Umeå Plant Science Centre - Associate Researchers

Eleni Stravrinidou in a lab looking on plants

Research

Photo: Thor Balkhed

The research in my group focuses on developing bioelectronic technologies for real time monitoring and dynamic modulation of plant physiology. Bioelectronics devices are very promising for interfacing with biology. Bioelectronic sensors can translate complex biological inputs to electronic readout signals while bioelectronic actuators can modulate biological networks via electronic addressing. Our aim is to develop bioelectronic technologies that overcome limitations of conventional methods and establish bioelectronics in plant biology. Focus is given on understanding and enhancing plant responses to environmental stress.

Recently we developed sensors based on the organic electrochemical transistor for monitoring sugar concentration in in-vitro and in-vivo plant systems. OECTs can operate in complex biological environment and directly detect analytes upon functionalization with biological recognition elements such as enzymes. OECTs also offer signal amplification and fast response times. In a first example we developed OECT glucose sensors and measured quantitively and in real-time the export of glucose from isolated chloroplasts¹. Glucose was detected only from chloroplasts isolated in night-time in agreement with our understanding of starch degradation in plants. With the OECT sensors we achieved a temporal resolution of 1min that surpass conventional methods. In another work we developed implantable OECT sugar sensors for in-vivo, real time monitoring of sugar transport in trees². Glucose and Sucrose sensors were implanted into the stem of Populus tremula x tremuloides (Hybrid Aspen tree) and could monitor sugar variations for 48h in the mature xylem tissue. The sensors revealed diurnal fluctuation in sucrose concentration while glucose concentration remained constant, something that was not observed before.

Collage of three images illustrating the principle of organic electrochemical transistor sensor measurement of sugar concentrations in plants

Figure 1: A. OECT-sensors for real time monitoring of sugars in trees. B. Photograph of the sensor implanted in the stem of Hybrid Aspen tree. C. Diurnal variation of sucrose concentration in xylem sap.

Furthermore, we developed a capillary based organic electronic ion pump (c-OEIP) for electronically controlled delivery of phytohormones. The OEIP is an electrophoretic delivery device that converts the electronic addressing signal into ionic fluxes allowing precise and dynamic delivery of ions and charged biomolecules with high spatiotemporal resolution. With the c-OEIP we could efficiently deliver the phytohormone Abscisic Acid, in the leaf apoplast of intact Nicotiana tabacum plants and induced stomata closure³. Our work revealed kinetics of ABA signal propagation in the leaf that were unknown.

Collage of three images illustrating the principle of capillary based organic electronic ion pumps delivering plant hormones in intact plants

Figure 2: OEIP for controlled and local delivery of phytohormones in intact plants. B. Micrograph of c-OEIP implanted in the leaf of tobacco plant. C. Temporal evolution of stomatal aperture upon ABA delivery with c-OEIP

Our proof-of-concept studies so far have shown that with bioelectronic devices, both sensors and actuators, we revealed biological processes that were not observed previously with conventional methods, highlighting the potential of bioelectronics for plant science.

References

Contact

CV E. Stavrinidou

Publications

Portrait photo of Sandra Jämtgård in a forest

Research

Photo: Andreas Palmén

My group’s research revolves around understanding the mechanisms governing plant nitrogen availability at the root-soil interface. A key tool in our research is the sampling technique microdialysis.
Our main aim is to develop microdialysis as a tool for root simulation, investigating key aspects of root physiology and plant-microbial interactions and how that influence plant nitrogen availability at the root surface, in a root growing in undisturbed soil.

In many ecosystems, nitrogen availability is limiting plant growth. Nitrogen is therefore applied to increase yields. Further insight into the plant perspective of nitrogen availability could lead to identifying ways to increase nitrogen use efficiency and decrease nitrogen pollution in managed environments. Critical in this seems to be the sampling methods used. Microdialysis is an approach for seeing nitrogen availability from a roots perspective.

We use microdialysis for measuring induced diffusive fluxes of foremost nitrogen, simulating what a plant root would experience in the field. An important factor in mirroring plant nitrogen availability at the root surface, particularly for the organic forms, in soil, is that this tool enables sampling with very little disturbance of the soil and that it allows continuous sampling. Due these sampling benefits, this technique has unveiled that in unfertilized soil, plant roots has access to a larger proportion of organic nitrogen than previously detected.

In a recent study, we used microdialysis to simulate root exudation by retrodialysis and its effect on nitrogen availability. Our study revealed that in a short-term perspective, nitrogen availability decreased, rather than increased most likely due to microbial immobilization.

Microdialysis allows repeated sampling, in situ in a small scale. This has led us to develop the application of this technique in additional directions. This includes sampling low molecular weight organic carbon compounds, enzymes and signalling molecules involved in plant-mycorrhiza interactions.

Our close collaboration with the Swedish Metabolomics Centre (SMC) enables our work on organic nitrogen in analysis of amino acids LC-MS (QQQ) and dipeptides and LC-MS (qTOF) quantification of isotopically labelled amino acids and metabolomic screening with GC-MS. This collaboration led to a recent study highlighting how critical the analysis is for evaluating the importance of plant uptake of organic nitrogen.

Microdialysis probe inserted into the soil organic layer in the boreal forest (photo: Sandra Jämtgård)

Key publications

Buckley S, Brackin R, Näsholm T, Schmidt S, Jämtgård S. 2022. The influence of sucrose on soil nitrogen availability–A root exudate simulation using microdialysis. Geoderma 409, 115645. https://doi.org/10.1016/j.geoderma.2021.115645
Svennerstam H, Jämtgård S. 2022. Timing is everything–obtaining accurate measures of plant uptake of amino acids. New Phytologist 234: 311-318. https://doi.org/10.1111/nph.17964
Plett K, Buckley S, Plett J, Anderson I, Lundberg-Felten J, Jämtgård S. 2021. Novel microdialysis technique reveals a dramatic shift in metabolite secretion during the early stages of the interaction between the ectomycorrhizal fungus Pisolithus microcarpus and its host Eucalyptus grandis. Microorganisms 9: 1817. https://doi.org/10.3390/microorganisms9091817
Buckley S, Brackin R, Jämtgård S, Näsholm T, Schmidt S, 2020. Microdialysis in soil environments: Current practice and future perspectives. Soil Biology & Biochemistry 143: 107743. https://doi.org/10.1016/j.soilbio.2020.107743
Buckley S, Brackin R, Näsholm T, Schmidt S, Jämtgård S. 2017. Improving in situ recovery of soil nitrogen using the microdialysis technique. Soil Biology & Biochemistry 114:93-103. https://doi.org/10.1016/j.soilbio.2017.07.009
Ganeteg U, Ahmad I, Jämtgård S, Aguetoni Cambui C, Inselsbacher E, Svennerstam H, Schmidt S and Näsholm T. 2017. Amino acid transporter mutants of Arabidopsis provides evidence that a non-mycorrhizal plant acquires organic nitrogen from agricultural soil. Plant Cell and Environment 40: 413-423. https://doi.org/10.1111/pce.12881
Jämtgård S, Näsholm T and Huss-Danell K. 2010. Nitrogen compounds in soil solutions of agricultural land. Soil Biology & Biochemistry 42: 2325-2330. https://doi.org/10.1016/j.soilbio.2010.09.011

Publications

Contact

Research

Photo: Mattias Pettersson

The ability of a species to sustain environmental change is primarily determined by its genetic reservoir, which is shaped over the course of history through demography and selection. We apply ecological and genomics tools to understand the origin and distribution of genetic diversity across landscapes in Eurasian conifer species. We use seed orchards as a study system to evaluate the impact of abiotic and biotic factors and management practices on genetic diversity and breeding gain in seed crops, and the adaptability of the regenerated production forests to future climate.

Ecological genomics

Local adaptation in which local genotypes have a fitness advantage than foreign genotypes is well known among long-lived tree species. Rapid climate change can break this genetic-environmental association much faster than trees’ ability to evolve in situ or migrate, thus creating a mismatch between genetic adaptation to altered environmental conditions. Inferences of genotype-environment associations due to polygenic nature of adaptive traits and the complexity of adaptive and dispersal-demographic factors that contribute to genetic differentiation across species range. Using landscape genomics approaches, we interrogate genome-wide variation across landscapes for understanding the extent to which evolutionary forces, e.g. demographic events, gene flow, introgression and selection, shape past and contemporary populations’ genetic structure, and identify those populations that may be most at risk under climate change. This research is conducted for major conifer species in Eurasia, e.g. Pinus sylvestris, Pinus tabuliformis, Pinus yunnanensis, Pinus densata and Picea abies.

A) Pinus densata on the Tibetan Plateau; B) Spatial structure of genomic diversity in P. densata; C) Hardiness variation in Scots pine; D) Controlled mating experiment in a Scots pine seed orchard

Seed orchards and adaptability of production forests

Efficient use of breeding resources requires a good understanding of the genetic composition of the founder materials for predicting the gain and diversity in future generations. For conifer trees, seed orchard is the link between tree breeding and the production forest. Well-functioning seed orchard is the most cost efficient and realistic way to increase timber production from forestland during the coming century. Our research in this area focuses on: 1) the assessment of diversity and coancestry in breeding populations of Scots pine (Pinus sylvestris) and Norway spruce (Picea abies); 2) the mating system in seed orchards of the two species, and pedigree structure and diversity in seed crops; and 3) the adaptation of orchard crops to different climate zones and thus formulating site-specific seedlot selection system for reforestation. These activities are in close collaboration with Skogforsk.

Key publications

Hall, D., Olsson, J., Zhao, W., Kroon, J., Wennström, U., Wang, X-R. 2021. Divergent patterns between phenotypic and genetic variation in Scots pine. Plant Communications，2:100139.
Zhao, W., Sun, Y-Q., Pan, J., Sullivan, A., Arnold, M.L., Mao, J-F., Wang, X-R. 2020. Effects of landscapes and range expansion on population structure and local adaptation. New Phytologist. 228: 330-343.
Sullivan, A.R., Schiffthaler, B., Thompson, S.L., Street, N.R., Wang, X-R. 2017. Interspecific plastome recombination reflects ancient reticulate evolution in Picea (Pinaceae). Molecular Biology and Evolution 34:1689-1701.
Funda, T., Wennström, U., Almqvist, C., Andersson Gull, B., Wang, X-R. 2016. Mating dynamics of Scots pine in isolation tents. Tree Genetics & Genomes 12:112.
Wang, B., Mao, J-F., Gao, J. Zhao, W., Wang, X-R. 2011. Colonization of the Tibetan Plateau by the homoploid hybrid pine Pinus densata. Molecular Ecology 20: 3796-3811.

Contact

CV X.-R. Wang

Publications

Svenska

Johanna Leppälä standing outside in a forest environment

Research

Plants commonly have strategies for both sexual and asexual reproduction. These reproductive functions do not evolve independently, but asexual reproduction e.g. through clonality, has consequences for sexual reproduction, typically by relaxing selection for sexual traits and allowing mutational degeneration in genes related to sexual functions. In my research, I am interested in both sexual and asexual reproduction of plants.

Related to sexual reproduction, I study genetics of speciation – i.e. genes involved in development of reproductive isolation. I have been using hybrids within and between outcrossing Arabidopsis species (A. lyrata, A. halleri and A. arenosa) to investigate reproductive barriers. Species barriers commonly manifest themselves as reduced hybrid viability and/or fertility. In these Arabidopsis species, reduction of hybrid pollen fertility is one of the first barriers to emerge between incipient species. Therefore, my main focus is on pollen related traits.

Three microscopy images of pollen grains of a hybrid between Arabidopsis species

Left: Light microscopy image of pollen grains of a hybrid between Arabidopsis species. Middle: DAPI staining (blue) of the same pollen grains, showing stained nuclei in two of the pollen grains, whereas two pollen grains (in the middle) remain unstained, as the cells are dead and DNA has degraded. Right: Scanning electron microscopy (SEM) image of pollen grains of a hybrid between Arabidopsis species: two smaller pollen grains in the middle are inviable.

Regarding asexual reproduction, my main interest is in clonality and its relation to sexual reproduction. Vegetative reproduction is typically associated with longevity and perenniality, and it can also be seen as a survival strategy, in conditions where sexual recruitment is low. Clonality has consequences for sexual reproduction, typically by relaxing selection for sexual traits and allowing mutational degeneration in genes related to sexual functions. The genetic basis of clonality has remained unknown, as the model plants of genetics are typically annuals. I use European aspen (Populus tremula) and Arabidopsis lyrata, as model species to study clonality and its genetic basis. In addition, I aim to identify whether clonality has affected sexual functions, specifically pollen quality and flowering frequency in these species.

Flowering Arabidopsis lyrata on the left side and Aspen trees with freshly green leaves photographed from below on the right.

Left: Arabidopsis lyrata in Höga Kusten, Sweden. Right: Aspen clones in a forest in Bjurholm.

Contact

CV J. Leppälä

Publications

Torgny Näsholm standing in front of a spruce tree

Research

Plant nitrogen (N) nutrition is a topic that challenges the researcher with a number of problems not encountered in other areas of plant mineral nutrition research. The diversity of N forms present in the soil, their interconversions, their different chemical and physical characteristics and not the least the multitude of adaptations and acclimatisations that plants display to optimize acquisition of various N forms all contribute to the complexity of plant N nutrition.

Thus, plants can use a wide array of chemical N forms, ranging from the simple inorganic N compounds such as NH4+ and NO3- as well as polymeric N forms such as proteins. My research deals with plant N physiology, particularly N acquisition and metabolism of forest plants. This research spans from detailed studies of uptake processes to forest fertilization and environmental effects of N.

Small tree seedlings growing in a nursery are seen on the left image, on the right side thale cress seedlings grown on a round agar plate that is divided in four parts is seen

Left: Tests with arginine based fertilizer in a seedling nursery Rotorua, New Zeeland. Right: Selection on D-amino acids.

We have studied uptake of various N forms and demonstrated how field-grown plants acquire different organic N compounds. These studies have stimulated us to characterize the molecular mechanisms underpinning plant organic N nutrition, specifically the specific transporters mediating uptake of various amino acids as well as metabolism of absorbed organic compounds.

We have discovered that plants have a well-developed capacity for using the common L-enantiomers of amino acids but a very restricted capacity to metabolise their D-counterparts. We have also shown how transgenic plants expressing genes encoding D-amino acid metabolising enzymes can detoxify and grow on D-amino acids. This finding has formed the basis for the development of a new selectable marker in plant biotechnology, now commercialized under the tradename SELDA. Basic L-amino acids, and in particular L-arginine, are absorbed at high rates by many plants and we have shown that such N forms have specific advantages for cultivation of woody plants such as conifer seedlings.

This finding forms the basis for the development of a new fertilizer – arGrow®, which is now commercialized by the company SweTree Technologies.

Key Publications

Näsholm, T., Kielland, K. & Ganeteg, U. (2009). Uptake of organic nitrogen by plants. Tansley Review New Phytologist, 182: 31- 48.
Svennerstam, H., Ganeteg, U., Bellini, C. & Näsholm, T. (2007). Comprehensive screening of Arabidopsis mutants suggests the Lysine Histidine Tranporter 1 to be involved in root uptake of amino acids. Plant Physiology 143: 1-8
Erikson, O., Hertzberg, M. & Näsholm, T. (2004). A conditional marker gene allowing both positive and negative selection in plants. Nature Biotechnology, 22: 455-458.
Lipson, D. and Näsholm, T. (2001). The unexpected versatility of plants: Organic Nitrogen Use and Availability in Terrestrial Ecosystems. Commissioned review. Oecologia 128: 305-316
Näsholm, T., Ekblad, A., Nordin, A., Giesler, R., Högberg, M. and Högberg, P. (1998). Boreal forest plants take up organic nitrogen. Nature 392, 914-916, 1998.

Contact

CV T. Näsholm

Svenska

Christiane Funk holding a flask with bacterial solution

Research

My research within the subject photosynthesis currently has developed into two different projects: 1. Investigating the potential of Nordic microalgae for wastewater reclamation and biomass generation and 2. Finding the function of plant proteases. Research objects in my group range from cyanobacteria, via green microalgae and cryptomonad algae to higher plants.

Wastewater reclamation and biomass generation by Nordic microalgae

With the expanding human population, we will need more food, more fuel and more water. At the same time, we have to reduce CO2 emissions by over 80%. One approach to address this problem is to recycle CO2 for fuel- or chemical-production using photosynthesis. Photosynthetic organisms use solar energy to incorporate atmospheric CO2 into organic molecules. We let microalgae perform photosynthesis and at the same time clean municipal and industrial wastewater. The algal biomass then can be used for biofuel, biogas, biofertilizer or even bioplastic. Our challenge is the sub-arctic climate we have in Northern Sweden with low temperatures and short-day lengths. Therefore, we investigate the potential of local, natural algal strains. We test their performance in cleaning wastewater, analyze their biomass and investigate, how to prolong their growth phase.

Plant proteases

Proteases are proteins that break down other proteins. They are involved in many different biological functions, e.g. the digestion of our food, cleaning the cell from malfunctioning proteins or cell signaling. Even though hundreds of proteases are encoded in the genomes of various plants, their biological roles are mostly unknown. Using molecular biological and biochemical methods, we try to find identify the function of some of them. Metacaspases, for example, are proteases thought to be involved in programmed cell death (PCD), the genetically encoded process leading to suicide of specific cells or tissues. In single-cell algae and cyanobacteria the necessity for PCD is less obvious, still these microorganisms contain metacaspases. The aim of our research is to investigate the broad network of PCD in photosynthetic single-cell organisms and at the same time to perform detailed functional, structural and evolutionary studies of the metacaspase homologues.

Microalgae and chlorophyll fluorescence in Arabidopsis shown in four inividual images. A) Various green microalgae found in municipal wastewater; B) Scanning electron microscope (SEM) image of the green microalga C. vulgaris 13-1 and its symbiotic bacterium Rhizobium sp. at 50 K magnification (Photos: Lorenza Ferro); C) Electron microscopy image of the cyanobacterium Synechocystis sp. 6803 (Photo: Tania Tibiletti); D) Chlorophyll fluorescence emitted from Arabidopsis thaliana leaves (Photo: Laxmi Mishra)

Key publications

Mehariya S, Plöhn M, Leon-Vaz A, Patel A, Funk C (2022) Improving the content of high value compounds in Nordic Desmodesmus microalgal strains. Bioresource Technology 359, 127445.
Spain O, Funk C (2022) Detailed characterisation of the cell wall structure and composition of Nordic green microalgae. J Agricultural and Food Chemistry 70, 9711-9721.
Martínez JM, Gojkovic Z, Ferro L, Maza M, Álvarez I, Raso J, Funk C. (2019) Use of Pulsed Electric Field permeabilization to extract astaxanthin from the Nordic microalga Haematococcus pluvialis. Bioresource Technology 289, 121694.
Mishra, L.S., Mielke, K., Wagner, R., Funk, C. (2019) Reduced expression of the presumably proteolytic inactive FtsHi members has impact on the Darwinian Figness of Arabidopsis thaliana. J. Exp. Botany 70, 2173-2184.
Karan, H.*, Funk, C.*, Grabert, M., Oey, M., Hankamer, B. (2019) Green bioplastics as part of a circular bioeconomy, Trends in Plant Science 24, 237-249.
Klemencic, M., Funk, C. (2018) Type III Metacaspases: calcium-dependent activity proposes new function for the p10 domain, New Phytologist 218, 1179-1191.

Contact

CV C. Funk

Publications

Svenska

Stefan Björklund standing in front of trees

Research

Plants need to integrate an array of signals to regulate complex patterns of gene expression. This is important since plants have specialized needs to respond to changes in the environment. Regulation of gene expression in plants is important for integration of external signals such as temperature, day length, concentration of different metabolites and light quality in the series of events that ultimately lead to owering. Finally, the regulation of gene expression during specific stages of seed development is an interesting example of tissue and developmental control which is of considerable agricultural importance.

In all eukaryotes, protein-encoding genes are transcribed by RNA polymerase II (pol II). To perform its most basal functions; promoter recognition, melting of the DNA template at the transcription start, formation of the first phosphodiester bonds and promoter escape, pol II requires five so called general transcription factors (GTFs). These GTFs, TBP, TFIIB, E, F, and H are conserved in all eukaryotes and together with pol II they form a preinitiation complex comprising nearly 30 polypeptides. Mediator is a multisubunit complex which functions as a connector between the promoter-bound transcriptional regulators and pol II.

The figure illustrates the eukaryotic transcription initiation complex.

A cartoon of a eukaryotic transcription initiation complex consisting of DNA, TBP, TFIIB, E, F and H, Mediator, Pol II and a specific transcription factor binding to an enhancer element.

Surprisingly, Mediator had not been identified in plants until we recently succeeded to purify Mediator from A. thaliana through conventional biochemical purification combined with reversed-phase LC-ESI-MS/MS. This was the first description of Mediator in a plant, and it was evident that it required a biochemical approach since most of the A. thaliana Mediator subunits show very low sequence homology to the corresponding proteins in yeast and metazoans. Plant Mediator is probably structurally conserved, but the amino acid sequences of individual subunits differ considerably when compared to other eukaryotes. Plants also contain a set of unique Mediator subunits, which are likely to be involved in regulation of plant-specific gene expression.

Link to Stefan Björklund's main research page

Key publications

Blomberg J, Aguilar X, Brännström K, Rautio L, Olofsson A, Wittung-Stafshede P, and Björklund S. (2012). Interactions between DNA, transcriptional regulator Dreb2a and the Med25 mediator subunit from Arabidopsis thaliana involve conformational changes Nucleic Acids Res. 40:5938-5950
Elfving, N., Davoine, C., Benlloch, R., Blomberg, J., Brännström, K., Müller, D., Nilsson, A., Ulfstedt, M., Ronne, H., Wingsle, G., Nilsson, O., and Björklund, S. (2011). The Arabidopsis thaliana Med25 mediator subunit integrates environmental cues to control plant development. Proc. Natl. Acad. Sci. USA. 108(20):8245-8250
Shaikhibrahim, Z., Rahaman, H., Wittung-Stafshede, P., and Björklund, S. (2009). Med8, Med18, and Med20 subunits of the Mediator head domain are interdependent upon each other for folding and complex formation. Proc. Natl. Acad. Sci. USA. 106:20728-20733
Bäckström, S., Elfving, N., Nilsson, R., Wingsle, G., and Björklund, S. (2007). Purification of a Plant Mediator from Arabidopsis thaliana identifies PFT1 as the Med25 subunit. Molecular Cell 5: 717-729.
Hallberg, M., Hu, G-Z., Balciunas, D., Sheikhibrahim, Z., Björklund, S., and Ronne, H. (2006). Functional and physical interactions of the Mediator subunit Med21/Srb7. Mol. Genet Genomics 276:197-210

Contact

CV S. Björklund

Publications

Svenska

Markus Schmid sitting at his desk in his office

Research

Photo: Fredrik Larsson

A fundamental difference between the development of plants and most animals is that the former maintains the potential to form new organs throughout their life. This capacity not only endows plants with the ability for continued growth, but also provides them with the means to rapidly and flexibly adjust to changes in their environment, resulting in a high degree of phenotypic plasticity. The aim of our research is to understand the molecular mechanisms that controls plant development, in particular the transition from vegetative to reproductive growth, in response to both endogenous and environmental stimuli.

Ambient temperature & alternative pre-mRNA splicing

An environmental signal that can have pronounced effects on plant growth and development is ambient temperature. We have recently identified a mutant in the plant model Arabidopsis thaliana that displays strong pleiotropic developmental defects in the shoot meristem and lateral organs specifically at low ambient temperature. The mutated gene, PORCUPINE, encodes a putative splice factor, suggesting that alternative splicing of pre-mRNA might be involved in modulating growth and development in response to changes in ambient temperature and might contribute to establish phenotypic plasticity in plants.

Illustration of the research done in Markus Schmid's group

Alternative splicing in the porcupine mutant

We are currently performing a number of experiments to:

identify the molecular mechanisms underlying the temperature-specific phenotype of the porcupine mutant
study the general effect of temperature on (alternative) pre-mRNA splicing and its consequences for plant growth and development
isolate and characterize new temperature-specific alleles affecting plant development

Regulation of flowering time & flower development

A trait that is in part controlled by ambient temperature is the induction of flowering. The transition from vegetative growth to flowering is a central event in the life cycle of plants, which requires correct timing to ensure reproductive success. In most plants flowering time is not fully deterministic but allows for some degree of phenotypic plasticity. Given that the decision to initiate flowering is made in a small number of cells in the leaf vasculature and the shoot meristem, any results obtained from complex tissues can be misleading as they likely mask tissue-specific regulatory processes. To overcome these limitations, we have adopted technologies such as INTACT and FACS to isolate nuclei from specific tissues for subsequent (epi-)genome and transcriptome analyses.

In collaboration with our colleagues at UPSC, Karin Ljung, Johannes Hanson and Ove Nilsson, we are:

investigating the dynamic changes of the epigenome, transcriptome, translatome, and metabolome during the switch to flowering in A. thaliana and hybrid aspen
isolating and characterizing novel flowering time regulators in A. thaliana
establishing methods for tissue- and cell-type specific “-omics” approaches in hybrid aspen

One of the first steps once plants are committed to flowering is the induction of the plant-specific transcription factor LEAFY in the incipient flower primordia. In collaboration with our colleagues Ove Nilsson (UPSC) and François Parcy (Grenoble) we are investigating how the LEAFY protein contributes to specifying the four different floral organs.

Trehalose 6 phosphate & SnRK1 signaling

The transition to flowering and subsequent seed filling are highly energy demanding processes. Thus, it is not surprising that the time of flowering is influenced by carbohydrate availability. Of particular importance in this regard is the phospho-disaccharide trehalose 6-phosphate (T6P), which plays a crucial role in carbohydrate signaling. T6P signals at least in part through the evolutionary conserved heterotrimeric kinase complex SUCROSE NON-FERMENTING1 RELATED KINASE 1 (SnRK1). We are studying how the T6P pathway and SnRK1 complex are integrated into the canonical network that regulates flowering.

Key publications:

Capovilla, G, Delhomme, N, Collani, S, Shutava, I, Bezrukov, I, Symeonidi, E, de Francisco Amorim, M, Laubinger, S, Schmid, M (2018) PORCUPINE regulates development in response to temperature through alternative splicing. Nature Plants 4: 534-539. doi: 10.1038/s41477-018-0176-z
You, Y, Sawikowska, A, Neumann, M, Posé, D, Capovilla, G, Langenecker, T, Neher, RA, Krajewski, P, Schmid, M (2017) Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering. Nature Communications 8: 15120, doi: 10.1038/ncomms15120
Posé D, Verhage L, Ott F, Yant L, Mathieu J, Angenent GC, Immink RGH and Schmid M (2013). Temperature-dependent regulation of flowering by antagonistic FLM variants. Nature 503: 414-417.
Wahl V, Ponnu P, Schlereth A, Arrivault S, Langenecker T, Franke A, Feil R, Lunn JE, Stitt M and Schmid M (2013). Regulation of flowering by trehalose-6-phosphate signaling in Arabidopsis thaliana. Science 339: 704-707.
Mathieu J, Warthmann N, Küttner F and Schmid M (2007). Export of FT protein from phloem companion cells is sufficient for floral induction in Arabidopsis. Current Biology 17: 1055-1060.

Team

CV M. Schmid

Publications

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2025 (1)

The Arabidopsis thaliana core splicing factor PORCUPINE/SmE1 requires intron-mediated expression. Dikaya, V., Rojas-Murcia, N., Benstein, R., Eiserhardt, W., & Schmid, M. PLoS ONE, 20(3 March). 2025.
doi link bibtex abstract

@article{dikaya_arabidopsis_2025,
	title = {The {Arabidopsis} thaliana core splicing factor {PORCUPINE}/{SmE1} requires intron-mediated expression},
	volume = {20},
	doi = {10.1371/journal.pone.0318163},
	abstract = {Plants are prone to genome duplications and tend to preserve multiple gene copies. This is also the case for the genes encoding the Sm proteins of Arabidopsis thaliana (L). The Sm proteins are best known for their roles in RNA processing such as pre-mRNA splicing and nonsense-mediated mRNA decay. In this study, we have taken a closer look at the phylogeny and differential regulation of the SmE-coding genes found in A. thaliana, PCP/SmE1, best known for its cold-sensitive phenotype, and its paralog, PCPL/SmE2. The phylogeny of the PCP homologs in the green lineage shows that SmE duplications happened multiple times independently in different plant clades and that the duplication that gave rise to PCP and PCPL occurred only in the Brassicaceae family. Our analysis revealed that A. thaliana PCP and PCPL proteins, which only differ in two amino acids, exhibit a very high level of functional conservation and can perform the same function in the cell. However, our results indicate that PCP is the prevailing copy of the two SmE genes in A. thaliana as it is more highly expressed and that the main difference between PCP and PCPL resides in their transcriptional regulation, which is strongly linked to intronic sequences. Our results provide insight into the complex mechanisms that underlie the differentiation of the paralogous gene expression as an adaptation to stress. © 2025 Dikaya et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},
	number = {3 March},
	journal = {PLoS ONE},
	author = {Dikaya, V. and Rojas-Murcia, N. and Benstein, R.M. and Eiserhardt, W.L. and Schmid, M.},
	year = {2025},
	keywords = {Arabidopsis thaliana, Gene expression, Genomics, Introns, Phenotypes, Phylogenetic analysis, Seedlings, Sequence alignment},
}

2024 (1)

The Arabidopsis splicing factor PORCUPINE/SmE1 orchestrates temperature-dependent root development via auxin homeostasis maintenance. El Arbi, N., Nardeli, S. M., Šimura, J., Ljung, K., & Schmid, M. New Phytologist, 244(4): 1408–1421. 2024. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20153

The Arabidopsis splicing factor PORCUPINE/SmE1 orchestrates temperature-dependent root development via auxin homeostasis maintenance [link]

Paper doi link bibtex abstract

@article{el_arbi_arabidopsis_2024,
	title = {The {Arabidopsis} splicing factor {PORCUPINE}/{SmE1} orchestrates temperature-dependent root development via auxin homeostasis maintenance},
	volume = {244},
	copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20153},
	doi = {10.1111/nph.20153},
	abstract = {Appropriate abiotic stress response is pivotal for plant survival and makes use of multiple signaling molecules and phytohormones to achieve specific and fast molecular adjustments. A multitude of studies has highlighted the role of alternative splicing in response to abiotic stress, including temperature, emphasizing the role of transcriptional regulation for stress response. Here we investigated the role of the core-splicing factor PORCUPINE (PCP) on temperature-dependent root development. We used marker lines and transcriptomic analyses to study the expression profiles of meristematic regulators and mitotic markers, and chemical treatments, as well as root hormone profiling to assess the effect of auxin signaling. The loss of PCP significantly alters RAM architecture in a temperature-dependent manner. Our results indicate that PCP modulates the expression of central meristematic regulators and is required to maintain appropriate levels of auxin in the RAM. We conclude that alternative pre-mRNA splicing is sensitive to moderate temperature fluctuations and contributes to root meristem maintenance, possibly through the regulation of phytohormone homeostasis and meristematic activity.},
	language = {en},
	number = {4},
	urldate = {2024-10-25},
	journal = {New Phytologist},
	author = {El Arbi, Nabila and Nardeli, Sarah Muniz and Šimura, Jan and Ljung, Karin and Schmid, Markus},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20153},
	keywords = {Arabidopsis thaliana, SmE, alternative RNA splicing, auxin signaling, root apical meristem, root development, temperature signaling},
	pages = {1408--1421},
}

2023 (1)

Isolation of Nuclei Tagged in Specific Cell Types (INTACT) in Arabidopsis. Benstein, R. M., Schmid, M., & You, Y. In Riechmann, J. L., & Ferrándiz, C., editor(s), Flower Development, volume 2686, pages 313–328. New York, NY, January 2023. Series Title: Methods in Molecular Biology

Isolation of Nuclei Tagged in Specific Cell Types (INTACT) in Arabidopsis [link]

Paper doi link bibtex abstract

@incollection{riechmann_isolation_2023,
	address = {New York, NY},
	title = {Isolation of {Nuclei} {Tagged} in {Specific} {Cell} {Types} ({INTACT}) in {Arabidopsis}},
	volume = {2686},
	isbn = {978-1-07-163298-7 978-1-07-163299-4},
	url = {https://link.springer.com/10.1007/978-1-0716-3299-4_16},
	abstract = {Many functionally distinct plant tissues have relatively low numbers of cells that are embedded within complex tissues. For example, the shoot apical meristem (SAM) consists of a small population of pluripotent stem cells surrounded by developing leaves and/or flowers at the growing tip of the plant. It is technically challenging to collect enough high-quality SAM samples for molecular analyses. Isolation of Nuclei Tagged in specific Cell Types (INTACT) is an easily reproducible method that allows the enrichment of biotin-tagged cell-type-specific nuclei from the total nuclei pool using biotin-streptavidin affinity purification. Here, we provide a detailed INTACT protocol for isolating nuclei from the Arabidopsis SAM. One can also adapt this protocol to isolate nuclei from other tissues and cell types for investigating tissue/cell-type-specific transcriptome and epigenome and their changes during developmental programs at a high spatiotemporal resolution. Furthermore, due to its low cost and simple procedures, INTACT can be conducted in any standard molecular laboratory.},
	language = {en},
	urldate = {2023-08-14},
	booktitle = {Flower {Development}},
	author = {Benstein, Ruben M. and Schmid, Markus and You, Yuan},
	editor = {Riechmann, José Luis and Ferrándiz, Cristina},
	month = jan,
	year = {2023},
	doi = {10.1007/978-1-0716-3299-4_16},
	note = {Series Title: Methods in Molecular Biology},
	pages = {313--328},
}

2022 (3)

FLOWERING LOCUS T paralogs control the annual growth cycle in Populus trees. André, D., Marcon, A., Lee, K. C., Goretti, D., Zhang, B., Delhomme, N., Schmid, M., & Nilsson, O. Current Biology, 32(13): 2988–2996.e4. July 2022. Publisher: Elsevier

FLOWERING LOCUS T paralogs control the annual growth cycle in Populus trees [link]

Paper doi link bibtex abstract

@article{andre_flowering_2022,
	title = {{FLOWERING} {LOCUS} {T} paralogs control the annual growth cycle in {Populus} trees},
	volume = {32},
	issn = {0960-9822},
	url = {https://www.cell.com/current-biology/abstract/S0960-9822(22)00782-5},
	doi = {10.1016/j.cub.2022.05.023},
	abstract = {In temperate and boreal regions, perennials adapt their annual growth cycle to the change of seasons. These adaptations ensure survival in harsh environmental conditions, allowing growth at different latitudes and altitudes, and are therefore tightly regulated. Populus tree species cease growth and form terminal buds in autumn when photoperiod falls below a certain threshold.1 This is followed by establishment of dormancy and cold hardiness over the winter. At the center of the photoperiodic pathway in Populus is the gene FLOWERING LOCUS T2 (FT2), which is expressed during summer and harbors significant SNPs in its locus associated with timing of bud set.1, 2, 3, 4 The paralogous gene FT1, on the other hand, is hyper-induced in chilling buds during winter.3,5 Even though its function is so far unknown, it has been suggested to be involved in the regulation of flowering and the release of winter dormancy.3,5 In this study, we employ CRISPR-Cas9-mediated gene editing to individually study the function of the FT-like genes in Populus trees. We show that while FT2 is required for vegetative growth during spring and summer and regulates the entry into dormancy, expression of FT1 is absolutely required for bud flush in spring. Gene expression profiling suggests that this function of FT1 is linked to the release of winter dormancy rather than to the regulation of bud flush per se. These data show how FT duplication and sub-functionalization have allowed Populus trees to regulate two completely different and major developmental control points during the yearly growth cycle.},
	language = {English},
	number = {13},
	urldate = {2022-08-12},
	journal = {Current Biology},
	author = {André, Domenique and Marcon, Alice and Lee, Keh Chien and Goretti, Daniela and Zhang, Bo and Delhomme, Nicolas and Schmid, Markus and Nilsson, Ove},
	month = jul,
	year = {2022},
	pmid = {35660141},
	note = {Publisher: Elsevier},
	keywords = {FLOWERING LOCUS T, Populus, annual growth cycle, bud flush, dormancy, paralogs},
	pages = {2988--2996.e4},
}

Impaired KIN10 function restores developmental defects in the Arabidopsis trehalose 6-phosphate synthase1 (tps1) mutant. Zacharaki, V., Ponnu, J., Crepin, N., Langenecker, T., Hagmann, J., Skorzinski, N., Musialak-Lange, M., Wahl, V., Rolland, F., & Schmid, M. New Phytologist, 235(1): 220–233. 2022.

Impaired KIN10 function restores developmental defects in the Arabidopsis trehalose 6-phosphate synthase1 (tps1) mutant [link]

Paper doi link bibtex abstract

@article{zacharaki_impaired_2022,
	title = {Impaired {KIN10} function restores developmental defects in the {Arabidopsis} trehalose 6-phosphate synthase1 (tps1) mutant},
	volume = {235},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18104},
	doi = {10.1111/nph.18104},
	abstract = {Sensing carbohydrate availability is essential for plants to coordinate their growth and development. In Arabidopsis thaliana, TREHALOSE 6-PHOSPHATE SYNTHASE 1 (TPS1) and its product, trehalose 6-phosphate (T6P), are important for the metabolic control of development. tps1 mutants are embryo-lethal and unable to flower when embryogenesis is rescued. T6P regulates development in part through inhibition of SUCROSE NON-FERMENTING1 RELATED KINASE1 (SnRK1). Here, we explored the role of SnRK1 in T6P-mediated plant growth and development using a combination of a mutant suppressor screen and genetic, cellular and transcriptomic approaches. We report nonsynonymous amino acid substitutions in the catalytic KIN10 and regulatory SNF4 subunits of SnRK1 that can restore both embryogenesis and flowering of tps1 mutant plants. The identified SNF4 point mutations disrupt the interaction with the catalytic subunit KIN10. Contrary to the common view that the two A. thaliana SnRK1 catalytic subunits act redundantly, we found that loss-of-function mutations in KIN11 are unable to restore embryogenesis and flowering, highlighting the important role of KIN10 in T6P signalling.},
	language = {en},
	number = {1},
	urldate = {2022-06-09},
	journal = {New Phytologist},
	author = {Zacharaki, Vasiliki and Ponnu, Jathish and Crepin, Nathalie and Langenecker, Tobias and Hagmann, Jörg and Skorzinski, Noemi and Musialak-Lange, Magdalena and Wahl, Vanessa and Rolland, Filip and Schmid, Markus},
	year = {2022},
	keywords = {Arabidopsis thaliana, SnRK1 complex, T6P pathway, TPS1, embryogenesis, flowering time},
	pages = {220--233},
}

PICLN modulates alternative splicing and light/temperature responses in plants. Mateos, J. L, Sanchez, S. E, Legris, M., Esteve-Bruna, D., Torchio, J. C, Petrillo, E., Goretti, D., Blanco-Touriñán, N., Seymour, D. K, Schmid, M., Weigel, D., Alabadí, D., & Yanovsky, M. J Plant Physiology,kiac527. November 2022.

PICLN modulates alternative splicing and light/temperature responses in plants [link]

Paper doi link bibtex abstract

@article{mateos_picln_2022,
	title = {{PICLN} modulates alternative splicing and light/temperature responses in plants},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac527},
	doi = {10.1093/plphys/kiac527},
	abstract = {Plants undergo transcriptome reprogramming to adapt to daily and seasonal fluctuations in light and temperature conditions. While most efforts have focused on the role of master transcription factors, the importance of splicing factors modulating these processes is now emerging. Efficient pre-mRNA splicing depends on proper spliceosome assembly, which in plants and animals requires the methylosome complex. Ion Chloride nucleotide-sensitive protein (PICLN) is part of the methylosome complex in both humans and Arabidopsis (Arabidopsis thaliana), and we show here that the human PICLN ortholog rescues phenotypes of Arabidopsis picln mutants. Altered photomorphogenic and photoperiodic responses in Arabidopsis picln mutants are associated with changes in pre-mRNA splicing that partially overlap with those in PROTEIN-ARGININE METHYL TRANSFERASE5 (prmt5) mutants. Mammalian PICLN also acts in concert with the Survival Motor Neuron (SMN) complex component GEMIN2 to modulate the late steps of UsnRNP assembly, and many alternative splicing events regulated by PICLN but not PRMT5, the main protein of the methylosome, are controlled by Arabidopsis GEMIN2. As with GEMIN2 and SM PROTEIN E1/PORCUPINE (SME1/PCP), low temperature, which increases PICLN expression, aggravates morphological and molecular defects of picln mutants. Taken together, these results establish a key role for PICLN in the regulation of pre-mRNA splicing and in mediating plant adaptation to daily and seasonal fluctuations in environmental conditions.},
	urldate = {2022-12-02},
	journal = {Plant Physiology},
	author = {Mateos, Julieta L and Sanchez, Sabrina E and Legris, Martina and Esteve-Bruna, David and Torchio, Jeanette C and Petrillo, Ezequiel and Goretti, Daniela and Blanco-Touriñán, Noel and Seymour, Danelle K and Schmid, Markus and Weigel, Detlef and Alabadí, David and Yanovsky, Marcelo J},
	month = nov,
	year = {2022},
	pages = {kiac527},
}

2021 (4)

Epigenetic Regulation of Temperature Responses – Past Successes and Future Challenges. Pandey, S. P., Benstein, R. M, Wang, Y., & Schmid, M. Journal of Experimental Botany, 72(21): 7482–7497. May 2021.

Epigenetic Regulation of Temperature Responses – Past Successes and Future Challenges [link]

Paper doi link bibtex abstract 8 downloads

@article{pandey_epigenetic_2021,
	title = {Epigenetic {Regulation} of {Temperature} {Responses} – {Past} {Successes} and {Future} {Challenges}},
	volume = {72},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erab248/6288481},
	doi = {10.1093/jxb/erab248},
	abstract = {Abstract
            In contrast to animals, plants cannot avoid unfavorable temperature conditions. Instead, plants have evolved intricate signaling pathways that enable them to perceive and respond to temperature. General acclimation processes that prepare the plant to respond to stressful heat and cold, usually occur throughout the whole plant. More specific temperature responses, however, are limited to certain tissues or cell types. While global responses are amenable to epigenomic analyses, responses which are highly localized are more problematic as the chromatin in question is not easily accessible. Here we review the current knowledge of the epigenetic regulation of FLOWERING LOCUS C and FLOWERING LOCUS T as examples of temperature-responsive flowering time regulators that are expressed broadly throughout the plants and in specific cell types, respectively. While undoubtably extremely successful, we reason that future analyses would benefit from higher spatiotemporal resolution. We conclude by reviewing methods and successful applications of tissue- and cell type-specific epigenomic analyses and provide a brief outlook into the future, single-cell epigenomics.},
	language = {en},
	number = {21},
	urldate = {2021-06-03},
	journal = {Journal of Experimental Botany},
	author = {Pandey, Saurabh Prakash and Benstein, Ruben M and Wang, Yanwei and Schmid, Markus},
	month = may,
	year = {2021},
	pages = {7482--7497},
}

Insights into the role of alternative splicing in plant temperature response. Dikaya, V., El Arbi, N., Rojas-Murcia, N., Nardeli, S. M., Goretti, D., & Schmid, M. Journal of Experimental Botany, 72(21): 7384–7403. November 2021.

Insights into the role of alternative splicing in plant temperature response [link]

Paper doi link bibtex abstract 12 downloads

@article{dikaya_insights_2021,
	title = {Insights into the role of alternative splicing in plant temperature response},
	volume = {72},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erab234},
	doi = {10/gkhp7j},
	abstract = {Alternative splicing occurs in all eukaryotic organisms. Since the first description of multiexon genes and the splicing machinery, the field has expanded rapidly, especially in animals and yeast. However, our knowledge about splicing in plants is still quite fragmented. Though eukaryotes show some similarity in the composition and dynamics of their splicing machinery, observations of unique plant traits are only starting to emerge. For instance, plant alternative splicing is closely linked to their ability to perceive various environmental stimuli. Due to their sessile lifestyle, temperature is a central source of information, allowing plants to adjust their development to match current growth conditions. Hence, seasonal temperature fluctuations and day–night cycles can strongly influence plant morphology across developmental stages. Here we discuss available data on temperature-dependent alternative splicing in plants. Given its fragmented state, it is not always possible to fit specific observations into a coherent picture, yet it is sufficient to estimate the complexity of this field and the need for further research. Better understanding of alternative splicing as a part of plant temperature response and adaptation may also prove to be a powerful tool for both fundamental and applied sciences.},
	number = {21},
	urldate = {2022-02-04},
	journal = {Journal of Experimental Botany},
	author = {Dikaya, Varvara and El Arbi, Nabila and Rojas-Murcia, Nelson and Nardeli, Sarah Muniz and Goretti, Daniela and Schmid, Markus},
	month = nov,
	year = {2021},
	pages = {7384--7403},
}

Perturbations in plant energy homeostasis prime lateral root initiation via SnRK1-bZIP63-ARF19 signaling. Muralidhara, P., Weiste, C., Collani, S., Krischke, M., Kreisz, P., Draken, J., Feil, R., Mair, A., Teige, M., Müller, M. J., Schmid, M., Becker, D., Lunn, J. E., Rolland, F., Hanson, J., & Dröge-Laser, W. Proceedings of the National Academy of Sciences, 118(37). September 2021.

Perturbations in plant energy homeostasis prime lateral root initiation via SnRK1-bZIP63-ARF19 signaling [link]

Paper doi link bibtex abstract 6 downloads

@article{muralidhara_perturbations_2021,
	title = {Perturbations in plant energy homeostasis prime lateral root initiation via {SnRK1}-{bZIP63}-{ARF19} signaling},
	volume = {118},
	copyright = {© 2021 . https://www.pnas.org/site/aboutpnas/licenses.xhtmlPublished under the PNAS license.},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/118/37/e2106961118},
	doi = {10/gmvnsg},
	abstract = {Plants adjust their energy metabolism to continuous environmental fluctuations, resulting in a tremendous plasticity in their architecture. The regulatory circuits involved, however, remain largely unresolved. In Arabidopsis, moderate perturbations in photosynthetic activity, administered by short-term low light exposure or unexpected darkness, lead to increased lateral root (LR) initiation. Consistent with expression of low-energy markers, these treatments alter energy homeostasis and reduce sugar availability in roots. Here, we demonstrate that the LR response requires the metabolic stress sensor kinase Snf1-RELATED-KINASE1 (SnRK1), which phosphorylates the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) that directly binds and activates the promoter of AUXIN RESPONSE FACTOR19 (ARF19), a key regulator of LR initiation. Consistently, starvation-induced ARF19 transcription is impaired in bzip63 mutants. This study highlights a positive developmental function of SnRK1. During energy limitation, LRs are initiated and primed for outgrowth upon recovery. Hence, this study provides mechanistic insights into how energy shapes the agronomically important root system.},
	language = {en},
	number = {37},
	urldate = {2021-11-12},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Muralidhara, Prathibha and Weiste, Christoph and Collani, Silvio and Krischke, Markus and Kreisz, Philipp and Draken, Jan and Feil, Regina and Mair, Andrea and Teige, Markus and Müller, Martin J. and Schmid, Markus and Becker, Dirk and Lunn, John E. and Rolland, Filip and Hanson, Johannes and Dröge-Laser, Wolfgang},
	month = sep,
	year = {2021},
	keywords = {ARF19, SnRK1, bZIP63, lateral root, metabolic homeostasis},
}

miRNA Mediated Regulation and Interaction between Plants and Pathogens. Yang, X., Zhang, L., Yang, Y., Schmid, M., & Wang, Y. International Journal of Molecular Sciences, 22(6): 2913. March 2021.

miRNA Mediated Regulation and Interaction between Plants and Pathogens [link]

Paper doi link bibtex abstract 3 downloads

@article{yang_mirna_2021,
	title = {{miRNA} {Mediated} {Regulation} and {Interaction} between {Plants} and {Pathogens}},
	volume = {22},
	issn = {1422-0067},
	url = {https://www.mdpi.com/1422-0067/22/6/2913},
	doi = {10/gjjv65},
	abstract = {Plants have evolved diverse molecular mechanisms that enable them to respond to a wide range of pathogens. It has become clear that microRNAs, a class of short single-stranded RNA molecules that regulate gene expression at the transcriptional or post-translational level, play a crucial role in coordinating plant-pathogen interactions. Specifically, miRNAs have been shown to be involved in the regulation of phytohormone signals, reactive oxygen species, and NBS-LRR gene expression, thereby modulating the arms race between hosts and pathogens. Adding another level of complexity, it has recently been shown that specific lncRNAs (ceRNAs) can act as decoys that interact with and modulate the activity of miRNAs. Here we review recent findings regarding the roles of miRNA in plant defense, with a focus on the regulatory modes of miRNAs and their possible applications in breeding pathogen-resistance plants including crops and trees. Special emphasis is placed on discussing the role of miRNA in the arms race between hosts and pathogens, and the interaction between disease-related miRNAs and lncRNAs.},
	language = {en},
	number = {6},
	urldate = {2021-06-03},
	journal = {International Journal of Molecular Sciences},
	author = {Yang, Xiaoqian and Zhang, Lichun and Yang, Yuzhang and Schmid, Markus and Wang, Yanwei},
	month = mar,
	year = {2021},
	pages = {2913},
}

2020 (4)

A gibberellin methyltransferase modulates the timing of floral transition at the Arabidopsis shoot meristem. Lee, J. E., Goretti, D., Neumann, M., Schmid, M., & You, Y. Physiologia Plantarum, 170(4): 474–487. December 2020.

A gibberellin methyltransferase modulates the timing of floral transition at the Arabidopsis shoot meristem [link]

Paper doi link bibtex 3 downloads

@article{lee_gibberellin_2020,
	title = {A gibberellin methyltransferase modulates the timing of floral transition at the {Arabidopsis} shoot meristem},
	volume = {170},
	issn = {0031-9317, 1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ppl.13146},
	doi = {10.1111/ppl.13146},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Lee, Joanne E. and Goretti, Daniela and Neumann, Manuela and Schmid, Markus and You, Yuan},
	month = dec,
	year = {2020},
	pages = {474--487},
}

Conifers exhibit a characteristic inactivation of auxin to maintain tissue homeostasis. Brunoni, F., Collani, S., Casanova‐Sáez, R., Šimura, J., Karady, M., Schmid, M., Ljung, K., & Bellini, C. New Phytologist, 226(6): 1753–1765. June 2020.

Conifers exhibit a characteristic inactivation of auxin to maintain tissue homeostasis [link]

Paper doi link bibtex 2 downloads

@article{brunoni_conifers_2020,
	title = {Conifers exhibit a characteristic inactivation of auxin to maintain tissue homeostasis},
	volume = {226},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16463},
	doi = {10.1111/nph.16463},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Brunoni, Federica and Collani, Silvio and Casanova‐Sáez, Rubén and Šimura, Jan and Karady, Michal and Schmid, Markus and Ljung, Karin and Bellini, Catherine},
	month = jun,
	year = {2020},
	pages = {1753--1765},
}

TERMINAL FLOWER1 Functions as a Mobile Transcriptional Cofactor in the Shoot Apical Meristem. Goretti, D., Silvestre, M., Collani, S., Langenecker, T., Méndez, C., Madueño, F., & Schmid, M. Plant Physiology, 182(4): 2081–2095. April 2020.

TERMINAL FLOWER1 Functions as a Mobile Transcriptional Cofactor in the Shoot Apical Meristem [link]

Paper doi link bibtex 2 downloads

@article{goretti_terminal_2020,
	title = {{TERMINAL} {FLOWER1} {Functions} as a {Mobile} {Transcriptional} {Cofactor} in the {Shoot} {Apical} {Meristem}},
	volume = {182},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/182/4/2081-2095/6116513},
	doi = {10/ghqb3x},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Goretti, Daniela and Silvestre, Marina and Collani, Silvio and Langenecker, Tobias and Méndez, Carla and Madueño, Francisco and Schmid, Markus},
	month = apr,
	year = {2020},
	pages = {2081--2095},
}

The trehalose 6‐phosphate pathway impacts vegetative phase change in Arabidopsis thaliana. Ponnu, J., Schlereth, A., Zacharaki, V., Działo, M. A., Abel, C., Feil, R., Schmid, M., & Wahl, V. The Plant Journal, 104(3): 768–780. November 2020.

The trehalose 6‐phosphate pathway impacts vegetative phase change in <i>Arabidopsis thaliana</i> [link]

Paper doi link bibtex 2 downloads

@article{ponnu_trehalose_2020,
	title = {The trehalose 6‐phosphate pathway impacts vegetative phase change in \textit{{Arabidopsis} thaliana}},
	volume = {104},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.14965},
	doi = {10.1111/tpj.14965},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Ponnu, Jathish and Schlereth, Armin and Zacharaki, Vasiliki and Działo, Magdalena A. and Abel, Christin and Feil, Regina and Schmid, Markus and Wahl, Vanessa},
	month = nov,
	year = {2020},
	pages = {768--780},
}

2019 (4)

A bacterial assay for rapid screening of IAA catabolic enzymes. Brunoni, F., Collani, S., Šimura, J., Schmid, M., Bellini, C., & Ljung, K. Plant Methods, 15(1): 126. December 2019.

A bacterial assay for rapid screening of IAA catabolic enzymes [link]

Paper doi link bibtex abstract

@article{brunoni_bacterial_2019,
	title = {A bacterial assay for rapid screening of {IAA} catabolic enzymes},
	volume = {15},
	issn = {1746-4811},
	url = {https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0509-6},
	doi = {10.1186/s13007-019-0509-6},
	abstract = {Abstract
            
              Background
              
                Plants rely on concentration gradients of the native auxin, indole-3-acetic acid (IAA), to modulate plant growth and development. Both metabolic and transport processes participate in the dynamic regulation of IAA homeostasis. Free IAA levels can be reduced by inactivation mechanisms, such as conjugation and degradation. IAA can be conjugated via ester linkage to glucose, or via amide linkage to amino acids, and degraded via oxidation. Members of the UDP glucosyl transferase (UGT) family catalyze the conversion of IAA to indole-3-acetyl-1-glucosyl ester (IAGlc); by contrast, IAA is irreversibly converted to indole-3-acetyl-
                l
                -aspartic acid (IAAsp) and indole-3-acetyl glutamic acid (IAGlu) by Group II of the GRETCHEN HAGEN3 (GH3) family of acyl amido synthetases. Dioxygenase for auxin oxidation (DAO) irreversibly oxidizes IAA to oxindole-3-acetic acid (oxIAA) and, in turn, oxIAA can be further glucosylated to oxindole-3-acetyl-1-glucosyl ester (oxIAGlc) by UGTs. These metabolic pathways have been identified based on mutant analyses, in vitro activity measurements, and
                in planta
                feeding assays. In vitro assays for studying protein activity are based on producing Arabidopsis enzymes in a recombinant form in bacteria or yeast followed by recombinant protein purification. However, the need to extract and purify the recombinant proteins represents a major obstacle when performing in vitro assays.
              
            
            
              Results
              In this work we report a rapid, reproducible and cheap method to screen the enzymatic activity of recombinant proteins that are known to inactivate IAA. The enzymatic reactions are carried out directly in bacteria that produce the recombinant protein. The enzymatic products can be measured by direct injection of a small supernatant fraction from the bacterial culture on ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem spectrometry (UHPLC–ESI-MS/MS). Experimental procedures were optimized for testing the activity of different classes of IAA-modifying enzymes without the need to purify recombinant protein.
            
            
              Conclusions
              This new method represents an alternative to existing in vitro assays. It can be applied to the analysis of IAA metabolites that are produced upon supplementation of substrate to engineered bacterial cultures and can be used for a rapid screening of orthologous candidate genes from non-model species.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Methods},
	author = {Brunoni, Federica and Collani, Silvio and Šimura, Jan and Schmid, Markus and Bellini, Catherine and Ljung, Karin},
	month = dec,
	year = {2019},
	pages = {126},
}

Abstract Background Plants rely on concentration gradients of the native auxin, indole-3-acetic acid (IAA), to modulate plant growth and development. Both metabolic and transport processes participate in the dynamic regulation of IAA homeostasis. Free IAA levels can be reduced by inactivation mechanisms, such as conjugation and degradation. IAA can be conjugated via ester linkage to glucose, or via amide linkage to amino acids, and degraded via oxidation. Members of the UDP glucosyl transferase (UGT) family catalyze the conversion of IAA to indole-3-acetyl-1-glucosyl ester (IAGlc); by contrast, IAA is irreversibly converted to indole-3-acetyl- l -aspartic acid (IAAsp) and indole-3-acetyl glutamic acid (IAGlu) by Group II of the GRETCHEN HAGEN3 (GH3) family of acyl amido synthetases. Dioxygenase for auxin oxidation (DAO) irreversibly oxidizes IAA to oxindole-3-acetic acid (oxIAA) and, in turn, oxIAA can be further glucosylated to oxindole-3-acetyl-1-glucosyl ester (oxIAGlc) by UGTs. These metabolic pathways have been identified based on mutant analyses, in vitro activity measurements, and in planta feeding assays. In vitro assays for studying protein activity are based on producing Arabidopsis enzymes in a recombinant form in bacteria or yeast followed by recombinant protein purification. However, the need to extract and purify the recombinant proteins represents a major obstacle when performing in vitro assays. Results In this work we report a rapid, reproducible and cheap method to screen the enzymatic activity of recombinant proteins that are known to inactivate IAA. The enzymatic reactions are carried out directly in bacteria that produce the recombinant protein. The enzymatic products can be measured by direct injection of a small supernatant fraction from the bacterial culture on ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem spectrometry (UHPLC–ESI-MS/MS). Experimental procedures were optimized for testing the activity of different classes of IAA-modifying enzymes without the need to purify recombinant protein. Conclusions This new method represents an alternative to existing in vitro assays. It can be applied to the analysis of IAA metabolites that are produced upon supplementation of substrate to engineered bacterial cultures and can be used for a rapid screening of orthologous candidate genes from non-model species.

CRISPR-based tools for targeted transcriptional and epigenetic regulation in plants. Lee, J. E., Neumann, M., Duro, D. I., & Schmid, M. PLOS ONE, 14(9): e0222778. September 2019.

CRISPR-based tools for targeted transcriptional and epigenetic regulation in plants [link]

Paper doi link bibtex 4 downloads

@article{lee_crispr-based_2019,
	title = {{CRISPR}-based tools for targeted transcriptional and epigenetic regulation in plants},
	volume = {14},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0222778},
	doi = {10.1371/journal.pone.0222778},
	language = {en},
	number = {9},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Lee, Joanne E. and Neumann, Manuela and Duro, Daniel Iglesias and Schmid, Markus},
	editor = {Candela, Hector},
	month = sep,
	year = {2019},
	pages = {e0222778},
}

FT Modulates Genome-Wide DNA-Binding of the bZIP Transcription Factor FD. Collani, S., Neumann, M., Yant, L., & Schmid, M. Plant Physiology, 180(1): 367–380. May 2019.

FT Modulates Genome-Wide DNA-Binding of the bZIP Transcription Factor FD [link]

Paper doi link bibtex

@article{collani_ft_2019,
	title = {{FT} {Modulates} {Genome}-{Wide} {DNA}-{Binding} of the {bZIP} {Transcription} {Factor} {FD}},
	volume = {180},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/180/1/367-380/6117581},
	doi = {10/gjdxbs},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Collani, Silvio and Neumann, Manuela and Yant, Levi and Schmid, Markus},
	month = may,
	year = {2019},
	pages = {367--380},
}

Phloem Companion Cell-Specific Transcriptomic and Epigenomic Analyses Identify MRF1, a Regulator of Flowering. You, Y., Sawikowska, A., Lee, J. E., Benstein, R. M., Neumann, M., Krajewski, P., & Schmid, M. The Plant Cell, 31(2): 325–345. February 2019.

Phloem Companion Cell-Specific Transcriptomic and Epigenomic Analyses Identify MRF1, a Regulator of Flowering [link]

Paper doi link bibtex 3 downloads

@article{you_phloem_2019,
	title = {Phloem {Companion} {Cell}-{Specific} {Transcriptomic} and {Epigenomic} {Analyses} {Identify} {MRF1}, a {Regulator} of {Flowering}},
	volume = {31},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/31/2/325-345/5985421},
	doi = {10/gjdw33},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {You, Yuan and Sawikowska, Aneta and Lee, Joanne E. and Benstein, Ruben M. and Neumann, Manuela and Krajewski, Paweł and Schmid, Markus},
	month = feb,
	year = {2019},
	pages = {325--345},
}

2018 (5)

Arabidopsis RNA processing factor SERRATE regulates the transcription of intronless genes. Speth, C., Szabo, E. X., Martinho, C., Collani, S., zur Oven-Krockhaus, S., Richter, S., Droste-Borel, I., Macek, B., Stierhof, Y., Schmid, M., Liu, C., & Laubinger, S. eLife, 7: e37078. August 2018.

Arabidopsis RNA processing factor SERRATE regulates the transcription of intronless genes [link]

Paper doi link bibtex abstract

@article{speth_arabidopsis_2018,
	title = {Arabidopsis {RNA} processing factor {SERRATE} regulates the transcription of intronless genes},
	volume = {7},
	issn = {2050-084X},
	url = {https://elifesciences.org/articles/37078},
	doi = {10/gd7w68},
	abstract = {Intron splicing increases proteome complexity, promotes RNA stability, and enhances transcription. However, introns and the concomitant need for splicing extend the time required for gene expression and can cause an undesirable delay in the activation of genes. Here, we show that the plant microRNA processing factor SERRATE (SE) plays an unexpected and pivotal role in the regulation of intronless genes. Arabidopsis SE associated with more than 1000, mainly intronless, genes in a transcription-dependent manner. Chromatin-bound SE liaised with paused and elongating polymerase II complexes and promoted their association with intronless target genes. Our results indicate that stress-responsive genes contain no or few introns, which negatively affects their expression strength, but that some genes circumvent this limitation via a novel SE-dependent transcriptional activation mechanism. Transcriptome analysis of a Drosophila mutant defective in ARS2, the metazoan homologue of SE, suggests that SE/ARS2 function in regulating intronless genes might be conserved across kingdoms.},
	language = {en},
	urldate = {2021-06-07},
	journal = {eLife},
	author = {Speth, Corinna and Szabo, Emese Xochitl and Martinho, Claudia and Collani, Silvio and zur Oven-Krockhaus, Sven and Richter, Sandra and Droste-Borel, Irina and Macek, Boris and Stierhof, York-Dieter and Schmid, Markus and Liu, Chang and Laubinger, Sascha},
	month = aug,
	year = {2018},
	pages = {e37078},
}

PORCUPINE regulates development in response to temperature through alternative splicing. Capovilla, G., Delhomme, N., Collani, S., Shutava, I., Bezrukov, I., Symeonidi, E., de Francisco Amorim, M., Laubinger, S., & Schmid, M. Nature Plants, 4(8): 534–539. August 2018.

PORCUPINE regulates development in response to temperature through alternative splicing [link]

Paper doi link bibtex

@article{capovilla_porcupine_2018,
	title = {{PORCUPINE} regulates development in response to temperature through alternative splicing},
	volume = {4},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/s41477-018-0176-z},
	doi = {10/gd9hnk},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Capovilla, Giovanna and Delhomme, Nicolas and Collani, Silvio and Shutava, Iryna and Bezrukov, Ilja and Symeonidi, Efthymia and de Francisco Amorim, Marcella and Laubinger, Sascha and Schmid, Markus},
	month = aug,
	year = {2018},
	pages = {534--539},
}

Ricinosomes and Aleurain-Containing Vacuoles (ACVs): Protease-Storing Organelles. Gietl, C., Schmid, M., & Simpson, D. In Annual Plant Reviews online, pages 96–118. American Cancer Society, 2018. Section: 5 _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119312994.apr0039

Ricinosomes and Aleurain-Containing Vacuoles (ACVs): Protease-Storing Organelles [link]

Paper doi link bibtex abstract

@incollection{gietl_ricinosomes_2018,
	title = {Ricinosomes and {Aleurain}-{Containing} {Vacuoles} ({ACVs}): {Protease}-{Storing} {Organelles}},
	isbn = {978-1-119-31299-4},
	shorttitle = {Ricinosomes and {Aleurain}-{Containing} {Vacuoles} ({ACVs})},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119312994.apr0039},
	abstract = {The sections in this article are},
	language = {en},
	urldate = {2021-10-22},
	booktitle = {Annual {Plant} {Reviews} online},
	publisher = {American Cancer Society},
	author = {Gietl, Christine and Schmid, Markus and Simpson, David},
	year = {2018},
	doi = {10.1002/9781119312994.apr0039},
	note = {Section: 5
\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119312994.apr0039},
	keywords = {Aleurone cell, aleurain-containing vacuoles, cotyledons, cysteine endopeptidase, endosperm, programmed cell death, ricinosomes},
	pages = {96--118},
}

Role of BASIC PENTACYSTEINE transcription factors in a subset of cytokinin signaling responses. Shanks, C. M., Hecker, A., Cheng, C., Brand, L., Collani, S., Schmid, M., Schaller, G. E., Wanke, D., Harter, K., & Kieber, J. J. The Plant Journal, 95(3): 458–473. August 2018.

Paper doi link bibtex

@article{shanks_role_2018,
	title = {Role of \textit{{BASIC} {PENTACYSTEINE}} transcription factors in a subset of cytokinin signaling responses},
	volume = {95},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.13962},
	doi = {10/gdqkns},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Shanks, Carly M. and Hecker, Andreas and Cheng, Chia-Yi and Brand, Luise and Collani, Silvio and Schmid, Markus and Schaller, G. Eric and Wanke, Dierk and Harter, Klaus and Kieber, Joseph J.},
	month = aug,
	year = {2018},
	pages = {458--473},
}

WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. Prát, T., Hajný, J., Grunewald, W., Vasileva, M., Molnár, G., Tejos, R., Schmid, M., Sauer, M., & Friml, J. PLOS Genetics, 14(1): e1007177. January 2018.

WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity [link]

Paper doi link bibtex

@article{prat_wrky23_2018,
	title = {{WRKY23} is a component of the transcriptional network mediating auxin feedback on {PIN} polarity},
	volume = {14},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1007177},
	doi = {10.1371/journal.pgen.1007177},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {PLOS Genetics},
	author = {Prát, Tomáš and Hajný, Jakub and Grunewald, Wim and Vasileva, Mina and Molnár, Gergely and Tejos, Ricardo and Schmid, Markus and Sauer, Michael and Friml, Jiří},
	editor = {Strader, Lucia},
	month = jan,
	year = {2018},
	pages = {e1007177},
}

2017 (4)

A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation. Conn, V. M., Hugouvieux, V., Nayak, A., Conos, S. A., Capovilla, G., Cildir, G., Jourdain, A., Tergaonkar, V., Schmid, M., Zubieta, C., & Conn, S. J. Nature Plants, 3(5): 17053. May 2017.

A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation [link]

Paper doi link bibtex

@article{conn_circrna_2017,
	title = {A {circRNA} from {SEPALLATA3} regulates splicing of its cognate {mRNA} through {R}-loop formation},
	volume = {3},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/nplants201753},
	doi = {10.1038/nplants.2017.53},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Conn, Vanessa M. and Hugouvieux, Véronique and Nayak, Aditya and Conos, Stephanie A. and Capovilla, Giovanna and Cildir, Gökhan and Jourdain, Agnès and Tergaonkar, Vinay and Schmid, Markus and Zubieta, Chloe and Conn, Simon J.},
	month = may,
	year = {2017},
	pages = {17053},
}

Contribution of major FLM isoforms to temperature-dependent flowering in Arabidopsis thaliana. Capovilla, G., Symeonidi, E., Wu, R., & Schmid, M. Journal of Experimental Botany, 68(18): 5117–5127. November 2017.

Contribution of major FLM isoforms to temperature-dependent flowering in Arabidopsis thaliana [link]

Paper doi link bibtex

@article{capovilla_contribution_2017,
	title = {Contribution of major {FLM} isoforms to temperature-dependent flowering in {Arabidopsis} thaliana},
	volume = {68},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/68/18/5117/4210925},
	doi = {10/gcjrww},
	language = {en},
	number = {18},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Capovilla, Giovanna and Symeonidi, Efthymia and Wu, Rui and Schmid, Markus},
	month = nov,
	year = {2017},
	pages = {5117--5127},
}

Dynamics of H3K4me3 Chromatin Marks Prevails over H3K27me3 for Gene Regulation during Flower Morphogenesis in Arabidopsis thaliana. Engelhorn, J., Blanvillain, R., Kröner, C., Parrinello, H., Rohmer, M., Posé, D., Ott, F., Schmid, M., & Carles, C. C. Epigenomes, 1(2): 8. September 2017. Number: 2 Publisher: Multidisciplinary Digital Publishing Institute

Dynamics of H3K4me3 Chromatin Marks Prevails over H3K27me3 for Gene Regulation during Flower Morphogenesis in Arabidopsis thaliana [link]

Paper doi link bibtex abstract

@article{engelhorn_dynamics_2017,
	title = {Dynamics of {H3K4me3} {Chromatin} {Marks} {Prevails} over {H3K27me3} for {Gene} {Regulation} during {Flower} {Morphogenesis} in {Arabidopsis} thaliana},
	volume = {1},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/2075-4655/1/2/8},
	doi = {10.3390/epigenomes1020008},
	abstract = {Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes (trxG), respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related Histone 3 trimethylation at lysine 4 (H3K4me3). However, the genome-wide dynamics in histone modifications that occur during developmental processes have remained elusive. Here, we report the distributions of H3K27me3 and H3K4me3 along with expression changes, in a developmental series including Arabidopsis thaliana leaf and three stages of flower development. We found that chromatin mark levels are highly dynamic over the time series on nearly half of all Arabidopsis genes. Moreover, during early flower morphogenesis, changes in H3K4me3 prevail over changes in H3K27me3 and quantitatively correlate with expression changes, while H3K27me3 changes occur later. Notably, we found that H3K4me3 increase during the early activation of PcG target genes while H3K27me3 level remain relatively constant at the locus. Our results reveal that H3K4me3 predicts changes in gene expression better than H3K27me3, unveil unexpected chromatin mechanisms at gene activation and underline the relevance of tissue-specific temporal epigenomics.},
	language = {en},
	number = {2},
	urldate = {2021-10-22},
	journal = {Epigenomes},
	author = {Engelhorn, Julia and Blanvillain, Robert and Kröner, Christian and Parrinello, Hugues and Rohmer, Marine and Posé, David and Ott, Felix and Schmid, Markus and Carles, Cristel C.},
	month = sep,
	year = {2017},
	note = {Number: 2
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {ChIP-seq, RNA-seq, chromatin and expression dynamics, differentiation, reproductive development},
	pages = {8},
}

Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering. You, Y., Sawikowska, A., Neumann, M., Posé, D., Capovilla, G., Langenecker, T., Neher, R. A., Krajewski, P., & Schmid, M. Nature Communications, 8(1): 15120. August 2017.

Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering [link]

Paper doi link bibtex 2 downloads

@article{you_temporal_2017,
	title = {Temporal dynamics of gene expression and histone marks at the {Arabidopsis} shoot meristem during flowering},
	volume = {8},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms15120},
	doi = {10.1038/ncomms15120},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {You, Yuan and Sawikowska, Aneta and Neumann, Manuela and Posé, David and Capovilla, Giovanna and Langenecker, Tobias and Neher, Richard A. and Krajewski, Paweł and Schmid, Markus},
	month = aug,
	year = {2017},
	pages = {15120},
}

2016 (2)

A SAM oligomerization domain shapes the genomic binding landscape of the LEAFY transcription factor. Sayou, C., Nanao, M. H., Jamin, M., Posé, D., Thévenon, E., Grégoire, L., Tichtinsky, G., Denay, G., Ott, F., Peirats Llobet, M., Schmid, M., Dumas, R., & Parcy, F. Nature Communications, 7(1): 11222. September 2016.

A SAM oligomerization domain shapes the genomic binding landscape of the LEAFY transcription factor [link]

Paper doi link bibtex

@article{sayou_sam_2016,
	title = {A {SAM} oligomerization domain shapes the genomic binding landscape of the {LEAFY} transcription factor},
	volume = {7},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms11222},
	doi = {10/f3tdv9},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Sayou, Camille and Nanao, Max H. and Jamin, Marc and Posé, David and Thévenon, Emmanuel and Grégoire, Laura and Tichtinsky, Gabrielle and Denay, Grégoire and Ott, Felix and Peirats Llobet, Marta and Schmid, Markus and Dumas, Renaud and Parcy, François},
	month = sep,
	year = {2016},
	pages = {11222},
}

Integration of light and metabolic signals for stem cell activation at the shoot apical meristem. Pfeiffer, A., Janocha, D., Dong, Y., Medzihradszky, A., Schöne, S., Daum, G., Suzaki, T., Forner, J., Langenecker, T., Rempel, E., Schmid, M., Wirtz, M., Hell, R., & Lohmann, J. U eLife, 5: e17023. July 2016.

Integration of light and metabolic signals for stem cell activation at the shoot apical meristem [link]

Paper doi link bibtex abstract

@article{pfeiffer_integration_2016,
title = {Integration of light and metabolic signals for stem cell activation at the shoot apical meristem},
volume = {5},
issn = {2050-084X},
url = {https://elifesciences.org/articles/17023},
doi = {10/f3r4bk},
abstract = {A major feature of embryogenesis is the specification of stem cell systems, but in contrast to the situation in most animals, plant stem cells remain quiescent until the postembryonic phase of development. Here, we dissect how light and metabolic signals are integrated to overcome stem cell dormancy at the shoot apical meristem. We show on the one hand that light is able to activate expression of the stem cell inducer WUSCHEL independently of photosynthesis and that this likely involves inter-regional cytokinin signaling. Metabolic signals, on the other hand, are transduced to the meristem through activation of the TARGET OF RAPAMYCIN (TOR) kinase. Surprisingly, TOR is also required for light signal dependent stem cell activation. Thus, the TOR kinase acts as a central integrator of light and metabolic signals and a key regulator of stem cell activation at the shoot apex.
,
Plants are able to grow and develop throughout their lives thanks to groups of stem cells at the tips of their shoots and roots, which can constantly divide to produce new cells. Energy captured from sunlight during a process called photosynthesis is the main source of energy for most plants. Therefore, the amount and quality of light in the environment has a big influence on how plants grow and develop. An enzyme called TOR kinase can sense energy levels in animal cells and regulate many processes including growth and cell division. Plants also have a TOR kinase, but it is less clear if it plays the same role in plants, and whether it can respond to light.
Plant stem cells only start to divide after the seed germinates. In shoots, a protein called WUSCHEL is required to maintain stem cells in an active state. Here, Pfeiffer et al. studied how shoot stem cells are activated in response to environmental signals in a plant known as Arabidopsis. The experiments show that light is able to activate the production of WUSCHEL independently of photosynthesis via a signal pathway that depends on TOR kinase. The stem cells do not directly sense light; instead other cells detect the light and relay the information to the stem cells with the help of a hormone called cytokinin.
Further experiments show that information about energy levels in cells is relayed via another signal pathway that also involves the TOR kinase. Therefore, Pfeiffer et al.’s findings suggest that the activation of TOR by light allows plant cells to anticipate how much energy will be available and efficiently tune their growth and development to cope with the environmental conditions. Future challenges are to understand how TOR kinase is regulated by light signals and how this enzyme is able to act on WUSCHEL to trigger stem cell division.},
language = {en},
urldate = {2021-06-07},
journal = {eLife},
author = {Pfeiffer, Anne and Janocha, Denis and Dong, Yihan and Medzihradszky, Anna and Schöne, Stefanie and Daum, Gabor and Suzaki, Takuya and Forner, Joachim and Langenecker, Tobias and Rempel, Eugen and Schmid, Markus and Wirtz, Markus and Hell, Rüdiger and Lohmann, Jan U},
month = jul,
year = {2016},
pages = {e17023},
}

A major feature of embryogenesis is the specification of stem cell systems, but in contrast to the situation in most animals, plant stem cells remain quiescent until the postembryonic phase of development. Here, we dissect how light and metabolic signals are integrated to overcome stem cell dormancy at the shoot apical meristem. We show on the one hand that light is able to activate expression of the stem cell inducer WUSCHEL independently of photosynthesis and that this likely involves inter-regional cytokinin signaling. Metabolic signals, on the other hand, are transduced to the meristem through activation of the TARGET OF RAPAMYCIN (TOR) kinase. Surprisingly, TOR is also required for light signal dependent stem cell activation. Thus, the TOR kinase acts as a central integrator of light and metabolic signals and a key regulator of stem cell activation at the shoot apex. , Plants are able to grow and develop throughout their lives thanks to groups of stem cells at the tips of their shoots and roots, which can constantly divide to produce new cells. Energy captured from sunlight during a process called photosynthesis is the main source of energy for most plants. Therefore, the amount and quality of light in the environment has a big influence on how plants grow and develop. An enzyme called TOR kinase can sense energy levels in animal cells and regulate many processes including growth and cell division. Plants also have a TOR kinase, but it is less clear if it plays the same role in plants, and whether it can respond to light. Plant stem cells only start to divide after the seed germinates. In shoots, a protein called WUSCHEL is required to maintain stem cells in an active state. Here, Pfeiffer et al. studied how shoot stem cells are activated in response to environmental signals in a plant known as Arabidopsis. The experiments show that light is able to activate the production of WUSCHEL independently of photosynthesis via a signal pathway that depends on TOR kinase. The stem cells do not directly sense light; instead other cells detect the light and relay the information to the stem cells with the help of a hormone called cytokinin. Further experiments show that information about energy levels in cells is relayed via another signal pathway that also involves the TOR kinase. Therefore, Pfeiffer et al.’s findings suggest that the activation of TOR by light allows plant cells to anticipate how much energy will be available and efficiently tune their growth and development to cope with the environmental conditions. Future challenges are to understand how TOR kinase is regulated by light signals and how this enzyme is able to act on WUSCHEL to trigger stem cell division.

2015 (6)

A quantitative and dynamic model of the Arabidopsis flowering time gene regulatory network. Leal Valentim, F., Mourik, S., Pose, D., Kim, M. C., Schmid, M., van Ham, R. C., Busscher, M., Sanchez-Perez, G. F., Molenaar, J., Angenent, G. C., Immink, R. G., & van Dijk, A. D. PLoS One, 10(2): e0116973. 2015. Edition: 2015/02/27

A quantitative and dynamic model of the Arabidopsis flowering time gene regulatory network [link]

Paper doi link bibtex abstract 1 download

@article{leal_valentim_quantitative_2015,
	title = {A quantitative and dynamic model of the {Arabidopsis} flowering time gene regulatory network},
	volume = {10},
	issn = {1932-6203 (Electronic) 1932-6203 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25719734},
	doi = {10.1371/journal.pone.0116973},
	abstract = {Various environmental signals integrate into a network of floral regulatory genes leading to the final decision on when to flower. Although a wealth of qualitative knowledge is available on how flowering time genes regulate each other, only a few studies incorporated this knowledge into predictive models. Such models are invaluable as they enable to investigate how various types of inputs are combined to give a quantitative readout. To investigate the effect of gene expression disturbances on flowering time, we developed a dynamic model for the regulation of flowering time in Arabidopsis thaliana. Model parameters were estimated based on expression time-courses for relevant genes, and a consistent set of flowering times for plants of various genetic backgrounds. Validation was performed by predicting changes in expression level in mutant backgrounds and comparing these predictions with independent expression data, and by comparison of predicted and experimental flowering times for several double mutants. Remarkably, the model predicts that a disturbance in a particular gene has not necessarily the largest impact on directly connected genes. For example, the model predicts that SUPPRESSOR OF OVEREXPRESSION OF CONSTANS (SOC1) mutation has a larger impact on APETALA1 (AP1), which is not directly regulated by SOC1, compared to its effect on LEAFY (LFY) which is under direct control of SOC1. This was confirmed by expression data. Another model prediction involves the importance of cooperativity in the regulation of APETALA1 (AP1) by LFY, a prediction supported by experimental evidence. Concluding, our model for flowering time gene regulation enables to address how different quantitative inputs are combined into one quantitative output, flowering time.},
	language = {eng},
	number = {2},
	journal = {PLoS One},
	author = {Leal Valentim, F. and Mourik, Sv and Pose, D. and Kim, M. C. and Schmid, M. and van Ham, R. C. and Busscher, M. and Sanchez-Perez, G. F. and Molenaar, J. and Angenent, G. C. and Immink, R. G. and van Dijk, A. D.},
	year = {2015},
	note = {Edition: 2015/02/27},
	keywords = {*Gene Expression Regulation, Plant, *Gene Regulatory Networks, Arabidopsis, Arabidopsis Proteins, Arabidopsis Proteins/genetics/metabolism, Arabidopsis/*genetics/growth \& development, Flowers, Flowers/*genetics/growth \& development, Gene Expression Regulation, Plant, Gene Regulatory Networks, MADS Domain Proteins, MADS Domain Proteins/genetics/metabolism, Models, Genetic, Transcription Factors, Transcription Factors/genetics/metabolism},
	pages = {e0116973},
}

Control of flowering by ambient temperature. Capovilla, G., Schmid, M., & Pose, D. J Exp Bot, 66(1): 59–69. January 2015. Edition: 2014/10/19

Control of flowering by ambient temperature [link]

Paper doi link bibtex abstract

@article{capovilla_control_2015,
	title = {Control of flowering by ambient temperature},
	volume = {66},
	issn = {1460-2431 (Electronic) 0022-0957 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25326628},
	doi = {10.1093/jxb/eru416},
	abstract = {The timing of flowering is a crucial decision in the life cycle of plants since favourable conditions are needed to maximize reproductive success and, hence, the survival of the species. It is therefore not surprising that plants constantly monitor endogenous and environmental signals, such as day length (photoperiod) and temperature, to adjust the timing of the floral transition. Temperature in particular has been shown to have a tremendous effect on the timing of flowering: the effect of prolonged periods of cold, called the vernalization response, has been extensively studied and the underlying epigenetic mechanisms are reasonably well understood in Arabidopsis thaliana. In contrast, the effect of moderate changes in ambient growth temperature on the progression of flowering, the thermosensory pathway, is only starting to be understood on the molecular level. Several genes and molecular mechanisms underlying the thermosensory pathway have already been identified and characterized in detail. At a time when global temperature is rising due to climate change, this knowledge will be pivotal to ensure crop production in the future.},
	language = {eng},
	number = {1},
	journal = {J Exp Bot},
	author = {Capovilla, G. and Schmid, M. and Pose, D.},
	month = jan,
	year = {2015},
	note = {Edition: 2014/10/19},
	keywords = {*Plant Development/genetics, *Temperature, Ambient temperature, Arabidopsis, Arabidopsis thaliana, Arabidopsis/genetics/growth \& development, Epigenesis, Genetic, Flowers, Flowers/genetics/*growth \& development, MADS, Mads, Plant Development, Temperature, flowering time, miRNA, thermosensory pathway.},
	pages = {59--69},
}

Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana. Galvao, V. C., Collani, S., Horrer, D., & Schmid, M. Plant J, 84(5): 949–62. December 2015. Edition: 2015/10/16

Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana [link]

Paper doi link bibtex abstract

@article{galvao_gibberellic_2015,
	title = {Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in {Arabidopsis} thaliana},
	volume = {84},
	issn = {1365-313X (Electronic) 0960-7412 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26466761},
	doi = {10.1111/tpj.13051},
	abstract = {Distinct molecular mechanisms integrate changes in ambient temperature into the genetic pathways that govern flowering time in Arabidopsis thaliana. Temperature-dependent eviction of the histone variant H2A.Z from nucleosomes has been suggested to facilitate the expression of FT by PIF4 at elevated ambient temperatures. Here we show that, in addition to PIF4, PIF3 and PIF5, but not PIF1 and PIF6, can promote flowering when expressed specifically in phloem companion cells (PCC), where they can induce FT and its close paralog, TSF. However, despite their strong potential to promote flowering, genetic analyses suggest that the PIF genes seem to have only a minor role in adjusting flowering in response to photoperiod or high ambient temperature. In addition, loss of PIF function only partially suppressed the early flowering phenotype and FT expression of the arp6 mutant, which is defective in H2A.Z deposition. In contrast, the chemical inhibition of gibberellic acid (GA) biosynthesis resulted in a strong attenuation of early flowering and FT expression in arp6. Furthermore, GA was able to induce flowering at low temperature (15 degrees C) independently of FT, TSF, and the PIF genes, probably directly at the shoot apical meristem. Together, our results suggest that the timing of the floral transition in response to ambient temperature is more complex than previously thought and that GA signaling might play a crucial role in this process.},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Plant J},
	author = {Galvao, V. C. and Collani, S. and Horrer, D. and Schmid, M.},
	month = dec,
	year = {2015},
	note = {Edition: 2015/10/16},
	keywords = {Arabidopsis Proteins/genetics/metabolism/physiology, Arabidopsis thaliana, Arabidopsis/genetics/*growth \& development/metabolism, Arp6, Basic Helix-Loop-Helix Transcription Factors/genetics/metabolism/physiology, Flm, Flowers/genetics/growth \& development/metabolism, Ft, Gibberellins/*metabolism/pharmacology, H2a.Z, Histones/metabolism, Microfilament Proteins/genetics/metabolism/physiology, Nucleosomes/metabolism, Phosphatidylethanolamine Binding Protein/genetics/metabolism/physiology, Photoperiod, Pif, Plant Growth Regulators/*metabolism/pharmacology, Signal Transduction, Svp, Temperature, ambient temperature, flowering, gibberellin},
	pages = {949--62},
}

Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M. Lutz, U., Posé, D., Pfeifer, M., Gundlach, H., Hagmann, J., Wang, C., Weigel, D., Mayer, K. F. X., Schmid, M., & Schwechheimer, C. PLOS Genetics, 11(10): e1005588. 2015. Publisher: Public Library of Science

Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M [link]

Paper doi link bibtex abstract

@article{lutz_modulation_2015,
	title = {Modulation of {Ambient} {Temperature}-{Dependent} {Flowering} in {Arabidopsis} thaliana by {Natural} {Variation} of {FLOWERING} {LOCUS} {M}},
	volume = {11},
	issn = {1553-7404},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005588},
	doi = {10.1371/journal.pgen.1005588},
	abstract = {Plants integrate seasonal cues such as temperature and day length to optimally adjust their flowering time to the environment. Compared to the control of flowering before and after winter by the vernalization and day length pathways, mechanisms that delay or promote flowering during a transient cool or warm period, especially during spring, are less well understood. Due to global warming, understanding this ambient temperature pathway has gained increasing importance. In Arabidopsis thaliana, FLOWERING LOCUS M (FLM) is a critical flowering regulator of the ambient temperature pathway. FLM is alternatively spliced in a temperature-dependent manner and the two predominant splice variants, FLM-ß and FLM-δ, can repress and activate flowering in the genetic background of the A. thaliana reference accession Columbia-0. The relevance of this regulatory mechanism for the environmental adaptation across the entire range of the species is, however, unknown. Here, we identify insertion polymorphisms in the first intron of FLM as causative for accelerated flowering in many natural A. thaliana accessions, especially in cool (15°C) temperatures. We present evidence for a potential adaptive role of this structural variation and link it specifically to changes in the abundance of FLM-ß. Our results may allow predicting flowering in response to ambient temperatures in the Brassicaceae.},
	language = {en},
	number = {10},
	urldate = {2021-10-22},
	journal = {PLOS Genetics},
	author = {Lutz, Ulrich and Posé, David and Pfeifer, Matthias and Gundlach, Heidrun and Hagmann, Jörg and Wang, Congmao and Weigel, Detlef and Mayer, Klaus F. X. and Schmid, Markus and Schwechheimer, Claus},
	year = {2015},
	note = {Publisher: Public Library of Science},
	keywords = {Arabidopsis thaliana, Flowering plants, Gene expression, Genetic loci, Genomics, Introns, Plant genomics, Polymerase chain reaction},
	pages = {e1005588},
}

Profiling of embryonic nuclear vs. cellular RNA in Arabidopsis thaliana. Slane, D., Kong, J., Schmid, M., Jürgens, G., & Bayer, M. Genomics Data, 4: 96–98. June 2015.
doi link bibtex abstract

@article{slane_profiling_2015,
	title = {Profiling of embryonic nuclear vs. cellular {RNA} in {Arabidopsis} thaliana},
	volume = {4},
	issn = {2213-5960},
	doi = {10.1016/j.gdata.2015.03.015},
	abstract = {In Arabidopsis, various cell type-specific whole-genome expression analyses have been conducted. However, the vast majority of these were performed with cellular RNA from root tissues or other easily accessible cell types [1]. Nuclear RNA was neglected for a long time as not being representative for transcriptomic studies. In recent years, however, there have been reports describing the validity of nuclear RNA for these types of studies [2,3]. Here we describe the generation, quality assessment and analysis of nuclear transcriptomic data from Arabidopsis embryos published by Slane et al. (2014) [4]. Comparison of nuclear with cellular gene expression demonstrated the usefulness of nuclear transcriptomics.},
	language = {eng},
	journal = {Genomics Data},
	author = {Slane, Daniel and Kong, Jixiang and Schmid, Markus and Jürgens, Gerd and Bayer, Martin},
	month = jun,
	year = {2015},
	pmid = {26484189},
	pmcid = {PMC4536148},
	keywords = {Arabidopsis thaliana, Gene expression, Microarray, Nuclear and cellular transcriptome, Pro-embryo and suspensor transcriptome},
	pages = {96--98},
}

Role of alternative pre-mRNA splicing in temperature signaling. Capovilla, G., Pajoro, A., Immink, R. G., & Schmid, M. Curr Opin Plant Biol, 27: 97–103. October 2015. Edition: 2015/07/21

Role of alternative pre-mRNA splicing in temperature signaling [link]

Paper doi link bibtex abstract

@article{capovilla_role_2015,
	title = {Role of alternative pre-{mRNA} splicing in temperature signaling},
	volume = {27},
	issn = {1879-0356 (Electronic) 1369-5266 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26190743},
	doi = {10/f3ndbf},
	abstract = {Developmental plasticity enables plants to respond rapidly to changing environmental conditions, such as temperature fluctuations. Understanding how plants measure temperature and integrate this information into developmental programs at the molecular level will be essential to breed thermo-tolerant crop varieties. Recent studies identified alternative splicing (AS) as a possible 'molecular thermometer', allowing plants to quickly adjust the abundance of functional transcripts to environmental perturbations. In this review, recent advances regarding the effects of temperature-responsive AS on plant development will be discussed, with emphasis on the circadian clock and flowering time control. The challenge for the near future will be to understand the molecular mechanisms by which temperature can influence AS regulation.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Curr Opin Plant Biol},
	author = {Capovilla, G. and Pajoro, A. and Immink, R. G. and Schmid, M.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/07/21},
	keywords = {*Alternative Splicing, *Gene Expression Regulation, Plant, *Genes, Regulator, *Plant Development, Circadian Clocks, Flowers/genetics/growth \& development, Plant Proteins/*genetics/metabolism, Temperature},
	pages = {97--103},
}

2014 (3)

Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo. Slane, D., Kong, J., Berendzen, K. W., Kilian, J., Henschen, A., Kolb, M., Schmid, M., Harter, K., Mayer, U., De Smet, I., Bayer, M., & Jürgens, G. Development (Cambridge, England), 141(24): 4831–4840. December 2014.
doi link bibtex abstract

@article{slane_cell_2014,
	title = {Cell type-specific transcriptome analysis in the early {Arabidopsis} thaliana embryo},
	volume = {141},
	issn = {1477-9129},
	doi = {10/f6s68v},
	abstract = {In multicellular organisms, cellular differences in gene activity are a prerequisite for differentiation and establishment of cell types. In order to study transcriptome profiles, specific cell types have to be isolated from a given tissue or even the whole organism. However, whole-transcriptome analysis of early embryos in flowering plants has been hampered by their size and inaccessibility. Here, we describe the purification of nuclear RNA from early stage Arabidopsis thaliana embryos using fluorescence-activated nuclear sorting (FANS) to generate expression profiles of early stages of the whole embryo, the proembryo and the suspensor. We validated our datasets of differentially expressed candidate genes by promoter-reporter gene fusions and in situ hybridization. Our study revealed that different classes of genes with respect to biological processes and molecular functions are preferentially expressed either in the proembryo or in the suspensor. This method can be used especially for tissues with a limited cell population and inaccessible tissue types. Furthermore, we provide a valuable resource for research on Arabidopsis early embryogenesis.},
	language = {eng},
	number = {24},
	journal = {Development (Cambridge, England)},
	author = {Slane, Daniel and Kong, Jixiang and Berendzen, Kenneth W. and Kilian, Joachim and Henschen, Agnes and Kolb, Martina and Schmid, Markus and Harter, Klaus and Mayer, Ulrike and De Smet, Ive and Bayer, Martin and Jürgens, Gerd},
	month = dec,
	year = {2014},
	pmid = {25411212},
	keywords = {Arabidopsis, Cell Nucleus, Cloning, Molecular, Fluorescence-activated nuclear sorting, Gene Expression Profiling, Genotype, In Situ Hybridization, Microarray Analysis, Microscopy, Fluorescence, Proembryo, RNA, Nuclear, Real-Time Polymerase Chain Reaction, Seeds, Suspensor, Transcriptome analysis},
	pages = {4831--4840},
}

Reciprocal responses in the interaction between Arabidopsis and the cell-content-feeding chelicerate herbivore spider mite. Zhurov, V., Navarro, M., Bruinsma, K. A., Arbona, V., Santamaria, M. E., Cazaux, M., Wybouw, N., Osborne, E. J., Ens, C., Rioja, C., Vermeirssen, V., Rubio-Somoza, I., Krishna, P., Diaz, I., Schmid, M., Gómez-Cadenas, A., Van de Peer, Y., Grbic, M., Clark, R. M., Van Leeuwen, T., & Grbic, V. Plant Physiology, 164(1): 384–399. January 2014.
doi link bibtex abstract

@article{zhurov_reciprocal_2014,
	title = {Reciprocal responses in the interaction between {Arabidopsis} and the cell-content-feeding chelicerate herbivore spider mite},
	volume = {164},
	issn = {1532-2548},
	doi = {10/f5m96t},
	abstract = {Most molecular-genetic studies of plant defense responses to arthropod herbivores have focused on insects. However, plant-feeding mites are also pests of diverse plants, and mites induce different patterns of damage to plant tissues than do well-studied insects (e.g. lepidopteran larvae or aphids). The two-spotted spider mite (Tetranychus urticae) is among the most significant mite pests in agriculture, feeding on a staggering number of plant hosts. To understand the interactions between spider mite and a plant at the molecular level, we examined reciprocal genome-wide responses of mites and its host Arabidopsis (Arabidopsis thaliana). Despite differences in feeding guilds, we found that transcriptional responses of Arabidopsis to mite herbivory resembled those observed for lepidopteran herbivores. Mutant analysis of induced plant defense pathways showed functionally that only a subset of induced programs, including jasmonic acid signaling and biosynthesis of indole glucosinolates, are central to Arabidopsis's defense to mite herbivory. On the herbivore side, indole glucosinolates dramatically increased mite mortality and development times. We identified an indole glucosinolate dose-dependent increase in the number of differentially expressed mite genes belonging to pathways associated with detoxification of xenobiotics. This demonstrates that spider mite is sensitive to Arabidopsis defenses that have also been associated with the deterrence of insect herbivores that are very distantly related to chelicerates. Our findings provide molecular insights into the nature of, and response to, herbivory for a representative of a major class of arthropod herbivores.},
	language = {eng},
	number = {1},
	journal = {Plant Physiology},
	author = {Zhurov, Vladimir and Navarro, Marie and Bruinsma, Kristie A. and Arbona, Vicent and Santamaria, M. Estrella and Cazaux, Marc and Wybouw, Nicky and Osborne, Edward J. and Ens, Cherise and Rioja, Cristina and Vermeirssen, Vanessa and Rubio-Somoza, Ignacio and Krishna, Priti and Diaz, Isabel and Schmid, Markus and Gómez-Cadenas, Aurelio and Van de Peer, Yves and Grbic, Miodrag and Clark, Richard M. and Van Leeuwen, Thomas and Grbic, Vojislava},
	month = jan,
	year = {2014},
	pmid = {24285850},
	pmcid = {PMC3875816},
	keywords = {Animals, Arabidopsis, Cyclopentanes, Female, Gene Expression Profiling, Gene Expression Regulation, Plant, Genetic Variation, Glucosinolates, Herbivory, Host-Parasite Interactions, Larva, Mutation, Oxylipins, Plant Growth Regulators, Signal Transduction, Tetranychidae},
	pages = {384--399},
}

Regulation of Flowering by Endogenous Signals. Galvão, V., & Schmid, M. In Advances in Botanical Research, volume 72, pages 63–102. December 2014. Journal Abbreviation: Advances in Botanical Research
doi link bibtex abstract

@incollection{galvao_regulation_2014,
	title = {Regulation of {Flowering} by {Endogenous} {Signals}},
	volume = {72},
	isbn = {978-0-12-417162-6},
	abstract = {The transition from vegetative to reproductive development, or floral transition, is a crucial event in the life cycle of plants. Work carried out over the last decades has shown how environmental signals, such as seasonal changes in the day length and temperature, are perceived and accurately integrated into genetically defined pathways to properly time the induction of flowering. In addition to seasonal fluctuations, plants must cope with a vast array of often stressful conditions that greatly affect metabolism and physiology. In this context, plant hormones and sugars have emerged as important endogenous signalling molecules mediating the transition to the reproductive phase. In this chapter we report the recent advances in understanding the molecular basis underlying the transition to flowering in response to these endogenous signals.},
	booktitle = {Advances in {Botanical} {Research}},
	author = {Galvão, Vinicius and Schmid, Markus},
	month = dec,
	year = {2014},
	doi = {10.1016/B978-0-12-417162-6.00003-1},
	note = {Journal Abbreviation: Advances in Botanical Research},
	pages = {63--102},
}

2013 (3)

Regulation of flowering by trehalose-6-phosphate signaling in Arabidopsis thaliana. Wahl, V., Ponnu, J., Schlereth, A., Arrivault, S., Langenecker, T., Franke, A., Feil, R., Lunn, J. E., Stitt, M., & Schmid, M. Science (New York, N.Y.), 339(6120): 704–707. February 2013.
doi link bibtex abstract 2 downloads

@article{wahl_regulation_2013,
	title = {Regulation of flowering by trehalose-6-phosphate signaling in {Arabidopsis} thaliana},
	volume = {339},
	issn = {1095-9203},
	doi = {10/f4kxph},
	abstract = {The timing of the induction of flowering determines to a large extent the reproductive success of plants. Plants integrate diverse environmental and endogenous signals to ensure the timely transition from vegetative growth to flowering. Carbohydrates are thought to play a crucial role in the regulation of flowering, and trehalose-6-phosphate (T6P) has been suggested to function as a proxy for carbohydrate status in plants. The loss of TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) causes Arabidopsis thaliana to flower extremely late, even under otherwise inductive environmental conditions. This suggests that TPS1 is required for the timely initiation of flowering. We show that the T6P pathway affects flowering both in the leaves and at the shoot meristem, and integrate TPS1 into the existing genetic framework of flowering-time control.},
	language = {eng},
	number = {6120},
	journal = {Science (New York, N.Y.)},
	author = {Wahl, Vanessa and Ponnu, Jathish and Schlereth, Armin and Arrivault, Stéphanie and Langenecker, Tobias and Franke, Annika and Feil, Regina and Lunn, John E. and Stitt, Mark and Schmid, Markus},
	month = feb,
	year = {2013},
	pmid = {23393265},
	keywords = {Arabidopsis, Arabidopsis Proteins, Circadian Rhythm, Flowers, Gene Expression Regulation, Plant, Glucosyltransferases, Meristem, MicroRNAs, Phosphatidylethanolamine Binding Protein, Photoperiod, Plant Leaves, Plant Shoots, Signal Transduction, Sugar Phosphates, Trehalose},
	pages = {704--707},
}

Regulation of temperature-responsive flowering by MADS-box transcription factor repressors. Lee, J. H., Ryu, H., Chung, K. S., Posé, D., Kim, S., Schmid, M., & Ahn, J. H. Science (New York, N.Y.), 342(6158): 628–632. November 2013.
doi link bibtex abstract 1 download

@article{lee_regulation_2013,
	title = {Regulation of temperature-responsive flowering by {MADS}-box transcription factor repressors},
	volume = {342},
	issn = {1095-9203},
	doi = {10/f5fmt6},
	abstract = {Changes in ambient temperature affect flowering time in plants; understanding this phenomenon will be crucial for buffering agricultural systems from the effects of climate change. Here, we show that levels of FLM-β, an alternatively spliced form of the flowering repressor FLOWERING LOCUS M, increase at lower temperatures, repressing flowering. FLM-β interacts with SHORT VEGETATIVE PHASE (SVP); SVP is degraded at high temperatures, reducing the abundance of the SVP-FLM-β repressor complex and, thus, allowing the plant to flower. The svp and flm mutants show temperature-insensitive flowering in different temperature ranges. Control of SVP-FLM-β repressor complex abundance via transcriptional and splicing regulation of FLM and posttranslational regulation of SVP protein stability provides an efficient, rapid mechanism for plants to respond to ambient temperature changes.},
	language = {eng},
	number = {6158},
	journal = {Science (New York, N.Y.)},
	author = {Lee, Jeong Hwan and Ryu, Hak-Seung and Chung, Kyung Sook and Posé, David and Kim, Soonkap and Schmid, Markus and Ahn, Ji Hoon},
	month = nov,
	year = {2013},
	pmid = {24030492},
	keywords = {Alternative Splicing, Arabidopsis, Arabidopsis Proteins, Flowers, Gene Expression Regulation, Plant, MADS Domain Proteins, Molecular Sequence Data, Mutation, Repressor Proteins, Temperature, Transcription Factors},
	pages = {628--632},
}

Temperature-dependent regulation of flowering by antagonistic FLM variants. Posé, D., Verhage, L., Ott, F., Yant, L., Mathieu, J., Angenent, G. C., Immink, R. G. H., & Schmid, M. Nature, 503(7476): 414–417. November 2013.
doi link bibtex abstract 2 downloads

@article{pose_temperature-dependent_2013,
	title = {Temperature-dependent regulation of flowering by antagonistic {FLM} variants},
	volume = {503},
	issn = {1476-4687},
	doi = {10/f5h734},
	abstract = {The appropriate timing of flowering is crucial for plant reproductive success. It is therefore not surprising that intricate genetic networks have evolved to perceive and integrate both endogenous and environmental signals, such as carbohydrate and hormonal status, photoperiod and temperature. In contrast to our detailed understanding of the vernalization pathway, little is known about how flowering time is controlled in response to changes in the ambient growth temperature. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles in this process. FLM is subject to temperature-dependent alternative splicing. Here we report that the two main FLM protein splice variants, FLM-β and FLM-δ, compete for interaction with the floral repressor SVP. The SVP-FLM-β complex is predominately formed at low temperatures and prevents precocious flowering. By contrast, the competing SVP-FLM-δ complex is impaired in DNA binding and acts as a dominant-negative activator of flowering at higher temperatures. Our results show a new mechanism that controls the timing of the floral transition in response to changes in ambient temperature. A better understanding of how temperature controls the molecular mechanisms of flowering will be important to cope with current changes in global climate.},
	language = {eng},
	number = {7476},
	journal = {Nature},
	author = {Posé, David and Verhage, Leonie and Ott, Felix and Yant, Levi and Mathieu, Johannes and Angenent, Gerco C. and Immink, Richard G. H. and Schmid, Markus},
	month = nov,
	year = {2013},
	pmid = {24067612},
	keywords = {Alternative Splicing, Arabidopsis, Arabidopsis Proteins, DNA-Binding Proteins, Flowers, Gene Expression Regulation, Plant, MADS Domain Proteins, Plants, Genetically Modified, Protein Binding, Protein Isoforms, Temperature, Time Factors, Transcription Factors},
	pages = {414--417},
}

2012 (7)

Characterization of SOC1's central role in flowering by the identification of its upstream and downstream regulators. Immink, R. G. H., Posé, D., Ferrario, S., Ott, F., Kaufmann, K., Valentim, F. L., de Folter, S., van der Wal, F., van Dijk, A. D. J., Schmid, M., & Angenent, G. C. Plant Physiology, 160(1): 433–449. September 2012.
doi link bibtex abstract

@article{immink_characterization_2012,
	title = {Characterization of {SOC1}'s central role in flowering by the identification of its upstream and downstream regulators},
	volume = {160},
	issn = {1532-2548},
	doi = {10/f36vk3},
	abstract = {The transition from vegetative to reproductive development is one of the most important phase changes in the plant life cycle. This step is controlled by various environmental signals that are integrated at the molecular level by so-called floral integrators. One such floral integrator in Arabidopsis (Arabidopsis thaliana) is the MADS domain transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). Despite extensive genetic studies, little is known about the transcriptional control of SOC1, and we are just starting to explore the network of genes under the direct control of SOC1 transcription factor complexes. Here, we show that several MADS domain proteins, including SOC1 heterodimers, are able to bind SOC1 regulatory sequences. Genome-wide target gene analysis by ChIP-seq confirmed the binding of SOC1 to its own locus and shows that it also binds to a plethora of flowering-time regulatory and floral homeotic genes. In turn, the encoded floral homeotic MADS domain proteins appear to bind SOC1 regulatory sequences. Subsequent in planta analyses revealed SOC1 repression by several floral homeotic MADS domain proteins, and we show that, mechanistically, this depends on the presence of the SOC1 protein. Together, our data show that SOC1 constitutes a major hub in the regulatory networks underlying floral timing and flower development and that these networks are composed of many positive and negative autoregulatory and feedback loops. The latter seems to be crucial for the generation of a robust flower-inducing signal, followed shortly after by repression of the SOC1 floral integrator.},
	language = {eng},
	number = {1},
	journal = {Plant Physiology},
	author = {Immink, Richard G. H. and Posé, David and Ferrario, Silvia and Ott, Felix and Kaufmann, Kerstin and Valentim, Felipe Leal and de Folter, Stefan and van der Wal, Froukje and van Dijk, Aalt D. J. and Schmid, Markus and Angenent, Gerco C.},
	month = sep,
	year = {2012},
	pmid = {22791302},
	pmcid = {PMC3440217},
	keywords = {Arabidopsis, Arabidopsis Proteins, Feedback, Physiological, Flowers, Gene Expression Regulation, Plant, Genes, Plant, Genes, Reporter, Genetic Complementation Test, Genetic Loci, Green Fluorescent Proteins, Immunoprecipitation, MADS Domain Proteins, Promoter Regions, Genetic, Protein Binding, Regulatory Sequences, Nucleic Acid, Signal Transduction, Time Factors, Transcription, Genetic, Two-Hybrid System Techniques},
	pages = {433--449},
}

Genome-wide binding-site analysis of REVOLUTA reveals a link between leaf patterning and light-mediated growth responses. Brandt, R., Salla-Martret, M., Bou-Torrent, J., Musielak, T., Stahl, M., Lanz, C., Ott, F., Schmid, M., Greb, T., Schwarz, M., Choi, S., Barton, M. K., Reinhart, B. J., Liu, T., Quint, M., Palauqui, J., Martínez-García, J. F., & Wenkel, S. The Plant Journal: For Cell and Molecular Biology, 72(1): 31–42. October 2012.
doi link bibtex abstract

@article{brandt_genome-wide_2012,
	title = {Genome-wide binding-site analysis of {REVOLUTA} reveals a link between leaf patterning and light-mediated growth responses},
	volume = {72},
	issn = {1365-313X},
	doi = {10/f3srjk},
	abstract = {Unlike the situation in animals, the final morphology of the plant body is highly modulated by the environment. During Arabidopsis development, intrinsic factors provide the framework for basic patterning processes. CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) transcription factors are involved in embryo, shoot and root patterning. During vegetative growth HD-ZIPIII proteins control several polarity set-up processes such as in leaves and the vascular system. We have identified several direct target genes of the HD-ZIPIII transcription factor REVOLUTA (REV) using a chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) approach. This analysis revealed that REV acts upstream of auxin biosynthesis and affects directly the expression of several class II HD-ZIP transcription factors that have been shown to act in the shade-avoidance response pathway. We show that, as well as involvement in basic patterning, HD-ZIPIII transcription factors have a critical role in the control of the elongation growth that is induced when plants experience shade. Leaf polarity is established by the opposed actions of HD-ZIPIII and KANADI transcription factors. Finally, our study reveals that the module that consists of HD-ZIPIII/KANADI transcription factors controls shade growth antagonistically and that this antagonism is manifested in the opposed regulation of shared target genes.},
	language = {eng},
	number = {1},
	journal = {The Plant Journal: For Cell and Molecular Biology},
	author = {Brandt, Ronny and Salla-Martret, Mercè and Bou-Torrent, Jordi and Musielak, Thomas and Stahl, Mark and Lanz, Christa and Ott, Felix and Schmid, Markus and Greb, Thomas and Schwarz, Martina and Choi, Sang-Bong and Barton, M. Kathryn and Reinhart, Brenda J. and Liu, Tie and Quint, Marcel and Palauqui, Jean-Christophe and Martínez-García, Jaime F. and Wenkel, Stephan},
	month = oct,
	year = {2012},
	keywords = {Adaptation, Physiological, Arabidopsis, Arabidopsis Proteins, Arabidopsis thaliana, Binding Sites, Body Patterning, Chromatin Immunoprecipitation, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Genome, Plant, HD-ZIPII, HD-ZIPIII, Homeodomain Proteins, Hypocotyl, In Situ Hybridization, Indoleacetic Acids, Light, Mutation, Phylogeny, Plant Leaves, Sequence Analysis, DNA, Signal Transduction, Transcription Factors, auxin, leaf development, shade avoidance},
	pages = {31--42},
}

Gibberellin Regulates the Arabidopsis Floral Transition through miR156-Targeted SQUAMOSA PROMOTER BINDING–LIKE Transcription Factors[W]. Yu, S., Galvão, V. C., Zhang, Y., Horrer, D., Zhang, T., Hao, Y., Feng, Y., Wang, S., Schmid, M., & Wang, J. The Plant Cell, 24(8): 3320–3332. August 2012.

Gibberellin Regulates the Arabidopsis Floral Transition through miR156-Targeted SQUAMOSA PROMOTER BINDING–LIKE Transcription Factors[W] [link]

Paper doi link bibtex abstract

@article{yu_gibberellin_2012,
	title = {Gibberellin {Regulates} the {Arabidopsis} {Floral} {Transition} through {miR156}-{Targeted} {SQUAMOSA} {PROMOTER} {BINDING}–{LIKE} {Transcription} {Factors}[{W}]},
	volume = {24},
	issn = {1040-4651},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3462634/},
	doi = {10.1105/tpc.112.101014},
	abstract = {This article examines the crosstalk between gibberellin responses, which result in degradation of DELLAs, and the microRNA-regulated SQUAMOSA PROMOTER BINDING LIKE (SPL) transcription factors, which activate miR172 and MADS box transcription factors. The authors find that DELLA binds to SPLs and interfere with SPL transcriptional activation of miR172 and MADS box genes, thereby delaying flowering., Gibberellin (), a diterpene hormone, plays diverse roles in plant growth and development, including seed germination, stem elongation, and flowering time. Although it is known that  accelerates flowering through degradation of transcription repressors, DELLAs, the underlying mechanism is poorly understood. We show here that DELLA directly binds to microRNA156 (miR156)-targeted SQUAMOSA PROMOTER BINDING–LIKE (SPL) transcription factors, which promote flowering by activating miR172 and MADS box genes. The interaction between DELLA and SPL interferes with SPL transcriptional activity and consequently delays floral transition through inactivating miR172 in leaves and MADS box genes at shoot apex under long-day conditions or through repressing MADS box genes at the shoot apex under short-day conditions. Our results elucidate the molecular mechanism by which  controls flowering and provide the missing link between DELLA and MADS box genes.},
	number = {8},
	urldate = {2021-10-22},
	journal = {The Plant Cell},
	author = {Yu, Sha and Galvão, Vinicius C. and Zhang, Yan-Chun and Horrer, Daniel and Zhang, Tian-Qi and Hao, Yan-Hong and Feng, Yu-Qi and Wang, Shui and Schmid, Markus and Wang, Jia-Wei},
	month = aug,
	year = {2012},
	pmid = {22942378},
	pmcid = {PMC3462634},
	pages = {3320--3332},
}

Spatial control of flowering by DELLA proteins in Arabidopsis thaliana. Galvão, V. C., Horrer, D., Küttner, F., & Schmid, M. Development (Cambridge, England), 139(21): 4072–4082. November 2012.
doi link bibtex abstract

@article{galvao_spatial_2012,
	title = {Spatial control of flowering by {DELLA} proteins in {Arabidopsis} thaliana},
	volume = {139},
	issn = {1477-9129},
	doi = {10/f4cgh5},
	abstract = {The transition from vegetative to reproductive development is a central event in the plant life cycle. To time the induction of flowering correctly, plants integrate environmental and endogenous signals such as photoperiod, temperature and hormonal status. The hormone gibberellic acid (GA) has long been known to regulate flowering. However, the spatial contribution of GA signaling in flowering time control is poorly understood. Here we have analyzed the effect of tissue-specific misexpression of wild-type and GA-insensitive (dellaΔ17) DELLA proteins on the floral transition in Arabidopsis thaliana. We demonstrate that under long days, GA affects the floral transition by promoting the expression of flowering time integrator genes such as FLOWERING LOCUS T (FT) and TWIN SISTER OF FT (TSF) in leaves independently of CONSTANS (CO) and GIGANTEA (GI). In addition, GA signaling promotes flowering independently of photoperiod through the regulation of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes in both the leaves and at the shoot meristem. Our data suggest that GA regulates flowering by controlling the spatial expression of floral regulatory genes throughout the plant in a day-length-specific manner.},
	language = {eng},
	number = {21},
	journal = {Development (Cambridge, England)},
	author = {Galvão, Vinicius C. and Horrer, Daniel and Küttner, Frank and Schmid, Markus},
	month = nov,
	year = {2012},
	pmid = {22992955},
	keywords = {Arabidopsis, Arabidopsis Proteins, Flowers, Gene Expression Regulation, Plant, Gibberellins},
	pages = {4072--4082},
}

Synteny-based mapping-by-sequencing enabled by targeted enrichment. Galvão, V. C., Nordström, K. J. V., Lanz, C., Sulz, P., Mathieu, J., Posé, D., Schmid, M., Weigel, D., & Schneeberger, K. The Plant Journal: For Cell and Molecular Biology, 71(3): 517–526. August 2012.
doi link bibtex abstract

@article{galvao_synteny-based_2012,
	title = {Synteny-based mapping-by-sequencing enabled by targeted enrichment},
	volume = {71},
	issn = {1365-313X},
	doi = {10/gkgdms},
	abstract = {Mapping-by-sequencing, as implemented in SHOREmap ('SHOREmapping'), is greatly accelerating the identification of causal mutations. The original SHOREmap approach based on resequencing of bulked segregants required a highly accurate and complete reference sequence. However, current whole-genome or transcriptome assemblies from next-generation sequencing data of non-model organisms do not produce chromosome-length scaffolds. We have therefore developed a method that exploits synteny with a related genome for genetic mapping. We first demonstrate how mapping-by-sequencing can be performed using a reduced number of markers, and how the associated decrease in the number of markers can be compensated for by enrichment of marker sequences. As proof of concept, we apply this method to Arabidopsis thaliana gene models ordered by synteny with the genome sequence of the distant relative Brassica rapa, whose genome has several large-scale rearrangements relative to A. thaliana. Our approach provides an alternative method for high-resolution genetic mapping in species that lack finished genome reference sequences or for which only RNA-seq assemblies are available. Finally, for improved identification of causal mutations by fine-mapping, we introduce a new likelihood ratio test statistic, transforming local allele frequency estimations into a confidence interval similar to conventional mapping intervals.},
	language = {eng},
	number = {3},
	journal = {The Plant Journal: For Cell and Molecular Biology},
	author = {Galvão, Vinicius C. and Nordström, Karl J. V. and Lanz, Christa and Sulz, Patric and Mathieu, Johannes and Posé, David and Schmid, Markus and Weigel, Detlef and Schneeberger, Korbinian},
	month = aug,
	year = {2012},
	pmid = {22409706},
	keywords = {Arabidopsis, Arabidopsis Proteins, Brassica rapa, Chromosome Mapping, DNA Mutational Analysis, DNA, Plant, Flowers, Gene Frequency, Gene Library, Genetic Linkage, Genome, Plant, High-Throughput Nucleotide Sequencing, MADS Domain Proteins, Mutation, Sequence Analysis, DNA, Synteny, Transcriptome},
	pages = {517--526},
}

The end of innocence: flowering networks explode in complexity. Posé, D., Yant, L., & Schmid, M. Current Opinion in Plant Biology, 15(1): 45–50. February 2012.
doi link bibtex abstract

@article{pose_end_2012,
	title = {The end of innocence: flowering networks explode in complexity},
	volume = {15},
	issn = {1879-0356},
	shorttitle = {The end of innocence},
	doi = {10/fphkmr},
	abstract = {Substantial recent advances in genome-scale transcription factor target mapping have provided a fresh view of the gene networks governing developmental transitions. In particular, our understanding of the fine-scale spatial and temporal dynamics underlying the floral transition at the shoot apex has seen great advances in the past two years. Single transcription factors are regularly observed to act in complex manners, directly promoting the expression of particular targets while directly repressing the expression of others, based at least partly on defined heterodimerization patterns. For single regulators this behavior reaches into distinct physiological processes, providing compelling evidence that particular transcription factors act to directly integrate diverse processes to orchestrate complex developmental transitions.},
	language = {eng},
	number = {1},
	journal = {Current Opinion in Plant Biology},
	author = {Posé, David and Yant, Levi and Schmid, Markus},
	month = feb,
	year = {2012},
	pmid = {21974961},
	keywords = {Flowers, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Gene Regulatory Networks, Genes, Plant, Plant Shoots},
	pages = {45--50},
}

The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element. Dinh, T. T., Girke, T., Liu, X., Yant, L., Schmid, M., & Chen, X. Development (Cambridge, England), 139(11): 1978–1986. June 2012.
doi link bibtex abstract

@article{dinh_floral_2012,
	title = {The floral homeotic protein {APETALA2} recognizes and acts through an {AT}-rich sequence element},
	volume = {139},
	issn = {1477-9129},
	doi = {10/f3xzq8},
	abstract = {Cell fate specification in development requires transcription factors for proper regulation of gene expression. In Arabidopsis, transcription factors encoded by four classes of homeotic genes, A, B, C and E, act in a combinatorial manner to control proper floral organ identity. The A-class gene APETALA2 (AP2) promotes sepal and petal identities in whorls 1 and 2 and restricts the expression of the C-class gene AGAMOUS (AG) from whorls 1 and 2. However, it is unknown how AP2 performs these functions. Unlike the other highly characterized floral homeotic proteins containing MADS domains, AP2 has two DNA-binding domains referred to as the AP2 domains and its DNA recognition sequence is still unknown. Here, we show that the second AP2 domain in AP2 binds a non-canonical AT-rich target sequence, and, using a GUS reporter system, we demonstrate that the presence of this sequence in the AG second intron is important for the restriction of AG expression in vivo. Furthermore, we show that AP2 binds the AG second intron and directly regulates AG expression through this sequence element. Computational analysis reveals that the binding site is highly conserved in the second intron of AG orthologs throughout Brassicaceae. By uncovering a biologically relevant AT-rich target sequence, this work shows that AP2 domains have wide-ranging target specificities and provides a missing link in the mechanisms that underlie flower development. It also sets the foundation for understanding the basis of the broad biological functions of AP2 in Arabidopsis, as well as the divergent biological functions of AP2 orthologs in dicotyledonous plants.},
	language = {eng},
	number = {11},
	journal = {Development (Cambridge, England)},
	author = {Dinh, Thanh Theresa and Girke, Thomas and Liu, Xigang and Yant, Levi and Schmid, Markus and Chen, Xuemei},
	month = jun,
	year = {2012},
	pmid = {22513376},
	pmcid = {PMC3347690},
	keywords = {AGAMOUS Protein, Arabidopsis, Arabidopsis, Arabidopsis Proteins, Base Sequence, Cell Differentiation, Chromatin Immunoprecipitation, Computational Biology, Electrophoretic Mobility Shift Assay, Flowers, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Homeodomain Proteins, Molecular Sequence Data, Nuclear Proteins, Sequence Analysis, DNA, Species Specificity},
	pages = {1978--1986},
}

2011 (4)

Prediction of regulatory interactions from genome sequences using a biophysical model for the Arabidopsis LEAFY transcription factor. Moyroud, E., Minguet, E. G., Ott, F., Yant, L., Posé, D., Monniaux, M., Blanchet, S., Bastien, O., Thévenon, E., Weigel, D., Schmid, M., & Parcy, F. The Plant Cell, 23(4): 1293–1306. April 2011.
doi link bibtex abstract

@article{moyroud_prediction_2011,
	title = {Prediction of regulatory interactions from genome sequences using a biophysical model for the {Arabidopsis} {LEAFY} transcription factor},
	volume = {23},
	issn = {1532-298X},
	doi = {10/dnkx8z},
	abstract = {Despite great advances in sequencing technologies, generating functional information for nonmodel organisms remains a challenge. One solution lies in an improved ability to predict genetic circuits based on primary DNA sequence in combination with detailed knowledge of regulatory proteins that have been characterized in model species. Here, we focus on the LEAFY (LFY) transcription factor, a conserved master regulator of floral development. Starting with biochemical and structural information, we built a biophysical model describing LFY DNA binding specificity in vitro that accurately predicts in vivo LFY binding sites in the Arabidopsis thaliana genome. Applying the model to other plant species, we could follow the evolution of the regulatory relationship between LFY and the AGAMOUS (AG) subfamily of MADS box genes and show that this link predates the divergence between monocots and eudicots. Remarkably, our model succeeds in detecting the connection between LFY and AG homologs despite extensive variation in binding sites. This demonstrates that the cis-element fluidity recently observed in animals also exists in plants, but the challenges it poses can be overcome with predictions grounded in a biophysical model. Therefore, our work opens new avenues to deduce the structure of regulatory networks from mere inspection of genomic sequences.},
	language = {eng},
	number = {4},
	journal = {The Plant Cell},
	author = {Moyroud, Edwige and Minguet, Eugenio Gómez and Ott, Felix and Yant, Levi and Posé, David and Monniaux, Marie and Blanchet, Sandrine and Bastien, Olivier and Thévenon, Emmanuel and Weigel, Detlef and Schmid, Markus and Parcy, François},
	month = apr,
	year = {2011},
	pmid = {21515819},
	pmcid = {PMC3101549},
	keywords = {AGAMOUS Protein, Arabidopsis, Arabidopsis, Arabidopsis Proteins, Base Sequence, Binding Sites, Biophysical Phenomena, Chromatin Immunoprecipitation, DNA, Plant, Evolution, Molecular, Flowers, Gene Expression Regulation, Plant, Genes, Plant, Genome, Plant, Introns, Models, Genetic, Molecular Sequence Data, Protein Binding, Regulatory Sequences, Nucleic Acid, Reproducibility of Results, Transcription Factors},
	pages = {1293--1306},
}

Regulation of flowering time: all roads lead to Rome. Srikanth, A., & Schmid, M. Cellular and molecular life sciences: CMLS, 68(12): 2013–2037. June 2011.
doi link bibtex abstract 2 downloads

@article{srikanth_regulation_2011,
	title = {Regulation of flowering time: all roads lead to {Rome}},
	volume = {68},
	issn = {1420-9071},
	shorttitle = {Regulation of flowering time},
	doi = {10/d99mmw},
	abstract = {Plants undergo a major physiological change as they transition from vegetative growth to reproductive development. This transition is a result of responses to various endogenous and exogenous signals that later integrate to result in flowering. Five genetically defined pathways have been identified that control flowering. The vernalization pathway refers to the acceleration of flowering on exposure to a long period of cold. The photoperiod pathway refers to regulation of flowering in response to day length and quality of light perceived. The gibberellin pathway refers to the requirement of gibberellic acid for normal flowering patterns. The autonomous pathway refers to endogenous regulators that are independent of the photoperiod and gibberellin pathways. Most recently, an endogenous pathway that adds plant age to the control of flowering time has been described. The molecular mechanisms of these pathways have been studied extensively in Arabidopsis thaliana and several other flowering plants.},
	language = {eng},
	number = {12},
	journal = {Cellular and molecular life sciences: CMLS},
	author = {Srikanth, Anusha and Schmid, Markus},
	month = jun,
	year = {2011},
	pmid = {21611891},
	keywords = {Arabidopsis, Flowers, Plant Physiological Phenomena, Signal Transduction},
	pages = {2013--2037},
}

The control of developmental phase transitions in plants. Huijser, P., & Schmid, M. Development (Cambridge, England), 138(19): 4117–4129. October 2011.
doi link bibtex abstract 1 download

@article{huijser_control_2011,
	title = {The control of developmental phase transitions in plants},
	volume = {138},
	issn = {1477-9129},
	doi = {10/ddvxq2},
	abstract = {Plant development progresses through distinct phases: vegetative growth, followed by a reproductive phase and eventually seed set and senescence. The transitions between these phases are controlled by distinct genetic circuits that integrate endogenous and environmental cues. In recent years, however, it has become evident that the genetic networks that underlie these phase transitions share some common factors. Here, we review recent advances in the field of plant phase transitions, highlighting the role of two microRNAs - miR156 and miR172 - and their respective targets during these transitions. In addition, we discuss the evolutionary conservation of the functions of these miRNAs in regulating the control of plant developmental phase transitions.},
	language = {eng},
	number = {19},
	journal = {Development (Cambridge, England)},
	author = {Huijser, Peter and Schmid, Markus},
	month = oct,
	year = {2011},
	pmid = {21896627},
	keywords = {Arabidopsis, Developmental Biology, Flowers, Gene Expression Regulation, Plant, Genes, Plant, MicroRNAs, Models, Biological, Models, Genetic, Plant Physiological Phenomena, Plants, Pollen, Transcription Factors},
	pages = {4117--4129},
}

Trehalose-6-phosphate: connecting plant metabolism and development. Ponnu, J., Wahl, V., & Schmid, M. Frontiers in Plant Science, 2: 70. 2011.
doi link bibtex abstract

@article{ponnu_trehalose-6-phosphate_2011,
	title = {Trehalose-6-phosphate: connecting plant metabolism and development},
	volume = {2},
	issn = {1664-462X},
	shorttitle = {Trehalose-6-phosphate},
	doi = {10/djjn5z},
	abstract = {Beyond their metabolic roles, sugars can also act as messengers in signal transduction. Trehalose, a sugar found in many species of plants and animals, is a non-reducing disaccharide composed of two glucose moieties. Its synthesis in plants is a two-step process, involving the production of trehalose-6-phosphate (T6P) catalyzed by trehalose-6-phosphate synthase (TPS) and its consecutive dephosphorylation to trehalose, catalyzed by trehalose-6-phosphate phosphatase (TPP). T6P has recently emerged as an important signaling metabolite, regulating carbon assimilation and sugar status in plants. In addition, T6P has also been demonstrated to play an essential role in plant development. This review recapitulates the recent advances we have made in understanding the role of T6P in coordinating diverse metabolic and developmental processes.},
	language = {eng},
	journal = {Frontiers in Plant Science},
	author = {Ponnu, Jathish and Wahl, Vanessa and Schmid, Markus},
	year = {2011},
	pmid = {22639606},
	pmcid = {PMC3355582},
	keywords = {TPP, TPS, development, trehalose, trehalose-6-phosphate},
	pages = {70},
}

2010 (4)

Control of lateral organ development and flowering time by the Arabidopsis thaliana MADS-box Gene AGAMOUS-LIKE6. Koo, S. C., Bracko, O., Park, M. S., Schwab, R., Chun, H. J., Park, K. M., Seo, J. S., Grbic, V., Balasubramanian, S., Schmid, M., Godard, F., Yun, D., Lee, S. Y., Cho, M. J., Weigel, D., & Kim, M. C. The Plant Journal: For Cell and Molecular Biology, 62(5): 807–816. June 2010.
doi link bibtex abstract

@article{koo_control_2010,
	title = {Control of lateral organ development and flowering time by the {Arabidopsis} thaliana {MADS}-box {Gene} {AGAMOUS}-{LIKE6}},
	volume = {62},
	issn = {1365-313X},
	doi = {10/d7dmk9},
	abstract = {MADS-domain transcription factors play pivotal roles in various developmental processes. The lack of simple loss-of-function phenotypes provides impediments to understand the biological function of some of the MADS-box transcription factors. Here we have characterized the potential role of the Arabidopsis thaliana AGAMOUS-LIKE6 (AGL6) gene by fusing full-length coding sequence with transcriptional activator and repressor domains and suggest a role for AGL6 in lateral organ development and flowering. Upon photoperiodic induction of flowering, AGL6 becomes expressed in abaxial and proximal regions of cauline leaf primordia, as well as the cryptic bracts subtending flowers. In developing flowers, AGL6 is detected in the proximal regions of all floral organs and in developing ovules. Converting AGL6 into a strong activator through fusion to the VP16 domain triggers bract outgrowth, implicating AGL6 in the development of bractless flowers in Arabidopsis. In addition, ectopic reproductive structures form on both bracts and flowers in gAGL6::VP16 transgenic plants, which is dependent on B and C class homeotic genes, but independent of LEAFY. Overexpression of both AGL6 and its transcriptional repressor form, AGL6::EAR, causes precocious flowering and terminal flower formation, suggesting that AGL6 suppresses the function of a floral repressor.},
	language = {eng},
	number = {5},
	journal = {The Plant Journal: For Cell and Molecular Biology},
	author = {Koo, Sung C. and Bracko, Oliver and Park, Mi S. and Schwab, Rebecca and Chun, Hyun J. and Park, Kyoung M. and Seo, Jun S. and Grbic, Vojislava and Balasubramanian, Sureshkumar and Schmid, Markus and Godard, François and Yun, Dae-Jin and Lee, Sang Y. and Cho, Moo J. and Weigel, Detlef and Kim, Min C.},
	month = jun,
	year = {2010},
	pmid = {20230491},
	keywords = {Arabidopsis, Arabidopsis Proteins, Flowers, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, MADS Domain Proteins, Microscopy, Electron, Scanning, Ovule, Plants, Genetically Modified, RNA, Plant},
	pages = {807--816},
}

MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor. Schlereth, A., Möller, B., Liu, W., Kientz, M., Flipse, J., Rademacher, E. H., Schmid, M., Jürgens, G., & Weijers, D. Nature, 464(7290): 913–916. April 2010.
doi link bibtex abstract

@article{schlereth_monopteros_2010,
	title = {{MONOPTEROS} controls embryonic root initiation by regulating a mobile transcription factor},
	volume = {464},
	issn = {1476-4687},
	doi = {10/fvkmp7},
	abstract = {Acquisition of cell identity in plants relies strongly on positional information, hence cell-cell communication and inductive signalling are instrumental for developmental patterning. During Arabidopsis embryogenesis, an extra-embryonic cell is specified to become the founder cell of the primary root meristem, hypophysis, in response to signals from adjacent embryonic cells. The auxin-dependent transcription factor MONOPTEROS (MP) drives hypophysis specification by promoting transport of the hormone auxin from the embryo to the hypophysis precursor. However, auxin accumulation is not sufficient for hypophysis specification, indicating that additional MP-dependent signals are required. Here we describe the microarray-based isolation of MP target genes that mediate signalling from embryo to hypophysis. Of three direct transcriptional target genes, TARGET OF MP 5 (TMO5) and TMO7 encode basic helix-loop-helix (bHLH) transcription factors that are expressed in the hypophysis-adjacent embryo cells, and are required and partially sufficient for MP-dependent root initiation. Importantly, the small TMO7 transcription factor moves from its site of synthesis in the embryo to the hypophysis precursor, thus representing a novel MP-dependent intercellular signal in embryonic root specification.},
	language = {eng},
	number = {7290},
	journal = {Nature},
	author = {Schlereth, Alexandra and Möller, Barbara and Liu, Weilin and Kientz, Marika and Flipse, Jacky and Rademacher, Eike H. and Schmid, Markus and Jürgens, Gerd and Weijers, Dolf},
	month = apr,
	year = {2010},
	pmid = {20220754},
	keywords = {Arabidopsis, Arabidopsis Proteins, Basic Helix-Loop-Helix Transcription Factors, DNA-Binding Proteins, Embryonic Development, Gene Expression Regulation, Plant, Genes, Plant, Indoleacetic Acids, Meristem, Oligonucleotide Array Sequence Analysis, Plant Roots, Signal Transduction, Transcription Factors},
	pages = {913--916},
}

Orchestration of the floral transition and floral development in Arabidopsis by the bifunctional transcription factor APETALA2. Yant, L., Mathieu, J., Dinh, T. T., Ott, F., Lanz, C., Wollmann, H., Chen, X., & Schmid, M. The Plant Cell, 22(7): 2156–2170. July 2010.
doi link bibtex abstract 1 download

@article{yant_orchestration_2010,
	title = {Orchestration of the floral transition and floral development in {Arabidopsis} by the bifunctional transcription factor {APETALA2}},
	volume = {22},
	issn = {1532-298X},
	doi = {10/bqpgn4},
	abstract = {The Arabidopsis thaliana transcription factor APETALA2 (AP2) has numerous functions, including roles in seed development, stem cell maintenance, and specification of floral organ identity. To understand the relationship between these different roles, we mapped direct targets of AP2 on a genome-wide scale in two tissue types. We find that AP2 binds to thousands of loci in the developing flower, many of which exhibit AP2-dependent transcription. Opposing, logical effects are evident in AP2 binding to two microRNA genes that influence AP2 expression, with AP2 positively regulating miR156 and negatively regulating miR172, forming a complex direct feedback loop, which also included all but one of the AP2-like miR172 target clade members. We compare the genome-wide direct target repertoire of AP2 with that of SCHLAFMUTZE, a closely related transcription factor that also represses the transition to flowering. We detect clear similarities and important differences in the direct target repertoires that are also tissue specific. Finally, using an inducible expression system, we demonstrate that AP2 has dual molecular roles. It functions as both a transcriptional activator and repressor, directly inducing the expression of the floral repressor AGAMOUS-LIKE15 and directly repressing the transcription of floral activators like SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1.},
	language = {eng},
	number = {7},
	journal = {The Plant Cell},
	author = {Yant, Levi and Mathieu, Johannes and Dinh, Thanh Theresa and Ott, Felix and Lanz, Christa and Wollmann, Heike and Chen, Xuemei and Schmid, Markus},
	month = jul,
	year = {2010},
	pmid = {20675573},
	pmcid = {PMC2929098},
	keywords = {Arabidopsis, Arabidopsis Proteins, Binding Sites, Flowers, Gene Expression, Genome, Plant, Homeodomain Proteins, Mutation, Nuclear Proteins},
	pages = {2156--2170},
}

The FANTASTIC FOUR proteins influence shoot meristem size in Arabidopsis thaliana. Wahl, V., Brand, L. H., Guo, Y., & Schmid, M. BMC plant biology, 10: 285. December 2010.
doi link bibtex abstract

@article{wahl_fantastic_2010,
	title = {The {FANTASTIC} {FOUR} proteins influence shoot meristem size in {Arabidopsis} thaliana},
	volume = {10},
	issn = {1471-2229},
	doi = {10/dt2kjb},
	abstract = {BACKGROUND: Throughout their lives plants produce new organs from groups of pluripotent cells called meristems, located at the tips of the shoot and the root. The size of the shoot meristem is tightly controlled by a feedback loop, which involves the homeodomain transcription factor WUSCHEL (WUS) and the CLAVATA (CLV) proteins. This regulatory circuit is further fine-tuned by morphogenic signals such as hormones and sugars.
RESULTS: Here we show that a family of four plant-specific proteins, encoded by the FANTASTIC FOUR (FAF) genes, has the potential to regulate shoot meristem size in Arabidopsis thaliana. FAF2 and FAF4 are expressed in the centre of the shoot meristem, overlapping with the site of WUS expression. Consistent with a regulatory interaction between the FAF gene family and WUS, our experiments indicate that the FAFs can repress WUS, which ultimately leads to an arrest of meristem activity in FAF overexpressing lines. The finding that meristematic expression of FAF2 and FAF4 is under negative control by CLV3 further supports the hypothesis that the FAFs are modulators of the genetic circuit that regulates the meristem.
CONCLUSION: This study reports the initial characterization of the Arabidopsis thaliana FAF gene family. Our data indicate that the FAF genes form a plant specific gene family, the members of which have the potential to regulate the size of the shoot meristem by modulating the CLV3-WUS feedback loop.},
	language = {eng},
	journal = {BMC plant biology},
	author = {Wahl, Vanessa and Brand, Luise H. and Guo, Ya-Long and Schmid, Markus},
	month = dec,
	year = {2010},
	pmid = {21176196},
	pmcid = {PMC3023791},
	keywords = {Arabidopsis, Arabidopsis Proteins, Flowers, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Glucuronidase, Homeodomain Proteins, In Situ Hybridization, Meristem, Microscopy, Electron, Scanning, Oligonucleotide Array Sequence Analysis, Plant Shoots, Plant Vascular Bundle, Repressor Proteins},
	pages = {285},
}

2009 (2)

Just say no: floral repressors help Arabidopsis bide the time. Yant, L., Mathieu, J., & Schmid, M. Current Opinion in Plant Biology, 12(5): 580–586. October 2009.
doi link bibtex abstract

@article{yant_just_2009,
	title = {Just say no: floral repressors help {Arabidopsis} bide the time},
	volume = {12},
	issn = {1879-0356},
	shorttitle = {Just say no},
	doi = {10/cnm97d},
	abstract = {Floral repressors ensure correct reproductive timing by safeguarding against premature flowering. In the past decade, several mechanisms of floral repression have come to light. Discrimination between direct and indirect repressors has been facilitated by increasing the use of chromatin immunoprecipitation assays. Certain MADS-domain transcription factors such as SHORT VEGETATIVE PHASE and FLOWERING LOCUS C bind directly to target euchromatin to repress specific loci including FLOWERING LOCUS T (FT) and FD. The AP2-domain transcription factor TEMPRANILLO 1 has also been shown to directly repress FT by binding its 5' UTR. We highlight emerging systems level approaches, including genome-scale direct binding studies (ChIP-chip and ChIP-Seq), which stand out in their promise to elucidate the complex network underlying the transition to flowering at an unprecedented level.},
	language = {eng},
	number = {5},
	journal = {Current Opinion in Plant Biology},
	author = {Yant, Levi and Mathieu, Johannes and Schmid, Markus},
	month = oct,
	year = {2009},
	pmid = {19695946},
	keywords = {Arabidopsis, Arabidopsis Proteins, Chromatin Immunoprecipitation, Flowers, Gene Expression Regulation, Plant, MADS Domain Proteins, Plant Leaves, Plant Shoots, Repressor Proteins, Transcription Factors},
	pages = {580--586},
}

Repression of flowering by the miR172 target SMZ. Mathieu, J., Yant, L. J., Mürdter, F., Küttner, F., & Schmid, M. PLoS biology, 7(7): e1000148. July 2009.
doi link bibtex abstract 1 download

@article{mathieu_repression_2009,
	title = {Repression of flowering by the {miR172} target {SMZ}},
	volume = {7},
	issn = {1545-7885},
	doi = {10/dcc259},
	abstract = {A small mobile protein, encoded by the FLOWERING LOCUS T (FT) locus, plays a central role in the control of flowering. FT is regulated positively by CONSTANS (CO), the output of the photoperiod pathway, and negatively by FLC, which integrates the effects of prolonged cold exposure. Here, we reveal the mechanisms of regulation by the microRNA miR172 target SCHLAFMUTZE (SMZ), a potent repressor of flowering. Whole-genome mapping of SMZ binding sites demonstrates not only direct regulation of FT, but also of many other flowering time regulators acting both upstream and downstream of FT, indicating an important role of miR172 and its targets in fine tuning the flowering response. A role for the miR172/SMZ module as a rheostat in flowering time is further supported by SMZ binding to several other genes encoding miR172 targets. Finally, we show that the action of SMZ is completely dependent on another floral repressor, FLM, providing the first direct connection between two important classes of flowering time regulators, AP2- and MADS-domain proteins.},
	language = {eng},
	number = {7},
	journal = {PLoS biology},
	author = {Mathieu, Johannes and Yant, Levi J. and Mürdter, Felix and Küttner, Frank and Schmid, Markus},
	month = jul,
	year = {2009},
	pmid = {19582143},
	pmcid = {PMC2701598},
	keywords = {Agrobacterium tumefaciens, Arabidopsis, Arabidopsis Proteins, Chromatin Immunoprecipitation, DNA-Binding Proteins, Flowers, Gene Expression Regulation, Plant, Genes, Reporter, MADS Domain Proteins, Meristem, MicroRNAs, Mutant Proteins, Oligonucleotide Array Sequence Analysis, Photoperiod, Plant Leaves, Plants, Genetically Modified, Protein Biosynthesis, RNA, Messenger, RNA, Plant, Reproduction, Transcription Factors, Transformation, Genetic},
	pages = {e1000148},
}

2008 (3)

Auxin Responses in Mutants of the Arabidopsis CONSTITUTIVE PHOTOMORPHOGENIC9 Signalosome. Dohmann, E. M. N., Levesque, M. P., Isono, E., Schmid, M., & Schwechheimer, C. Plant Physiology, 147(3): 1369–1379. July 2008.

Auxin Responses in Mutants of the Arabidopsis CONSTITUTIVE PHOTOMORPHOGENIC9 Signalosome [link]

Paper doi link bibtex abstract

@article{dohmann_auxin_2008,
	title = {Auxin {Responses} in {Mutants} of the {Arabidopsis} {CONSTITUTIVE} {PHOTOMORPHOGENIC9} {Signalosome}},
	volume = {147},
	issn = {0032-0889},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2442533/},
	doi = {10.1104/pp.108.121061},
	abstract = {The CONSTITUTIVE PHOTOMORPHOGENIC9 (COP9) signalosome (CSN) is an evolutionarily conserved multiprotein complex that interacts with cullin-RING type E3 ubiquitin ligases (CRLs). CSN subunit 5 (CSN5), which, when incorporated into CSN, can deconjugate the NEDD8 modification from the cullin subunit of CRLs, is essential for CSN's role in controlling CRL activity. Whether the CSN5 monomer, which is maintained in csn mutants such as csn3 or csn4, has a functional role, remains to be established. We performed a comparative gene expression-profiling experiment with Arabidopsis (Arabidopsis thaliana) csn3, csn4, and csn5 mutants, and we show here that these mutants cannot be distinguished at the transcriptional level. Furthermore, we show that csn3 csn5 mutants are morphologically indistinguishable from csn3 or csn5 mutants. Taken together, these data suggest that the CSN5 monomer does not have a function that leads to transcriptional or morphological changes in the csn mutants. We further examined auxin responses in csn mutants. Whereas CSN had previously been shown to be required for the auxin response-regulatory E3 complexes, specifically SCFTIR1, the csn mutant phenotype suggests that CSN is not essential for auxin responses. We present physiological and genetic data that indicate that auxin responses are indeed only partially impaired in csn mutants and that this is not the result of maternally contributed CSN. Finally, we discuss these findings in the context of the current understanding of the role of neddylation and CSN-mediated deneddylation for CRL activity.},
	number = {3},
	urldate = {2021-10-22},
	journal = {Plant Physiology},
	author = {Dohmann, Esther Mirjam Natascha and Levesque, Mitchell Paul and Isono, Erika and Schmid, Markus and Schwechheimer, Claus},
	month = jul,
	year = {2008},
	pmid = {18467458},
	pmcid = {PMC2442533},
	pages = {1369--1379},
}

KDEL-tailed cysteine endopeptidases involved in programmed cell death, intercalation of new cells, and dismantling of extensin scaffolds. Helm, M., Schmid, M., Hierl, G., Terneus, K., Tan, L., Lottspeich, F., Kieliszewski, M. J., & Gietl, C. American Journal of Botany, 95(9): 1049–1062. 2008. _eprint: https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.3732/ajb.2007404

KDEL-tailed cysteine endopeptidases involved in programmed cell death, intercalation of new cells, and dismantling of extensin scaffolds [link]

Paper doi link bibtex abstract

@article{helm_kdel-tailed_2008,
	title = {{KDEL}-tailed cysteine endopeptidases involved in programmed cell death, intercalation of new cells, and dismantling of extensin scaffolds},
	volume = {95},
	copyright = {© 2008 Botanical Society of America},
	issn = {1537-2197},
	url = {https://bsapubs.onlinelibrary.wiley.com/doi/abs/10.3732/ajb.2007404},
	doi = {10/ddb996},
	abstract = {KDEL-tailed cysteine endopeptidases are a group of papain-type peptidases found in senescing tissue undergoing programmed cell death (PCD). Their genes have so far been cloned and analyzed in 12 angiosperms. They are synthesized as proenzymes with a C-terminal KDEL endoplasmatic reticulum retention signal, which is removed with the prosequence to activate enzyme activity. We previously identified three genes for KDEL-tailed cysteine endopeptidases (AtCEP1, AtCEP2, AtCEP3) in Arabidopsis thaliana. Transgenic plants of A. thaliana expressing β-glucuronidase (GUS) under the control of the promoters for the three genes were produced and analyzed histochemically. GUS activity was promoter- and tissue-specific GUS activity during seedling, flower, and root development, especially in tissues that collapse during final stages of PCD, and in the course of lateral root formation. KDEL-tailed cysteine endopeptidases are unique in being able to digest the extensins that form the basic scaffold for cell wall formation. The broad substrate specificity is due to the structure of the active site cleft of the KDEL-tailed cysteine endopeptidase that accepts a wide variety of amino acids, including proline and glycosylated hydroxyproline of the hydroxyproline rich glycoproteins of the cell wall.},
	language = {en},
	number = {9},
	urldate = {2021-06-10},
	journal = {American Journal of Botany},
	author = {Helm, Michael and Schmid, Markus and Hierl, Georg and Terneus, Kimberly and Tan, Li and Lottspeich, Friedrich and Kieliszewski, Marcia J. and Gietl, Christine},
	year = {2008},
	note = {\_eprint: https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.3732/ajb.2007404},
	keywords = {Arabidopsis thaliana, Brassicaceae, Euphorbiaceae, KDEL-tailed cysteine endopeptidases, Ricinus communis, cell wall degradation, development in generative and vegetative tissues, programmed cell death, ricinosome, β-glucuronidase (GUS)},
	pages = {1049--1062},
}

The Arabidopsis COP9 signalosome is essential for G2 phase progression and genomic stability. Dohmann, E. M. N., Levesque, M. P., De Veylder, L., Reichardt, I., Jürgens, G., Schmid, M., & Schwechheimer, C. Development (Cambridge, England), 135(11): 2013–2022. June 2008.
doi link bibtex abstract

@article{dohmann_arabidopsis_2008,
	title = {The {Arabidopsis} {COP9} signalosome is essential for {G2} phase progression and genomic stability},
	volume = {135},
	issn = {0950-1991},
	doi = {10/b8t2wz},
	abstract = {The COP9 signalosome (CSN) is required for the full activity of cullin-RING E3 ubiquitin ligases (CRLs) in eukaryotes. CSN exerts its function on CRLs by removing the ubiquitin-related NEDD8 conjugate from the cullin subunit of CRLs. CSN seems, thereby, to control CRL disassembly or CRL subunit stability. In Arabidopsis thaliana, loss of CSN function leads to constitutive photomorphogenic (cop) seedling development and a post-germination growth arrest. The underlying molecular cause of this growth arrest is currently unknown. Here, we show that Arabidopsis csn mutants are delayed in G2 phase progression. This cell cycle arrest correlates with the induction of the DNA damage response pathway and is suggestive of the activation of a DNA damage checkpoint. In support of this hypothesis, we detected gene conversion events in csn mutants that are indicative of DNA double-strand breaks. DNA damage is also apparent in mutants of the NEDD8 conjugation pathway and in mutants of the E3 ligase subunits CULLIN4, COP1 and DET1, which share phenotypes with csn mutants. In summary, our data suggest that Arabidopsis csn mutants undergo DNA damage, which might be the cause of the delay in G2 cell cycle progression.},
	language = {eng},
	number = {11},
	journal = {Development (Cambridge, England)},
	author = {Dohmann, Esther M. N. and Levesque, Mitchell P. and De Veylder, Lieven and Reichardt, Ilka and Jürgens, Gerd and Schmid, Markus and Schwechheimer, Claus},
	month = jun,
	year = {2008},
	pmid = {18434413},
	keywords = {ATP-Binding Cassette Transporters, Arabidopsis Proteins, COP9 Signalosome Complex, Cell Cycle, Cell Division, Cullin Proteins, Cyclin B, DNA Damage, Flow Cytometry, G2 Phase, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Genomic Instability, Immunoblotting, In Situ Nick-End Labeling, Intracellular Signaling Peptides and Proteins, Multiprotein Complexes, Nuclear Proteins, Oligonucleotide Array Sequence Analysis, Peptide Hydrolases, Plant Roots, Protein Kinases, Protein-Serine-Threonine Kinases, Seedlings, Ubiquitin-Protein Ligases, Ubiquitins},
	pages = {2013--2022},
}

2007 (2)

Distinct expression patterns of natural antisense transcripts in Arabidopsis. Henz, S. R., Cumbie, J. S., Kasschau, K. D., Lohmann, J. U., Carrington, J. C., Weigel, D., & Schmid, M. Plant Physiology, 144(3): 1247–1255. July 2007.
doi link bibtex abstract

@article{henz_distinct_2007,
	title = {Distinct expression patterns of natural antisense transcripts in {Arabidopsis}},
	volume = {144},
	issn = {0032-0889},
	doi = {10/d6krth},
	abstract = {It has been shown that overlapping cis-natural antisense transcripts (cis-NATs) can form a regulatory circuit in which small RNAs derived from one transcript regulate stability of the other transcript, which manifests itself as anticorrelated expression. However, little is known about how widespread antagonistic expression of cis-NATs is. We have determined how frequently cis-NAT pairs, which make up 7.4\% of annotated transcription units in the Arabidopsis (Arabidopsis thaliana) genome, show anticorrelated expression patterns. Indeed, global expression profiles of pairs of cis-NATs on average have significantly lower pairwise Pearson correlation coefficients than other pairs of neighboring genes whose transcripts do not overlap. However, anticorrelated expression that is greater than expected by chance is found in only a small number of cis-NAT pairs. The degree of anticorrelation does not depend on the length of the overlap or on the distance of the 5' ends of the transcripts. Consistent with earlier findings, cis-NATs do not exhibit an increased likelihood to give rise to small RNAs, as determined from available small RNA sequences and massively parallel signature sequencing tags. However, the overlapping regions of cis-NATs appeared to be enriched for small RNA loci compared to nonoverlapping regions. Furthermore, expression of cis-NATs was not disproportionately affected in various RNA-silencing mutants. Our results demonstrate that there is a trend toward anticorrelated expression of cis-NAT pairs in Arabidopsis, but currently available data do not produce a strong signature of small RNA-mediated silencing for this process.},
	language = {eng},
	number = {3},
	journal = {Plant Physiology},
	author = {Henz, Stefan R. and Cumbie, Jason S. and Kasschau, Kristin D. and Lohmann, Jan U. and Carrington, James C. and Weigel, Detlef and Schmid, Markus},
	month = jul,
	year = {2007},
	pmid = {17496106},
	pmcid = {PMC1914114},
	keywords = {Arabidopsis, Gene Expression Regulation, Plant, Genome, Plant, Oligonucleotide Array Sequence Analysis, Promoter Regions, Genetic, RNA Interference, RNA, Antisense},
	pages = {1247--1255},
}

Export of FT protein from phloem companion cells is sufficient for floral induction in Arabidopsis. Mathieu, J., Warthmann, N., Küttner, F., & Schmid, M. Current biology: CB, 17(12): 1055–1060. June 2007.
doi link bibtex abstract

@article{mathieu_export_2007,
	title = {Export of {FT} protein from phloem companion cells is sufficient for floral induction in {Arabidopsis}},
	volume = {17},
	issn = {0960-9822},
	doi = {10/bts4m3},
	abstract = {Several endogenous and environmental factors need to be integrated to time the onset of flowering. Genetic and molecular analyses, primarily in Arabidopsis thaliana and rice, have shown that CONSTANS (CO) and FLOWERING LOCUS T (FT) play central roles in photoperiod-dependent flowering. The overall picture is that CO acts in the phloem companion cells of leaves and that its main effect is to induce FT mRNA in these cells. Surprisingly, FT, a small globular protein of 20 kDa, interacts at the shoot apex with the bZIP transcription factor FLOWERING LOCUS D (FD) to induce downstream targets. Given that green fluorescent protein (GFP), which as a monomer is 27 kDa, can be easily exported to sink tissue including flowers when expressed in phloem companion cells, the latter finding strongly implied that FT protein is the mobile floral-inductive signal. In agreement with this hypothesis, an FT-GFP fusion, just like GFP, can be exported from the phloem of both rice and Arabidopsis. It has been unknown, however, whether mobile FT protein is sufficient for transmitting the flowering signal. Here we show that FT mRNA is required in phloem companion cells where it acts partially redundant with its paralog TWIN SISTER OF FT (TSF) to induce flowering. Furthermore, we have devised a method that uncouples FT mRNA and protein effects in vivo. We demonstrate that export of FT protein from phloem companion cells is sufficient to induce flowering.},
	language = {eng},
	number = {12},
	journal = {Current biology: CB},
	author = {Mathieu, Johannes and Warthmann, Norman and Küttner, Frank and Schmid, Markus},
	month = jun,
	year = {2007},
	pmid = {17540570},
	keywords = {Arabidopsis, Arabidopsis Proteins, Flowers, Gene Expression Regulation, Plant, Phloem, Phosphatidylethanolamine Binding Protein, RNA, Messenger, Signal Transduction},
	pages = {1055--1060},
}

2005 (4)

A gene expression map of Arabidopsis thaliana development. Schmid, M., Davison, T. S., Henz, S. R., Pape, U. J., Demar, M., Vingron, M., Schölkopf, B., Weigel, D., & Lohmann, J. U. Nature Genetics, 37(5): 501–506. May 2005.
doi link bibtex abstract

@article{schmid_gene_2005,
	title = {A gene expression map of {Arabidopsis} thaliana development},
	volume = {37},
	issn = {1061-4036},
	doi = {10.1038/ng1543},
	abstract = {Regulatory regions of plant genes tend to be more compact than those of animal genes, but the complement of transcription factors encoded in plant genomes is as large or larger than that found in those of animals. Plants therefore provide an opportunity to study how transcriptional programs control multicellular development. We analyzed global gene expression during development of the reference plant Arabidopsis thaliana in samples covering many stages, from embryogenesis to senescence, and diverse organs. Here, we provide a first analysis of this data set, which is part of the AtGenExpress expression atlas. We observed that the expression levels of transcription factor genes and signal transduction components are similar to those of metabolic genes. Examining the expression patterns of large gene families, we found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.},
	language = {eng},
	number = {5},
	journal = {Nature Genetics},
	author = {Schmid, Markus and Davison, Timothy S. and Henz, Stefan R. and Pape, Utz J. and Demar, Monika and Vingron, Martin and Schölkopf, Bernhard and Weigel, Detlef and Lohmann, Jan U.},
	month = may,
	year = {2005},
	pmid = {15806101},
	keywords = {Arabidopsis, Gene Expression, Gene Expression Profiling, Genetic Markers},
	pages = {501--506},
}

Diversity of flowering responses in wild Arabidopsis thaliana strains. Lempe, J., Balasubramanian, S., Sureshkumar, S., Singh, A., Schmid, M., & Weigel, D. PLoS genetics, 1(1): 109–118. July 2005.
doi link bibtex abstract

@article{lempe_diversity_2005,
	title = {Diversity of flowering responses in wild {Arabidopsis} thaliana strains},
	volume = {1},
	issn = {1553-7390},
	doi = {10.1371/journal.pgen.0010006},
	abstract = {Although multiple environmental cues regulate the transition to flowering in Arabidopsis thaliana, previous studies have suggested that wild A. thaliana accessions fall primarily into two classes, distinguished by their requirement for vernalization (extended winter-like temperatures), which enables rapid flowering under long days. Much of the difference in vernalization response is apparently due to variation at two epistatically acting loci, FRI and FLC. We present the response of over 150 wild accessions to three different environmental variables. In long days, FLC is among those genes whose expression is most highly correlated with flowering. In short days, FRI and FLC are less important, although their contribution is still significant. In addition, there is considerable variation not only in vernalization response, but also in the response to differences in day length or ambient growth temperature. The identification of accessions that flower relatively early or late in specific environments suggests that many of the flowering-time pathways identified by mutagenesis, such as those that respond to day length, contribute to flowering-time variation in the wild. In contrast to differences in vernalization requirement, which are mainly mediated by FRI and FLC, it seems that variation in these other pathways is due to allelic effects at several different loci.},
	language = {eng},
	number = {1},
	journal = {PLoS genetics},
	author = {Lempe, Janne and Balasubramanian, Sureshkumar and Sureshkumar, Sridevi and Singh, Anandita and Schmid, Markus and Weigel, Detlef},
	month = jul,
	year = {2005},
	pmid = {16103920},
	pmcid = {PMC1183525},
	pages = {109--118},
}

Integration of spatial and temporal information during floral induction in Arabidopsis. Wigge, P. A., Kim, M. C., Jaeger, K. E., Busch, W., Schmid, M., Lohmann, J. U., & Weigel, D. Science (New York, N.Y.), 309(5737): 1056–1059. August 2005.
doi link bibtex abstract

@article{wigge_integration_2005,
	title = {Integration of spatial and temporal information during floral induction in {Arabidopsis}},
	volume = {309},
	issn = {1095-9203},
	doi = {10/c6nzdx},
	abstract = {Flowering of Arabidopsis is regulated by several environmental and endogenous signals. An important integrator of these inputs is the FLOWERING LOCUS T (FT) gene, which encodes a small, possibly mobile protein. A primary response to floral induction is the activation of FT RNA expression in leaves. Because flowers form at a distant site, the shoot apex, these data suggest that FT primarily controls the timing of flowering. Integration of temporal and spatial information is mediated in part by the bZIP transcription factor FD, which is already expressed at the shoot apex before floral induction. A complex of FT and FD proteins in turn can activate floral identity genes such as APETALA1 (AP1).},
	language = {eng},
	number = {5737},
	journal = {Science (New York, N.Y.)},
	author = {Wigge, Philip A. and Kim, Min Chul and Jaeger, Katja E. and Busch, Wolfgang and Schmid, Markus and Lohmann, Jan U. and Weigel, Detlef},
	month = aug,
	year = {2005},
	pmid = {16099980},
	keywords = {Arabidopsis, Arabidopsis Proteins, Chromatin Immunoprecipitation, DNA-Binding Proteins, Flowers, Gene Expression Regulation, Plant, Homeodomain Proteins, MADS Domain Proteins, Models, Biological, Mutation, Oligonucleotide Array Sequence Analysis, Phenotype, Plant Leaves, Plant Proteins, Plant Shoots, Protein Interaction Mapping, Recombinant Fusion Proteins, Signal Transduction, Time Factors, Transcription Factors, Transcription, Genetic, Two-Hybrid System Techniques},
	pages = {1056--1059},
}

Specific effects of microRNAs on the plant transcriptome. Schwab, R., Palatnik, J. F., Riester, M., Schommer, C., Schmid, M., & Weigel, D. Developmental Cell, 8(4): 517–527. April 2005.
doi link bibtex abstract

@article{schwab_specific_2005,
	title = {Specific effects of {microRNAs} on the plant transcriptome},
	volume = {8},
	issn = {1534-5807},
	doi = {10.1016/j.devcel.2005.01.018},
	abstract = {Most plant microRNAs (miRNAs) have perfect or near-perfect complementarity with their targets. This is consistent with their primary mode of action being cleavage of target mRNAs, similar to that induced by perfectly complementary small interfering RNAs (siRNAs). However, there are natural targets with up to five mismatches. Furthermore, artificial siRNAs can have substantial effects on so-called off-targets, to which they have only limited complementarity. By analyzing the transcriptome of plants overexpressing different miRNAs, we have deduced a set of empirical parameters for target recognition. Compared to artificial siRNAs, authentic plant miRNAs appear to have much higher specificity, which may reflect their coevolution with the remainder of the transcriptome. We also demonstrate that miR172, previously thought to act primarily by translational repression, can efficiently guide mRNA cleavage, although the effects on steady-state levels of target transcripts are obscured by strong feedback regulation. This finding unifies the view of plant miRNA action.},
	language = {eng},
	number = {4},
	journal = {Developmental Cell},
	author = {Schwab, Rebecca and Palatnik, Javier F. and Riester, Markus and Schommer, Carla and Schmid, Markus and Weigel, Detlef},
	month = apr,
	year = {2005},
	pmid = {15809034},
	keywords = {Base Pairing, Base Sequence, Gene Expression Profiling, Gene Expression Regulation, Plant, MicroRNAs, Nucleic Acid Conformation, Oligonucleotide Array Sequence Analysis, Phenotype, Plant Proteins, Plants, Genetically Modified, RNA, Plant, Reproducibility of Results, Transcription, Genetic},
	pages = {517--527},
}

2003 (3)

AthPEX10, a nuclear gene essential for peroxisome and storage organelle formation during Arabidopsis embryogenesis. Schumann, U., Wanner, G., Veenhuis, M., Schmid, M., & Gietl, C. Proceedings of the National Academy of Sciences of the United States of America, 100(16): 9626–9631. August 2003.
doi link bibtex abstract

@article{schumann_athpex10_2003,
	title = {{AthPEX10}, a nuclear gene essential for peroxisome and storage organelle formation during {Arabidopsis} embryogenesis},
	volume = {100},
	issn = {0027-8424},
	doi = {10/dzx29q},
	abstract = {In yeasts and mammals, PEX10 encodes an integral membrane protein with a C3HC4 RING finger motif in its C-terminal domain and is required for peroxisome biogenesis and matrix protein import. In humans, its dysfunction in peroxisome biogenesis leads to severe Zellweger Syndrome and infantile Refsum disease. Here we show that dysfunction of a homologous gene in Arabidopsis leads to lethality at the heart stage of embryogenesis, impairing the biogenesis of peroxisomes, lipid bodies, and protein bodies. In a T-DNA insertion mutant disrupting the fourth exon of the AthPEX10 gene, ultrastructural analyses fail to detect peroxisomes characteristic for wild-type embryogenesis. Storage triacyl glycerides are not assembled into lipid bodies (oil bodies; oleosomes) surrounded by the phospholipid-protein monolayer membrane. Instead, the dysfunctional monolayer membranes, which derive from the bilayer membrane of the endoplasmic reticulum, accumulate in the cytosol. Concomitantly the transfer of the storage proteins from their site of synthesis at the endoplasmic reticulum to the vacuoles is disturbed. The mutant can be rescued by transformation with wild-type AthPEX10 cDNA. Transformants of wild-type Hansenula polymorpha cells with the AthPEX10 cDNA did produce the encoded protein without targeting it to peroxisomes. Additionally, the cDNA could not complement a Hansenula pex10 mutant unable to form peroxisomes. The ultrastructural knockout phenotype of AthPEX10p suggests that this protein in Arabidopsis is essential for peroxisome, oleosome, and protein transport vesicle formation.},
	language = {eng},
	number = {16},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Schumann, Uwe and Wanner, Gerhard and Veenhuis, Marten and Schmid, Markus and Gietl, Christine},
	month = aug,
	year = {2003},
	pmid = {12883010},
	pmcid = {PMC170968},
	keywords = {Amino Acid Sequence, Arabidopsis, Arabidopsis Proteins, Carrier Proteins, Cell Membrane, Cell Nucleus, Cytosol, DNA, Complementary, Endoplasmic Reticulum, Exons, Lipid Bilayers, Lipid Metabolism, Membrane Transport Proteins, Microscopy, Electron, Molecular Sequence Data, Mutation, Organelles, Peroxins, Peroxisomes, Phospholipids, Plants, Genetically Modified, Protein Structure, Tertiary, Receptors, Cytoplasmic and Nuclear},
	pages = {9626--9631},
}

Dissection of floral induction pathways using global expression analysis. Schmid, M., Uhlenhaut, N. H., Godard, F., Demar, M., Bressan, R., Weigel, D., & Lohmann, J. U. Development (Cambridge, England), 130(24): 6001–6012. December 2003.
doi link bibtex abstract

@article{schmid_dissection_2003,
	title = {Dissection of floral induction pathways using global expression analysis},
	volume = {130},
	issn = {0950-1991},
	doi = {10/c56qz2},
	abstract = {Flowering of the reference plant Arabidopsis thaliana is controlled by several signaling pathways, which converge on a small set of genes that function as pathway integrators. We have analyzed the genomic response to one type of floral inductive signal, photoperiod, to dissect the function of several genes transducing this stimulus, including CONSTANS, thought to be the major output of the photoperiod pathway. Comparing the effects of CONSTANS with those of FLOWERING LOCUS T, which integrates inputs from CONSTANS and other floral inductive pathways, we find that expression profiles of shoot apices from plants with mutations in either gene are very similar. In contrast, a mutation in LEAFY, which also acts downstream of CONSTANS, has much more limited effects. Another pathway integrator, SUPPRESSOR OF OVEREXPRESSION OF CO 1, is responsive to acute induction by photoperiod even in the presence of the floral repressor encoded by FLOWERING LOCUS C. We have discovered a large group of potential floral repressors that are down-regulated upon photoperiodic induction. These include two AP2 domain-encoding genes that can repress flowering. The two paralogous genes, SCHLAFMUTZE and SCHNARCHZAPFEN, share a signature with partial complementarity to the miR172 microRNA, whose precursor we show to be induced upon flowering. These and related findings on SPL genes suggest that microRNAs play an important role in the regulation of flowering.},
	language = {eng},
	number = {24},
	journal = {Development (Cambridge, England)},
	author = {Schmid, Markus and Uhlenhaut, N. Henriette and Godard, François and Demar, Monika and Bressan, Ray and Weigel, Detlef and Lohmann, Jan U.},
	month = dec,
	year = {2003},
	pmid = {14573523},
	keywords = {Animals, Arabidopsis, Arabidopsis Proteins, DNA-Binding Proteins, Flowers, Gene Expression Profiling, Gene Expression Regulation, Plant, MicroRNAs, Photoperiod, Polymorphism, Genetic, Signal Transduction, Statistics as Topic, Transcription Factors},
	pages = {6001--6012},
}

Genome-wide insertional mutagenesis of Arabidopsis thaliana. Alonso, J. M., Stepanova, A. N., Leisse, T. J., Kim, C. J., Chen, H., Shinn, P., Stevenson, D. K., Zimmerman, J., Barajas, P., Cheuk, R., Gadrinab, C., Heller, C., Jeske, A., Koesema, E., Meyers, C. C., Parker, H., Prednis, L., Ansari, Y., Choy, N., Deen, H., Geralt, M., Hazari, N., Hom, E., Karnes, M., Mulholland, C., Ndubaku, R., Schmidt, I., Guzman, P., Aguilar-Henonin, L., Schmid, M., Weigel, D., Carter, D. E., Marchand, T., Risseeuw, E., Brogden, D., Zeko, A., Crosby, W. L., Berry, C. C., & Ecker, J. R. Science (New York, N.Y.), 301(5633): 653–657. August 2003.
doi link bibtex abstract

@article{alonso_genome-wide_2003,
	title = {Genome-wide insertional mutagenesis of {Arabidopsis} thaliana},
	volume = {301},
	issn = {1095-9203},
	doi = {10/fqhtnq},
	abstract = {Over 225,000 independent Agrobacterium transferred DNA (T-DNA) insertion events in the genome of the reference plant Arabidopsis thaliana have been created that represent near saturation of the gene space. The precise locations were determined for more than 88,000 T-DNA insertions, which resulted in the identification of mutations in more than 21,700 of the approximately 29,454 predicted Arabidopsis genes. Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels. Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.},
	language = {eng},
	number = {5633},
	journal = {Science (New York, N.Y.)},
	author = {Alonso, José M. and Stepanova, Anna N. and Leisse, Thomas J. and Kim, Christopher J. and Chen, Huaming and Shinn, Paul and Stevenson, Denise K. and Zimmerman, Justin and Barajas, Pascual and Cheuk, Rosa and Gadrinab, Carmelita and Heller, Collen and Jeske, Albert and Koesema, Eric and Meyers, Cristina C. and Parker, Holly and Prednis, Lance and Ansari, Yasser and Choy, Nathan and Deen, Hashim and Geralt, Michael and Hazari, Nisha and Hom, Emily and Karnes, Meagan and Mulholland, Celene and Ndubaku, Ral and Schmidt, Ian and Guzman, Plinio and Aguilar-Henonin, Laura and Schmid, Markus and Weigel, Detlef and Carter, David E. and Marchand, Trudy and Risseeuw, Eddy and Brogden, Debra and Zeko, Albana and Crosby, William L. and Berry, Charles C. and Ecker, Joseph R.},
	month = aug,
	year = {2003},
	pmid = {12893945},
	keywords = {3' Untranslated Regions, 5' Untranslated Regions, Alleles, Arabidopsis, Arabidopsis Proteins, Base Composition, Chromosomes, Plant, DNA, Bacterial, DNA, Plant, Ethylenes, Exons, Expressed Sequence Tags, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Plant, Genes, Plant, Genome, Plant, Introns, Mutagenesis, Insertional, Mutation, Oligonucleotide Array Sequence Analysis, Promoter Regions, Genetic, Recombination, Genetic, Rhizobium},
	pages = {653--657},
}

2001 (2)

Ricinosomes: an organelle for developmentally regulated programmed cell death in senescing plant tissues. Gietl, C., & Schmid, M. Naturwissenschaften, 88(2): 49–58. February 2001.

Ricinosomes: an organelle for developmentally regulated programmed cell death in senescing plant tissues [link]

Paper doi link bibtex abstract

@article{gietl_ricinosomes_2001,
	title = {Ricinosomes: an organelle for developmentally regulated programmed cell death in senescing plant tissues},
	volume = {88},
	issn = {1432-1904},
	shorttitle = {Ricinosomes},
	url = {https://doi.org/10.1007/s001140000203},
	doi = {10.1007/s001140000203},
	abstract = {This review describes aspects of programmed cell death (PCD). Present research maps the enzymes involved and explores the signal transduction pathways involved in their synthesis. A special organelle (the ricinosome) has been discovered in the senescing endosperm of germinating castor beans (Ricinus communis) that develops at the beginning of PCD and delivers large amounts of a papain-type cysteine endopeptidase (CysEP) in the final stages of cellular disintegration. Castor beans store oil and proteins in a living endosperm surrounding the cotyledons. These stores are mobilized during germination and transferred into the cotyledons. PCD is initiated after this transfer is complete. The CysEP is synthesized in the lumen of the endoplasmic reticulum (ER) where it is retained by its C-terminal KDEL peptide as a rather inactive pro-enzyme. Large number of ricinosomes bud from the ER at the same time as the nuclear DNA is characteristically fragmented during PCD. The mitochondria, glyoxysomes and ribosomes are degraded in autophagic vacuoles, while the endopeptidase is activated by removal of the propeptide and the KDEL tail and enters the cytosol. The endosperm dries and detaches from the cotyledons. A homologous KDEL-tailed cysteine endopeptidase has been found in several senescing tissues; it has been localized in ricinosomes of withering day-lily petals and dying seed coats. Three genes for a KDEL-tailed cysteine endopeptidase have been identified in Arabidopsis. One is expressed in senescing ovules, the second in the vascular vessels and the third in maturing siliques. These genes open the way to exploring PCD in plants.},
	language = {en},
	number = {2},
	urldate = {2021-10-22},
	journal = {Naturwissenschaften},
	author = {Gietl, C. and Schmid, M.},
	month = feb,
	year = {2001},
	pages = {49--58},
}

The ricinosomes of senescing plant tissue bud from the endoplasmic reticulum. Schmid, M., Simpson, D. J., Sarioglu, H., Lottspeich, F., & Gietl, C. Proceedings of the National Academy of Sciences, 98(9): 5353–5358. April 2001. Publisher: National Academy of Sciences Section: Biological Sciences

The ricinosomes of senescing plant tissue bud from the endoplasmic reticulum [link]

Paper doi link bibtex abstract

@article{schmid_ricinosomes_2001,
	title = {The ricinosomes of senescing plant tissue bud from the endoplasmic reticulum},
	volume = {98},
	copyright = {Copyright © 2001, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/98/9/5353},
	doi = {10.1073/pnas.061038298},
	abstract = {The ricinosome (synonym, precursor protease vesicle) is a novel organelle, found so far exclusively in plant cells. Electron microscopic studies suggest that it buds off from the endoplasmic reticulum in senescing tissues. Biochemical support for this unusual origin now comes from the composition of the purified organelle, which contains large amounts of a 45-kDa cysteine endoprotease precursor with a C-terminal KDEL motif and the endoplasmic reticulum lumen residents BiP (binding protein) and protein disulfide isomerase. Western blot analysis, peptide sequencing, and mass spectrometry demonstrate retention of KDEL in the protease proform. Acidification of isolated ricinosomes causes castor bean cysteine endopeptidase activation, with cleavage of the N-terminal propeptide and the C-terminal KDEL motif. We propose that ricinosomes accumulate during senescence by programmed cell death and are activated by release of protons from acidic vacuoles.},
	language = {en},
	number = {9},
	urldate = {2021-11-02},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Schmid, Markus and Simpson, David J. and Sarioglu, Hakan and Lottspeich, Friedrich and Gietl, Christine},
	month = apr,
	year = {2001},
	pmid = {11296243},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {Ricinus communis, papain-type KDEL peptidase},
	pages = {5353--5358},
}

1999 (1)

Programmed cell death in castor bean endosperm is associated with the accumulation and release of a cysteine endopeptidase from ricinosomes. Schmid, M., Simpson, D., & Gietl, C. Proceedings of the National Academy of Sciences, 96(24): 14159–14164. November 1999. Publisher: National Academy of Sciences Section: Biological Sciences

Paper doi link bibtex abstract

@article{schmid_programmed_1999,
	title = {Programmed cell death in castor bean endosperm is associated with the accumulation and release of a cysteine endopeptidase from ricinosomes},
	volume = {96},
	copyright = {Copyright © 1999, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/96/24/14159},
	doi = {10/fwpzcr},
	abstract = {The cells of the endosperm of castor bean seeds (Ricinus communis) undergo programmed cell death during germination, after their oil and protein reserves have been mobilized. Nuclear DNA fragmentation first was observed at day 3 in the endosperm cells immediately adjacent to the cotyledons and progressed across to the outermost cell layers by day 5. We also detected the accumulation of small organelles known as ricinosomes, by using an antibody against a cysteine endoprotease. By the time the nuclear DNA was susceptible to heavy label by terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling, the ricinosomes had released into the cytoplasm their content of cysteine endoprotease, which became activated because of the cleavage of its propeptide. The cysteine endoprotease is distinguished by a C-terminal KDEL sequence, although it is not retained in the lumen of the endoplasmic reticulum and is a marker for ricinosomes. Homologous proteases are found in the senescing tissues of other plants, including the petals of the daylily. Ricinosomes were identified in this tissue by electron microscopy and immunocytochemistry. It seems that ricinosomes are not unique to Ricinus and play an important role in the degradation of plant cell contents during programmed cell death.},
	language = {en},
	number = {24},
	urldate = {2021-11-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Schmid, Markus and Simpson, David and Gietl, Christine},
	month = nov,
	year = {1999},
	pmid = {10570215},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {Apoptosis, Castor Bean, Cell Nucleus, Cysteine Endopeptidases, DNA Fragmentation, DNA, Plant, Germination, Hemerocallis sp., In Situ Hybridization, Organelles, Plants, Toxic, Ricinus communis, Seeds, papain-type KDEL peptidase},
	pages = {14159--14164},
}

1998 (2)

A cysteine endopeptidase with a C-terminal KDEL motif isolated from castor bean endosperm is a marker enzyme for the ricinosome, a putative lytic compartment. Schmid, M., Simpson, D., Kalousek, F., & Gietl, C. Planta, 206(3): 466–475. October 1998.
doi link bibtex abstract

@article{schmid_cysteine_1998,
	title = {A cysteine endopeptidase with a {C}-terminal {KDEL} motif isolated from castor bean endosperm is a marker enzyme for the ricinosome, a putative lytic compartment},
	volume = {206},
	issn = {0032-0935},
	doi = {10.1007/s004250050423},
	abstract = {A papain-type cysteine endopeptidase with a molecular mass of 35 kDa for the mature enzyme, was purified from germinating castor bean (Ricinus communis L.) endosperm by virtue of its capacity to process the glyoxysomal malate dehydrogenase precursor protein to the mature subunit in vitro (C. Gietl et al., 1997, Plant Physiol 113: 863-871). The cDNA clones from endosperm of germinating seedlings and from developing seeds were isolated and sequence analysis revealed that a very similar or identical peptidase is synthesised in both tissues. Sequencing established a presequence for co-translational targeting into the endoplasmic reticulum, an N-terminal propeptide and a C-terminal KDEL motif for the castor bean cysteine endopeptidase precursor. The 45-kDa pro-enzyme stably present in isolated organelles was enzymatically active. Immunocytochemistry with antibodies raised against the purified cysteine endopeptidase revealed highly specific labelling of ricinosomes, organelles which co-purify with glyoxysomes from germinating Ricinus endosperm. The cysteine endopeptidase from castor bean endosperm, which represents a senescing tissue, is homologous to cysteine endopeptidases from other senescing tissues such as the cotyledons of germinating mung bean (Vigna mungo) and vetch (Vicia sativa), the seed pods of maturing French bean (Phaseolus vulgaris) and the flowers of daylily (Hemerocallis sp.).},
	language = {eng},
	number = {3},
	journal = {Planta},
	author = {Schmid, M. and Simpson, D. and Kalousek, F. and Gietl, C.},
	month = oct,
	year = {1998},
	pmid = {9763713},
	keywords = {Base Sequence, Biomarkers, Castor Bean, Cell Compartmentation, Centrifugation, Density Gradient, Cysteine Endopeptidases, DNA, Complementary, DNA, Plant, Enzyme Precursors, Molecular Sequence Data, Oligopeptides, Organelles, Plants, Toxic, Protein Sorting Signals, Sucrose},
	pages = {466--475},
}

The plant PTS1 receptor: similarities and differences to its human and yeast counterparts. Wimmer, C., Schmid, M., Veenhuis, M., & Gietl, C. The Plant Journal, 16(4): 453–464. 1998. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313x.1998.00320.x

The plant PTS1 receptor: similarities and differences to its human and yeast counterparts [link]

Paper doi link bibtex abstract

@article{wimmer_plant_1998,
	title = {The plant {PTS1} receptor: similarities and differences to its human and yeast counterparts},
	volume = {16},
	issn = {1365-313X},
	shorttitle = {The plant {PTS1} receptor},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-313x.1998.00320.x},
	doi = {10.1046/j.1365-313x.1998.00320.x},
	abstract = {Two targeting signals, PTS1 and PTS2, mediate import of proteins into the peroxisomal matrix. We have cloned and sequenced the watermelon ( Citrullus vulgaris ) cDNA homologue to the PTS1 receptor gene (PEX5). Its gene product, CvPex5p, belongs to the family of tetratricopeptide repeat (TPR) containing proteins like the human and yeast counterparts, and exhibits 11 repeats of the sequence W-X2-(E/S)-(Y/F/Q) in its N-terminal half. According to fractionation studies the plant Pex5p is located mainly in the cytosolic fraction and therefore could function as a cycling receptor between the cytosol and glyoxysomes, as has been proposed for the Pex5p of human and some yeast peroxisomes. Transformation of the Hansenula polymorpha peroxisome deficient pex5 mutant with watermelon PEX5 resulted in restoration of peroxisome formation and the synthesis of additional membranes surrounding the peroxisomes. These structures are labeled in immunogold experiments using antibodies against the Hansenula polymorpha integral membrane protein Pex3p, confirming their peroxisomal nature. The plant Pex5p was localized by immunogold labelling mainly in the cytosol of the yeast, but also inside the newly formed peroxisomes. However, import of the PTS1 protein alcohol oxidase is only partially restored by CvPex5p.},
	language = {en},
	number = {4},
	urldate = {2021-10-22},
	journal = {The Plant Journal},
	author = {Wimmer, Christine and Schmid, Markus and Veenhuis, Marten and Gietl, Christine},
	year = {1998},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313x.1998.00320.x},
	pages = {453--464},
}

Thomas Moritz in front of a mass spectrometer

Research

The aim of my research is to understand the mechanisms of metabolic control of shoot elongation and wood formation in the model plant Populus. We want to understand how plant hormones and other metabolites are involved in the control of plant development, and how different environmental cues, such as photoperiod, affect the metabolic control of growth and development. The metabolic control of growth and development are studied by using both targeted and untargeted metabolomics approaches.

Gibberellins (GAs) are a group of tetracyclic diterpenes, some of which are essential endogenous regulators that influence growth and development events throughout the life cycle of a plant, e.g. shoot elongation, expansion and shape of leaves, flowering and seed germination. Our project is concerned with the role of GAs in plant development, and daylength responses, focusing on the tree hybrid aspen (Populus tremula x P. tremuloides) as a model system. Our approach for studying the role of GAs in trees is to study endogenous expression of GA biosynthetic and signalling genes and to transform Populus with genes encoding those genes.

Populus transformed with the AtGA20ox1 under the control of the 35S promoter shows elongated internodes, longer petioles and larger leaves, reduced root formation and increased shoot biomass.We have also char- acterized the GA receptor, GID1 in Populus. Four orthologs of GID1 have been identified in Populus tremula x P. tremuloides (PttGID1.1 to 1.4). When PttGID1.1 and PttGID1.3 were overexpressed in Populus with a 35S promoter, overexpressors shared several similar phenotypic traits with previously described 35S:AtGA20ox1 overexpressors, including rapid growth and increased elongation.

Three photos showing parts of a mass spectrometer instrument that is used to measure metabolites

We are also studying the role of GAs and other signaling compounds in wood formation. The role of GAs is done by both using transgenic Populus with increased levels of GAs and signalling and by predicting where GAs are formed and perceived during wood formation. For example, we have quantified GAs and analyzed the expression of GA biosynthesis genes and genes with predicted roles in GA signalling in tangential sections across the cambial region of aspen trees (Populus tremula). The results show, for example inter alia, that the bioactive GA and GA 14 predominantly occur in the zone of expansion of xylem cells.

Studies with transgenic Populus overexpressing AtGA20ox1 or PttGID1 with 35S or a xylem-specific promoter, suggest that GAs are required for two distinct processes in wood formation with tissue-specific signalling pathways: xylogenesis, mediated by GA signalling in the cambium, and fibre elongation in developing xylem.

By using a metabolomics approach we are also studying how specific patterns of metabolites, including signalling compounds, are vary in different regions of the wood-forming zone in Populus. From the data we can conclude that cambial activity, cell expansion and secondary cell wall thickening are tightly coupled processes, Many of these patterns can be explained on the basis of the developmental processes taking place within these regions, e.g. in the cambium.

Many woody species with indeterminate growth show complete cessation of elongation growth after only a few weeks in short photoperiods. In hybrid aspen transformed with the oat PHYA gene, the dwarf phenotype is correlated with a reduction in GA levels, but in short photoperiods there is no further reduction in GA contents, in marked contrast to the pattern in wild-type plants. These observations imply that GAs have an important role as signals in the photoperiodic regulation of shoot elongation. We have also been studying transgenic GA plants to elucidate how changes in GA levels and signalling affect photoperiodic growth. Studies in PHYA and GA biosynthesis/signalling overexpressors are used with transcriptomic and metabolomic approaches to elucidate the early signalling pathways in short-day induced growth cessation, including identification of new putative signalling compounds.

Key Publications

Davoine, C., Abreu, I. N. Khajeh, K., Blomberg, J., Kidd, B. N., Kazan, K., Schenk, P. M., Gerber, L., Nilsson, O., Moritz, T. , Bjorklund, S. 2017. Functional metabolomics as a tool to analyze mediator function and structure in plants. Plos One 12(6).
Lindén, P., Keech, O., Stenlund, H., Gardeström, P., Moritz, T. 2016 Reduced mitochondrial malate dehydrogenase activity has a strong effect on photorespiratory metabolism as revealed by 13C-labelling. J. Exp. Bot., 67: 3123-3135
Eriksson, M.E., Hoffman, D., Kaduk, M., Mauriat, M., Moritz, T. 2015 Transgenic hybrid aspen trees with increased gibberellin (GA) concentrations suggest that GA acts in parallel with FLOWERING LOCUS T2 to control shoot elongation. New Phytologist, 205, 1288-1295.
Mauriat M., Sandberg L., Moritz T. 2011 Proper gibberellin localization in vascular tissue is required to control auxin dependent leaf development and bud outgrowth in hybrid aspen. Plant J. 67: 805-816.
Mauriat M., Moritz T. 2009 Analyses of GA20ox- and GID1-overexpressing Populus suggest gibberellins play two distinct roles in wood formation. Plant J. 58: 989-1003.
Israelsson M., Sundberg B., Moritz T. 2005 Tissue-specific localisation of gibberellins in wood-forming tissues in aspen. Plant J. 44: 494-504.
Jonsson P., Johansson A., Gullberg J., Trygg J., A J., Grung B., Marklund S., Sjöström M., Antti H., Moritz T. 2005 High through-put data analysis for detecting and identifying differences between samples in GC/MS-based metabolomic analyses Anal. Chem. 77: 5635-5642.
Eriksson M., Israelsson M., Olsson O., Moritz T. 2000. Increased gibberellin biosynthesis in transgenic trees promotes growth, biomass production and xylem fibre length. Nature Biotech. 784-788.

Team

CV T. Moritz

Publications

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2025 (5)

Epigenetic suppression of creatine kinase B in adipocytes links endoplasmic reticulum stress to obesity-associated inflammation. Renzi, G., Vlassakev, I., Hansen, M., Higos, R., Lecoutre, S., Elmastas, M., Hodek, O., Moritz, T., Alaeddine, L. M., Frendo–Cumbo, S., Dahlman, I., Kerr, A., Maqdasy, S., Mejhert, N., & Rydén, M. Molecular Metabolism, 92: 102082. February 2025.

Epigenetic suppression of creatine kinase B in adipocytes links endoplasmic reticulum stress to obesity-associated inflammation [link]

Paper doi link bibtex abstract

@article{renzi_epigenetic_2025,
	title = {Epigenetic suppression of creatine kinase {B} in adipocytes links endoplasmic reticulum stress to obesity-associated inflammation},
	volume = {92},
	issn = {2212-8778},
	url = {https://www.sciencedirect.com/science/article/pii/S2212877824002138},
	doi = {10.1016/j.molmet.2024.102082},
	abstract = {In white adipose tissue, disturbed creatine metabolism through reduced creatine kinase B (CKB) transcription contributes to obesity-related inflammation. However, the mechanisms regulating CKB expression in human white adipocytes remain unclear. By screening conditions perturbed in obesity, we identified endoplasmic reticulum (ER) stress as a key suppressor of CKB transcription across multiple cell types. Through follow-up studies, we found that ER stress through the IRE1–XBP1s pathway, promotes CKB promoter methylation via the methyltransferase DNMT3A. This epigenetic change represses CKB transcription, shifting metabolism towards glycolysis and increasing the production of the pro-inflammatory chemokine CCL2. We validated our findings in vivo, demonstrating that individuals living with obesity show an inverse relationship between CKB expression and promoter methylation in white adipocytes, along with elevated CCL2 secretion. Overall, our study uncovers a regulatory axis where ER stress drives inflammation in obesity by reducing CKB abundance, and consequently altering the bioenergetic state of the cell.},
	urldate = {2025-01-10},
	journal = {Molecular Metabolism},
	author = {Renzi, Gianluca and Vlassakev, Ivan and Hansen, Mattias and Higos, Romane and Lecoutre, Simon and Elmastas, Merve and Hodek, Ondrej and Moritz, Thomas and Alaeddine, Lynn M. and Frendo–Cumbo, Scott and Dahlman, Ingrid and Kerr, Alastair and Maqdasy, Salwan and Mejhert, Niklas and Rydén, Mikael},
	month = feb,
	year = {2025},
	keywords = {Chromatin remodeling, Creatine pathway, Glycolysis, Immunometabolism, Tunicamycin},
	pages = {102082},
}

Marked mucosal lipid shifts in treatment refractory inflammatory bowel disease: a lipidomic study. Moe, Ø. K., Gao, Q., Geng, D., Jensen, E., Goll, R., Nestegard, O., Gundersen, M. D., Florholmen, J. R., & Moritz, T. BMC Gastroenterology, 25(1): 389. May 2025.
$Marked mucosal lipid shifts in treatment refractory inflammatory bowel disease: a lipidomic study [link]$ Paper doi link bibtex abstract

@article{moe_marked_2025,
	title = {Marked mucosal lipid shifts in treatment refractory inflammatory bowel disease: a lipidomic study},
	volume = {25},
	issn = {1471-230X},
	shorttitle = {Marked mucosal lipid shifts in treatment refractory inflammatory bowel disease},
	url = {https://doi.org/10.1186/s12876-025-03944-6},
	doi = {10.1186/s12876-025-03944-6},
	abstract = {Mechanisms causing non-response to biological agents in IBD remain to be fully understood. Thus, we aimed to characterize the lipid profile in treatment refractory non-immunogenic patients with adequate trough-levels.},
	number = {1},
	urldate = {2025-05-23},
	journal = {BMC Gastroenterology},
	author = {Moe, Øystein K. and Gao, Qian and Geng, Dawei and Jensen, Einar and Goll, Rasmus and Nestegard, Oddmund and Gundersen, Mona D. and Florholmen, Jon R. and Moritz, T.},
	month = may,
	year = {2025},
	keywords = {Biological therapy, Inflammatory bowel disease, Lipids, Non-response},
	pages = {389},
}

NAD depletion in skeletal muscle does not compromise muscle function or accelerate aging. Chubanava, S., Karavaeva, I., Ehrlich, A. M., Justicia, R. M., Basse, A. L., Kulik, I., Dalbram, E., Ahwazi, D., Heaselgrave, S. R., Trošt, K., Stocks, B., Hodek, O., Rodrigues, R. N., Havelund, J. F., Schlabs, F. L., Larsen, S., Yonamine, C. Y., Henriquez-Olguín, C., Giustarini, D., Rossi, R., Gerhart-Hines, Z., Moritz, T., Zierath, J. R., Sakamoto, K., Jensen, T. E., Færgeman, N. J., Lavery, G. G., Deshmukh, A. S., & Treebak, J. T. Cell Metabolism. April 2025.

NAD depletion in skeletal muscle does not compromise muscle function or accelerate aging [link]

Paper doi link bibtex abstract

@article{chubanava_nad_2025,
	title = {{NAD} depletion in skeletal muscle does not compromise muscle function or accelerate aging},
	issn = {1550-4131},
	url = {https://www.sciencedirect.com/science/article/pii/S1550413125002128},
	doi = {10.1016/j.cmet.2025.04.002},
	abstract = {Nicotinamide adenine dinucleotide (NAD) is a ubiquitous electron carrier essential for energy metabolism and post-translational modification of numerous regulatory proteins. Dysregulations of NAD metabolism are widely regarded as detrimental to health, with NAD depletion commonly implicated in aging. However, the extent to which cellular NAD concentration can decline without adverse consequences remains unclear. To investigate this, we generated a mouse model in which nicotinamide phosphoribosyltransferase (NAMPT)-mediated NAD+ biosynthesis was disrupted in adult skeletal muscle. The intervention resulted in an 85\% reduction in muscle NAD+ abundance while maintaining tissue integrity and functionality, as demonstrated by preserved muscle morphology, contractility, and exercise tolerance. This absence of functional impairments was further supported by intact mitochondrial respiratory capacity and unaltered muscle transcriptomic and proteomic profiles. Furthermore, lifelong NAD depletion did not accelerate muscle aging or impair whole-body metabolism. Collectively, these findings suggest that NAD depletion does not contribute to age-related decline in skeletal muscle function.},
	urldate = {2025-05-09},
	journal = {Cell Metabolism},
	author = {Chubanava, Sabina and Karavaeva, Iuliia and Ehrlich, Amy M. and Justicia, Roger M. and Basse, Astrid L. and Kulik, Ivan and Dalbram, Emilie and Ahwazi, Danial and Heaselgrave, Samuel R. and Trošt, Kajetan and Stocks, Ben and Hodek, Ondřej and Rodrigues, Raissa N. and Havelund, Jesper F. and Schlabs, Farina L. and Larsen, Steen and Yonamine, Caio Y. and Henriquez-Olguín, Carlos and Giustarini, Daniela and Rossi, Ranieri and Gerhart-Hines, Zachary and Moritz, Thomas and Zierath, Juleen R. and Sakamoto, Kei and Jensen, Thomas E. and Færgeman, Nils J. and Lavery, Gareth G. and Deshmukh, Atul S. and Treebak, Jonas T.},
	month = apr,
	year = {2025},
	keywords = {NAD biosynthesis, NAD metabolism, NAMPT, aging, epigenetic clock, exercise, mitochondrial supercomplexes, nicotinamide, reactive oxygen species, skeletal muscle},
}

Nature’s Master of Ceremony: The Populus Circadian Clock as Orchestrator of Tree Growth and Phenology. Mariën, B., Robinson, K. M., Jurca, M., Michelson, I. H., Takata, N., Kozarewa, I., Pin, P. A., Ingvarsson, P. K., Moritz, T., Ibáñez, C., Nilsson, O., Jansson, S., Penfield, S., Yu, J., & Eriksson, M. E. npj Biological Timing and Sleep, 2(1): 1–19. April 2025. Publisher: Nature Publishing Group

Paper doi link bibtex abstract

@article{marien_natures_2025,
	title = {Nature’s {Master} of {Ceremony}: {The} {Populus} {Circadian} {Clock} as {Orchestrator} of {Tree} {Growth} and {Phenology}},
	volume = {2},
	copyright = {2025 The Author(s)},
	issn = {2948-281X},
	shorttitle = {Nature’s {Master} of {Ceremony}},
	url = {https://www.nature.com/articles/s44323-025-00034-4},
	doi = {10.1038/s44323-025-00034-4},
	abstract = {Understanding the timely regulation of plant growth and phenology is crucial for assessing a terrestrial ecosystem’s productivity and carbon budget. The circadian clock, a system of genetic oscillators, acts as ‘Master of Ceremony’ during plant physiological processes. The mechanism is particularly elusive in trees despite its relevance. The primary and secondary tree growth, leaf senescence, bud set, and bud burst timing were investigated in 68 constructs transformed into Populus hybrids and compared with untransformed or transformed controls grown in natural or controlled conditions. The results were analyzed using generalized additive models with ordered-factor-smooth interaction smoothers. This meta-analysis shows that several genetic components are associated with the clock. Especially core clock-regulated genes affected tree growth and phenology in both controlled and field conditions. Our results highlight the importance of field trials and the potential of using the clock to generate trees with improved characteristics for sustainable silviculture (e.g., reprogrammed to new photoperiodic regimes and increased growth).},
	language = {en},
	number = {1},
	urldate = {2025-04-11},
	journal = {npj Biological Timing and Sleep},
	author = {Mariën, Bertold and Robinson, Kathryn M. and Jurca, Manuela and Michelson, Ingrid H. and Takata, Naoki and Kozarewa, Iwanka and Pin, Pierre A. and Ingvarsson, Pär K. and Moritz, Thomas and Ibáñez, Cristian and Nilsson, Ove and Jansson, Stefan and Penfield, Steve and Yu, Jun and Eriksson, Maria E.},
	month = apr,
	year = {2025},
	note = {Publisher: Nature Publishing Group},
	keywords = {Biological techniques, Plant sciences},
	pages = {1--19},
}

Pantothenate kinase 4 controls skeletal muscle substrate metabolism. Miranda-Cervantes, A., Fritzen, A. M., Raun, S. H., Hodek, O., Møller, L. L. V., Johann, K., Deisen, L., Gregorevic, P., Gudiksen, A., Artati, A., Adamski, J., Andersen, N. R., Sigvardsen, C. M., Carl, C. S., Voldstedlund, C. T., Kjøbsted, R., Hauck, S. M., Schjerling, P., Jensen, T. E., Cebrian-Serrano, A., Jähnert, M., Gottmann, P., Burtscher, I., Lickert, H., Pilegaard, H., Schürmann, A., Tschöp, M. H., Moritz, T., Müller, T. D., Sylow, L., Kiens, B., Richter, E. A., & Kleinert, M. Nature Communications, 16(1): 345. January 2025. Publisher: Nature Publishing Group

Pantothenate kinase 4 controls skeletal muscle substrate metabolism [link]

Paper doi link bibtex abstract

@article{miranda-cervantes_pantothenate_2025,
	title = {Pantothenate kinase 4 controls skeletal muscle substrate metabolism},
	volume = {16},
	copyright = {2025 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-024-55036-w},
	doi = {10.1038/s41467-024-55036-w},
	abstract = {Metabolic flexibility in skeletal muscle is essential for maintaining healthy glucose and lipid metabolism, and its dysfunction is closely linked to metabolic diseases. Exercise enhances metabolic flexibility, making it an important tool for discovering mechanisms that promote metabolic health. Here we show that pantothenate kinase 4 (PanK4) is a new conserved exercise target with high abundance in muscle. Muscle-specific deletion of PanK4 impairs fatty acid oxidation which is related to higher intramuscular acetyl-CoA and malonyl-CoA levels. Elevated acetyl-CoA levels persist regardless of feeding state and are associated with whole-body glucose intolerance, reduced insulin-stimulated glucose uptake in glycolytic muscle, and impaired glucose uptake during exercise. Conversely, increasing PanK4 levels in glycolytic muscle lowers acetyl-CoA and enhances glucose uptake. Our findings highlight PanK4 as an important regulator of acetyl-CoA levels, playing a key role in both muscle lipid and glucose metabolism.},
	language = {en},
	number = {1},
	urldate = {2025-01-10},
	journal = {Nature Communications},
	author = {Miranda-Cervantes, Adriana and Fritzen, Andreas M. and Raun, Steffen H. and Hodek, Ondřej and Møller, Lisbeth L. V. and Johann, Kornelia and Deisen, Luisa and Gregorevic, Paul and Gudiksen, Anders and Artati, Anna and Adamski, Jerzy and Andersen, Nicoline R. and Sigvardsen, Casper M. and Carl, Christian S. and Voldstedlund, Christian T. and Kjøbsted, Rasmus and Hauck, Stefanie M. and Schjerling, Peter and Jensen, Thomas E. and Cebrian-Serrano, Alberto and Jähnert, Markus and Gottmann, Pascal and Burtscher, Ingo and Lickert, Heiko and Pilegaard, Henriette and Schürmann, Annette and Tschöp, Matthias H. and Moritz, Thomas and Müller, Timo D. and Sylow, Lykke and Kiens, Bente and Richter, Erik A. and Kleinert, Maximilian},
	month = jan,
	year = {2025},
	note = {Publisher: Nature Publishing Group},
	keywords = {Diabetes, Fat metabolism, Homeostasis, Metabolomics},
	pages = {345},
}

2024 (2)

Reduced adipocyte glutaminase activity promotes energy expenditure and metabolic health. Lecoutre, S., Maqdasy, S., Rizo-Roca, D., Renzi, G., Vlassakev, I., Alaeddine, L. M., Higos, R., Jalkanen, J., Zhong, J., Zareifi, D. S., Frendo-Cumbo, S., Massier, L., Hodek, O., Juvany, M., Moritz, T., de Castro Barbosa, T., Omar-Hmeadi, M., López-Yus, M., Merabtene, F., Abatan, J. B., Marcelin, G., El Hachem, E., Rouault, C., Bergo, M. O., Petrus, P., Zierath, J. R., Clément, K., Krook, A., Mejhert, N., & Rydén, M. Nature Metabolism, 6(7): 1329–1346. July 2024. Publisher: Nature Publishing Group

Reduced adipocyte glutaminase activity promotes energy expenditure and metabolic health [link]

Paper doi link bibtex abstract

@article{lecoutre_reduced_2024,
	title = {Reduced adipocyte glutaminase activity promotes energy expenditure and metabolic health},
	volume = {6},
	copyright = {2024 The Author(s)},
	issn = {2522-5812},
	url = {https://www.nature.com/articles/s42255-024-01083-y},
	doi = {10.1038/s42255-024-01083-y},
	abstract = {Glutamine and glutamate are interconverted by several enzymes and alterations in this metabolic cycle are linked to cardiometabolic traits. Herein, we show that obesity-associated insulin resistance is characterized by decreased plasma and white adipose tissue glutamine-to-glutamate ratios. We couple these stoichiometric changes to perturbed fat cell glutaminase and glutamine synthase messenger RNA and protein abundance, which together promote glutaminolysis. In human white adipocytes, reductions in glutaminase activity promote aerobic glycolysis and mitochondrial oxidative capacity via increases in hypoxia-inducible factor 1α abundance, lactate levels and p38 mitogen-activated protein kinase signalling. Systemic glutaminase inhibition in male and female mice, or genetically in adipocytes of male mice, triggers the activation of thermogenic gene programs in inguinal adipocytes. Consequently, the knockout mice display higher energy expenditure and improved glucose tolerance compared to control littermates, even under high-fat diet conditions. Altogether, our findings highlight white adipocyte glutamine turnover as an important determinant of energy expenditure and metabolic health.},
	language = {en},
	number = {7},
	urldate = {2024-07-29},
	journal = {Nature Metabolism},
	author = {Lecoutre, Simon and Maqdasy, Salwan and Rizo-Roca, David and Renzi, Gianluca and Vlassakev, Ivan and Alaeddine, Lynn M. and Higos, Romane and Jalkanen, Jutta and Zhong, Jiawei and Zareifi, Danae S. and Frendo-Cumbo, Scott and Massier, Lucas and Hodek, Ondrej and Juvany, Marta and Moritz, Thomas and de Castro Barbosa, Thais and Omar-Hmeadi, Muhmmad and López-Yus, Marta and Merabtene, Fatiha and Abatan, Jimon Boniface and Marcelin, Geneviève and El Hachem, Elie-Julien and Rouault, Christine and Bergo, Martin O. and Petrus, Paul and Zierath, Juleen R. and Clément, Karine and Krook, Anna and Mejhert, Niklas and Rydén, Mikael},
	month = jul,
	year = {2024},
	note = {Publisher: Nature Publishing Group},
	keywords = {Fat metabolism, Obesity},
	pages = {1329--1346},
}

Schinus terebinthifolia Raddi—Untargeted Metabolomics Approach to Investigate the Chemical Variation in Volatile and Non-Volatile Compounds. Carneiro, M. J., Pinheiro, G. P., Antunes, E. R. M., Hantao, L. W., Moritz, T., & Sawaya, A. C. H. F. Metabolites, 14(11): 612. November 2024. Number: 11 Publisher: Multidisciplinary Digital Publishing Institute

Paper doi link bibtex abstract

@article{carneiro_schinus_2024,
	title = {Schinus terebinthifolia {Raddi}—{Untargeted} {Metabolomics} {Approach} to {Investigate} the {Chemical} {Variation} in {Volatile} and {Non}-{Volatile} {Compounds}},
	volume = {14},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2218-1989},
	url = {https://www.mdpi.com/2218-1989/14/11/612},
	doi = {10.3390/metabo14110612},
	abstract = {Context: Schinus terebinthifolia Raddi is used in Brazilian folk medicine due to the wound healing and antiseptic properties of its bark, and its fruit are used as a condiment. However, the aerial parts of this plant have been studied and present some bioactive compounds as well. Objectives: The aim of this study was to investigate the variation in volatile and non-volatile composition of S. terebinthifolia leaves using untargeted metabolomics. Material and Methods: The leaves of four trees were collected over one year; ethanolic extracts were analyzed by UHPLC-MS and fresh leaves were analyzed by GC-MS using HS-SPME. The data were processed using online software. Results: The results suggest seasonality interfered little with the chemical composition of leaves. On the other hand, the sex of the plant clearly determined the chemical composition of both volatile and non-volatile compounds. Discussion and conclusions: Chemical variability between plants with male and female flowers is fundamental information for the standardized use of its leaves. Compounds with important biological activities were putatively identified, confirming the potential use of S. terebinthifolia leaves as a source of bioactive compounds, reducing waste and increasing economic gains for local farmers throughout the year.},
	language = {en},
	number = {11},
	urldate = {2024-11-29},
	journal = {Metabolites},
	author = {Carneiro, Mara Junqueira and Pinheiro, Guilherme Perez and Antunes, Elisa Ribeiro Miranda and Hantao, Leandro Wang and Moritz, Thomas and Sawaya, Alexandra Christine Helena Frankland},
	month = nov,
	year = {2024},
	note = {Number: 11
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{Aroeira}, GC-MS, UHPLC-MS, pink pepper, plant sex, seasonality},
	pages = {612},
}

2023 (3)

Oak stands along an elevation gradient have different molecular strategies for regulating bud phenology. Le Provost, G., Lalanne, C., Lesur, I., Louvet, J., Delzon, S., Kremer, A., Labadie, K., Aury, J., Da Silva, C., Moritz, T., & Plomion, C. BMC Plant Biology, 23(1): 108. February 2023.

Oak stands along an elevation gradient have different molecular strategies for regulating bud phenology [link]

Paper doi link bibtex abstract

@article{le_provost_oak_2023,
	title = {Oak stands along an elevation gradient have different molecular strategies for regulating bud phenology},
	volume = {23},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-023-04069-2},
	doi = {10.1186/s12870-023-04069-2},
	abstract = {Global warming raises serious concerns about the persistence of species and populations locally adapted to their environment, simply because of the shift it produces in their adaptive landscape. For instance, the phenological cycle of tree species may be strongly affected by higher winter temperatures and late frost in spring. Given the variety of ecosystem services they provide, the question of forest tree adaptation has received increasing attention in the scientific community and catalyzed research efforts in ecology, evolutionary biology and functional genomics to study their adaptive capacity to respond to such perturbations.},
	number = {1},
	urldate = {2023-03-03},
	journal = {BMC Plant Biology},
	author = {Le Provost, Gregoire and Lalanne, Céline and Lesur, Isabelle and Louvet, Jean-Marc and Delzon, Sylvain and Kremer, Antoine and Labadie, Karine and Aury, Jean-Marc and Da Silva, Corinne and Moritz, Thomas and Plomion, Christophe},
	month = feb,
	year = {2023},
	keywords = {Bud phenology, Elevation cline, Gene expression, Hormone quantification, Response to temperature, Sessile oak},
	pages = {108},
}

Structural elucidation of 3-nitrophenylhydrazine derivatives of tricarboxylic acid cycle acids and optimization of their fragmentation to boost sensitivity in liquid chromatography-mass spectrometry. Hodek, O., Henderson, J., Argemi-Muntadas, L., Khan, A., & Moritz, T. Journal of Chromatography B, 1222: 123719. April 2023.

Paper doi link bibtex abstract

@article{hodek_structural_2023,
	title = {Structural elucidation of 3-nitrophenylhydrazine derivatives of tricarboxylic acid cycle acids and optimization of their fragmentation to boost sensitivity in liquid chromatography-mass spectrometry},
	volume = {1222},
	issn = {1570-0232},
	url = {https://www.sciencedirect.com/science/article/pii/S1570023223001290},
	doi = {10.1016/j.jchromb.2023.123719},
	abstract = {Carboxylic acids participate in many metabolic pathways including tricarboxylic acid (TCA) cycle. Therefore, there have been ongoing attempts to develop sensitive liquid chromatography-mass spectrometry methods over the last decades. Derivatization of the carboxylic acids with 3-nitrophenylhydrazine presents a well-established methodology, and yet the derivatized species of polycarboxylic acids and their fragmentation in collision-induced dissociation have not been fully studied before. In our study, we elucidated how annotation of most abundant 3-nitrophenylhydrazine derivatives and optimization of their fragmentation in multiple reaction monitoring can boost the sensitivity, especially for polycarboxylic acids. Finally, the optimized liquid chromatography-tandem mass spectrometry method allowed for low detection limits ranging from 10 pM for 2-oxoglutaric acid to 800 pM for pyruvic acid. All TCA carboxylates were quantified in 20 µL of human plasma and the targeted method was validated in the same matrix. The same methodology with a modified gradient elution was also applied to untargeted screening of fatty acids by using high-resolution mass spectrometry enabling identification of 29 medium- to long-chain fatty acids in human plasma. The TCA carboxylates were also quantified in 105 of C2C12 mouse myuotube cells grown under different treatments to proof applicability of the methodology to biological studies in a wider sense. However, unfortunately all the TCA carboxylates were also found in the derivatized blanks in substantial amounts, which prevents from using the methodology for quantification of the carboxylates in less than 105 cells.},
	language = {en},
	urldate = {2023-04-21},
	journal = {Journal of Chromatography B},
	author = {Hodek, Ondřej and Henderson, John and Argemi-Muntadas, Lidia and Khan, Adnan and Moritz, Thomas},
	month = apr,
	year = {2023},
	keywords = {3-nitrophenylhydrazine, Carboxylic acid, Derivatization, Liquid chromatography-mass spectrometry},
	pages = {123719},
}

Xylan glucuronic acid side chains fix suberin-like aliphatic compounds to wood cell walls. Derba-Maceluch, M., Mitra, M., Hedenström, M., Liu, X., Gandla, M. L., Barbut, F. R., Abreu, I. N., Donev, E. N., Urbancsok, J., Moritz, T., Jönsson, L. J., Tsang, A., Powlowski, J., Master, E. R., & Mellerowicz, E. J. New Phytologist, 238(1): 297–312. January 2023. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18712

Xylan glucuronic acid side chains fix suberin-like aliphatic compounds to wood cell walls [link]

Paper doi link bibtex abstract

@article{derba-maceluch_xylan_2023,
	title = {Xylan glucuronic acid side chains fix suberin-like aliphatic compounds to wood cell walls},
	volume = {238},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18712},
	doi = {10.1111/nph.18712},
	abstract = {Wood is the most important repository of assimilated carbon in the biosphere, in the form of large polymers (cellulose, hemicelluloses including glucuronoxylan, and lignin) that interactively form a composite, together with soluble extractives including phenolic and aliphatic compounds. Molecular interactions among these compounds are not fully understood. We have targeted the expression of a fungal α-glucuronidase to the wood cell wall of aspen (Populus tremula L. × tremuloides Michx.) and Arabidopsis (Arabidopsis thaliana (L.) Heynh), to decrease contents of the 4-O-methyl glucuronopyranose acid (mGlcA) substituent of xylan, to elucidate mGlcA's functions. The enzyme affected the content of aliphatic insoluble cell wall components having composition similar to suberin, which required mGlcA for binding to cell walls. Such suberin-like compounds have been previously identified in decayed wood, but here, we show their presence in healthy wood of both hardwood and softwood species. By contrast, γ-ester bonds between mGlcA and lignin were insensitive to cell wall-localized α-glucuronidase, supporting the intracellular formation of these bonds. These findings challenge the current view of the wood cell wall composition and reveal a novel function of mGlcA substituent of xylan in fastening of suberin-like compounds to cell wall. They also suggest an intracellular initiation of lignin–carbohydrate complex assembly.},
	language = {en},
	number = {1},
	urldate = {2023-03-10},
	journal = {New Phytologist},
	author = {Derba-Maceluch, Marta and Mitra, Madhusree and Hedenström, Mattias and Liu, Xiaokun and Gandla, Madhavi L. and Barbut, Félix R. and Abreu, Ilka N. and Donev, Evgeniy N. and Urbancsok, János and Moritz, Thomas and Jönsson, Leif J. and Tsang, Adrian and Powlowski, Justin and Master, Emma R. and Mellerowicz, Ewa J.},
	month = jan,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18712},
	keywords = {Populus, lignin-carbohydrate complexes (LCCs), lignin–carbohydrate complexes, saccharification, suberin, wood cell wall, xylan},
	pages = {297--312},
}

2022 (7)

Circum-Arctic distribution of chemical anti-herbivore compounds suggests biome-wide trade-off in defence strategies in Arctic shrubs. Lindén, E., te Beest, M., Aubreu, I., Moritz, T., Sundqvist, M. K., Barrio, I. C., Boike, J., Bryant, J. P., Bråthen, K. A., Buchwal, A., Bueno, C. G., Currier, A., Egelkraut, D. D., Forbes, B. C., Hallinger, M., Heijmans, M., Hermanutz, L., Hik, D. S., Hofgaard, A., Holmgren, M., Huebner, D. C., Høye, T. T., Jónsdóttir, I. S., Kaarlejärvi, E., Kissler, E., Kumpula, T., Limpens, J., Myers-Smith, I. H., Normand, S., Post, E., Rocha, A. V., Schmidt, N. M., Skarin, A., Soininen, E. M., Sokolov, A., Sokolova, N., Speed, J. D. M., Street, L., Tananaev, N., Tremblay, J., Urbanowicz, C., Watts, D. A., Zimmermann, H., & Olofsson, J. Ecography,e06166. August 2022.

Circum-Arctic distribution of chemical anti-herbivore compounds suggests biome-wide trade-off in defence strategies in Arctic shrubs [link]

Paper doi link bibtex abstract

@article{linden_circum-arctic_2022,
title = {Circum-{Arctic} distribution of chemical anti-herbivore compounds suggests biome-wide trade-off in defence strategies in {Arctic} shrubs},
issn = {1600-0587},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ecog.06166},
doi = {10.1111/ecog.06166},
abstract = {Spatial variation in plant chemical defence towards herbivores can help us understand variation in herbivore top–down control of shrubs in the Arctic and possibly also shrub responses to global warming. Less defended, non-resinous shrubs could be more influenced by herbivores than more defended, resinous shrubs. However, sparse field measurements limit our current understanding of how much of the circum-Arctic variation in defence compounds is explained by taxa or defence functional groups (resinous/non-resinous). We measured circum-Arctic chemical defence and leaf digestibility in resinous (Betula glandulosa, B. nana ssp. exilis) and non-resinous (B. nana ssp. nana, B. pumila) shrub birches to see how they vary among and within taxa and functional groups. Using liquid chromatography–mass spectrometry (LC–MS) metabolomic analyses and in vitro leaf digestibility via incubation in cattle rumen fluid, we analysed defence composition and leaf digestibility in 128 samples from 44 tundra locations. We found biogeographical patterns in anti-herbivore defence where mean leaf triterpene concentrations and twig resin gland density were greater in resinous taxa and mean concentrations of condensing tannins were greater in non-resinous taxa. This indicates a biome-wide trade-off between triterpene- or tannin-dominated defences. However, we also found variations in chemical defence composition and resin gland density both within and among functional groups (resinous/non-resinous) and taxa, suggesting these categorisations only partly predict chemical herbivore defence. Complex tannins were the only defence compounds negatively related to in vitro digestibility, identifying this previously neglected tannin group as having a potential key role in birch anti-herbivore defence. We conclude that circum-Arctic variation in birch anti-herbivore defence can be partly derived from biogeographical distributions of birch taxa, although our detailed mapping of plant defence provides more information on this variation and can be used for better predictions of herbivore effects on Arctic vegetation.},
language = {en},
urldate = {2022-09-08},
journal = {Ecography},
author = {Lindén, Elin and te Beest, Mariska and Aubreu, Ilka and Moritz, Thomas and Sundqvist, Maja K. and Barrio, Isabel C. and Boike, Julia and Bryant, John P. and Bråthen, Kari Anne and Buchwal, Agata and Bueno, C. Guillermo and Currier, Alain and Egelkraut, Dagmar D. and Forbes, Bruce C. and Hallinger, Martin and Heijmans, Monique and Hermanutz, Luise and Hik, David S. and Hofgaard, Annika and Holmgren, Milena and Huebner, Diane C. and Høye, Toke T. and Jónsdóttir, Ingibjörg S. and Kaarlejärvi, Elina and Kissler, Emilie and Kumpula, Timo and Limpens, Juul and Myers-Smith, Isla H. and Normand, Signe and Post, Eric and Rocha, Adrian V. and Schmidt, Niels Martin and Skarin, Anna and Soininen, Eeva M. and Sokolov, Aleksandr and Sokolova, Natalia and Speed, James D. M. and Street, Lorna and Tananaev, Nikita and Tremblay, Jean-Pierre and Urbanowicz, Christine and Watts, David A. and Zimmermann, Heike and Olofsson, Johan},
month = aug,
year = {2022},
keywords = {Arctic, Betula, birch, herbivory, metabolomics, plant chemical defence, shrubs, tundra},
pages = {e06166},
}

Spatial variation in plant chemical defence towards herbivores can help us understand variation in herbivore top–down control of shrubs in the Arctic and possibly also shrub responses to global warming. Less defended, non-resinous shrubs could be more influenced by herbivores than more defended, resinous shrubs. However, sparse field measurements limit our current understanding of how much of the circum-Arctic variation in defence compounds is explained by taxa or defence functional groups (resinous/non-resinous). We measured circum-Arctic chemical defence and leaf digestibility in resinous (Betula glandulosa, B. nana ssp. exilis) and non-resinous (B. nana ssp. nana, B. pumila) shrub birches to see how they vary among and within taxa and functional groups. Using liquid chromatography–mass spectrometry (LC–MS) metabolomic analyses and in vitro leaf digestibility via incubation in cattle rumen fluid, we analysed defence composition and leaf digestibility in 128 samples from 44 tundra locations. We found biogeographical patterns in anti-herbivore defence where mean leaf triterpene concentrations and twig resin gland density were greater in resinous taxa and mean concentrations of condensing tannins were greater in non-resinous taxa. This indicates a biome-wide trade-off between triterpene- or tannin-dominated defences. However, we also found variations in chemical defence composition and resin gland density both within and among functional groups (resinous/non-resinous) and taxa, suggesting these categorisations only partly predict chemical herbivore defence. Complex tannins were the only defence compounds negatively related to in vitro digestibility, identifying this previously neglected tannin group as having a potential key role in birch anti-herbivore defence. We conclude that circum-Arctic variation in birch anti-herbivore defence can be partly derived from biogeographical distributions of birch taxa, although our detailed mapping of plant defence provides more information on this variation and can be used for better predictions of herbivore effects on Arctic vegetation.

Impaired phosphocreatine metabolism in white adipocytes promotes inflammation. Maqdasy, S., Lecoutre, S., Renzi, G., Frendo-Cumbo, S., Rizo-Roca, D., Moritz, T., Juvany, M., Hodek, O., Gao, H., Couchet, M., Witting, M., Kerr, A., Bergo, M. O., Choudhury, R. P., Aouadi, M., Zierath, J. R., Krook, A., Mejhert, N., & Rydén, M. Nature Metabolism, 4(2): 1–13. February 2022.

Impaired phosphocreatine metabolism in white adipocytes promotes inflammation [link]

Paper doi link bibtex abstract

@article{maqdasy_impaired_2022,
	title = {Impaired phosphocreatine metabolism in white adipocytes promotes inflammation},
	volume = {4},
	copyright = {2022 The Author(s)},
	issn = {2522-5812},
	url = {https://www.nature.com/articles/s42255-022-00525-9},
	doi = {10.1038/s42255-022-00525-9},
	abstract = {The mechanisms promoting disturbed white adipocyte function in obesity remain largely unclear. Herein, we integrate white adipose tissue (WAT) metabolomic and transcriptomic data from clinical cohorts and find that the WAT phosphocreatine/creatine ratio is increased and creatine kinase-B expression and activity is decreased in the obese state. In human in vitro and murine in vivo models, we demonstrate that decreased phosphocreatine metabolism in white adipocytes alters adenosine monophosphate-activated protein kinase activity via effects on adenosine triphosphate/adenosine diphosphate levels, independently of WAT beigeing. This disturbance promotes a pro-inflammatory profile characterized, in part, by increased chemokine (C-C motif) ligand 2 (CCL2) production. These data suggest that the phosphocreatine/creatine system links cellular energy shuttling with pro-inflammatory responses in human and murine white adipocytes. Our findings provide unexpected perspectives on the mechanisms driving WAT inflammation in obesity and may present avenues to target adipocyte dysfunction.},
	language = {en},
	number = {2},
	urldate = {2022-02-17},
	journal = {Nature Metabolism},
	author = {Maqdasy, Salwan and Lecoutre, Simon and Renzi, Gianluca and Frendo-Cumbo, Scott and Rizo-Roca, David and Moritz, Thomas and Juvany, Marta and Hodek, Ondrej and Gao, Hui and Couchet, Morgane and Witting, Michael and Kerr, Alastair and Bergo, Martin O. and Choudhury, Robin P. and Aouadi, Myriam and Zierath, Juleen R. and Krook, Anna and Mejhert, Niklas and Rydén, Mikael},
	month = feb,
	year = {2022},
	keywords = {Fat metabolism, Mechanisms of disease, Obesity},
	pages = {1--13},
}

Metabolic control of arginine and ornithine levels paces the progression of leaf senescence. Liebsch, D., Juvany, M., Li, Z., Wang, H., Ziolkowska, A., Chrobok, D., Boussardon, C., Wen, X., Law, S. R, Janečková, H., Brouwer, B., Lindén, P., Delhomme, N., Stenlund, H., Moritz, T., Gardeström, P., Guo, H., & Keech, O. Plant Physiology, 189(4): 1943–1960. August 2022.

Metabolic control of arginine and ornithine levels paces the progression of leaf senescence [link]

Paper doi link bibtex abstract

@article{liebsch_metabolic_2022,
	title = {Metabolic control of arginine and ornithine levels paces the progression of leaf senescence},
	volume = {189},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac244},
	doi = {10.1093/plphys/kiac244},
	abstract = {Leaf senescence can be induced by stress or aging, sometimes in a synergistic manner. It is generally acknowledged that the ability to withstand senescence-inducing conditions can provide plants with stress resilience. Although the signaling and transcriptional networks responsible for a delayed senescence phenotype, often referred to as a functional stay-green trait, have been actively investigated, very little is known about the subsequent metabolic adjustments conferring this aptitude to survival. First, using the individually darkened leaf (IDL) experimental setup, we compared IDLs of wild-type (WT) Arabidopsis (Arabidopsis thaliana) to several stay-green contexts, that is IDLs of two functional stay-green mutant lines, oresara1-2 (ore1-2) and an allele of phytochrome-interacting factor 5 (pif5), as well as to leaves from a WT plant entirely darkened (DP). We provide compelling evidence that arginine and ornithine, which accumulate in all stay-green contexts—likely due to the lack of induction of amino acids (AAs) transport—can delay the progression of senescence by fueling the Krebs cycle or the production of polyamines (PAs). Secondly, we show that the conversion of putrescine to spermidine (SPD) is controlled in an age-dependent manner. Thirdly, we demonstrate that SPD represses senescence via interference with ethylene signaling by stabilizing the ETHYLENE BINDING FACTOR1 and 2 (EBF1/2) complex. Taken together, our results identify arginine and ornithine as central metabolites influencing the stress- and age-dependent progression of leaf senescence. We propose that the regulatory loop between the pace of the AA export and the progression of leaf senescence provides the plant with a mechanism to fine-tune the induction of cell death in leaves, which, if triggered unnecessarily, can impede nutrient remobilization and thus plant growth and survival.},
	number = {4},
	urldate = {2022-08-08},
	journal = {Plant Physiology},
	author = {Liebsch, Daniela and Juvany, Marta and Li, Zhonghai and Wang, Hou-Ling and Ziolkowska, Agnieszka and Chrobok, Daria and Boussardon, Clément and Wen, Xing and Law, Simon R and Janečková, Helena and Brouwer, Bastiaan and Lindén, Pernilla and Delhomme, Nicolas and Stenlund, Hans and Moritz, Thomas and Gardeström, Per and Guo, Hongwei and Keech, Olivier},
	month = aug,
	year = {2022},
	pages = {1943--1960},
}

Mixed-mode chromatography-mass spectrometry enables targeted and untargeted screening of carboxylic acids in biological samples. Hodek, O., Argemi-Muntadas, L., Khan, A., & Moritz, T. Analytical Methods, 14(10): 1015–1022. January 2022.

Mixed-mode chromatography-mass spectrometry enables targeted and untargeted screening of carboxylic acids in biological samples [link]

Paper doi link bibtex abstract

@article{hodek_mixed-mode_2022,
	title = {Mixed-mode chromatography-mass spectrometry enables targeted and untargeted screening of carboxylic acids in biological samples},
	volume = {14},
	issn = {1759-9679},
	url = {https://pubs.rsc.org/en/content/articlelanding/2022/ay/d1ay02143e},
	doi = {10/gpkx25},
	abstract = {Carboxylic acids are crucial metabolites in the tricarboxylic acid (TCA) cycle and thus participate in central carbon metabolism (CCM). Research dependent on the analysis of metabolites involved in central carbon metabolism requires fast separation and sensitive detection of carboxylic acids using liquid chromatography-mass spectrometry (LC-MS). However, successful separation of all carboxylic acids from the TCA cycle by liquid chromatography remains a challenging task because of their high polarity and thus low retention on the conventional reversed-phase columns. In this study, we tested a reversed-phase/anion exchange mixed-mode stationary phase (Waters BEH C18 AX) using liquid chromatography-tandem mass spectrometry (LC-MS/MS). We developed and optimized a method that enables a 10 minute separation of all carboxylic acids from the TCA cycle and lactic acid without prior derivatization or addition of ion-pair reagents in the mobile phase. The developed method was validated for quantification of 8 acids in murine brown preadipocytes, 5 acids in human plasma and 6 acids in Arabidopsis thaliana leaves with limits of quantification ranging from 0.1 μM for malic acid to 10 μM for isocitric acid. Moreover, the mixed-mode chromatography enabled untargeted screening of medium- to long-chain fatty acids in murine brown preadipocytes, Arabidopsis thaliana, and human plasma, where 23 fatty acids were identified by using liquid chromatography with high-resolution mass spectrometry (HRMS).},
	language = {en},
	number = {10},
	urldate = {2022-02-25},
	journal = {Analytical Methods},
	author = {Hodek, Ondřej and Argemi-Muntadas, Lidia and Khan, Adnan and Moritz, Thomas},
	month = jan,
	year = {2022},
	pages = {1015--1022},
}

Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health. Marabita, F., James, T., Karhu, A., Virtanen, H., Kettunen, K., Stenlund, H., Boulund, F., Hellström, C., Neiman, M., Mills, R., Perheentupa, T., Laivuori, H., Helkkula, P., Byrne, M., Jokinen, I., Honko, H., Kallonen, A., Ermes, M., Similä, H., Lindholm, M., Widén, E., Ripatti, S., Perälä-Heape, M., Engstrand, L., Nilsson, P., Moritz, T., Miettinen, T., Sallinen, R., & Kallioniemi, O. Cell Systems, 13(3): 241–255.e7. March 2022.

Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health [link]

Paper doi link bibtex

@article{marabita_multiomics_2022,
	title = {Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health},
	volume = {13},
	issn = {2405-4712},
	url = {https://www.cell.com/cell-systems/abstract/S2405-4712(21)00451-8},
	doi = {10.1016/j.cels.2021.11.001},
	language = {English},
	number = {3},
	urldate = {2022-04-08},
	journal = {Cell Systems},
	author = {Marabita, Francesco and James, Tojo and Karhu, Anu and Virtanen, Heidi and Kettunen, Kaisa and Stenlund, Hans and Boulund, Fredrik and Hellström, Cecilia and Neiman, Maja and Mills, Robert and Perheentupa, Teemu and Laivuori, Hannele and Helkkula, Pyry and Byrne, Myles and Jokinen, Ilkka and Honko, Harri and Kallonen, Antti and Ermes, Miikka and Similä, Heidi and Lindholm, Mikko and Widén, Elisabeth and Ripatti, Samuli and Perälä-Heape, Maritta and Engstrand, Lars and Nilsson, Peter and Moritz, Thomas and Miettinen, Timo and Sallinen, Riitta and Kallioniemi, Olli},
	month = mar,
	year = {2022},
	keywords = {P4 medicine, lifestyle changes, multiomics data integration, personalized medicine, precision health, precision medicine, systems medicine},
	pages = {241--255.e7},
}

Sucrose synthase activity is not required for cellulose biosynthesis in Arabidopsis. Wang, W., Viljamaa, S., Hodek, O., Moritz, T., & Niittylä, T. The Plant Journal, 110(5): 1493–1497. 2022.

Sucrose synthase activity is not required for cellulose biosynthesis in Arabidopsis [link]

Paper doi link bibtex abstract

@article{wang_sucrose_2022,
	title = {Sucrose synthase activity is not required for cellulose biosynthesis in {Arabidopsis}},
	volume = {110},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15752},
	doi = {10.1111/tpj.15752},
	abstract = {Biosynthesis of plant cell walls requires UDP-glucose as the substrate for cellulose biosynthesis, and as an intermediate for the synthesis of other matrix polysaccharides. The sucrose cleaving enzyme sucrose synthase (SUS) is thought to have a central role in UDP-glucose biosynthesis, and a long-held and much debated hypothesis postulates that SUS is required to supply UDP-glucose to cellulose biosynthesis. To investigate the role of SUS in cellulose biosynthesis of Arabidopsis thaliana we characterized mutants in which four or all six Arabidopsis SUS genes were disrupted. These sus mutants showed no growth phenotypes, vascular tissue cell wall defects, or changes in cellulose content. Moreover, the UDP-glucose content of rosette leaves of the sextuple sus mutants was increased by approximately 20\% compared with wild type. It can thus be concluded that cellulose biosynthesis is able to employ alternative UDP-glucose biosynthesis pathway(s), and thereby the model of SUS requirements for cellulose biosynthesis in Arabidopsis can be refuted.},
	language = {en},
	number = {5},
	urldate = {2022-06-09},
	journal = {The Plant Journal},
	author = {Wang, Wei and Viljamaa, Sonja and Hodek, Ondrej and Moritz, Thomas and Niittylä, Totte},
	year = {2022},
	keywords = {Arabidopsis thaliana, UDP-glucose, cellulose, sucrose synthase},
	pages = {1493--1497},
}

The human batokine EPDR1 regulates β-cell metabolism and function. Cataldo, L. R., Gao, Q., Argemi-Muntadas, L., Hodek, O., Cowan, E., Hladkou, S., Gheibi, S., Spégel, P., Prasad, R. B., Eliasson, L., Scheele, C., Fex, M., Mulder, H., & Moritz, T. Molecular Metabolism, 66: 101629. December 2022.

The human batokine EPDR1 regulates β-cell metabolism and function [link]

Paper doi link bibtex abstract

@article{cataldo_human_2022,
	title = {The human batokine {EPDR1} regulates β-cell metabolism and function},
	volume = {66},
	issn = {2212-8778},
	url = {https://www.sciencedirect.com/science/article/pii/S2212877822001983},
	doi = {10.1016/j.molmet.2022.101629},
	abstract = {Objective
Ependymin-Related Protein 1 (EPDR1) was recently identified as a secreted human batokine regulating mitochondrial respiration linked to thermogenesis in brown fat. Despite that EPDR1 is expressed in human pancreatic β-cells and that glucose-stimulated mitochondrial metabolism is critical for stimulus-secretion coupling in β-cells, the role of EPDR1 in β-cell metabolism and function has not been investigated.
Methods
EPDR1 mRNA levels in human pancreatic islets from non-diabetic (ND) and type 2 diabetes (T2D) subjects were assessed. Human islets, EndoC-βH1 and INS1 832/13 cells were transfected with scramble (control) and EPDR1 siRNAs (EPDR1-KD) or treated with human EPDR1 protein, and glucose-stimulated insulin secretion (GSIS) assessed by ELISA. Mitochondrial metabolism was investigated by extracellular flux analyzer, confocal microscopy and mass spectrometry-based metabolomics analysis.
Results
EPDR1 mRNA expression was upregulated in human islets from T2D and obese donors and positively correlated to BMI of donors. In T2D donors, EPDR1 mRNA levels negatively correlated with HbA1c and positively correlated with GSIS. EPDR1 silencing in human islets and β-cell lines reduced GSIS whereas treatment with human EPDR1 protein increased GSIS. Epdr1 silencing in INS1 832/13 cells reduced glucose- and pyruvate- but not K+-stimulated insulin secretion. Metabolomics analysis in Epdr1-KD INS1 832/13 cells suggests diversion of glucose-derived pyruvate to lactate production and decreased malate-aspartate shuttle and the tricarboxylic acid (TCA) cycle activity. The glucose-stimulated rise in mitochondrial respiration and ATP/ADP-ratio was impaired in Epdr1-deficient cells.
Conclusion
These results suggests that to maintain glucose homeostasis in obese people, upregulation of EPDR1 may improve β-cell function via channelling glycolysis-derived pyruvate to the mitochondrial TCA cycle.},
	language = {en},
	urldate = {2022-12-22},
	journal = {Molecular Metabolism},
	author = {Cataldo, Luis Rodrigo and Gao, Qian and Argemi-Muntadas, Lidia and Hodek, Ondrej and Cowan, Elaine and Hladkou, Sergey and Gheibi, Sevda and Spégel, Peter and Prasad, Rashmi B. and Eliasson, Lena and Scheele, Camilla and Fex, Malin and Mulder, Hindrik and Moritz, Thomas},
	month = dec,
	year = {2022},
	keywords = {Beta cells, Insulin secretion, Lactate, Mitochondrial metabolism, TCA cycle, Type 2 diabetes},
	pages = {101629},
}

2021 (3)

A metabolomic study of Gomphrena agrestis in Brazilian Cerrado suggests drought-adaptive strategies on metabolism. Melo, G. A., Abreu, I. N., de Oliveira, M. B., Budzinski, I. G. F., Silva, L. V., Pimenta, M. A. S., & Moritz, T. Scientific Reports, 11(1): 12933. June 2021.

A metabolomic study of Gomphrena agrestis in Brazilian Cerrado suggests drought-adaptive strategies on metabolism [link]

Paper doi link bibtex abstract 1 download

@article{melo_metabolomic_2021,
	title = {A metabolomic study of {Gomphrena} agrestis in {Brazilian} {Cerrado} suggests drought-adaptive strategies on metabolism},
	volume = {11},
	copyright = {2021 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-021-92449-9},
	doi = {10.1038/s41598-021-92449-9},
	abstract = {Drought is the main factor that limits the distribution and productivity of plant species. In the Brazilian Cerrado, the vegetation is adapted to a seasonal climate with long- and short-term periods of drought. To analyze the metabolic strategies under such conditions, a metabolomic approach was used to characterize Gomphrena agrestis Mart. (Amaranthaceae) a native species that grows under natural conditions, in a rock-field area. Roots and leaves material from native specimens were sampled along different seasons of the year and LC–MS and GC–MS analyzed for multiple chemical constituents. The datasets derived from the different measurements were combined and evaluated using multivariate analysis. Principal component analysis was used to obtain an overview of the samples and identify outliers. Later, the data was analyzed with orthogonal projection to latent structures discriminant analysis to obtain valid models that could explain the metabolite variations in the different seasons. Two hundred and eighty metabolites were annotated, generating a unique database to characterize metabolic strategies used to cope with the effects of drought. The accumulation of fructans in the thickened roots is consistent with the storage of carbons during the rainy season to support the energy demand during a long period of drought. The accumulation of Abscisic acid, sugars and sugar alcohols, phenolics, and pigment in the leaves suggests physiological adaptations. To cope with long-term drought, the data suggests that tissue water status and storage of reserves are important to support plant survival and regrowth. However, during short-term drought, osmoregulation and oxidative protection seems to be essential, probably to support the maintenance of active photosynthesis.},
	language = {en},
	number = {1},
	urldate = {2021-11-04},
	journal = {Scientific Reports},
	author = {Melo, Geraldo Aclécio and Abreu, Ilka Nacif and de Oliveira, Maíra Baista and Budzinski, Ilara Gabriela Frasson and Silva, Lucinélia Vieira and Pimenta, Marcio Antônio Silva and Moritz, Thomas},
	month = jun,
	year = {2021},
	keywords = {Plant physiology, Plant sciences, Plant stress responses},
	pages = {12933},
}

Branched-chain amino acid metabolism is regulated by ERRα in primary human myotubes and is further impaired by glucose loading in type 2 diabetes. Sjögren, R. J. O., Rizo-Roca, D., Chibalin, A. V., Chorell, E., Furrer, R., Katayama, S., Harada, J., Karlsson, H. K. R., Handschin, C., Moritz, T., Krook, A., Näslund, E., & Zierath, J. R. Diabetologia, 64(9): 2077–2091. September 2021.

Paper doi link bibtex abstract 1 download

@article{sjogren_branched-chain_2021,
	title = {Branched-chain amino acid metabolism is regulated by {ERRα} in primary human myotubes and is further impaired by glucose loading in type 2 diabetes},
	volume = {64},
	issn = {1432-0428},
	url = {https://doi.org/10.1007/s00125-021-05481-9},
	doi = {10.1007/s00125-021-05481-9},
	abstract = {Increased levels of branched-chain amino acids (BCAAs) are associated with type 2 diabetes pathogenesis. However, most metabolomic studies are limited to an analysis of plasma metabolites under fasting conditions, rather than the dynamic shift in response to a metabolic challenge. Moreover, metabolomic profiles of peripheral tissues involved in glucose homeostasis are scarce and the transcriptomic regulation of genes involved in BCAA catabolism is partially unknown. This study aimed to identify differences in circulating and skeletal muscle BCAA levels in response to an OGTT in individuals with normal glucose tolerance (NGT) or type 2 diabetes. Additionally, transcription factors involved in the regulation of the BCAA gene set were identified.},
	language = {en},
	number = {9},
	urldate = {2022-04-08},
	journal = {Diabetologia},
	author = {Sjögren, Rasmus J. O. and Rizo-Roca, David and Chibalin, Alexander V. and Chorell, Elin and Furrer, Regula and Katayama, Shintaro and Harada, Jun and Karlsson, Håkan K. R. and Handschin, Christoph and Moritz, Thomas and Krook, Anna and Näslund, Erik and Zierath, Juleen R.},
	month = sep,
	year = {2021},
	pages = {2077--2091},
}

Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees. Gandla, M. L., Mähler, N., Escamez, S., Skotare, T., Obudulu, O., Möller, L., Abreu, I. N., Bygdell, J., Hertzberg, M., Hvidsten, T. R., Moritz, T., Wingsle, G., Trygg, J., Tuominen, H., & Jönsson, L. J. Biotechnology for Biofuels, 14(1): 43. December 2021.

Paper doi link bibtex abstract 6 downloads

@article{gandla_overexpression_2021,
	title = {Overexpression of vesicle-associated membrane protein {PttVAP27}-17 as a tool to improve biomass production and the overall saccharification yields in {Populus} trees},
	volume = {14},
	issn = {1754-6834},
	url = {https://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/s13068-021-01895-0},
	doi = {10/gjd7kj},
	abstract = {Abstract
            
              Background
              Bioconversion of wood into bioproducts and biofuels is hindered by the recalcitrance of woody raw material to bioprocesses such as enzymatic saccharification. Targeted modification of the chemical composition of the feedstock can improve saccharification but this gain is often abrogated by concomitant reduction in tree growth.
            
            
              Results
              
                In this study, we report on transgenic hybrid aspen (
                Populus tremula
                ×
                tremuloides
                ) lines that showed potential to increase biomass production both in the greenhouse and after 5 years of growth in the field. The transgenic lines carried an overexpression construct for
                Populus tremula
                ×
                tremuloides
                vesicle-associated membrane protein (VAMP)-associated protein
                PttVAP27-17
                that was selected from a gene-mining program for novel regulators of wood formation. Analytical-scale enzymatic saccharification without any pretreatment revealed for all greenhouse-grown transgenic lines, compared to the wild type, a 20–44\% increase in the glucose yield per dry weight after enzymatic saccharification, even though it was statistically significant only for one line. The glucose yield after enzymatic saccharification with a prior hydrothermal pretreatment step with sulfuric acid was not increased in the greenhouse-grown transgenic trees on a dry-weight basis, but increased by 26–50\% when calculated on a whole biomass basis in comparison to the wild-type control. Tendencies to increased glucose yields by up to 24\% were present on a whole tree biomass basis after acidic pretreatment and enzymatic saccharification also in the transgenic trees grown for 5 years on the field when compared to the wild-type control.
              
            
            
              Conclusions
              The results demonstrate the usefulness of gene-mining programs to identify novel genes with the potential to improve biofuel production in tree biotechnology programs. Furthermore, multi-omic analyses, including transcriptomic, proteomic and metabolomic analyses, performed here provide a toolbox for future studies on the function of VAP27 proteins in plants.},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {Biotechnology for Biofuels},
	author = {Gandla, Madhavi Latha and Mähler, Niklas and Escamez, Sacha and Skotare, Tomas and Obudulu, Ogonna and Möller, Linus and Abreu, Ilka N. and Bygdell, Joakim and Hertzberg, Magnus and Hvidsten, Torgeir R. and Moritz, Thomas and Wingsle, Gunnar and Trygg, Johan and Tuominen, Hannele and Jönsson, Leif J.},
	month = dec,
	year = {2021},
	pages = {43},
}

Abstract Background Bioconversion of wood into bioproducts and biofuels is hindered by the recalcitrance of woody raw material to bioprocesses such as enzymatic saccharification. Targeted modification of the chemical composition of the feedstock can improve saccharification but this gain is often abrogated by concomitant reduction in tree growth. Results In this study, we report on transgenic hybrid aspen ( Populus tremula × tremuloides ) lines that showed potential to increase biomass production both in the greenhouse and after 5 years of growth in the field. The transgenic lines carried an overexpression construct for Populus tremula × tremuloides vesicle-associated membrane protein (VAMP)-associated protein PttVAP27-17 that was selected from a gene-mining program for novel regulators of wood formation. Analytical-scale enzymatic saccharification without any pretreatment revealed for all greenhouse-grown transgenic lines, compared to the wild type, a 20–44% increase in the glucose yield per dry weight after enzymatic saccharification, even though it was statistically significant only for one line. The glucose yield after enzymatic saccharification with a prior hydrothermal pretreatment step with sulfuric acid was not increased in the greenhouse-grown transgenic trees on a dry-weight basis, but increased by 26–50% when calculated on a whole biomass basis in comparison to the wild-type control. Tendencies to increased glucose yields by up to 24% were present on a whole tree biomass basis after acidic pretreatment and enzymatic saccharification also in the transgenic trees grown for 5 years on the field when compared to the wild-type control. Conclusions The results demonstrate the usefulness of gene-mining programs to identify novel genes with the potential to improve biofuel production in tree biotechnology programs. Furthermore, multi-omic analyses, including transcriptomic, proteomic and metabolomic analyses, performed here provide a toolbox for future studies on the function of VAP27 proteins in plants.

2020 (5)

A metabolite roadmap of the wood‐forming tissue in Populus tremula. Abreu, I. N., Johansson, A. I., Sokołowska, K., Niittylä, T., Sundberg, B., Hvidsten, T. R., Street, N. R., & Moritz, T. New Phytologist, 228(5): 1559–1572. December 2020.

A metabolite roadmap of the wood‐forming tissue in Populus tremula [link]

Paper doi link bibtex 2 downloads

@article{abreu_metabolite_2020,
	title = {A metabolite roadmap of the wood‐forming tissue in {Populus} tremula},
	volume = {228},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16799},
	doi = {10.1111/nph.16799},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Abreu, Ilka N. and Johansson, Annika I. and Sokołowska, Katarzyna and Niittylä, Totte and Sundberg, Björn and Hvidsten, Torgeir R. and Street, Nathaniel R. and Moritz, Thomas},
	month = dec,
	year = {2020},
	pages = {1559--1572},
}

Changes in lipid and carotenoid metabolism in Chlamydomonas reinhardtii during induction of CO2-concentrating mechanism: Cellular response to low CO2 stress. Abreu, I. N., Aksmann, A., Bajhaiya, A. K., Benlloch, R., Giordano, M., Pokora, W., Selstam, E., & Moritz, T. Algal Research, 52: 102099. December 2020.

Paper doi link bibtex

@article{abreu_changes_2020,
	title = {Changes in lipid and carotenoid metabolism in {Chlamydomonas} reinhardtii during induction of {CO2}-concentrating mechanism: {Cellular} response to low {CO2} stress},
	volume = {52},
	issn = {22119264},
	shorttitle = {Changes in lipid and carotenoid metabolism in {Chlamydomonas} reinhardtii during induction of {CO2}-concentrating mechanism},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S221192642030967X},
	doi = {10/gjcxj6},
	language = {en},
	urldate = {2021-06-07},
	journal = {Algal Research},
	author = {Abreu, Ilka N. and Aksmann, Anna and Bajhaiya, Amit K. and Benlloch, Reyes and Giordano, Mario and Pokora, Wojciech and Selstam, Eva and Moritz, Thomas},
	month = dec,
	year = {2020},
	pages = {102099},
}

Differentiation of two Maytenus species and their hybrid via untargeted metabolomics. Antunes, E. R. M., Duarte, R. S., Moritz, T., & Sawaya, A. C. H. F. Industrial Crops and Products, 158: 113014. December 2020.

Differentiation of two Maytenus species and their hybrid via untargeted metabolomics [link]

Paper doi link bibtex

@article{antunes_differentiation_2020,
	title = {Differentiation of two {Maytenus} species and their hybrid via untargeted metabolomics},
	volume = {158},
	issn = {09266690},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0926669020309316},
	doi = {10/gjcxhq},
	language = {en},
	urldate = {2021-06-07},
	journal = {Industrial Crops and Products},
	author = {Antunes, Elisa Ribeiro Miranda and Duarte, Rodolfo Santos and Moritz, Thomas and Sawaya, Alexandra Christine Helena Frankland},
	month = dec,
	year = {2020},
	pages = {113014},
}

Integration of molecular profiles in a longitudinal wellness profiling cohort. Tebani, A., Gummesson, A., Zhong, W., Koistinen, I. S., Lakshmikanth, T., Olsson, L. M., Boulund, F., Neiman, M., Stenlund, H., Hellström, C., Karlsson, M. J., Arif, M., Dodig-Crnković, T., Mardinoglu, A., Lee, S., Zhang, C., Chen, Y., Olin, A., Mikes, J., Danielsson, H., von Feilitzen, K., Jansson, P., Angerås, O., Huss, M., Kjellqvist, S., Odeberg, J., Edfors, F., Tremaroli, V., Forsström, B., Schwenk, J. M., Nilsson, P., Moritz, T., Bäckhed, F., Engstrand, L., Brodin, P., Bergström, G., Uhlen, M., & Fagerberg, L. Nature Communications, 11(1): 4487. December 2020.

Integration of molecular profiles in a longitudinal wellness profiling cohort [link]

Paper doi link bibtex abstract

@article{tebani_integration_2020,
	title = {Integration of molecular profiles in a longitudinal wellness profiling cohort},
	volume = {11},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-020-18148-7},
	doi = {10.1038/s41467-020-18148-7},
	abstract = {Abstract
            An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies and immune cell profiling, complemented with gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Tebani, Abdellah and Gummesson, Anders and Zhong, Wen and Koistinen, Ina Schuppe and Lakshmikanth, Tadepally and Olsson, Lisa M. and Boulund, Fredrik and Neiman, Maja and Stenlund, Hans and Hellström, Cecilia and Karlsson, Max J. and Arif, Muhammad and Dodig-Crnković, Tea and Mardinoglu, Adil and Lee, Sunjae and Zhang, Cheng and Chen, Yang and Olin, Axel and Mikes, Jaromir and Danielsson, Hanna and von Feilitzen, Kalle and Jansson, Per-Anders and Angerås, Oskar and Huss, Mikael and Kjellqvist, Sanela and Odeberg, Jacob and Edfors, Fredrik and Tremaroli, Valentina and Forsström, Björn and Schwenk, Jochen M. and Nilsson, Peter and Moritz, Thomas and Bäckhed, Fredrik and Engstrand, Lars and Brodin, Petter and Bergström, Göran and Uhlen, Mathias and Fagerberg, Linn},
	month = dec,
	year = {2020},
	pages = {4487},
}

Metabolic Profiling and Compound-Class Identification Reveal Alterations in Serum Triglyceride Levels in Mice Immunized with Human Vaccine Adjuvant Alum. Khoomrung, S., Nookaew, I., Sen, P., Olafsdottir, T. A., Persson, J., Moritz, T., Andersen, P., Harandi, A. M., & Nielsen, J. Journal of Proteome Research, 19(1): 269–278. January 2020.

Paper doi link bibtex

@article{khoomrung_metabolic_2020,
	title = {Metabolic {Profiling} and {Compound}-{Class} {Identification} {Reveal} {Alterations} in {Serum} {Triglyceride} {Levels} in {Mice} {Immunized} with {Human} {Vaccine} {Adjuvant} {Alum}},
	volume = {19},
	issn = {1535-3893, 1535-3907},
	url = {https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00517},
	doi = {10.1021/acs.jproteome.9b00517},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Journal of Proteome Research},
	author = {Khoomrung, Sakda and Nookaew, Intawat and Sen, Partho and Olafsdottir, Thorunn A. and Persson, Josefine and Moritz, Thomas and Andersen, Peter and Harandi, Ali M. and Nielsen, Jens},
	month = jan,
	year = {2020},
	pages = {269--278},
}

2019 (5)

Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in Saccharomyces cerevisiae. Bergman, A., Hellgren, J., Moritz, T., Siewers, V., Nielsen, J., & Chen, Y. Microbial Cell Factories, 18(1): 25. December 2019.

Paper doi link bibtex

@article{bergman_heterologous_2019,
	title = {Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in {Saccharomyces} cerevisiae},
	volume = {18},
	issn = {1475-2859},
	url = {https://microbialcellfactories.biomedcentral.com/articles/10.1186/s12934-019-1072-6},
	doi = {10/gh8zrg},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Microbial Cell Factories},
	author = {Bergman, Alexandra and Hellgren, John and Moritz, Thomas and Siewers, Verena and Nielsen, Jens and Chen, Yun},
	month = dec,
	year = {2019},
	pages = {25},
}

Leaf metabolic signatures induced by real and simulated herbivory in black mustard (Brassica nigra). Papazian, S., Girdwood, T., Wessels, B. A., Poelman, E. H., Dicke, M., Moritz, T., & Albrectsen, B. R. Metabolomics, 15(10): 130. October 2019.

Leaf metabolic signatures induced by real and simulated herbivory in black mustard (Brassica nigra) [link]

Paper doi link bibtex abstract 2 downloads

@article{papazian_leaf_2019,
	title = {Leaf metabolic signatures induced by real and simulated herbivory in black mustard ({Brassica} nigra)},
	volume = {15},
	issn = {1573-3882, 1573-3890},
	url = {http://link.springer.com/10.1007/s11306-019-1592-4},
	doi = {10.1007/s11306-019-1592-4},
	abstract = {Abstract
            
              Introduction
              The oxylipin methyl jasmonate (MeJA) is a plant hormone active in response signalling and defence against herbivores. Although MeJA is applied experimentally to mimic herbivory and induce plant defences, its downstream effects on the plant metabolome are largely uncharacterized, especially in the context of primary growth and tissue-specificity of the response.
            
            
              Objectives
              
                We investigated the effects of MeJA-simulated and real caterpillar herbivory on the foliar metabolome of the wild plant
                Brassica nigra
                and monitored the herbivore-induced responses in relation to leaf ontogeny.
              
            
            
              Methods
              As single or multiple herbivory treatments, MeJA- and mock-sprayed plants were consecutively exposed to caterpillars or left untreated. Gas chromatography (GC) and liquid chromatography (LC) time-of-flight mass-spectrometry (TOF-MS) were combined to analyse foliar compounds, including central primary and specialized defensive plant metabolites.
            
            
              Results
              Plant responses were stronger in young leaves, which simultaneously induced higher chlorophyll levels. Both MeJA and caterpillar herbivory induced similar, but not identical, accumulation of tricarboxylic acids (TCAs), glucosinolates (GSLs) and phenylpropanoids (PPs), but only caterpillar feeding led to depletion of amino acids. MeJA followed by caterpillars caused higher induction of defence compounds, including a three-fold increase in the major defence compound allyl-GSL (sinigrin). When feeding on MeJA-treated plants, caterpillars gained less weight indicative of the reduced host-plant quality and enhanced resistance.
            
            
              Conclusions
              The metabolomics approach showed that plant responses induced by herbivory extend beyond the regulation of defence metabolism and are tightly modulated throughout leaf development. This leads to a new understanding of the plant metabolic potential that can be exploited for future plant protection strategies.},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Metabolomics},
	author = {Papazian, Stefano and Girdwood, Tristan and Wessels, Bernard A. and Poelman, Erik H. and Dicke, Marcel and Moritz, Thomas and Albrectsen, Benedicte R.},
	month = oct,
	year = {2019},
	pages = {130},
}

PECTIN ACETYLESTERASE9 Affects the Transcriptome and Metabolome and Delays Aphid Feeding. Kloth, K. J., Abreu, I. N., Delhomme, N., Petřík, I., Villard, C., Ström, C., Amini, F., Novák, O., Moritz, T., & Albrectsen, B. R. Plant Physiology, 181(4): 1704–1720. December 2019.

PECTIN ACETYLESTERASE9 Affects the Transcriptome and Metabolome and Delays Aphid Feeding [link]

Paper doi link bibtex

@article{kloth_pectin_2019,
	title = {{PECTIN} {ACETYLESTERASE9} {Affects} the {Transcriptome} and {Metabolome} and {Delays} {Aphid} {Feeding}},
	volume = {181},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/181/4/1704-1720/6000543},
	doi = {10.1104/pp.19.00635},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Kloth, Karen J. and Abreu, Ilka N. and Delhomme, Nicolas and Petřík, Ivan and Villard, Cloé and Ström, Cecilia and Amini, Fariba and Novák, Ondřej and Moritz, Thomas and Albrectsen, Benedicte R.},
	month = dec,
	year = {2019},
	pages = {1704--1720},
}

Targeted Multiple Reaction Monitoring Analysis of CSF Identifies UCHL1 and GPNMB as Candidate Biomarkers for ALS. Zhu, S., Wuolikainen, A., Wu, J., Öhman, A., Wingsle, G., Moritz, T., Andersen, P. M., Forsgren, L., & Trupp, M. Journal of Molecular Neuroscience, 69(4): 643–657. December 2019.

Targeted Multiple Reaction Monitoring Analysis of CSF Identifies UCHL1 and GPNMB as Candidate Biomarkers for ALS [link]

Paper doi link bibtex abstract

@article{zhu_targeted_2019,
	title = {Targeted {Multiple} {Reaction} {Monitoring} {Analysis} of {CSF} {Identifies} {UCHL1} and {GPNMB} as {Candidate} {Biomarkers} for {ALS}},
	volume = {69},
	issn = {0895-8696, 1559-1166},
	url = {http://link.springer.com/10.1007/s12031-019-01411-y},
	doi = {10.1007/s12031-019-01411-y},
	abstract = {Abstract
            The neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and Parkinson’s disease (PD) share some common molecular deficits including disruption of protein homeostasis leading to disease-specific protein aggregation. While insoluble protein aggregates are the defining pathological confirmation of diagnosis, patient stratification based on early molecular etiologies may identify distinct subgroups within a clinical diagnosis that would respond differently in therapeutic development programs. We are developing targeted multiple reaction monitoring (MRM) mass spectrometry methods to rigorously quantify CSF proteins from known disease genes involved in lysosomal, ubiquitin-proteasomal, and autophagy pathways. Analysis of CSF from 21 PD, 21 ALS, and 25 control patients, rigorously matched for gender, age, and age of sample, revealed significant changes in peptide levels between PD, ALS, and control. In patients with PD, levels of two peptides for chromogranin B (CHGB, secretogranin 1) were significantly reduced. In CSF of patients with ALS, levels of two peptides from ubiquitin carboxy-terminal hydrolase like protein 1 (UCHL1) and one peptide each for glycoprotein non-metastatic melanoma protein B (GPNMB) and cathepsin D (CTSD) were all increased. Analysis of patients with ALS separated into two groups based on length of survival after CSF sampling revealed that the increases in GPNMB and UCHL1 were specific for short-lived ALS patients. While analysis of additional cohorts is required to validate these candidate biomarkers, this study suggests methods for stratification of ALS patients for clinical trials and identifies targets for drug efficacy measurements during therapeutic development.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Journal of Molecular Neuroscience},
	author = {Zhu, Shaochun and Wuolikainen, Anna and Wu, Junfang and Öhman, Anders and Wingsle, Gunnar and Moritz, Thomas and Andersen, Peter M. and Forsgren, Lars and Trupp, Miles},
	month = dec,
	year = {2019},
	pages = {643--657},
}

Two-step derivatization for determination of sugar phosphates in plants by combined reversed phase chromatography/tandem mass spectrometry. Rende, U., Niittylä, T., & Moritz, T. Plant Methods, 15(1): 127. December 2019.

Paper doi link bibtex abstract

@article{rende_two-step_2019,
	title = {Two-step derivatization for determination of sugar phosphates in plants by combined reversed phase chromatography/tandem mass spectrometry},
	volume = {15},
	issn = {1746-4811},
	url = {https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0514-9},
	doi = {10.1186/s13007-019-0514-9},
	abstract = {Abstract
            
              Background
              Sugar phosphates are important intermediates of central carbon metabolism in biological systems, with roles in glycolysis, the pentose–phosphate pathway, tricarboxylic acid (TCA) cycle, and many other biosynthesis pathways. Understanding central carbon metabolism requires a simple, robust and comprehensive analytical method. However, sugar phosphates are notoriously difficult to analyze by traditional reversed phase liquid chromatography.
            
            
              Results
              
                Here, we show a two-step derivatization of sugar phosphates by methoxylamine and propionic acid anhydride after chloroform/methanol (3:7) extraction from
                Populus
                leaf and developing wood that improves separation, identification and quantification of sugar phosphates by ultra high performance liquid chromatography–electrospray ionization–mass spectrometry (UHPLC–ESI–MS). Standard curves of authentic sugar phosphates were generated for concentrations from pg to ng/μl with a correlation coefficient
                R
                2
                 {\textgreater} 0.99. The method showed high sensitivity and repeatability with relative standard deviation (RSD) {\textless} 20\% based on repeated extraction, derivatization and detection. The analytical accuracy for
                Populus
                leaf extracts, determined by a two-level spiking approach of selected metabolites, was 79–107\%.
              
            
            
              Conclusion
              
                The results show the reliability of combined reversed phase liquid chromatography–tandem mass spectrometry for sugar phosphate analysis and demonstrate the presence of two unknown sugar phosphates in
                Populus
                extracts.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Methods},
	author = {Rende, Umut and Niittylä, Totte and Moritz, Thomas},
	month = dec,
	year = {2019},
	pages = {127},
}

2018 (5)

A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees. Obudulu, O., Mähler, N., Skotare, T., Bygdell, J., Abreu, I. N., Ahnlund, M., Latha Gandla, M., Petterle, A., Moritz, T., Hvidsten, T. R., Jönsson, L. J., Wingsle, G., Trygg, J., & Tuominen, H. BMC Genomics, 19(1): 11. December 2018.

A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees [link]

Paper doi link bibtex 1 download

@article{obudulu_multi-omics_2018,
	title = {A multi-omics approach reveals function of {Secretory} {Carrier}-{Associated} {Membrane} {Proteins} in wood formation of {Populus} trees},
	volume = {19},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4411-1},
	doi = {10.1186/s12864-017-4411-1},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Obudulu, Ogonna and Mähler, Niklas and Skotare, Tomas and Bygdell, Joakim and Abreu, Ilka N. and Ahnlund, Maria and Latha Gandla, Madhavi and Petterle, Anna and Moritz, Thomas and Hvidsten, Torgeir R. and Jönsson, Leif J. and Wingsle, Gunnar and Trygg, Johan and Tuominen, Hannele},
	month = dec,
	year = {2018},
	pages = {11},
}

Darkened Leaves Use Different Metabolic Strategies for Senescence and Survival. Law, S. R., Chrobok, D., Juvany, M., Delhomme, N., Lindén, P., Brouwer, B., Ahad, A., Moritz, T., Jansson, S., Gardeström, P., & Keech, O. Plant Physiology, 177(1): 132–150. May 2018.

Darkened Leaves Use Different Metabolic Strategies for Senescence and Survival [link]

Paper doi link bibtex 2 downloads

@article{law_darkened_2018,
	title = {Darkened {Leaves} {Use} {Different} {Metabolic} {Strategies} for {Senescence} and {Survival}},
	volume = {177},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/177/1/132-150/6116945},
	doi = {10.1104/pp.18.00062},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Law, Simon R. and Chrobok, Daria and Juvany, Marta and Delhomme, Nicolas and Lindén, Pernilla and Brouwer, Bastiaan and Ahad, Abdul and Moritz, Thomas and Jansson, Stefan and Gardeström, Per and Keech, Olivier},
	month = may,
	year = {2018},
	pages = {132--150},
}

Metabolic Profiling of Multiorgan Samples: Evaluation of MODY5/RCAD Mutant Mice. Torell, F., Bennett, K., Cereghini, S., Fabre, M., Rännar, S., Lundstedt-Enkel, K., Moritz, T., Haumaitre, C., Trygg, J., & Lundstedt, T. Journal of Proteome Research, 17(7): 2293–2306. July 2018.

Metabolic Profiling of Multiorgan Samples: Evaluation of MODY5/RCAD Mutant Mice [link]

Paper doi link bibtex

@article{torell_metabolic_2018,
	title = {Metabolic {Profiling} of {Multiorgan} {Samples}: {Evaluation} of {MODY5}/{RCAD} {Mutant} {Mice}},
	volume = {17},
	issn = {1535-3893, 1535-3907},
	shorttitle = {Metabolic {Profiling} of {Multiorgan} {Samples}},
	url = {https://pubs.acs.org/doi/10.1021/acs.jproteome.7b00821},
	doi = {10/gdxhnh},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Journal of Proteome Research},
	author = {Torell, Frida and Bennett, Kate and Cereghini, Silvia and Fabre, Mélanie and Rännar, Stefan and Lundstedt-Enkel, Katrin and Moritz, Thomas and Haumaitre, Cécile and Trygg, Johan and Lundstedt, Torbjörn},
	month = jul,
	year = {2018},
	pages = {2293--2306},
}

Optimising methods for the recovery and quantification of di- and tripeptides in soil. Jämtgård, S., Robinson, N., Moritz, T., Colgrave, M. L., & Schmidt, S. Soil Research, 56(4): 404. 2018.

Optimising methods for the recovery and quantification of di- and tripeptides in soil [link]

Paper doi link bibtex abstract

@article{jamtgard_optimising_2018,
	title = {Optimising methods for the recovery and quantification of di- and tripeptides in soil},
	volume = {56},
	issn = {1838-675X},
	url = {http://www.publish.csiro.au/?paper=SR17279},
	doi = {10.1071/SR17279},
	abstract = {Di- and tripeptides are intermediaries in the nitrogen cycle and are likely to have roles in the soil–microbe–plant continuum, but they have hitherto been difficult to measure in soils. To lay the base for future studies of oligopeptides in soil, we added 10 known di- and tripeptides with diverse chemical properties to forest and agricultural soils and then recovered the peptides by means of induced diffusive fluxes using microdialysis, a minimally-intrusive soil sampling technique. The concentration of the peptides recovered with the probes was 25–39\% (relative recovery) of the concentration in the external solution, and followed the same trend as previously observed for amino acids, with smaller peptides (e.g. Gly-Gly) recovered at a higher rate than larger ones (e.g. Tyr-Phe). After derivatisation with AccQ-Tag™, a standard method for amino acids, peptides were analysed by ultra-high-pressure liquid chromatography-triple quadrupole mass spectrometry. Multiple reaction monitoring mass spectrometry was used to quantify specific peptides with a short run time of 15 min and a detection limit of 0.01–0.02 pmol injected (0.005–0.01 pmol µL–1) for the different peptides. This methodology allowed successful analysis of all standard di- and tripeptides tested here. We conclude that microdialysis in combination with UHPLC-MS will allow measurement of plant-relevant fluxes of di- and tripeptides in undisturbed soil.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Soil Research},
	author = {Jämtgård, Sandra and Robinson, Nicole and Moritz, Thomas and Colgrave, Michelle L. and Schmidt, Susanne},
	year = {2018},
	pages = {404},
}

Simultaneous determination of ribonucleoside and deoxyribonucleoside triphosphates in biological samples by hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry. Kong, Z., Jia, S., Chabes, A. L., Appelblad, P., Lundmark, R., Moritz, T., & Chabes, A. Nucleic Acids Research, 46(11): e66–e66. June 2018.

Paper doi link bibtex

@article{kong_simultaneous_2018,
	title = {Simultaneous determination of ribonucleoside and deoxyribonucleoside triphosphates in biological samples by hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry},
	volume = {46},
	issn = {0305-1048, 1362-4962},
	url = {https://academic.oup.com/nar/article/46/11/e66/4937551},
	doi = {10.1093/nar/gky203},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Nucleic Acids Research},
	author = {Kong, Ziqing and Jia, Shaodong and Chabes, Anna Lena and Appelblad, Patrik and Lundmark, Richard and Moritz, Thomas and Chabes, Andrei},
	month = jun,
	year = {2018},
	pages = {e66--e66},
}

2017 (6)

At bHLH68 transcription factor contributes to the regulation of ABA homeostasis and drought stress tolerance in Arabidopsis thaliana. Le Hir, R., Castelain, M., Chakraborti, D., Moritz, T., Dinant, S., & Bellini, C. Physiologia Plantarum, 160(3): 312–327. July 2017.

At <i>bHLH68</i> transcription factor contributes to the regulation of ABA homeostasis and drought stress tolerance in <i>Arabidopsis thaliana</i> [link]

Paper doi link bibtex

@article{le_hir_at_2017,
	title = {At \textit{{bHLH68}} transcription factor contributes to the regulation of {ABA} homeostasis and drought stress tolerance in \textit{{Arabidopsis} thaliana}},
	volume = {160},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12549},
	doi = {10.1111/ppl.12549},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Le Hir, Rozenn and Castelain, Mathieu and Chakraborti, Dipankar and Moritz, Thomas and Dinant, Sylvie and Bellini, Catherine},
	month = jul,
	year = {2017},
	pages = {312--327},
}

Defense Responses in Aspen with Altered Pectin Methylesterase Activity Reveal the Hormonal Inducers of Tyloses. Leśniewska, J., Öhman, D., Krzesłowska, M., Kushwah, S., Barciszewska-Pacak, M., Kleczkowski, L. A., Sundberg, B., Moritz, T., & Mellerowicz, E. J. Plant Physiology, 173(2): 1409–1419. February 2017.

Defense Responses in Aspen with Altered Pectin Methylesterase Activity Reveal the Hormonal Inducers of Tyloses [link]

Paper doi link bibtex 1 download

@article{lesniewska_defense_2017,
	title = {Defense {Responses} in {Aspen} with {Altered} {Pectin} {Methylesterase} {Activity} {Reveal} the {Hormonal} {Inducers} of {Tyloses}},
	volume = {173},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/173/2/1409-1419/6116100},
	doi = {10.1104/pp.16.01443},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Leśniewska, Joanna and Öhman, David and Krzesłowska, Magdalena and Kushwah, Sunita and Barciszewska-Pacak, Maria and Kleczkowski, Leszek A. and Sundberg, Björn and Moritz, Thomas and Mellerowicz, Ewa J.},
	month = feb,
	year = {2017},
	pages = {1409--1419},
}

Enhanced Secondary- and Hormone Metabolism in Leaves of Arbuscular Mycorrhizal Medicago truncatula. Adolfsson, L., Nziengui, H., Abreu, I. N, Šimura, J., Beebo, A., Herdean, A., Aboalizadeh, J., Široká, J., Moritz, T., Novák, O., Ljung, K., Schoefs, B., & Spetea, C. Plant Physiology, 175(1): 392–411. September 2017.

Enhanced Secondary- and Hormone Metabolism in Leaves of Arbuscular Mycorrhizal <i>Medicago truncatula</i> [link]

Paper doi link bibtex

@article{adolfsson_enhanced_2017,
	title = {Enhanced {Secondary}- and {Hormone} {Metabolism} in {Leaves} of {Arbuscular} {Mycorrhizal} \textit{{Medicago} truncatula}},
	volume = {175},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/175/1/392-411/6117013},
	doi = {10/gbvxq8},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Adolfsson, Lisa and Nziengui, Hugues and Abreu, Ilka N and Šimura, Jan and Beebo, Azeez and Herdean, Andrei and Aboalizadeh, Jila and Široká, Jitka and Moritz, Thomas and Novák, Ondřej and Ljung, Karin and Schoefs, Benoît and Spetea, Cornelia},
	month = sep,
	year = {2017},
	pages = {392--411},
}

Functional metabolomics as a tool to analyze Mediator function and structure in plants. Davoine, C., Abreu, I. N., Khajeh, K., Blomberg, J., Kidd, B. N., Kazan, K., Schenk, P. M., Gerber, L., Nilsson, O., Moritz, T., & Björklund, S. PLOS ONE, 12(6): e0179640. June 2017.

Functional metabolomics as a tool to analyze Mediator function and structure in plants [link]

Paper doi link bibtex

@article{davoine_functional_2017,
	title = {Functional metabolomics as a tool to analyze {Mediator} function and structure in plants},
	volume = {12},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0179640},
	doi = {10/gcjk93},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Davoine, Celine and Abreu, Ilka N. and Khajeh, Khalil and Blomberg, Jeanette and Kidd, Brendan N. and Kazan, Kemal and Schenk, Peer M. and Gerber, Lorenz and Nilsson, Ove and Moritz, Thomas and Björklund, Stefan},
	editor = {Mantovani, Roberto},
	month = jun,
	year = {2017},
	pages = {e0179640},
}

Metabolome and transcriptome profiling reveal new insights into somatic embryo germination in Norway spruce (Picea abies). Dobrowolska, I., Businge, E., Abreu, I. N, Moritz, T., & Egertsdotter, U. Tree Physiology, 37(12): 1752–1766. December 2017.

Metabolome and transcriptome profiling reveal new insights into somatic embryo germination in Norway spruce (Picea abies) [link]

Paper doi link bibtex

@article{dobrowolska_metabolome_2017,
	title = {Metabolome and transcriptome profiling reveal new insights into somatic embryo germination in {Norway} spruce ({Picea} abies)},
	volume = {37},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article/37/12/1752/3896382},
	doi = {10/gcwvts},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {Tree Physiology},
	author = {Dobrowolska, Izabela and Businge, Edward and Abreu, Ilka N and Moritz, Thomas and Egertsdotter, Ulrika},
	month = dec,
	year = {2017},
	pages = {1752--1766},
}

Nitrogen uptake and assimilation in proliferating embryogenic cultures of Norway spruce—Investigating the specific role of glutamine. Carlsson, J., Svennerstam, H., Moritz, T., Egertsdotter, U., & Ganeteg, U. PLOS ONE, 12(8): e0181785. August 2017.

Nitrogen uptake and assimilation in proliferating embryogenic cultures of Norway spruce—Investigating the specific role of glutamine [link]

Paper doi link bibtex

@article{carlsson_nitrogen_2017,
	title = {Nitrogen uptake and assimilation in proliferating embryogenic cultures of {Norway} spruce—{Investigating} the specific role of glutamine},
	volume = {12},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0181785},
	doi = {10/gcjnr5},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Carlsson, Johanna and Svennerstam, Henrik and Moritz, Thomas and Egertsdotter, Ulrika and Ganeteg, Ulrika},
	editor = {Min, Xiang Jia},
	month = aug,
	year = {2017},
	pages = {e0181785},
}

2016 (8)

Central Metabolic Responses to Ozone and Herbivory Affect Photosynthesis and Stomatal Closure. Papazian, S., Khaling, E., Bonnet, C., Lassueur, S., Reymond, P., Moritz, T., Blande, J. D., & Albrectsen, B. R. Plant Physiology, 172(3): 2057–2078. November 2016.

Central Metabolic Responses to Ozone and Herbivory Affect Photosynthesis and Stomatal Closure [link]

Paper doi link bibtex 2 downloads

@article{papazian_central_2016,
	title = {Central {Metabolic} {Responses} to {Ozone} and {Herbivory} {Affect} {Photosynthesis} and {Stomatal} {Closure}},
	volume = {172},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/172/3/2057-2078/6115987},
	doi = {10/f3vft5},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Papazian, Stefano and Khaling, Eliezer and Bonnet, Christelle and Lassueur, Steve and Reymond, Philippe and Moritz, Thomas and Blande, James D. and Albrectsen, Benedicte R.},
	month = nov,
	year = {2016},
	pages = {2057--2078},
}

Dissecting the Metabolic Role of Mitochondria during Developmental Leaf Senescence. Chrobok, D., Law, S. R., Brouwer, B., Lindén, P., Ziolkowska, A., Liebsch, D., Narsai, R., Szal, B., Moritz, T., Rouhier, N., Whelan, J., Gardeström, P., & Keech, O. Plant Physiology, 172(4): 2132–2153. December 2016.

Dissecting the Metabolic Role of Mitochondria during Developmental Leaf Senescence [link]

Paper doi link bibtex

@article{chrobok_dissecting_2016,
	title = {Dissecting the {Metabolic} {Role} of {Mitochondria} during {Developmental} {Leaf} {Senescence}},
	volume = {172},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/172/4/2132-2153/6115841},
	doi = {10/f3vc6g},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Chrobok, Daria and Law, Simon R. and Brouwer, Bastiaan and Lindén, Pernilla and Ziolkowska, Agnieszka and Liebsch, Daniela and Narsai, Reena and Szal, Bozena and Moritz, Thomas and Rouhier, Nicolas and Whelan, James and Gardeström, Per and Keech, Olivier},
	month = dec,
	year = {2016},
	pages = {2132--2153},
}

Integrated analysis of gene expression from carbon metabolism, proteome and metabolome, reveals altered primary metabolism in Eucalyptus grandis bark, in response to seasonal variation. Budzinski, I. G. F., Moon, D. H., Morosini, J. S., Lindén, P., Bragatto, J., Moritz, T., & Labate, C. A. BMC Plant Biology, 16(1): 149. December 2016.

Paper doi link bibtex

@article{budzinski_integrated_2016,
	title = {Integrated analysis of gene expression from carbon metabolism, proteome and metabolome, reveals altered primary metabolism in {Eucalyptus} grandis bark, in response to seasonal variation},
	volume = {16},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-016-0839-8},
	doi = {10/f3vbf9},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Plant Biology},
	author = {Budzinski, Ilara Gabriela Frasson and Moon, David H. and Morosini, Júlia Silva and Lindén, Pernilla and Bragatto, Juliano and Moritz, Thomaz and Labate, Carlos Alberto},
	month = dec,
	year = {2016},
	pages = {149},
}

Metabolomic Quality Assessment of EDTA Plasma and Serum Samples. Malm, L., Tybring, G., Moritz, T., Landin, B., & Galli, J. Biopreservation and Biobanking, 14(5): 416–423. October 2016.

Metabolomic Quality Assessment of EDTA Plasma and Serum Samples [link]

Paper doi link bibtex

@article{malm_metabolomic_2016,
	title = {Metabolomic {Quality} {Assessment} of {EDTA} {Plasma} and {Serum} {Samples}},
	volume = {14},
	issn = {1947-5535, 1947-5543},
	url = {http://www.liebertpub.com/doi/10.1089/bio.2015.0092},
	doi = {10/f3tq4s},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Biopreservation and Biobanking},
	author = {Malm, Linus and Tybring, Gunnel and Moritz, Thomas and Landin, Britta and Galli, Joakim},
	month = oct,
	year = {2016},
	pages = {416--423},
}

Multi-platform mass spectrometry analysis of the CSF and plasma metabolomes of rigorously matched amyotrophic lateral sclerosis, Parkinson's disease and control subjects. Wuolikainen, A., Jonsson, P., Ahnlund, M., Antti, H., Marklund, S. L., Moritz, T., Forsgren, L., Andersen, P. M., & Trupp, M. Molecular BioSystems, 12(4): 1287–1298. 2016.

Paper doi link bibtex abstract

@article{wuolikainen_multi-platform_2016,
	title = {Multi-platform mass spectrometry analysis of the {CSF} and plasma metabolomes of rigorously matched amyotrophic lateral sclerosis, {Parkinson}'s disease and control subjects},
	volume = {12},
	issn = {1742-206X, 1742-2051},
	url = {http://xlink.rsc.org/?DOI=C5MB00711A},
	doi = {10.1039/C5MB00711A},
	abstract = {Schematic view of the study design and the mass spectrometry platforms used for metabolomics analysis.
          , 
            Amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD) are protein-aggregation diseases that lack clear molecular etiologies. Biomarkers could aid in diagnosis, prognosis, planning of care, drug target identification and stratification of patients into clinical trials. We sought to characterize shared and unique metabolite perturbations between ALS and PD and matched controls selected from patients with other diagnoses, including differential diagnoses to ALS or PD that visited our clinic for a lumbar puncture. Cerebrospinal fluid (CSF) and plasma from rigorously age-, sex- and sampling-date matched patients were analyzed on multiple platforms using gas chromatography (GC) and liquid chromatography (LC)–mass spectrometry (MS). We applied constrained randomization of run orders and orthogonal partial least squares projection to latent structure-effect projections (OPLS-EP) to capitalize upon the study design. The combined platforms identified 144 CSF and 196 plasma metabolites with diverse molecular properties. Creatine was found to be increased and creatinine decreased in CSF of ALS patients compared to matched controls. Glucose was increased in CSF of ALS patients and α-hydroxybutyrate was increased in CSF and plasma of ALS patients compared to matched controls. Leucine, isoleucine and ketoleucine were increased in CSF of both ALS and PD. Together, these studies, in conjunction with earlier studies, suggest alterations in energy utilization pathways and have identified and further validated perturbed metabolites to be used in panels of biomarkers for the diagnosis of ALS and PD.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Molecular BioSystems},
	author = {Wuolikainen, Anna and Jonsson, Pär and Ahnlund, Maria and Antti, Henrik and Marklund, Stefan L. and Moritz, Thomas and Forsgren, Lars and Andersen, Peter M. and Trupp, Miles},
	year = {2016},
	pages = {1287--1298},
}

Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development. Obudulu, O., Bygdell, J., Sundberg, B., Moritz, T., Hvidsten, T. R., Trygg, J., & Wingsle, G. BMC Genomics, 17(1): 119. December 2016.

Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development [link]

Paper doi link bibtex

@article{obudulu_quantitative_2016,
	title = {Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development},
	volume = {17},
	issn = {1471-2164},
	url = {http://www.biomedcentral.com/1471-2164/17/119},
	doi = {10.1186/s12864-016-2458-z},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Obudulu, Ogonna and Bygdell, Joakim and Sundberg, Björn and Moritz, Thomas and Hvidsten, Torgeir R. and Trygg, Johan and Wingsle, Gunnar},
	month = dec,
	year = {2016},
	pages = {119},
}

Reduced mitochondrial malate dehydrogenase activity has a strong effect on photorespiratory metabolism as revealed by $^{\textrm{13}}$ C labelling. Lindén, P., Keech, O., Stenlund, H., Gardeström, P., & Moritz, T. Journal of Experimental Botany, 67(10): 3123–3135. May 2016.
$Reduced mitochondrial malate dehydrogenase activity has a strong effect on photorespiratory metabolism as revealed by $^{\textrm{13}}$ C labelling [link]$ Paper doi link bibtex

@article{linden_reduced_2016,
	title = {Reduced mitochondrial malate dehydrogenase activity has a strong effect on photorespiratory metabolism as revealed by $^{\textrm{13}}$ {C} labelling},
	volume = {67},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erw030},
	doi = {10.1093/jxb/erw030},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Lindén, Pernilla and Keech, Olivier and Stenlund, Hans and Gardeström, Per and Moritz, Thomas},
	month = may,
	year = {2016},
	pages = {3123--3135},
}

Seasonal Variation of Carbon Metabolism in the Cambial Zone of Eucalyptus grandis. Budzinski, I. G. F., Moon, D. H., Lindén, P., Moritz, T., & Labate, C. A. Frontiers in Plant Science, 7. June 2016.

Seasonal Variation of Carbon Metabolism in the Cambial Zone of Eucalyptus grandis [link]

Paper doi link bibtex

@article{budzinski_seasonal_2016,
	title = {Seasonal {Variation} of {Carbon} {Metabolism} in the {Cambial} {Zone} of {Eucalyptus} grandis},
	volume = {7},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/Article/10.3389/fpls.2016.00932/abstract},
	doi = {10/f3vjsv},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Budzinski, Ilara G. F. and Moon, David H. and Lindén, Pernilla and Moritz, Thomas and Labate, Carlos A.},
	month = jun,
	year = {2016},
}

2015 (4)

13C Tracking after 13CO2 Supply Revealed Diurnal Patterns of Wood Formation in Aspen. Mahboubi, A., Linden, P., Hedenstrom, M., Moritz, T., & Niittylä, T. Plant Physiol, 168(2): 478–89. June 2015.

13C Tracking after 13CO2 Supply Revealed Diurnal Patterns of Wood Formation in Aspen [link]

Paper doi link bibtex abstract

@article{mahboubi_13c_2015,
	title = {{13C} {Tracking} after {13CO2} {Supply} {Revealed} {Diurnal} {Patterns} of {Wood} {Formation} in {Aspen}},
	volume = {168},
	issn = {1532-2548 (Electronic) 0032-0889 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25931520},
	doi = {10.1104/pp.15.00292},
	abstract = {Wood of trees is formed from carbon assimilated in the photosynthetic tissues. Determining the temporal dynamics of carbon assimilation, subsequent transport into developing wood, and incorporation to cell walls would further our understanding of wood formation in particular and tree growth in general. To investigate these questions, we designed a (13)CO2 labeling system to study carbon transport and incorporation to developing wood of hybrid aspen (Populus tremula x tremuloides). Tracking of (13)C incorporation to wood over a time course using nuclear magnetic resonance spectroscopy revealed diurnal patterns in wood cell wall biosynthesis. The dark period had a differential effect on (13)C incorporation to lignin and cell wall carbohydrates. No (13)C was incorporated into aromatic amino acids of cell wall proteins in the dark, suggesting that cell wall protein biosynthesis ceased during the night. The results show previously unrecognized temporal patterns in wood cell wall biosynthesis, suggest diurnal cycle as a possible cue in the regulation of carbon incorporation to wood, and establish a unique (13)C labeling method for the analysis of wood formation and secondary growth in trees.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiol},
	author = {Mahboubi, A. and Linden, P. and Hedenstrom, M. and Moritz, T. and Niittylä, T.},
	month = jun,
	year = {2015},
	keywords = {*Circadian Rhythm, Analysis of Variance, Carbon Dioxide/*metabolism, Carbon Isotopes, Cell Wall/metabolism, Cellulose/metabolism, Magnetic Resonance Spectroscopy, Metabolic Networks and Pathways, Metabolome, Models, Biological, Phloem/metabolism, Plant Leaves/metabolism, Populus/*physiology, Principal Component Analysis, Sucrose/metabolism, Wood/*growth \& development},
	pages = {478--89},
}

Cell-type specific metabolic profiling of Arabidopsis thaliana protoplasts as a tool for plant systems biology. Petersson, S. V., Linden, P., Moritz, T., & Ljung, K. Metabolomics, 11(6): 1679–1689. December 2015. Edition: 2015/10/23

Cell-type specific metabolic profiling of Arabidopsis thaliana protoplasts as a tool for plant systems biology [link]

Paper doi link bibtex abstract

@article{petersson_cell-type_2015,
	title = {Cell-type specific metabolic profiling of {Arabidopsis} thaliana protoplasts as a tool for plant systems biology},
	volume = {11},
	issn = {1573-3882 (Print) 1573-3882 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26491421},
	doi = {10.1007/s11306-015-0814-7},
	abstract = {Flow cytometry combined with cell sorting of protoplasts has previously been used successfully for transcript profiling of the Arabidopsis thaliana root. We have developed the technique further, and in this paper we present a robust and reliable method for metabolite profiling in specific cell types isolated from Arabidopsis roots. The method uses a combination of fluorescence-activated cell sorting and gas chromatography-time of flight-mass spectrometry analysis. Cortical and endodermal cells from the green fluorescent protein (GFP)-expressing enhancer trap line J0571 were analysed and compared with non-GFP-expressing cells and intact root tissue. Of the metabolites identified, several showed significant differences in concentration between cell types. Multivariate statistical analysis was used to compare metabolite patterns between cell and tissue types, showing that the patterns differed substantially. Isolation of specific cell populations combined with highly sensitive MS-analysis will be a powerful tool for future studies of plant metabolism, and can also be combined with transcript and protein profiling for in-depth analyses of cellular processes.},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Metabolomics},
	author = {Petersson, S. V. and Linden, P. and Moritz, T. and Ljung, K.},
	month = dec,
	year = {2015},
	note = {Edition: 2015/10/23},
	keywords = {Arabidopsis thaliana, Flow cytometry, Gas chromatography-mass spectrometry, Metabolite profiling, Multivariate statistical analysis, Untargeted metabolomics},
	pages = {1679--1689},
}

Silencing C19-GA 2-oxidases induces parthenocarpic development and inhibits lateral branching in tomato plants. Martinez-Bello, L., Moritz, T., & Lopez-Diaz, I. J Exp Bot, 66(19): 5897–910. September 2015. Edition: 2015/06/21

Silencing C19-GA 2-oxidases induces parthenocarpic development and inhibits lateral branching in tomato plants [link]

Paper doi link bibtex abstract

@article{martinez-bello_silencing_2015,
	title = {Silencing {C19}-{GA} 2-oxidases induces parthenocarpic development and inhibits lateral branching in tomato plants},
	volume = {66},
	issn = {1460-2431 (Electronic) 0022-0957 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26093022},
	doi = {10/f3p6nj},
	abstract = {Gibberellins (GAs) are phytohormones that regulate a wide range of developmental processes in plants. Levels of active GAs are regulated by biosynthetic and catabolic enzymes like the GA 2-oxidases (GA2oxs). In tomato (Solanum lycopersicum L.) C19 GA2oxs are encoded by a small multigenic family of five members with some degree of redundancy. In order to investigate their roles in tomato, the silencing of all five genes in transgenic plants was induced. A significant increase in active GA4 content was found in the ovaries of transgenic plants. In addition, the transgenic unfertilized ovaries were much bigger than wild-type ovaries (about 30 times) and a certain proportion (5-37\%) were able to develop parthenocarpically. Among the GA2ox family, genes GA2ox1 and -2 seem to be the most relevant for this phenotype since their expression was induced in unfertilized ovaries and repressed in developing fruits, inversely correlating with ovary growth. Interestingly, transgenic lines exhibited a significant inhibition of branching and a higher content of active GA4 in axillary buds. This phenotype was reverted, in transgenic plants, by the application of paclobutrazol, a GA biosynthesis inhibitor, suggesting a role for GAs as repressors of branching. In summary, this work demonstrates that GA 2-oxidases regulate gibberellin levels in ovaries and axillary buds of tomato plants and their silencing is responsible for parthenocarpic fruit growth and branching inhibition.},
	language = {en},
	number = {19},
	urldate = {2021-06-07},
	journal = {J Exp Bot},
	author = {Martinez-Bello, L. and Moritz, T. and Lopez-Diaz, I.},
	month = sep,
	year = {2015},
	note = {Edition: 2015/06/21},
	keywords = {*Gene Expression Regulation, Plant, Branching, Fruit/genetics/growth \& development/metabolism, GA 2-oxidases, Gene Expression Regulation, Developmental, Gene Silencing, Gibberellins/metabolism, Lycopersicon esculentum/*genetics/*growth \& development/metabolism, Mixed Function Oxygenases/*genetics/metabolism, Plant Proteins/*genetics/metabolism, Plant Stems/genetics/growth \& development/metabolism, Plants, Genetically Modified/genetics/growth \& development/metabolism, Sequence Analysis, DNA, gibberellins, parthenocarpy, silencing, tomato.},
	pages = {5897--910},
}

Transgenic hybrid aspen trees with increased gibberellin (GA) concentrations suggest that GA acts in parallel with FLOWERING LOCUS T2 to control shoot elongation. Eriksson, M. E., Hoffman, D., Kaduk, M., Mauriat, M., & Moritz, T. New Phytologist, 205(3): 1288–1295. 2015. _eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.13144

Paper doi link bibtex abstract

@article{eriksson_transgenic_2015,
	title = {Transgenic hybrid aspen trees with increased gibberellin ({GA}) concentrations suggest that {GA} acts in parallel with {FLOWERING} {LOCUS} {T2} to control shoot elongation},
	volume = {205},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.13144},
	doi = {10/f3nxc2},
	abstract = {Bioactive gibberellins (GAs) have been implicated in short day (SD)-induced growth cessation in Populus, because exogenous applications of bioactive GAs to hybrid aspens (Populus tremula × tremuloides) under SD conditions delay growth cessation. However, this effect diminishes with time, suggesting that plants may cease growth following exposure to SDs due to a reduction in sensitivity to GAs. In order to validate and further explore the role of GAs in growth cessation, we perturbed GA biosynthesis or signalling in hybrid aspen plants by overexpressing AtGA20ox1, AtGA2ox2 and PttGID1.3 (encoding GA biosynthesis enzymes and a GA receptor). We found trees with elevated concentrations of bioactive GA, due to overexpression of AtGA20ox1, continued to grow in SD conditions and were insensitive to the level of FLOWERING LOCUS T2 (FT2) expression. As transgenic plants overexpressing the PttGID1.3 GA receptor responded in a wild-type (WT) manner to SD conditions, this insensitivity did not result from limited receptor availability. As high concentrations of bioactive GA during SD conditions were sufficient to sustain shoot elongation growth in hybrid aspen trees, independent of FT2 expression levels, we conclude elongation growth in trees is regulated by both GA- and long day-responsive pathways, similar to the regulation of flowering in Arabidopsis thaliana.},
	language = {en},
	number = {3},
	urldate = {2021-08-31},
	journal = {New Phytologist},
	author = {Eriksson, Maria E. and Hoffman, Daniel and Kaduk, Mateusz and Mauriat, Mélanie and Moritz, Thomas},
	year = {2015},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.13144},
	keywords = {Flowering Locus T2 (FT2), Populus, gibberellins (GA), growth cessation, photoperiod},
	pages = {1288--1295},
}

2014 (9)

A quantitative LC/MS method targeting urinary 1-methyl-4-imidazoleacetic acid for safety monitoring of the global histamine turnover in clinical studies. Kolmert, J., Forngren, B., Lindberg, J., Öhd, J., Åberg, K. M., Nilsson, G., Moritz, T., & Nordström, A. Analytical and Bioanalytical Chemistry, 406(6): 1751–1762. February 2014.

Paper doi link bibtex

@article{kolmert_quantitative_2014,
	title = {A quantitative {LC}/{MS} method targeting urinary 1-methyl-4-imidazoleacetic acid for safety monitoring of the global histamine turnover in clinical studies},
	volume = {406},
	issn = {1618-2642, 1618-2650},
	url = {http://link.springer.com/10.1007/s00216-013-7594-6},
	doi = {10/f225w6},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Analytical and Bioanalytical Chemistry},
	author = {Kolmert, J. and Forngren, B. and Lindberg, J. and Öhd, J. and Åberg, K. M. and Nilsson, G. and Moritz, T. and Nordström, A.},
	month = feb,
	year = {2014},
	pages = {1751--1762},
}

Aspen pectate lyase PtxtPL1-27 mobilizes matrix polysaccharides from woody tissues and improves saccharification yield. Biswal, A. K, Soeno, K., Gandla, M., Immerzeel, P., Pattathil, S., Lucenius, J., Serimaa, R., Hahn, M. G, Moritz, T., Jönsson, L. J, Israelsson-Nordström, M., & Mellerowicz, E. J Biotechnology for Biofuels, 7(1): 11. 2014.

Aspen pectate lyase PtxtPL1-27 mobilizes matrix polysaccharides from woody tissues and improves saccharification yield [link]

Paper doi link bibtex

@article{biswal_aspen_2014,
	title = {Aspen pectate lyase {PtxtPL1}-27 mobilizes matrix polysaccharides from woody tissues and improves saccharification yield},
	volume = {7},
	issn = {1754-6834},
	url = {http://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/1754-6834-7-11},
	doi = {10/f22tkm},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Biotechnology for Biofuels},
	author = {Biswal, Ajaya K and Soeno, Kazuo and Gandla, Madhavi and Immerzeel, Peter and Pattathil, Sivakumar and Lucenius, Jessica and Serimaa, Ritva and Hahn, Michael G and Moritz, Thomas and Jönsson, Leif J and Israelsson-Nordström, Maria and Mellerowicz, Ewa J},
	year = {2014},
	pages = {11},
}

CHOLINE TRANSPORTER-LIKE1 is required for sieve plate development to mediate long-distance cell-to-cell communication. Dettmer, J., Ursache, R., Campilho, A., Miyashima, S., Belevich, I., O’Regan, S., Mullendore, D. L., Yadav, S. R., Lanz, C., Beverina, L., Papagni, A., Schneeberger, K., Weigel, D., Stierhof, Y., Moritz, T., Knoblauch, M., Jokitalo, E., & Helariutta, Y. Nature Communications, 5(1): 4276. September 2014.

CHOLINE TRANSPORTER-LIKE1 is required for sieve plate development to mediate long-distance cell-to-cell communication [link]

Paper doi link bibtex

@article{dettmer_choline_2014,
	title = {{CHOLINE} {TRANSPORTER}-{LIKE1} is required for sieve plate development to mediate long-distance cell-to-cell communication},
	volume = {5},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms5276},
	doi = {10/f3p42k},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Nature Communications},
	author = {Dettmer, Jan and Ursache, Robertas and Campilho, Ana and Miyashima, Shunsuke and Belevich, Ilya and O’Regan, Seana and Mullendore, Daniel Leroy and Yadav, Shri Ram and Lanz, Christa and Beverina, Luca and Papagni, Antonio and Schneeberger, Korbinian and Weigel, Detlef and Stierhof, York-Dieter and Moritz, Thomas and Knoblauch, Michael and Jokitalo, Eija and Helariutta, Ykä},
	month = sep,
	year = {2014},
	pages = {4276},
}

Gibberellins inhibit adventitious rooting in hybrid aspen and Arabidopsis by affecting auxin transport. Mauriat, M., Petterle, A., Bellini, C., & Moritz, T. The Plant Journal, 78(3): 372–384. May 2014.

Gibberellins inhibit adventitious rooting in hybrid aspen and Arabidopsis by affecting auxin transport [link]

Paper doi link bibtex

@article{mauriat_gibberellins_2014,
	title = {Gibberellins inhibit adventitious rooting in hybrid aspen and {Arabidopsis} by affecting auxin transport},
	volume = {78},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.12478},
	doi = {10/f22tk3},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Mauriat, Mélanie and Petterle, Anna and Bellini, Catherine and Moritz, Thomas},
	month = may,
	year = {2014},
	pages = {372--384},
}

High lipid order of Arabidopsis cell‐plate membranes mediated by sterol and DYNAMIN‐RELATED PROTEIN1A function. Frescatada‐Rosa, M., Stanislas, T., Backues, S. K., Reichardt, I., Men, S., Boutté, Y., Jürgens, G., Moritz, T., Bednarek, S. Y., & Grebe, M. The Plant Journal, 80(5): 745–757. December 2014.

High lipid order of Arabidopsis cell‐plate membranes mediated by sterol and DYNAMIN‐RELATED PROTEIN1A function [link]

Paper doi link bibtex

@article{frescatadarosa_high_2014,
	title = {High lipid order of {Arabidopsis} cell‐plate membranes mediated by sterol and {DYNAMIN}‐{RELATED} {PROTEIN1A} function},
	volume = {80},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.12674},
	doi = {10/f3nxhn},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Frescatada‐Rosa, Márcia and Stanislas, Thomas and Backues, Steven K. and Reichardt, Ilka and Men, Shuzhen and Boutté, Yohann and Jürgens, Gerd and Moritz, Thomas and Bednarek, Sebastian Y. and Grebe, Markus},
	month = dec,
	year = {2014},
	pages = {745--757},
}

Maladjusted Host Immune Responses Induce Experimental Cerebral Malaria-Like Pathology in a Murine Borrelia and Plasmodium Co-Infection Model. Normark, J., Nelson, M., Engström, P., Andersson, M., Björk, R., Moritz, T., Fahlgren, A., & Bergström, S. PLoS ONE, 9(7): e103295. July 2014.

Paper doi link bibtex

@article{normark_maladjusted_2014,
	title = {Maladjusted {Host} {Immune} {Responses} {Induce} {Experimental} {Cerebral} {Malaria}-{Like} {Pathology} in a {Murine} {Borrelia} and {Plasmodium} {Co}-{Infection} {Model}},
	volume = {9},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0103295},
	doi = {10/f22k7v},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Normark, Johan and Nelson, Maria and Engström, Patrik and Andersson, Marie and Björk, Rafael and Moritz, Thomas and Fahlgren, Anna and Bergström, Sven},
	editor = {Wooten, R. Mark},
	month = jul,
	year = {2014},
	pages = {e103295},
}

Metabolite and Peptide Levels in Plasma and CSF Differentiating Healthy Controls from Patients with Newly Diagnosed Parkinson's Disease. Trupp, M., Jonsson, P., Öhrfelt, A., Zetterberg, H., Obudulu, O., Malm, L., Wuolikainen, A., Linder, J., Moritz, T., Blennow, K., Antti, H., & Forsgren, L. Journal of Parkinson's Disease, 4(3): 549–560. 2014.

Metabolite and Peptide Levels in Plasma and CSF Differentiating Healthy Controls from Patients with Newly Diagnosed Parkinson's Disease [link]

Paper doi link bibtex

@article{trupp_metabolite_2014,
	title = {Metabolite and {Peptide} {Levels} in {Plasma} and {CSF} {Differentiating} {Healthy} {Controls} from {Patients} with {Newly} {Diagnosed} {Parkinson}'s {Disease}},
	volume = {4},
	issn = {1877718X, 18777171},
	url = {https://www.medra.org/servlet/aliasResolver?alias=iospress&doi=10.3233/JPD-140389},
	doi = {10/f23vd3},
	number = {3},
	urldate = {2021-06-08},
	journal = {Journal of Parkinson's Disease},
	author = {Trupp, Miles and Jonsson, Pär and Öhrfelt, Annika and Zetterberg, Henrik and Obudulu, Ogonna and Malm, Linus and Wuolikainen, Anna and Linder, Jan and Moritz, Thomas and Blennow, Kaj and Antti, Henrik and Forsgren, Lars},
	year = {2014},
	pages = {549--560},
}

No Evidence of Geographical Structure of Salicinoid Chemotypes within Populus Tremula. Keefover-Ring, K., Ahnlund, M., Abreu, I. N., Jansson, S., Moritz, T., & Albrectsen, B. R. PLoS ONE, 9(10): e107189. October 2014.

No Evidence of Geographical Structure of Salicinoid Chemotypes within Populus Tremula [link]

Paper doi link bibtex

@article{keefover-ring_no_2014,
	title = {No {Evidence} of {Geographical} {Structure} of {Salicinoid} {Chemotypes} within {Populus} {Tremula}},
	volume = {9},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0107189},
	doi = {10/f25fhm},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Keefover-Ring, Ken and Ahnlund, Maria and Abreu, Ilka Nacif and Jansson, Stefan and Moritz, Thomas and Albrectsen, Benedicte Riber},
	editor = {Yin, Tongming},
	month = oct,
	year = {2014},
	pages = {e107189},
}

Serum Metabolomic Biomarkers of Dementia. Mousavi, M., Jonsson, P., Antti, H., Adolfsson, R., Nordin, A., Bergdahl, J., Eriksson, K., Moritz, T., Nilsson, L., & Nyberg, L. Dementia and Geriatric Cognitive Disorders Extra, 4(2): 252–262. July 2014.

Serum Metabolomic Biomarkers of Dementia [link]

Paper doi link bibtex

@article{mousavi_serum_2014,
	title = {Serum {Metabolomic} {Biomarkers} of {Dementia}},
	volume = {4},
	issn = {1664-5464},
	url = {https://www.karger.com/Article/FullText/364816},
	doi = {10/f242b6},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Dementia and Geriatric Cognitive Disorders Extra},
	author = {Mousavi, Malahat and Jonsson, P�r and Antti, Henrik and Adolfsson, Rolf and Nordin, Annelie and Bergdahl, Jan and Eriksson, K�re and Moritz, Thomas and Nilsson, Lars-G�ran and Nyberg, Lars},
	month = jul,
	year = {2014},
	pages = {252--262},
}

2013 (4)

ABCG9, ABCG11 and ABCG14 ABC transporters are required for vascular development in Arabidopsis. Le Hir, R., Sorin, C., Chakraborti, D., Moritz, T., Schaller, H., Tellier, F., Robert, S., Morin, H., Bakó, L., & Bellini, C. The Plant Journal, 76(5): 811–824. December 2013.

ABCG9, ABCG11 and ABCG14 ABC transporters are required for vascular development in Arabidopsis [link]

Paper doi link bibtex

@article{le_hir_abcg9_2013,
	title = {{ABCG9}, {ABCG11} and {ABCG14} {ABC} transporters are required for vascular development in {Arabidopsis}},
	volume = {76},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.12334},
	doi = {10/f22xd4},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Le Hir, Rozenn and Sorin, Clément and Chakraborti, Dipankar and Moritz, Thomas and Schaller, Hubert and Tellier, Frédérique and Robert, Stéphanie and Morin, Halima and Bakó, Laszlo and Bellini, Catherine},
	month = dec,
	year = {2013},
	pages = {811--824},
}

Co-expression analysis, proteomic and metabolomic study on the impact of a Deg/HtrA protease triple mutant in Synechocystis sp. PCC 6803 exposed to temperature and high light stress. Miranda, H., Cheregi, O., Netotea, S., Hvidsten, T. R., Moritz, T., & Funk, C. Journal of Proteomics, 78: 294–311. January 2013.

Paper doi link bibtex

@article{miranda_co-expression_2013,
	title = {Co-expression analysis, proteomic and metabolomic study on the impact of a {Deg}/{HtrA} protease triple mutant in {Synechocystis} sp. {PCC} 6803 exposed to temperature and high light stress},
	volume = {78},
	issn = {18743919},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1874391912006926},
	doi = {10/f2z4z6},
	language = {en},
	urldate = {2021-06-08},
	journal = {Journal of Proteomics},
	author = {Miranda, Hélder and Cheregi, Otilia and Netotea, Sergiu and Hvidsten, Torgeir R. and Moritz, Thomas and Funk, Christiane},
	month = jan,
	year = {2013},
	pages = {294--311},
}

OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants. Srivastava, V., Obudulu, O., Bygdell, J., Löfstedt, T., Rydén, P., Nilsson, R., Ahnlund, M., Johansson, A., Jonsson, P., Freyhult, E., Qvarnström, J., Karlsson, J., Melzer, M., Moritz, T., Trygg, J., Hvidsten, T. R., & Wingsle, G. BMC Genomics, 14(1): 893. December 2013.

Paper doi link bibtex abstract

@article{srivastava_onpls_2013,
	title = {{OnPLS} integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic {hipI}- superoxide dismutase {Populus} plants},
	volume = {14},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/1471-2164-14-893},
	doi = {10/f2zk6q},
	abstract = {Reactive oxygen species (ROS) are involved in the regulation of diverse physiological processes in plants, including various biotic and abiotic stress responses. Thus, oxidative stress tolerance mechanisms in plants are complex, and diverse responses at multiple levels need to be characterized in order to understand them. Here we present system responses to oxidative stress in Populus by integrating data from analyses of the cambial region of wild-type controls and plants expressing high-isoelectric-point superoxide dismutase (hipI-SOD) transcripts in antisense orientation showing a higher production of superoxide. The cambium, a thin cell layer, generates cells that differentiate to form either phloem or xylem and is hypothesized to be a major reason for phenotypic perturbations in the transgenic plants. Data from multiple platforms including transcriptomics (microarray analysis), proteomics (UPLC/QTOF-MS), and metabolomics (GC-TOF/MS, UPLC/MS, and UHPLC-LTQ/MS) were integrated using the most recent development of orthogonal projections to latent structures called OnPLS. OnPLS is a symmetrical multi-block method that does not depend on the order of analysis when more than two blocks are analysed. Significantly affected genes, proteins and metabolites were then visualized in painted pathway diagrams.},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Srivastava, Vaibhav and Obudulu, Ogonna and Bygdell, Joakim and Löfstedt, Tommy and Rydén, Patrik and Nilsson, Robert and Ahnlund, Maria and Johansson, Annika and Jonsson, Pär and Freyhult, Eva and Qvarnström, Johanna and Karlsson, Jan and Melzer, Michael and Moritz, Thomas and Trygg, Johan and Hvidsten, Torgeir R. and Wingsle, Gunnar},
	month = dec,
	year = {2013},
	keywords = {OnPLS, Oxidative stress, Poplar, Statistical integration, Systems biology},
	pages = {893},
}

The effect of carbohydrates and osmoticum on storage reserve accumulation and germination of Norway spruce somatic embryos. Businge, E., Bygdell, J., Wingsle, G., Moritz, T., & Egertsdotter, U. Physiologia Plantarum, 149(2): 273–285. October 2013.

The effect of carbohydrates and osmoticum on storage reserve accumulation and germination of Norway spruce somatic embryos [link]

Paper doi link bibtex 1 download

@article{businge_effect_2013,
	title = {The effect of carbohydrates and osmoticum on storage reserve accumulation and germination of {Norway} spruce somatic embryos},
	volume = {149},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12039},
	doi = {10/f2zr7w},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Businge, Edward and Bygdell, Joakim and Wingsle, Gunnar and Moritz, Thomas and Egertsdotter, Ulrika},
	month = oct,
	year = {2013},
	pages = {273--285},
}

2012 (9)

ALS patients with mutations in the SOD1 gene have an unique metabolomic profile in the cerebrospinal fluid compared with ALS patients without mutations. Wuolikainen, A., Andersen, P. M., Moritz, T., Marklund, S. L., & Antti, H. Molecular Genetics and Metabolism, 105(3): 472–478. March 2012.

Paper doi link bibtex

@article{wuolikainen_als_2012,
	title = {{ALS} patients with mutations in the {SOD1} gene have an unique metabolomic profile in the cerebrospinal fluid compared with {ALS} patients without mutations},
	volume = {105},
	issn = {10967192},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1096719211006184},
	doi = {10/ffcrdm},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Molecular Genetics and Metabolism},
	author = {Wuolikainen, Anna and Andersen, Peter M. and Moritz, Thomas and Marklund, Stefan L. and Antti, Henrik},
	month = mar,
	year = {2012},
	pages = {472--478},
}

Altered Metabolic Signature in Pre-Diabetic NOD Mice. Madsen, R., Banday, V. S., Moritz, T., Trygg, J., & Lejon, K. PLoS ONE, 7(4): e35445. April 2012.

Altered Metabolic Signature in Pre-Diabetic NOD Mice [link]

Paper doi link bibtex

@article{madsen_altered_2012,
	title = {Altered {Metabolic} {Signature} in {Pre}-{Diabetic} {NOD} {Mice}},
	volume = {7},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0035445},
	doi = {10/f23mgb},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Madsen, Rasmus and Banday, Viqar Showkat and Moritz, Thomas and Trygg, Johan and Lejon, Kristina},
	editor = {Maedler, Kathrin},
	month = apr,
	year = {2012},
	pages = {e35445},
}

Development of a gas chromatography/mass spectrometry based metabolomics protocol by means of statistical experimental design. Danielsson, A. P. H., Moritz, T., Mulder, H., & Spégel, P. Metabolomics, 8(1): 50–63. February 2012.

Development of a gas chromatography/mass spectrometry based metabolomics protocol by means of statistical experimental design [link]

Paper doi link bibtex

@article{danielsson_development_2012,
	title = {Development of a gas chromatography/mass spectrometry based metabolomics protocol by means of statistical experimental design},
	volume = {8},
	issn = {1573-3882, 1573-3890},
	url = {http://link.springer.com/10.1007/s11306-011-0283-6},
	doi = {10/cbcwmc},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Metabolomics},
	author = {Danielsson, Anders P. H. and Moritz, Thomas and Mulder, Hindrik and Spégel, Peter},
	month = feb,
	year = {2012},
	pages = {50--63},
}

Effects of oestrogen and testosterone therapy on serum metabolites in postmenopausal women. Zang, H., Moritz, T., Norstedt, G., Hirschberg, A. L., & Tollet-Egnell, P. Clinical Endocrinology, 77(2): 288–295. August 2012.

Effects of oestrogen and testosterone therapy on serum metabolites in postmenopausal women [link]

Paper doi link bibtex

@article{zang_effects_2012,
	title = {Effects of oestrogen and testosterone therapy on serum metabolites in postmenopausal women},
	volume = {77},
	issn = {03000664},
	url = {http://doi.wiley.com/10.1111/j.1365-2265.2012.04374.x},
	doi = {10/f2znjv},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Clinical Endocrinology},
	author = {Zang, Hong and Moritz, Thomas and Norstedt, Gunnar and Hirschberg, Angelica L. and Tollet-Egnell, Petra},
	month = aug,
	year = {2012},
	pages = {288--295},
}

Mass spectrometric identification of new minor indigoids in shellfish purple dye from Hexaplex trunculus. Surowiec, I., Nowik, W., & Moritz, T. Dyes and Pigments, 94(2): 363–369. August 2012.

Mass spectrometric identification of new minor indigoids in shellfish purple dye from Hexaplex trunculus [link]

Paper doi link bibtex

@article{surowiec_mass_2012,
	title = {Mass spectrometric identification of new minor indigoids in shellfish purple dye from {Hexaplex} trunculus},
	volume = {94},
	issn = {01437208},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0143720812000320},
	doi = {10/f2zz55},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Dyes and Pigments},
	author = {Surowiec, Izabella and Nowik, Witold and Moritz, Thomas},
	month = aug,
	year = {2012},
	pages = {363--369},
}

Metabolic Responses to Change in Disease Activity during Tumor Necrosis Factor Inhibition in Patients with Rheumatoid Arthritis. Madsen, R., Rantapää-Dahlqvist, S., Lundstedt, T., Moritz, T., & Trygg, J. Journal of Proteome Research, 11(7): 3796–3804. July 2012.

Metabolic Responses to Change in Disease Activity during Tumor Necrosis Factor Inhibition in Patients with Rheumatoid Arthritis [link]

Paper doi link bibtex

@article{madsen_metabolic_2012,
	title = {Metabolic {Responses} to {Change} in {Disease} {Activity} during {Tumor} {Necrosis} {Factor} {Inhibition} in {Patients} with {Rheumatoid} {Arthritis}},
	volume = {11},
	issn = {1535-3893, 1535-3907},
	url = {https://pubs.acs.org/doi/10.1021/pr300296v},
	doi = {10/f24g7h},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Journal of Proteome Research},
	author = {Madsen, Rasmus and Rantapää-Dahlqvist, Solbritt and Lundstedt, Torbjörn and Moritz, Thomas and Trygg, Johan},
	month = jul,
	year = {2012},
	pages = {3796--3804},
}

Metabolite profiling reveals clear metabolic changes during somatic embryo development of Norway spruce (Picea abies). Businge, E., Brackmann, K., Moritz, T., & Egertsdotter, U. Tree Physiology, 32(2): 232–244. February 2012.

Metabolite profiling reveals clear metabolic changes during somatic embryo development of Norway spruce (Picea abies) [link]

Paper doi link bibtex

@article{businge_metabolite_2012,
	title = {Metabolite profiling reveals clear metabolic changes during somatic embryo development of {Norway} spruce ({Picea} abies)},
	volume = {32},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpr142},
	doi = {10/f24n88},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Tree Physiology},
	author = {Businge, E. and Brackmann, K. and Moritz, T. and Egertsdotter, U.},
	month = feb,
	year = {2012},
	pages = {232--244},
}

Multivariate curve resolution provides a high-throughput data processing pipeline for pyrolysis-gas chromatography/mass spectrometry. Gerber, L., Eliasson, M., Trygg, J., Moritz, T., & Sundberg, B. Journal of Analytical and Applied Pyrolysis, 95: 95–100. May 2012.

Multivariate curve resolution provides a high-throughput data processing pipeline for pyrolysis-gas chromatography/mass spectrometry [link]

Paper doi link bibtex

@article{gerber_multivariate_2012,
	title = {Multivariate curve resolution provides a high-throughput data processing pipeline for pyrolysis-gas chromatography/mass spectrometry},
	volume = {95},
	issn = {01652370},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0165237012000137},
	doi = {10/fxs9zf},
	language = {en},
	urldate = {2021-06-08},
	journal = {Journal of Analytical and Applied Pyrolysis},
	author = {Gerber, Lorenz and Eliasson, Mattias and Trygg, Johan and Moritz, Thomas and Sundberg, Björn},
	month = may,
	year = {2012},
	pages = {95--100},
}

Physical fitness level is reflected by alterations in the human plasma metabolome. Chorell, E., Svensson, M. B., Moritz, T., & Antti, H. Molecular BioSystems, 8(4): 1187. 2012.

Physical fitness level is reflected by alterations in the human plasma metabolome [link]

Paper doi link bibtex

@article{chorell_physical_2012,
	title = {Physical fitness level is reflected by alterations in the human plasma metabolome},
	volume = {8},
	issn = {1742-206X, 1742-2051},
	url = {http://xlink.rsc.org/?DOI=c2mb05428k},
	doi = {10/fxnw3m},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Molecular BioSystems},
	author = {Chorell, Elin and Svensson, Michael B. and Moritz, Thomas and Antti, Henrik},
	year = {2012},
	pages = {1187},
}

2011 (6)

Comparison of the role of gibberellins and ethylene in response to submergence of two lowland rice cultivars, Senia and Bomba. Dubois, V., Moritz, T., & García-Martínez, J. L. Journal of Plant Physiology, 168(3): 233–241. February 2011.

Comparison of the role of gibberellins and ethylene in response to submergence of two lowland rice cultivars, Senia and Bomba [link]

Paper doi link bibtex

@article{dubois_comparison_2011,
	title = {Comparison of the role of gibberellins and ethylene in response to submergence of two lowland rice cultivars, {Senia} and {Bomba}},
	volume = {168},
	issn = {01761617},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0176161710004050},
	doi = {10/b3z5h8},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Journal of Plant Physiology},
	author = {Dubois, Vincent and Moritz, Thomas and García-Martínez, José L.},
	month = feb,
	year = {2011},
	pages = {233--241},
}

Diagnostic properties of metabolic perturbations in rheumatoid arthritis. Madsen, R. K, Lundstedt, T., Gabrielsson, J., Sennbro, C., Alenius, G., Moritz, T., Rantapää-Dahlqvist, S., & Trygg, J. Arthritis Research & Therapy, 13(1): R19. February 2011.

Diagnostic properties of metabolic perturbations in rheumatoid arthritis [link]

Paper doi link bibtex

@article{madsen_diagnostic_2011,
	title = {Diagnostic properties of metabolic perturbations in rheumatoid arthritis},
	volume = {13},
	issn = {1478-6362},
	url = {https://arthritis-research.biomedcentral.com/articles/10.1186/ar3243},
	doi = {10/fdbqs3},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Arthritis Research \& Therapy},
	author = {Madsen, Rasmus K and Lundstedt, Torbjörn and Gabrielsson, Jon and Sennbro, Carl-Johan and Alenius, Gerd-Marie and Moritz, Thomas and Rantapää-Dahlqvist, Solbritt and Trygg, Johan},
	month = feb,
	year = {2011},
	pages = {R19},
}

Disease-Related Changes in the Cerebrospinal Fluid Metabolome in Amyotrophic Lateral Sclerosis Detected by GC/TOFMS. Wuolikainen, A., Moritz, T., Marklund, S. L., Antti, H., & Andersen, P. M. PLOS ONE, 6(4): e17947. April 2011. Publisher: Public Library of Science

Disease-Related Changes in the Cerebrospinal Fluid Metabolome in Amyotrophic Lateral Sclerosis Detected by GC/TOFMS [link]

Paper doi link bibtex abstract

@article{wuolikainen_disease-related_2011,
	title = {Disease-{Related} {Changes} in the {Cerebrospinal} {Fluid} {Metabolome} in {Amyotrophic} {Lateral} {Sclerosis} {Detected} by {GC}/{TOFMS}},
	volume = {6},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017947},
	doi = {10/fkwd4d},
	abstract = {Background/Aim The changes in the cerebrospinal fluid (CSF) metabolome associated with the fatal neurodegenerative disease amyotrophic lateral sclerosis (ALS) are poorly understood and earlier smaller studies have shown conflicting results. The metabolomic methodology is suitable for screening large cohorts of samples. Global metabolomics can be used for detecting changes of metabolite concentrations in samples of fluids such as CSF. Methodology Using gas chromatography coupled to mass spectrometry (GC/TOFMS) and multivariate statistical modeling, we simultaneously studied the metabolome signature of ∼120 small metabolites in the CSF of patients with ALS, stratified according to hereditary disposition and clinical subtypes of ALS in relation to controls. Principal Findings The study is the first to report data validated over two sub-sets of ALS vs. control patients for a large set of metabolites analyzed by GC/TOFMS. We find that patients with sporadic amyotrophic lateral sclerosis (SALS) have a heterogeneous metabolite signature in the cerebrospinal fluid, in some patients being almost identical to controls. However, familial amyotrophic lateral sclerosis (FALS) without superoxide dismutase-1 gene (SOD1) mutation is less heterogeneous than SALS. The metabolome of the cerebrospinal fluid of 17 ALS patients with a SOD1 gene mutation was found to form a separate homogeneous group. Analysis of metabolites revealed that glutamate and glutamine were reduced, in particular in patients with a familial predisposition. There are significant differences in the metabolite profile and composition among patients with FALS, SALS and patients carrying a mutation in the SOD1 gene suggesting that the neurodegenerative process in different subtypes of ALS may be partially dissimilar. Conclusions/Significance Patients with a genetic predisposition to amyotrophic lateral sclerosis have a more distinct and homogeneous signature than patients with a sporadic disease.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {PLOS ONE},
	author = {Wuolikainen, Anna and Moritz, Thomas and Marklund, Stefan L. and Antti, Henrik and Andersen, Peter Munch},
	month = apr,
	year = {2011},
	note = {Publisher: Public Library of Science},
	keywords = {Amyotrophic lateral sclerosis, Cerebrospinal fluid, Drug metabolism, Glutamic acid, Metabolic analysis, Metabolites, Metabolomics, Mutation},
	pages = {e17947},
}

Proper gibberellin localization in vascular tissue is required to control auxin-dependent leaf development and bud outgrowth in hybrid aspen: GA-dependent auxin transport in vascular tissue. Mauriat, M., Sandberg, L. G., & Moritz, T. The Plant Journal, 67(5): 805–816. September 2011.

Paper doi link bibtex

@article{mauriat_proper_2011,
	title = {Proper gibberellin localization in vascular tissue is required to control auxin-dependent leaf development and bud outgrowth in hybrid aspen: {GA}-dependent auxin transport in vascular tissue},
	volume = {67},
	issn = {09607412},
	shorttitle = {Proper gibberellin localization in vascular tissue is required to control auxin-dependent leaf development and bud outgrowth in hybrid aspen},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2011.04635.x},
	doi = {10/bnx4nt},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Mauriat, Mélanie and Sandberg, Linda G. and Moritz, Thomas},
	month = sep,
	year = {2011},
	pages = {805--816},
}

The sucrose‐regulated Arabidopsis transcription factor bZIP11 reprograms metabolism and regulates trehalose metabolism. Ma, J., Hanssen, M., Lundgren, K., Hernández, L., Delatte, T., Ehlert, A., Liu, C., Schluepmann, H., Dröge‐Laser, W., Moritz, T., Smeekens, S., & Hanson, J. New Phytologist, 191(3): 733–745. August 2011.

The sucrose‐regulated Arabidopsis transcription factor bZIP11 reprograms metabolism and regulates trehalose metabolism [link]

Paper doi link bibtex

@article{ma_sucroseregulated_2011,
	title = {The sucrose‐regulated {Arabidopsis} transcription factor {bZIP11} reprograms metabolism and regulates trehalose metabolism},
	volume = {191},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2011.03735.x},
	doi = {10/b9vhbj},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Ma, Jingkun and Hanssen, Micha and Lundgren, Krister and Hernández, Lázaro and Delatte, Thierry and Ehlert, Andrea and Liu, Chun‐Ming and Schluepmann, Henriette and Dröge‐Laser, Wolfgang and Moritz, Thomas and Smeekens, Sjef and Hanson, Johannes},
	month = aug,
	year = {2011},
	pages = {733--745},
}

UHPLC-ESI/TOFMS Determination of salicylate-like phenolic gycosides in Populus tremula leaves. Abreu, I., Ahnlund, M., Moritz, T., & Albrectsen, B. Journal of chemical ecology, 37: 857–70. August 2011.
doi link bibtex abstract

@article{abreu_uhplc-esitofms_2011,
	title = {{UHPLC}-{ESI}/{TOFMS} {Determination} of salicylate-like phenolic gycosides in {Populus} tremula leaves},
	volume = {37},
	doi = {10/c8755j},
	abstract = {Associations of salicylate-like phenolic glycosides (PGs) with biological activity have been reported in Salix and Populus trees, but only for a few compounds, and in relation to a limited number of herbivores. By considering the full diversity of PGs, we may improve our ability to recognize genotypes or chemotype groups and enhance our understanding of their ecological function. Here, we present a fast and efficient general method for salicylate determination in leaves of Eurasian aspen that uses ultra-high performance liquid chromatography-electrospray ionization/time-of-flight mass spectrometry (UHPLC-ESI/TOFMS). The time required for the liquid chromatography separations was 13.5 min per sample, compared to around 60 min per sample for most HPLC protocols. In leaf samples from identical P. tremula genotypes with diverse propagation and treatment histories, we identified nine PGs. We found the compound-specific mass chromatograms to be more informative than the UV-visible chromatograms for compound identification and when quantitating samples with large variability in PG content. Signature compounds previously reported for P. tremoloides (tremulacin, tremuloidin, salicin, and salicortin) always were present, and five PGs (2'-O-cinnamoyl-salicortin, 2'-O-acetyl-salicortin, 2'-O-acetyl-salicin, acetyl-tremulacin, and salicyloyl-salicin) were detected for the first time in P. tremula. By using information about the formic acid adduct that appeared for PGs in the LTQ-Orbitrap MS environment, novel compounds like acetyl-tremulacin could be tentatively identified without the use of standards. The novel PGs were consistently either present in genotypes regardless of propagation and damage treatment or were not detectable. In some genotypes, concentrations of 2'-O-acetyl-salicortin and 2'-O-cinnamoyl-salicortin were similar to levels of biologically active PGs in other Salicaceous trees. Our study suggests that we may expect a wide variation in PG content in aspen populations which is of interest both for studies of interactions with herbivores and for mapping population structure.

Electronic supplementary material
The online version of this article (doi:10.1007/s10886-011-9991-7) contains supplementary material, which is available to authorized users.},
	journal = {Journal of chemical ecology},
	author = {Abreu, Ilka and Ahnlund, Maria and Moritz, Thomas and Albrectsen, Benedicte},
	month = aug,
	year = {2011},
	pages = {857--70},
}

Associations of salicylate-like phenolic glycosides (PGs) with biological activity have been reported in Salix and Populus trees, but only for a few compounds, and in relation to a limited number of herbivores. By considering the full diversity of PGs, we may improve our ability to recognize genotypes or chemotype groups and enhance our understanding of their ecological function. Here, we present a fast and efficient general method for salicylate determination in leaves of Eurasian aspen that uses ultra-high performance liquid chromatography-electrospray ionization/time-of-flight mass spectrometry (UHPLC-ESI/TOFMS). The time required for the liquid chromatography separations was 13.5 min per sample, compared to around 60 min per sample for most HPLC protocols. In leaf samples from identical P. tremula genotypes with diverse propagation and treatment histories, we identified nine PGs. We found the compound-specific mass chromatograms to be more informative than the UV-visible chromatograms for compound identification and when quantitating samples with large variability in PG content. Signature compounds previously reported for P. tremoloides (tremulacin, tremuloidin, salicin, and salicortin) always were present, and five PGs (2'-O-cinnamoyl-salicortin, 2'-O-acetyl-salicortin, 2'-O-acetyl-salicin, acetyl-tremulacin, and salicyloyl-salicin) were detected for the first time in P. tremula. By using information about the formic acid adduct that appeared for PGs in the LTQ-Orbitrap MS environment, novel compounds like acetyl-tremulacin could be tentatively identified without the use of standards. The novel PGs were consistently either present in genotypes regardless of propagation and damage treatment or were not detectable. In some genotypes, concentrations of 2'-O-acetyl-salicortin and 2'-O-cinnamoyl-salicortin were similar to levels of biologically active PGs in other Salicaceous trees. Our study suggests that we may expect a wide variation in PG content in aspen populations which is of interest both for studies of interactions with herbivores and for mapping population structure. Electronic supplementary material The online version of this article (doi:10.1007/s10886-011-9991-7) contains supplementary material, which is available to authorized users.

2010 (8)

A Metabolomic Approach to Study Major Metabolite Changes during Acclimation to Limiting CO2 in Chlamydomonas reinhardtii. Renberg, L., Johansson, A. I., Shutova, T., Stenlund, H., Aksmann, A., Raven, J. A., Gardeström, P., Moritz, T., & Samuelsson, G. Plant Physiology, 154(1): 187–196. September 2010.

A Metabolomic Approach to Study Major Metabolite Changes during Acclimation to Limiting CO2 in <i>Chlamydomonas reinhardtii</i> [link]

Paper doi link bibtex abstract

@article{renberg_metabolomic_2010,
	title = {A {Metabolomic} {Approach} to {Study} {Major} {Metabolite} {Changes} during {Acclimation} to {Limiting} {CO2} in \textit{{Chlamydomonas} reinhardtii}},
	volume = {154},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/154/1/187/6111228},
	doi = {10/b3xzqv},
	abstract = {Abstract
            Using a gas chromatography-mass spectrometry-time of flight technique, we determined major metabolite changes during induction of the carbon-concentrating mechanism in the unicellular green alga Chlamydomonas reinhardtii. In total, 128 metabolites with significant differences between high- and low-CO2-grown cells were detected, of which 82 were wholly or partially identified, including amino acids, lipids, and carbohydrates. In a 24-h time course experiment, we show that the amino acids serine and phenylalanine increase transiently while aspartate and glutamate decrease after transfer to low CO2. The biggest differences were typically observed 3 h after transfer to low-CO2 conditions. Therefore, we made a careful metabolomic examination at the 3-h time point, comparing low-CO2 treatment to high-CO2 control. Five metabolites involved in photorespiration, 11 amino acids, and one lipid were increased, while six amino acids and, interestingly, 21 lipids were significantly lower. Our conclusion is that the metabolic pattern during early induction of the carbon-concentrating mechanism fit a model where photorespiration is increasing.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Renberg, Linda and Johansson, Annika I. and Shutova, Tatiana and Stenlund, Hans and Aksmann, Anna and Raven, John A. and Gardeström, Per and Moritz, Thomas and Samuelsson, Göran},
	month = sep,
	year = {2010},
	pages = {187--196},
}

Alteration of PHYA expression change circadian rhythms and timing of bud set in Populus. Kozarewa, I., Ibáñez, C., Johansson, M., Ögren, E., Mozley, D., Nylander, E., Chono, M., Moritz, T., & Eriksson, M. E. Plant Molecular Biology, 73(1-2): 143–156. May 2010.

Alteration of PHYA expression change circadian rhythms and timing of bud set in Populus [link]

Paper doi link bibtex

@article{kozarewa_alteration_2010,
	title = {Alteration of {PHYA} expression change circadian rhythms and timing of bud set in {Populus}},
	volume = {73},
	issn = {0167-4412, 1573-5028},
	url = {http://link.springer.com/10.1007/s11103-010-9619-2},
	doi = {10/dp553q},
	language = {en},
	number = {1-2},
	urldate = {2021-06-08},
	journal = {Plant Molecular Biology},
	author = {Kozarewa, Iwanka and Ibáñez, Cristian and Johansson, Mikael and Ögren, Erling and Mozley, David and Nylander, Eva and Chono, Makiko and Moritz, Thomas and Eriksson, Maria E.},
	month = may,
	year = {2010},
	pages = {143--156},
}

Changes in diurnal patterns within the Populus transcriptome and metabolome in response to photoperiod variation. Hoffman, D. E., Jonsson, P., Bylesjö, M., Trygg, J., Antti, H., Eriksson, M. E., & Moritz, T. Plant, Cell & Environment, 33(8): 1298–1313. August 2010.
doi link bibtex abstract 1 download

@article{hoffman_changes_2010,
	title = {Changes in diurnal patterns within the {Populus} transcriptome and metabolome in response to photoperiod variation},
	volume = {33},
	issn = {1365-3040},
	doi = {10/d2xk8m},
	abstract = {Changes in seasonal photoperiod provides an important environmental signal that affects the timing of winter dormancy in perennial, deciduous, temperate tree species, such as hybrid aspen (Populus tremula x Populus tremuloides). In this species, growth cessation, cold acclimation and dormancy are induced in the autumn by the detection of day-length shortening that occurs at a given critical day length. Important components in the detection of such day-length changes are photoreceptors and the circadian clock, and many plant responses at both the gene regulation and metabolite levels are expected to be diurnal. To directly examine this expectation and study components in these events, here we report transcriptomic and metabolomic responses to a change in photoperiod from long to short days in hybrid aspen. We found about 16\% of genes represented on the arrays to be diurnally regulated, as assessed by our pre-defined criteria. Furthermore, several of these genes were involved in circadian-associated processes, including photosynthesis and primary and secondary metabolism. Metabolites affected by the change in photoperiod were mostly involved in carbon metabolism. Taken together, we have thus established a molecular catalog of events that precede a response to winter.},
	language = {eng},
	number = {8},
	journal = {Plant, Cell \& Environment},
	author = {Hoffman, Daniel E. and Jonsson, Pär and Bylesjö, Max and Trygg, Johan and Antti, Henrik and Eriksson, Maria E. and Moritz, Thomas},
	month = aug,
	year = {2010},
	pmid = {20302601},
	keywords = {Carbohydrate Metabolism, Circadian Rhythm, DNA, Complementary, Gene Expression Profiling, Gene Expression Regulation, Plant, Genes, Plant, Metabolome, Oligonucleotide Array Sequence Analysis, Photoperiod, Populus, Seasons},
	pages = {1298--1313},
}

Development and optimization of a metabolomic method for analysis of adherent cell cultures. Danielsson, A. P., Moritz, T., Mulder, H., & Spégel, P. Analytical Biochemistry, 404(1): 30–39. September 2010.

Development and optimization of a metabolomic method for analysis of adherent cell cultures [link]

Paper doi link bibtex

@article{danielsson_development_2010,
	title = {Development and optimization of a metabolomic method for analysis of adherent cell cultures},
	volume = {404},
	issn = {00032697},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0003269710002502},
	doi = {10/fhmpbx},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Analytical Biochemistry},
	author = {Danielsson, Anders P.H. and Moritz, Thomas and Mulder, Hindrik and Spégel, Peter},
	month = sep,
	year = {2010},
	pages = {30--39},
}

Ischaemic preconditioning is related to decreasing levels of extracellular adenosine that may be metabolically useful in the at-risk myocardium: an experimental study in the pig. Waldenström, A., Haney, M., Biber, B., Kavianipour, M., Moritz, T., Strandén, P., Wikström, G., & Ronquist, G. Acta Physiologica, 199(1): 1–9. May 2010.

Paper doi link bibtex

@article{waldenstrom_ischaemic_2010,
	title = {Ischaemic preconditioning is related to decreasing levels of extracellular adenosine that may be metabolically useful in the at-risk myocardium: an experimental study in the pig},
	volume = {199},
	issn = {17481708, 17481716},
	shorttitle = {Ischaemic preconditioning is related to decreasing levels of extracellular adenosine that may be metabolically useful in the at-risk myocardium},
	url = {http://doi.wiley.com/10.1111/j.1748-1716.2009.02071.x},
	doi = {10/dsp97q},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Acta Physiologica},
	author = {Waldenström, A. and Haney, M. and Biber, B. and Kavianipour, M. and Moritz, T. and Strandén, P. and Wikström, G. and Ronquist, G.},
	month = may,
	year = {2010},
	pages = {1--9},
}

Metabolomic Characterization of Human Prostate Cancer Bone Metastases Reveals Increased Levels of Cholesterol. Thysell, E., Surowiec, I., Hörnberg, E., Crnalic, S., Widmark, A., Johansson, A. I., Stattin, P., Bergh, A., Moritz, T., Antti, H., & Wikström, P. PLoS ONE, 5(12): e14175. December 2010.

Metabolomic Characterization of Human Prostate Cancer Bone Metastases Reveals Increased Levels of Cholesterol [link]

Paper doi link bibtex

@article{thysell_metabolomic_2010,
	title = {Metabolomic {Characterization} of {Human} {Prostate} {Cancer} {Bone} {Metastases} {Reveals} {Increased} {Levels} of {Cholesterol}},
	volume = {5},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0014175},
	doi = {10/d69xb9},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Thysell, Elin and Surowiec, Izabella and Hörnberg, Emma and Crnalic, Sead and Widmark, Anders and Johansson, Annika I. and Stattin, Pär and Bergh, Anders and Moritz, Thomas and Antti, Henrik and Wikström, Pernilla},
	editor = {Creighton, Chad},
	month = dec,
	year = {2010},
	pages = {e14175},
}

Metabolomic analysis of a human oral glucose tolerance test reveals fatty acids as reliable indicators of regulated metabolism. Spégel, P., Danielsson, A. P. H., Bacos, K., Nagorny, C. L. F., Moritz, T., Mulder, H., & Filipsson, K. Metabolomics, 6(1): 56–66. March 2010.

Metabolomic analysis of a human oral glucose tolerance test reveals fatty acids as reliable indicators of regulated metabolism [link]

Paper doi link bibtex

@article{spegel_metabolomic_2010,
	title = {Metabolomic analysis of a human oral glucose tolerance test reveals fatty acids as reliable indicators of regulated metabolism},
	volume = {6},
	issn = {1573-3882, 1573-3890},
	url = {http://link.springer.com/10.1007/s11306-009-0177-z},
	doi = {10/frw67z},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Metabolomics},
	author = {Spégel, Peter and Danielsson, Anders P. H. and Bacos, Karl and Nagorny, Cecilia L. F. and Moritz, Thomas and Mulder, Hindrik and Filipsson, Karin},
	month = mar,
	year = {2010},
	pages = {56--66},
}

Pyruvate dehydrogenase kinase 1 controls mitochondrial metabolism and insulin secretion in INS-1 832/13 clonal β-cells. Krus, U., Kotova, O., Spégel, P., Hallgard, E., Sharoyko, V., Vedin, A., Moritz, T., Sugden, M., Koeck, T., & Mulder, H. Biochemical Journal, 429(1): 205–213. July 2010.

Pyruvate dehydrogenase kinase 1 controls mitochondrial metabolism and insulin secretion in INS-1 832/13 clonal β-cells [link]

Paper doi link bibtex abstract

@article{krus_pyruvate_2010,
	title = {Pyruvate dehydrogenase kinase 1 controls mitochondrial metabolism and insulin secretion in {INS}-1 832/13 clonal β-cells},
	volume = {429},
	issn = {0264-6021, 1470-8728},
	url = {https://portlandpress.com/biochemj/article/429/1/205/45438/Pyruvate-dehydrogenase-kinase-1-controls},
	doi = {10/d2d23m},
	abstract = {Tight coupling between cytosolic and mitochondrial metabolism is key for GSIS (glucose-stimulated insulin secretion). In the present study we examined the regulatory contribution of PDH (pyruvate dehydrogenase) kinase 1, a negative regulator of PDH, to metabolic coupling in 832/13 clonal β-cells. Knockdown of PDH kinase 1 with siRNA (small interfering RNA) reduced its mRNA ({\textgreater}80\%) and protein level ({\textgreater}40\%) after 72 h. PDH activity, glucose-stimulated cellular oxygen consumption and pyruvate-stimulated mitochondrial oxygen consumption increased 1.7- (P{\textless}0.05), 1.6- (P{\textless}0.05) and 1.6-fold (P{\textless}0.05) respectively. Gas chromatography/MS revealed an altered metabolite profile upon silencing of PDH kinase 1, determined by increased levels of the tricarboxylic acid cycle intermediates malate, fumarate and α-ketoglutarate. These metabolic alterations were associated with exaggerated GSIS (5-fold compared with 3.1-fold in control cells; P{\textless}0.01). Insulin secretion, provoked by leucine and dimethylsuccinate, which feed into the tricarboxylic acid cycle bypassing PDH, was unaffected. The oxygen consumption and metabolic data strongly suggest that knockdown of PDH kinase 1 in β-cells permits increased metabolic flux of glucose-derived carbons into the tricarboxylic acid cycle via PDH. Enhanced insulin secretion is probably caused by increased generation of tricarboxylic acid cycle-derived reducing equivalents for mitochondrial electron transport to generate ATP and/or stimulatory metabolic intermediates. On the basis of these findings, we suggest that PDH kinase 1 is an important regulator of PDH in clonal β-cells and that PDH kinase 1 and PDH are important for efficient metabolic coupling. Maintaining low PDH kinase 1 expression/activity, keeping PDH in a dephosphorylated and active state, may be important for β-cells to achieve the metabolic flux rates necessary for maximal GSIS.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Biochemical Journal},
	author = {Krus, Ulrika and Kotova, Olga and Spégel, Peter and Hallgard, Elna and Sharoyko, Vladimir V. and Vedin, Anna and Moritz, Thomas and Sugden, Mary C. and Koeck, Thomas and Mulder, Hindrik},
	month = jul,
	year = {2010},
	pages = {205--213},
}

2009 (11)

An Auxin Gradient and Maximum in the Arabidopsis Root Apex Shown by High-Resolution Cell-Specific Analysis of IAA Distribution and Synthesis. Petersson, S. V., Johansson, A. I., Kowalczyk, M., Makoveychuk, A., Wang, J. Y., Moritz, T., Grebe, M., Benfey, P. N., Sandberg, G., & Ljung, K. The Plant Cell, 21(6): 1659–1668. August 2009.

An Auxin Gradient and Maximum in the <i>Arabidopsis</i> Root Apex Shown by High-Resolution Cell-Specific Analysis of IAA Distribution and Synthesis [link]

Paper doi link bibtex abstract 1 download

@article{petersson_auxin_2009,
	title = {An {Auxin} {Gradient} and {Maximum} in the \textit{{Arabidopsis}} {Root} {Apex} {Shown} by {High}-{Resolution} {Cell}-{Specific} {Analysis} of {IAA} {Distribution} and {Synthesis}},
	volume = {21},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/21/6/1659/6095411},
	doi = {10/ddgn83},
	abstract = {Abstract
            Local concentration gradients of the plant growth regulator auxin (indole-3-acetic acid [IAA]) are thought to instruct the positioning of organ primordia and stem cell niches and to direct cell division, expansion, and differentiation. High-resolution measurements of endogenous IAA concentrations in support of the gradient hypothesis are required to substantiate this hypothesis. Here, we introduce fluorescence-activated cell sorting of green fluorescent protein–marked cell types combined with highly sensitive mass spectrometry methods as a novel means for analyses of IAA distribution and metabolism at cellular resolution. Our results reveal the presence of IAA concentration gradients within the Arabidopsis thaliana root tip with a distinct maximum in the organizing quiescent center of the root apex. We also demonstrate that the root apex provides an important source of IAA and that cells of all types display a high synthesis capacity, suggesting a substantial contribution of local biosynthesis to auxin homeostasis in the root tip. Our results indicate that local biosynthesis and polar transport combine to produce auxin gradients and maxima in the root tip.},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Petersson, Sara V. and Johansson, Annika I. and Kowalczyk, Mariusz and Makoveychuk, Alexander and Wang, Jean Y. and Moritz, Thomas and Grebe, Markus and Benfey, Philip N. and Sandberg, Göran and Ljung, Karin},
	month = aug,
	year = {2009},
	pages = {1659--1668},
}

Analyses of GA20ox- and GID1-over-expressing aspen suggest that gibberellins play two distinct roles in wood formation. Mauriat, M., & Moritz, T. The Plant Journal: For Cell and Molecular Biology, 58(6): 989–1003. June 2009.
doi link bibtex abstract

@article{mauriat_analyses_2009,
	title = {Analyses of {GA20ox}- and {GID1}-over-expressing aspen suggest that gibberellins play two distinct roles in wood formation},
	volume = {58},
	issn = {1365-313X},
	doi = {10/cqnj6n},
	abstract = {Gibberellins (GAs) are involved in many aspects of plant development, including shoot growth, flowering and wood formation. Increased levels of bioactive GAs are known to induce xylogenesis and xylem fiber elongation in aspen. However, there is currently little information on the response pathway(s) that mediate GA effects on wood formation. Here we characterize an important element of the GA pathway in hybrid aspen: the GA receptor, GID1. Four orthologs of GID1 were identified in Populus tremula x P. tremuloides (PttGID1.1-1.4). These were functional when expressed in Arabidopsis thaliana, and appear to present a degree of sub-functionalization in hybrid aspen. PttGID1.1 and PttGID1.3 were over-expressed in independent lines of hybrid aspen using either the 35S promoter or a xylem-specific promoter (LMX5). The 35S:PttGID1 over-expressors shared several phenotypic traits previously described in 35S:AtGA20ox1 over-expressors, including rapid growth, increased elongation, and increased xylogenesis. However, their xylem fibers were not elongated, unlike those of 35S:AtGA20ox1 plants. Similar differences in the xylem fiber phenotype were observed when PttGID1.1, PttGID1.3 or AtGA20ox1 were expressed under the control of the LMX5 promoter, suggesting either that PttGID1.1 and PttGID1.3 play no role in fiber elongation or that GA homeostasis is strongly controlled when GA signaling is altered. Our data suggest that GAs are required in two distinct wood-formation processes that have tissue-specific signaling pathways: xylogenesis, as mediated by GA signaling in the cambium, and fiber elongation in the developing xylem.},
	language = {eng},
	number = {6},
	journal = {The Plant Journal: For Cell and Molecular Biology},
	author = {Mauriat, Mélanie and Moritz, Thomas},
	month = jun,
	year = {2009},
	pmid = {19228336},
	keywords = {Amino Acid Sequence, Arabidopsis, Cloning, Molecular, Gene Expression Regulation, Enzymologic, Gene Expression Regulation, Plant, Gibberellins, Mixed Function Oxygenases, Molecular Sequence Data, Plant Proteins, Plants, Genetically Modified, Populus, Promoter Regions, Genetic, RNA, Plant, Receptors, Cell Surface, Sequence Alignment, Wood},
	pages = {989--1003},
}

Compensation for Systematic Cross-Contribution Improves Normalization of Mass Spectrometry Based Metabolomics Data. Redestig, H., Fukushima, A., Stenlund, H., Moritz, T., Arita, M., Saito, K., & Kusano, M. Analytical Chemistry, 81(19): 7974–7980. October 2009.

Compensation for Systematic Cross-Contribution Improves Normalization of Mass Spectrometry Based Metabolomics Data [link]

Paper doi link bibtex

@article{redestig_compensation_2009,
	title = {Compensation for {Systematic} {Cross}-{Contribution} {Improves} {Normalization} of {Mass} {Spectrometry} {Based} {Metabolomics} {Data}},
	volume = {81},
	issn = {0003-2700, 1520-6882},
	url = {https://pubs.acs.org/doi/10.1021/ac901143w},
	doi = {10/fr25p2},
	language = {en},
	number = {19},
	urldate = {2021-06-08},
	journal = {Analytical Chemistry},
	author = {Redestig, Henning and Fukushima, Atsushi and Stenlund, Hans and Moritz, Thomas and Arita, Masanori and Saito, Kazuki and Kusano, Miyako},
	month = oct,
	year = {2009},
	pages = {7974--7980},
}

Decreased Mitochondrial Activities of Malate Dehydrogenase and Fumarase in Tomato Lead to Altered Root Growth and Architecture via Diverse Mechanisms. van der Merwe, M. J., Osorio, S., Moritz, T., Nunes-Nesi, A., & Fernie, A. R. Plant Physiology, 149(2): 653–669. February 2009.

Paper doi link bibtex abstract

@article{van_der_merwe_decreased_2009,
	title = {Decreased {Mitochondrial} {Activities} of {Malate} {Dehydrogenase} and {Fumarase} in {Tomato} {Lead} to {Altered} {Root} {Growth} and {Architecture} via {Diverse} {Mechanisms}},
	volume = {149},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/149/2/653/6107909},
	doi = {10/dnz8fc},
	abstract = {Abstract
            Transgenic tomato (Solanum lycopersicum) plants in which either mitochondrial malate dehydrogenase or fumarase was antisense inhibited have previously been characterized to exhibit altered photosynthetic metabolism. Here, we demonstrate that these manipulations also resulted in differences in root growth, with both transgenics being characterized by a dramatic reduction of root dry matter deposition and respiratory activity but opposite changes with respect to root area. A range of physiological, molecular, and biochemical experiments were carried out in order to determine whether changes in root morphology were due to altered metabolism within the root itself, alterations in the nature of the transformants' root exudation, consequences of alteration in the efficiency of photoassimilate delivery to the root, or a combination of these factors. Grafting experiments in which the transformants were reciprocally grafted to wild-type controls suggested that root length and area were determined by the aerial part of the plant but that biomass was not. Despite the transgenic roots displaying alteration in the expression of phytohormone-associated genes, evaluation of the levels of the hormones themselves revealed that, with the exception of gibberellins, they were largely unaltered. When taken together, these combined experiments suggest that root biomass and growth are retarded by root-specific alterations in metabolism and gibberellin contents. These data are discussed in the context of current models of root growth and biomass partitioning.},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {van der Merwe, Margaretha J. and Osorio, Sonia and Moritz, Thomas and Nunes-Nesi, Adriano and Fernie, Alisdair R.},
	month = feb,
	year = {2009},
	pages = {653--669},
}

Gibberellin mediates daylength-controlled differentiation of vegetative meristems in strawberry (Fragaria × ananassa Duch). Hytönen, T., Elomaa, P., Moritz, T., & Junttila, O. BMC Plant Biology, 9(1): 18. 2009.

Gibberellin mediates daylength-controlled differentiation of vegetative meristems in strawberry (Fragaria × ananassa Duch) [link]

Paper doi link bibtex

@article{hytonen_gibberellin_2009,
	title = {Gibberellin mediates daylength-controlled differentiation of vegetative meristems in strawberry ({Fragaria} × ananassa {Duch})},
	volume = {9},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-9-18},
	doi = {10/fk39gx},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Hytönen, Timo and Elomaa, Paula and Moritz, Thomas and Junttila, Olavi},
	year = {2009},
	pages = {18},
}

Improper excess light energy dissipation in Arabidopsis results in a metabolic reprogramming. Frenkel, M., Külheim, C., Jänkänpää, H. J., Skogström, O., Dall'Osto, L., Ågren, J., Bassi, R., Moritz, T., Moen, J., & Jansson, S. BMC Plant Biology, 9(1): 12. January 2009.

Improper excess light energy dissipation in Arabidopsis results in a metabolic reprogramming [link]

Paper doi link bibtex abstract

@article{frenkel_improper_2009,
	title = {Improper excess light energy dissipation in {Arabidopsis} results in a metabolic reprogramming},
	volume = {9},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/1471-2229-9-12},
	doi = {10/ffdbr8},
	abstract = {Plant performance is affected by the level of expression of PsbS, a key photoprotective protein involved in the process of feedback de-excitation (FDE), or the qE component of non-photochemical quenching, NPQ.},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Frenkel, Martin and Külheim, Carsten and Jänkänpää, Hanna Johansson and Skogström, Oskar and Dall'Osto, Luca and Ågren, Jon and Bassi, Roberto and Moritz, Thomas and Moen, Jon and Jansson, Stefan},
	month = jan,
	year = {2009},
	keywords = {Herbivore Preference, Partial Little Square Discriminant Analysis, Partial Little Square Discriminant Analysis Model, Photooxidative Stress, Photosynthetic Light Reaction},
	pages = {12},
}

Integrated Analysis of Transcript, Protein and Metabolite Data To Study Lignin Biosynthesis in Hybrid Aspen. Bylesjö, M., Nilsson, R., Srivastava, V., Grönlund, A., Johansson, A. I., Jansson, S., Karlsson, J., Moritz, T., Wingsle, G., & Trygg, J. Journal of Proteome Research, 8(1): 199–210. January 2009.

Integrated Analysis of Transcript, Protein and Metabolite Data To Study Lignin Biosynthesis in Hybrid Aspen [link]

Paper doi link bibtex

@article{bylesjo_integrated_2009,
	title = {Integrated {Analysis} of {Transcript}, {Protein} and {Metabolite} {Data} {To} {Study} {Lignin} {Biosynthesis} in {Hybrid} {Aspen}},
	volume = {8},
	issn = {1535-3893, 1535-3907},
	url = {https://pubs.acs.org/doi/10.1021/pr800298s},
	doi = {10/ddqkpn},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Journal of Proteome Research},
	author = {Bylesjö, Max and Nilsson, Robert and Srivastava, Vaibhav and Grönlund, Andreas and Johansson, Annika I. and Jansson, Stefan and Karlsson, Jan and Moritz, Thomas and Wingsle, Gunnar and Trygg, Johan},
	month = jan,
	year = {2009},
	pages = {199--210},
}

Metabolomic evaluation of pulsed electric field-induced stress on potato tissue. Galindo, F. G., Dejmek, P., Lundgren, K., Rasmusson, A. G., Vicente, A., & Moritz, T. Planta, 230(3): 469–479. August 2009.

Metabolomic evaluation of pulsed electric field-induced stress on potato tissue [link]

Paper doi link bibtex

@article{galindo_metabolomic_2009,
	title = {Metabolomic evaluation of pulsed electric field-induced stress on potato tissue},
	volume = {230},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-009-0950-2},
	doi = {10/bg94jg},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Planta},
	author = {Galindo, Federico Gómez and Dejmek, Petr and Lundgren, Krister and Rasmusson, Allan G. and Vicente, António and Moritz, Thomas},
	month = aug,
	year = {2009},
	pages = {469--479},
}

Optimization of procedures for collecting and storing of CSF for studying the metabolome in ALS. Wuolikainen, A., Hedenström, M., Moritz, T., Marklund, S. L., Antti, H., & Andersen, P. M. Amyotrophic Lateral Sclerosis, 10(4): 229–236. January 2009.

Optimization of procedures for collecting and storing of CSF for studying the metabolome in ALS [link]

Paper doi link bibtex

@article{wuolikainen_optimization_2009,
	title = {Optimization of procedures for collecting and storing of {CSF} for studying the metabolome in {ALS}},
	volume = {10},
	issn = {1748-2968, 1471-180X},
	url = {http://www.tandfonline.com/doi/full/10.1080/17482960902871009},
	doi = {10/cjcnvg},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Amyotrophic Lateral Sclerosis},
	author = {Wuolikainen, Anna and Hedenström, Mattias and Moritz, Thomas and Marklund, Stefan L. and Antti, Henrik and Andersen, Peter M.},
	month = jan,
	year = {2009},
	pages = {229--236},
}

Predictive Metabolomics Evaluation of Nutrition-Modulated Metabolic Stress Responses in Human Blood Serum During the Early Recovery Phase of Strenuous Physical Exercise. Chorell, E., Moritz, T., Branth, S., Antti, H., & Svensson, M. B. Journal of Proteome Research, 8(6): 2966–2977. June 2009.

Paper doi link bibtex

@article{chorell_predictive_2009,
	title = {Predictive {Metabolomics} {Evaluation} of {Nutrition}-{Modulated} {Metabolic} {Stress} {Responses} in {Human} {Blood} {Serum} {During} the {Early} {Recovery} {Phase} of {Strenuous} {Physical} {Exercise}},
	volume = {8},
	issn = {1535-3893, 1535-3907},
	url = {https://pubs.acs.org/doi/10.1021/pr900081q},
	doi = {10/fn674z},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Journal of Proteome Research},
	author = {Chorell, Elin and Moritz, Thomas and Branth, Stefan and Antti, Henrik and Svensson, Michael B.},
	month = jun,
	year = {2009},
	pages = {2966--2977},
}

The role and regulation of the tricarboxylic acid cycle in Solanum lycopersicum roots. Van der Merwe, M., Osorio, S., Moritz, T., Nunes-Nesi, A., & Fernie, A. South African Journal of Botany, 75(2): 424. April 2009.

The role and regulation of the tricarboxylic acid cycle in Solanum lycopersicum roots [link]

Paper doi link bibtex

@article{van_der_merwe_role_2009,
	title = {The role and regulation of the tricarboxylic acid cycle in {Solanum} lycopersicum roots},
	volume = {75},
	issn = {02546299},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0254629909001203},
	doi = {10/d84qt3},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {South African Journal of Botany},
	author = {Van der Merwe, M.J. and Osorio, S. and Moritz, T. and Nunes-Nesi, A. and Fernie, A.R.},
	month = apr,
	year = {2009},
	pages = {424},
}

2008 (9)

A Second Pathway to Degrade Pyrimidine Nucleic Acid Precursors in Eukaryotes. Andersen, G., Björnberg, O., Polakova, S., Pynyaha, Y., Rasmussen, A., Møller, K., Hofer, A., Moritz, T., Sandrini, M. P. B., Merico, A., Compagno, C., Åkerlund, H., Gojković, Z., & Piškur, J. Journal of Molecular Biology, 380(4): 656–666. July 2008.

A Second Pathway to Degrade Pyrimidine Nucleic Acid Precursors in Eukaryotes [link]

Paper doi link bibtex

@article{andersen_second_2008,
	title = {A {Second} {Pathway} to {Degrade} {Pyrimidine} {Nucleic} {Acid} {Precursors} in {Eukaryotes}},
	volume = {380},
	issn = {00222836},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0022283608005846},
	doi = {10/dbbqnk},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Journal of Molecular Biology},
	author = {Andersen, Gorm and Björnberg, Olof and Polakova, Silvia and Pynyaha, Yuriy and Rasmussen, Anna and Møller, Kasper and Hofer, Anders and Moritz, Thomas and Sandrini, Michael Paolo Bastner and Merico, Anna-Maria and Compagno, Concetta and Åkerlund, Hans-Erik and Gojković, Zoran and Piškur, Jure},
	month = jul,
	year = {2008},
	pages = {656--666},
}

Arabidopsis sterol carrier protein-2 is required for normal development of seeds and seedlings. Zheng, B. S., Rönnberg, E., Viitanen, L., Salminen, T. A., Lundgren, K., Moritz, T., & Edqvist, J. Journal of Experimental Botany, 59(12): 3485–3499. September 2008.

Arabidopsis sterol carrier protein-2 is required for normal development of seeds and seedlings [link]

Paper doi link bibtex

@article{zheng_arabidopsis_2008,
	title = {Arabidopsis sterol carrier protein-2 is required for normal development of seeds and seedlings},
	volume = {59},
	issn = {1460-2431, 0022-0957},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/ern201},
	doi = {10/c2pqd9},
	language = {en},
	number = {12},
	urldate = {2021-06-10},
	journal = {Journal of Experimental Botany},
	author = {Zheng, Bing Song and Rönnberg, Elin and Viitanen, Lenita and Salminen, Tiina A. and Lundgren, Krister and Moritz, Thomas and Edqvist, Johan},
	month = sep,
	year = {2008},
	pages = {3485--3499},
}

Evaluation of a protocol for metabolic profiling studies on human blood plasma by combined ultra-performance liquid chromatography/mass spectrometry: From extraction to data analysis. Bruce, S. J., Jonsson, P., Antti, H., Cloarec, O., Trygg, J., Marklund, S. L., & Moritz, T. Analytical Biochemistry, 372(2): 237–249. January 2008.

Paper doi link bibtex

@article{bruce_evaluation_2008,
	title = {Evaluation of a protocol for metabolic profiling studies on human blood plasma by combined ultra-performance liquid chromatography/mass spectrometry: {From} extraction to data analysis},
	volume = {372},
	issn = {00032697},
	shorttitle = {Evaluation of a protocol for metabolic profiling studies on human blood plasma by combined ultra-performance liquid chromatography/mass spectrometry},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0003269707006161},
	doi = {10/fm7np6},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Analytical Biochemistry},
	author = {Bruce, Stephen J. and Jonsson, Pär and Antti, Henrik and Cloarec, Olivier and Trygg, Johan and Marklund, Stefan L. and Moritz, Thomas},
	month = jan,
	year = {2008},
	pages = {237--249},
}

Gibberellin Homeostasis in Tobacco is Regulated by Gibberellin Metabolism Genes with Different Gibberellin Sensitivity. Gallego-Giraldo, L., Ubeda-Tomás, S., Gisbert, C., García-Martínez, J. L., Moritz, T., & López-Díaz, I. Plant and Cell Physiology, 49(5): 679–690. May 2008.

Gibberellin Homeostasis in Tobacco is Regulated by Gibberellin Metabolism Genes with Different Gibberellin Sensitivity [link]

Paper doi link bibtex

@article{gallego-giraldo_gibberellin_2008,
	title = {Gibberellin {Homeostasis} in {Tobacco} is {Regulated} by {Gibberellin} {Metabolism} {Genes} with {Different} {Gibberellin} {Sensitivity}},
	volume = {49},
	issn = {1471-9053, 0032-0781},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcn042},
	doi = {10/ckqdfn},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {Plant and Cell Physiology},
	author = {Gallego-Giraldo, Lina and Ubeda-Tomás, Susana and Gisbert, Carmina and García-Martínez, José L. and Moritz, Thomas and López-Díaz, Isabel},
	month = may,
	year = {2008},
	pages = {679--690},
}

Modulation of the Hormone Setting by Rhodococcus fascians Results in Ectopic KNOX Activation in Arabidopsis. Depuydt, S., Doležal, K., Van Lijsebettens, M., Moritz, T., Holsters, M., & Vereecke, D. Plant Physiology, 146(3): 1267–1281. March 2008.

Modulation of the Hormone Setting by <i>Rhodococcus fascians</i> Results in Ectopic <i>KNOX</i> Activation in Arabidopsis [link]

Paper doi link bibtex abstract

@article{depuydt_modulation_2008,
	title = {Modulation of the {Hormone} {Setting} by \textit{{Rhodococcus} fascians} {Results} in {Ectopic} \textit{{KNOX}} {Activation} in {Arabidopsis}},
	volume = {146},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/146/3/1267/6107230},
	doi = {10/dkp574},
	abstract = {Abstract
            The biotrophic actinomycete Rhodococcus fascians has a profound impact on plant development and a common aspect of the symptomatology is the deformation of infected leaves. In Arabidopsis (Arabidopsis thaliana), the serrated leaf margins formed upon infection resemble the leaf phenotype of transgenic plants with ectopic expression of KNOTTED-like homeobox (KNOX) genes. Through transcript profiling, we demonstrate that class-I KNOX genes are transcribed in symptomatic leaves. Functional analysis revealed that BREVIPEDICELLUS/KNOTTED-LIKE1 and mainly SHOOT MERISTEMLESS were essential for the observed leaf dissection. However, these results also positioned the KNOX genes downstream in the signaling cascade triggered by R. fascians infection. The much faster activation of ARABIDOPSIS RESPONSE REGULATOR5 and the establishment of homeostatic and feedback mechanisms to control cytokinin (CK) levels support the overrepresentation of this hormone in infected plants due to the secretion by the pathogen, thereby placing the CK response high up in the cascade. Hormone measurements show a net decrease of tested CKs, indicating either that secretion by the bacterium and degradation by the plant are in balance, or, as suggested by the strong reaction of 35S:CKX plants, that other CKs are at play. At early time points of the interaction, activation of gibberellin 2-oxidase presumably installs a local hormonal setting favorable for meristematic activity that provokes leaf serrations. The results are discussed in the context of symptom development, evasion of plant defense, and the establishment of a specific niche by R. fascians.},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Plant Physiology},
	author = {Depuydt, Stephen and Doležal, Karel and Van Lijsebettens, Mieke and Moritz, Thomas and Holsters, Marcelle and Vereecke, Danny},
	month = mar,
	year = {2008},
	pages = {1267--1281},
}

Reduced gibberellin response affects ethylene biosynthesis and responsiveness in the Arabidopsis gai eto2‐1 double mutant. De Grauwe, L., Chaerle, L., Dugardeyn, J., Decat, J., Rieu, I., Vriezen, W. H., Moritz, T., Beemster, G. T. S., Phillips, A. L., Harberd, N. P., Hedden, P., & Van Der Straeten, D. New Phytologist, 177(1): 128–141. January 2008.

Reduced gibberellin response affects ethylene biosynthesis and responsiveness in the Arabidopsis <i>gai eto2‐1</i> double mutant [link]

Paper doi link bibtex

@article{de_grauwe_reduced_2008,
	title = {Reduced gibberellin response affects ethylene biosynthesis and responsiveness in the {Arabidopsis} \textit{gai eto2‐1} double mutant},
	volume = {177},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2007.02263.x},
	doi = {10/bjkq86},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {De Grauwe, Liesbeth and Chaerle, Laury and Dugardeyn, Jasper and Decat, Jan and Rieu, Ivo and Vriezen, Wim H. and Moritz, Thomas and Beemster, Gerrit T. S. and Phillips, Andy L. and Harberd, Nicholas P. and Hedden, Peter and Van Der Straeten, Dominique},
	month = jan,
	year = {2008},
	pages = {128--141},
}

Sterol-dependent endocytosis mediates post-cytokinetic acquisition of PIN2 auxin efflux carrier polarity. Men, S., Boutté, Y., Ikeda, Y., Li, X., Palme, K., Stierhof, Y., Hartmann, M., Moritz, T., & Grebe, M. Nature Cell Biology, 10(2): 237–244. February 2008.

Sterol-dependent endocytosis mediates post-cytokinetic acquisition of PIN2 auxin efflux carrier polarity [link]

Paper doi link bibtex

@article{men_sterol-dependent_2008,
	title = {Sterol-dependent endocytosis mediates post-cytokinetic acquisition of {PIN2} auxin efflux carrier polarity},
	volume = {10},
	issn = {1465-7392, 1476-4679},
	url = {http://www.nature.com/articles/ncb1686},
	doi = {10/chxrxg},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Nature Cell Biology},
	author = {Men, Shuzhen and Boutté, Yohann and Ikeda, Yoshihisa and Li, Xugang and Palme, Klaus and Stierhof, York-Dieter and Hartmann, Marie-Andrée and Moritz, Thomas and Grebe, Markus},
	month = feb,
	year = {2008},
	pages = {237--244},
}

The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction (RT-PCR) analysis in plants. Gutierrez, L., Mauriat, M., Gunin, S., Pelloux, J., Lefebvre, J., Louvet, R., Rusterucci, C., Moritz, T., Guerineau, F., Bellini, C., & Van Wuytswinkel, O. Plant Biotechnology Journal, 6(6): 609–618. August 2008.

Paper doi link bibtex

@article{gutierrez_lack_2008,
	title = {The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction ({RT}-{PCR}) analysis in plants},
	volume = {6},
	issn = {14677644, 14677652},
	shorttitle = {The lack of a systematic validation of reference genes},
	url = {http://doi.wiley.com/10.1111/j.1467-7652.2008.00346.x},
	doi = {10/d6bcb9},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {Plant Biotechnology Journal},
	author = {Gutierrez, Laurent and Mauriat, Mlanie and Gunin, Stphanie and Pelloux, Jrme and Lefebvre, Jean-Franois and Louvet, Romain and Rusterucci, Christine and Moritz, Thomas and Guerineau, Franois and Bellini, Catherine and Van Wuytswinkel, Olivier},
	month = aug,
	year = {2008},
	pages = {609--618},
}

Visualization of GC/TOF-MS-Based Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class Models. Wiklund, S., Johansson, E., Sjöström, L., Mellerowicz, E. J., Edlund, U., Shockcor, J. P., Gottfries, J., Moritz, T., & Trygg, J. Analytical Chemistry, 80(1): 115–122. January 2008.

Visualization of GC/TOF-MS-Based Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class Models [link]

Paper doi link bibtex

@article{wiklund_visualization_2008,
	title = {Visualization of {GC}/{TOF}-{MS}-{Based} {Metabolomics} {Data} for {Identification} of {Biochemically} {Interesting} {Compounds} {Using} {OPLS} {Class} {Models}},
	volume = {80},
	issn = {0003-2700, 1520-6882},
	url = {https://pubs.acs.org/doi/10.1021/ac0713510},
	doi = {10/bjbc4d},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Analytical Chemistry},
	author = {Wiklund, Susanne and Johansson, Erik and Sjöström, Lina and Mellerowicz, Ewa J. and Edlund, Ulf and Shockcor, John P. and Gottfries, Johan and Moritz, Thomas and Trygg, Johan},
	month = jan,
	year = {2008},
	pages = {115--122},
}

2007 (10)

Application of a metabolomic method combining one-dimensional and two-dimensional gas chromatography-time-of-flight/mass spectrometry to metabolic phenotyping of natural variants in rice. Kusano, M., Fukushima, A., Kobayashi, M., Hayashi, N., Jonsson, P., Moritz, T., Ebana, K., & Saito, K. Journal of Chromatography B, 855(1): 71–79. August 2007.

Paper doi link bibtex

@article{kusano_application_2007,
	title = {Application of a metabolomic method combining one-dimensional and two-dimensional gas chromatography-time-of-flight/mass spectrometry to metabolic phenotyping of natural variants in rice},
	volume = {855},
	issn = {15700232},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1570023207003479},
	doi = {10/ds6j34},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Journal of Chromatography B},
	author = {Kusano, Miyako and Fukushima, Atsushi and Kobayashi, Makoto and Hayashi, Naomi and Jonsson, Pär and Moritz, Thomas and Ebana, Kaworu and Saito, Kazuki},
	month = aug,
	year = {2007},
	pages = {71--79},
}

Cross-talk between gibberellin and auxin in development of Populus wood: gibberellin stimulates polar auxin transport and has a common transcriptome with auxin: Cross-talk between GA and auxin in wood development. Björklund, S., Antti, H., Uddestrand, I., Moritz, T., & Sundberg, B. The Plant Journal, 52(3): 499–511. September 2007.

Paper doi link bibtex

@article{bjorklund_cross-talk_2007,
	title = {Cross-talk between gibberellin and auxin in development of {Populus} wood: gibberellin stimulates polar auxin transport and has a common transcriptome with auxin: {Cross}-talk between {GA} and auxin in wood development},
	volume = {52},
	issn = {09607412},
	shorttitle = {Cross-talk between gibberellin and auxin in development of {Populus} wood},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2007.03250.x},
	doi = {10/chbxht},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Björklund, Simon and Antti, Henrik and Uddestrand, Ida and Moritz, Thomas and Sundberg, Björn},
	month = sep,
	year = {2007},
	pages = {499--511},
}

Data integration in plant biology: the O2PLS method for combined modeling of transcript and metabolite data. Bylesjö, M., Eriksson, D., Kusano, M., Moritz, T., & Trygg, J. The Plant Journal, 52(6): 1181–1191. December 2007.

Data integration in plant biology: the O2PLS method for combined modeling of transcript and metabolite data [link]

Paper doi link bibtex

@article{bylesjo_data_2007,
	title = {Data integration in plant biology: the {O2PLS} method for combined modeling of transcript and metabolite data},
	volume = {52},
	issn = {09607412, 1365313X},
	shorttitle = {Data integration in plant biology},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2007.03293.x},
	doi = {10/dq2z2k},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Bylesjö, Max and Eriksson, Daniel and Kusano, Miyako and Moritz, Thomas and Trygg, Johan},
	month = dec,
	year = {2007},
	pages = {1181--1191},
}

Environmental and hormonal regulation of the activity-dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks: Molecular analysis of cambial activity-dormancy cycle. Druart, N., Johansson, A., Baba, K., Schrader, J., Sjödin, A., Bhalerao, R. R., Resman, L., Trygg, J., Moritz, T., & Bhalerao, R. P. The Plant Journal, 50(4): 557–573. April 2007.

Paper doi link bibtex

@article{druart_environmental_2007,
	title = {Environmental and hormonal regulation of the activity-dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks: {Molecular} analysis of cambial activity-dormancy cycle},
	volume = {50},
	issn = {09607412, 1365313X},
	shorttitle = {Environmental and hormonal regulation of the activity-dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2007.03077.x},
	doi = {10/cgt589},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Druart, Nathalie and Johansson, Annika and Baba, Kyoko and Schrader, Jarmo and Sjödin, Andreas and Bhalerao, Rupali R. and Resman, Lars and Trygg, Johan and Moritz, Thomas and Bhalerao, Rishikesh P.},
	month = apr,
	year = {2007},
	pages = {557--573},
}

Ethylene-induced Arabidopsis hypocotyl elongation is dependent on but not mediated by gibberellins. Vandenbussche, F., Vancompernolle, B., Rieu, I., Ahmad, M., Phillips, A., Moritz, T., Hedden, P., & Van Der Straeten, D. Journal of Experimental Botany, 58(15-16): 4269–4281. November 2007.

Ethylene-induced Arabidopsis hypocotyl elongation is dependent on but not mediated by gibberellins [link]

Paper doi link bibtex

@article{vandenbussche_ethylene-induced_2007,
	title = {Ethylene-induced {Arabidopsis} hypocotyl elongation is dependent on but not mediated by gibberellins},
	volume = {58},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erm288},
	doi = {10/c9kqxg},
	language = {en},
	number = {15-16},
	urldate = {2021-06-10},
	journal = {Journal of Experimental Botany},
	author = {Vandenbussche, F. and Vancompernolle, B. and Rieu, I. and Ahmad, M. and Phillips, A. and Moritz, T. and Hedden, P. and Van Der Straeten, D.},
	month = nov,
	year = {2007},
	pages = {4269--4281},
}

Orthogonal projections to latent structures as a strategy for microarray data normalization. Bylesjö, M., Eriksson, D., Sjödin, A., Jansson, S., Moritz, T., & Trygg, J. BMC Bioinformatics, 8(1): 207. December 2007.

Orthogonal projections to latent structures as a strategy for microarray data normalization [link]

Paper doi link bibtex

@article{bylesjo_orthogonal_2007,
	title = {Orthogonal projections to latent structures as a strategy for microarray data normalization},
	volume = {8},
	issn = {1471-2105},
	url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-207},
	doi = {10/dfs78z},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Bioinformatics},
	author = {Bylesjö, Max and Eriksson, Daniel and Sjödin, Andreas and Jansson, Stefan and Moritz, Thomas and Trygg, Johan},
	month = dec,
	year = {2007},
	pages = {207},
}

Plant metabolomics coming of age. Guy, C., Kopka, J., & Moritz, T. Physiologia Plantarum, 132(2): 113–116. December 2007.

Paper doi link bibtex

@article{guy_plant_2007,
	title = {Plant metabolomics coming of age},
	volume = {132},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2007.01020.x},
	doi = {10/dt585v},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Physiologia Plantarum},
	author = {Guy, Charles and Kopka, Joachim and Moritz, Thomas},
	month = dec,
	year = {2007},
	pages = {113--116},
}

Reliable Profile Detection in Comparative Metabolomics. Thysell, E., Pohjanen, E., Lindberg, J., Schuppe-Koistinen, I., Moritz, T., Jonsson, P., & Antti, H. OMICS: A Journal of Integrative Biology, 11(2): 209–224. June 2007.

Paper doi link bibtex

@article{thysell_reliable_2007,
	title = {Reliable {Profile} {Detection} in {Comparative} {Metabolomics}},
	volume = {11},
	issn = {1536-2310, 1557-8100},
	url = {http://www.liebertpub.com/doi/10.1089/omi.2007.0006},
	doi = {10/cvvjjh},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {OMICS: A Journal of Integrative Biology},
	author = {Thysell, Elin and Pohjanen, Elin and Lindberg, Johan and Schuppe-Koistinen, Ina and Moritz, Thomas and Jonsson, Pär and Antti, Henrik},
	month = jun,
	year = {2007},
	pages = {209--224},
}

The plant stress hormone ethylene controls floral transition via DELLA-dependent regulation of floral meristem-identity genes. Achard, P., Baghour, M., Chapple, A., Hedden, P., Van Der Straeten, D., Genschik, P., Moritz, T., & Harberd, N. P. Proceedings of the National Academy of Sciences, 104(15): 6484–6489. April 2007.

The plant stress hormone ethylene controls floral transition via DELLA-dependent regulation of floral meristem-identity genes [link]

Paper doi link bibtex

@article{achard_plant_2007,
	title = {The plant stress hormone ethylene controls floral transition via {DELLA}-dependent regulation of floral meristem-identity genes},
	volume = {104},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0610717104},
	doi = {10/d92wbd},
	language = {en},
	number = {15},
	urldate = {2021-06-10},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Achard, P. and Baghour, M. and Chapple, A. and Hedden, P. and Van Der Straeten, D. and Genschik, P. and Moritz, T. and Harberd, N. P.},
	month = apr,
	year = {2007},
	pages = {6484--6489},
}

Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana. Kusano, M., Fukushima, A., Arita, M., Jonsson, P., Moritz, T., Kobayashi, M., Hayashi, N., Tohge, T., & Saito, K. BMC Systems Biology, 1(1): 53. 2007.

Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana [link]

Paper doi link bibtex

@article{kusano_unbiased_2007,
	title = {Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in {Arabidopsis} thaliana},
	volume = {1},
	issn = {1752-0509},
	url = {http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-1-53},
	doi = {10/djdc4c},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Systems Biology},
	author = {Kusano, Miyako and Fukushima, Atsushi and Arita, Masanori and Jonsson, Pär and Moritz, Thomas and Kobayashi, Makoto and Hayashi, Naomi and Tohge, Takayuki and Saito, Kazuki},
	year = {2007},
	pages = {53},
}

2006 (10)

Arabidopsis REGULATOR OF AXILLARY MERISTEMS1 controls a leaf axil stem cell niche and modulates vegetative development. Keller, T., Abbott, J., Moritz, T., & Doerner, P. Plant Cell, 18(3): 598–611. March 2006. Place: Rockville Publisher: Amer Soc Plant Biologists WOS:000236004900009
doi link bibtex abstract

@article{keller_arabidopsis_2006,
	title = {Arabidopsis {REGULATOR} {OF} {AXILLARY} {MERISTEMS1} controls a leaf axil stem cell niche and modulates vegetative development},
	volume = {18},
	issn = {1040-4651},
	doi = {10.1105/tpc.105.038588},
	abstract = {Shoot branching is a major determinant of variation in plant stature. Branches, which form secondary growth axes, originate from stem cells activated in leaf axils. The initial steps by which axillary meristems (AMs) are specified and their stem cells organized are still poorly understood. We identified gain- and loss-of-function alleles at the Arabidopsis thaliana REGULATOR OF AXILLARY MERISTEMS1 (RAX1) locus. RAX1 is encoded by the Myb-like transcription factor MYB37 and is an Arabidopsis homolog of the tomato ( Solanum lycopersicum) Blind gene. RAX1 is transiently expressed in a small central domain within the boundary zone separating shoot apical meristem and leaf primordia early in leaf primordium development. RAX1 genetically interacts with CUP-SHAPED COTYLEDON (CUC) genes and is required for the expression of CUC2 in the RAX1 expression domain, suggesting that RAX1 acts through CUC2. We propose that RAX1 functions to positionally specify a stem cell niche for AM formation. RAX1 also affects the timing of developmental phase transitions by negatively regulating gibberellic acid levels in the shoot apex. RAX1 thus defines a novel activity that links the specification of AM formation with the modulation of the rate of progression through developmental phases.},
	language = {English},
	number = {3},
	journal = {Plant Cell},
	author = {Keller, T. and Abbott, J. and Moritz, T. and Doerner, P.},
	month = mar,
	year = {2006},
	note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000236004900009},
	keywords = {arabidopsis-thaliana, cup-shaped-cotyledon, expression, gene   family, gibberellin, growth, initiation, organogenesis, shoot apical meristem, t-dna},
	pages = {598--611},
}

Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis. Andersson-Gunnerås, S., Mellerowicz, E. J., Love, J., Segerman, B., Ohmiya, Y., Coutinho, P. M., Nilsson, P., Henrissat, B., Moritz, T., & Sundberg, B. The Plant Journal, 45(2): 144–165. 2006. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2005.02584.x

Paper doi link bibtex abstract

@article{andersson-gunneras_biosynthesis_2006,
	title = {Biosynthesis of cellulose-enriched tension wood in {Populus}: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis},
	volume = {45},
	issn = {1365-313X},
	shorttitle = {Biosynthesis of cellulose-enriched tension wood in {Populus}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2005.02584.x},
	doi = {10/fkwhm3},
	abstract = {Stems and branches of angiosperm trees form tension wood (TW) when exposed to a gravitational stimulus. One of the main characteristics of TW, which distinguishes it from normal wood, is the formation of fibers with a thick inner gelatinous cell wall layer mainly composed of crystalline cellulose. Hence TW is enriched in cellulose, and deficient in lignin and hemicelluloses. An expressed sequence tag library made from TW-forming tissues in Populus tremula (L.) × tremuloides (Michx.) and data from transcript profiling using microarray and metabolite analysis were obtained during TW formation in Populus tremula (L.) in two growing seasons. The data were examined with the aim of identifying the genes responsible for the change in carbon (C) flow into various cell wall components, and the mechanisms important for the formation of the gelatinous cell wall layer (G-layer). A specific effort was made to identify carbohydrate-active enzymes with a putative function in cell wall biosynthesis. An increased C flux to cellulose was suggested by a higher abundance of sucrose synthase transcripts. However, genes related to the cellulose biosynthetic machinery were not generally affected, although the expression of secondary wall-specific CesA genes was modified in both directions. Other pathways for which the data suggested increased activity included lipid and glucosamine biosynthesis and the pectin degradation machinery. In addition, transcripts encoding fasciclin-like arabinogalactan proteins were particularly increased and found to lack true Arabidopsis orthologs. Major pathways for which the transcriptome and metabolome analysis suggested decreased activity were the pathway for C flux through guanosine 5′-diphosphate (GDP) sugars to mannans, the pentose phosphate pathway, lignin biosynthesis, and biosynthesis of cell wall matrix carbohydrates. Several differentially expressed auxin- and ethylene-related genes and transcription factors were also identified.},
	language = {en},
	number = {2},
	urldate = {2021-06-11},
	journal = {The Plant Journal},
	author = {Andersson-Gunnerås, Sara and Mellerowicz, Ewa J. and Love, Jonathan and Segerman, Bo and Ohmiya, Yasunori and Coutinho, Pedro M. and Nilsson, Peter and Henrissat, Bernard and Moritz, Thomas and Sundberg, Björn},
	year = {2006},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2005.02584.x},
	keywords = {cell walls, cellulose, development, hemicellulose, lignin, poplar},
	pages = {144--165},
}

GA4 Is the Active Gibberellin in the Regulation of LEAFY Transcription and Arabidopsis Floral Initiation. Eriksson, S., Böhlenius, H., Moritz, T., & Nilsson, O. The Plant Cell, 18(9): 2172–2181. September 2006.

GA4 Is the Active Gibberellin in the Regulation of LEAFY Transcription and Arabidopsis Floral Initiation [link]

Paper doi link bibtex abstract

@article{eriksson_ga4_2006,
	title = {{GA4} {Is} the {Active} {Gibberellin} in the {Regulation} of {LEAFY} {Transcription} and {Arabidopsis} {Floral} {Initiation}},
	volume = {18},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.106.042317},
	doi = {10.1105/tpc.106.042317},
	abstract = {Flower initiation in Arabidopsis thaliana under noninductive short-day conditions is dependent on the biosynthesis of the plant hormone gibberellin (GA). This dependency can be explained, at least partly, by GA regulation of the flower meristem identity gene LEAFY (LFY) and the flowering time gene SUPPRESSOR OF CONSTANS1. Although it is well established that GA4 is the active GA in the regulation of Arabidopsis shoot elongation, the identity of the GA responsible for the regulation of Arabidopsis flowering has not been established. Through a combination of GA quantifications and sensitivity assays, we show that GA4 is the active GA in the regulation of LFY transcription and Arabidopsis flowering time under short-day conditions. The levels of GA4 and sucrose increase dramatically in the shoot apex shortly before floral initiation, and the regulation of genes involved in GA metabolism suggests that this increase is possibly due to transport of GAs and sucrose from outside sources to the shoot apex. Our results demonstrate that in the dicot Arabidopsis, in contrast with the monocot Lolium temulentum, GA4 is the active GA in the regulation of both shoot elongation and flower initiation.},
	number = {9},
	urldate = {2024-10-07},
	journal = {The Plant Cell},
	author = {Eriksson, Sven and Böhlenius, Henrik and Moritz, Thomas and Nilsson, Ove},
	month = sep,
	year = {2006},
	pages = {2172--2181},
}

Integration of plant responses to environmentally activated phytohormonal signals. Achard, P., Cheng, H., De Grauwe, L., Decat, J., Schoutteten, H., Moritz, T., Van Der Straeten, D., Peng, J. R., & Harberd, N. P. Science, 311(5757): 91–94. January 2006. Place: Washington Publisher: Amer Assoc Advancement Science WOS:000234546300040
doi link bibtex abstract

@article{achard_integration_2006,
	title = {Integration of plant responses to environmentally activated phytohormonal signals},
	volume = {311},
	issn = {0036-8075},
	doi = {10/fd7637},
	abstract = {Plants live in fixed locations and survive adversity by integrating growth responses to diverse environmental signals. Here, we show that the nuclear-localized growth-repressing DELLA proteins of Arabidopsis integrate responses to independent hormonal and environmental signals of adverse conditions. The growth restraint conferred by DELLA proteins is beneficial and promotes survival. We propose that DELLAs permit flexible and appropriate modulation of plant growth in response to changes in natural environments.},
	language = {English},
	number = {5757},
	journal = {Science},
	author = {Achard, P. and Cheng, H. and De Grauwe, L. and Decat, J. and Schoutteten, H. and Moritz, T. and Van Der Straeten, D. and Peng, J. R. and Harberd, N. P.},
	month = jan,
	year = {2006},
	note = {Place: Washington
Publisher: Amer Assoc Advancement Science
WOS:000234546300040},
	keywords = {arabidopsis-thaliana, floral   development, gene-expression, gibberellin response, growth, modulation, overexpression, protein, transcription factor, transduction},
	pages = {91--94},
}

Long-term submergence-induced elongation in Rumex palustris requires abscisic acid-dependent biosynthesis of gibberellin. Benschop, J. J., Bou, J., Peeters, A. J. M., Wagemaker, N., Guhl, K., Ward, D., Hedden, P., Moritz, T., & Voesenek, L. A. C. J. Plant Physiology, 141(4): 1644–1652. August 2006. Place: Rockville Publisher: Amer Soc Plant Biologists WOS:000239636800044
doi link bibtex abstract

@article{benschop_long-term_2006,
	title = {Long-term submergence-induced elongation in {Rumex} palustris requires abscisic acid-dependent biosynthesis of gibberellin},
	volume = {141},
	issn = {0032-0889},
	doi = {10/fpnvsb},
	abstract = {Rumex palustris (polygonceae) responds to complete submergence with enhanced elongation of its youngest petioles. This process requires the presence of gibberellin (GA) and is associated with an increase in the concentration of GA 1 in elongating petioles. We have examined how GA biosynthesis was regulated in submerged plants. Therefore, cDNAs encoding GA-biosynthetic enzymes GA20-oxidase and GA3-oxidase, and the GA-deactivating enzyme GA2-oxidase were cloned from R. palustris and the kinetics of transcription of the corresponding genes was determined during a 24 h submergence period. The submergence-induced elongation response could be separated into several phases: (1) during the first phase of 4 h, petiole elongation was insensitive to GA; (2) from 4 to 6 h onward growth was limited by GA; and (3) from 15 h onward underwater elongation was dependent, but not limited by GA. Submergence induced an increase of GA 1 concentration, as well as enhanced transcript levels of RpGA3ox1. Exogenous abscisic acid repressed the transcript levels of RpGA20ox1 and RpGA3ox1 and thus inhibited the submergence-induced increase in GA(1). Abscisic acid had no effect on the tissue responsiveness to GA.},
	language = {English},
	number = {4},
	journal = {Plant Physiology},
	author = {Benschop, Joris J. and Bou, Jordi and Peeters, Anton J. M. and Wagemaker, Niels and Guhl, Kerstin and Ward, Dennis and Hedden, Peter and Moritz, Thomas and Voesenek, Laurentius A. C. J.},
	month = aug,
	year = {2006},
	note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000239636800044},
	keywords = {20-oxidase genes, arabidopsis, ethylene, expression, pea, petiole elongation, plant, rice, shoot elongation, stem elongation},
	pages = {1644--1652},
}

MASQOT-GUI: spot quality assessment for the two-channel microarray platform. Bylesjö, M., Sjödin, A., Eriksson, D., Antti, H., Moritz, T., Jansson, S., & Trygg, J. Bioinformatics, 22(20): 2554–2555. October 2006.

MASQOT-GUI: spot quality assessment for the two-channel microarray platform [link]

Paper doi link bibtex abstract

@article{bylesjo_masqot-gui_2006,
	title = {{MASQOT}-{GUI}: spot quality assessment for the two-channel microarray platform},
	volume = {22},
	issn = {1367-4803},
	shorttitle = {{MASQOT}-{GUI}},
	url = {https://doi.org/10.1093/bioinformatics/btl434},
	doi = {10.1093/bioinformatics/btl434},
	abstract = {Summary: MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts a set of independent applications, with interactions between the tools as well as import and export support for external software. The implementation of automated multivariate quality control assessment, which is a unique feature of MASQOT-GUI, is based on the previously documented and evaluated MASQOT methodology. Further abilities of the application are outlined and illustrated.Availability: MASQOT-GUI is Java-based and licensed under the GNU LGPL. Source code and installation files are available for download at Contact: This email address is being protected from spambots. You need JavaScript enabled to view it. information: Supplementary data are available at Bioinformatics online},
	number = {20},
	urldate = {2021-06-11},
	journal = {Bioinformatics},
	author = {Bylesjö, Max and Sjödin, Andreas and Eriksson, Daniel and Antti, Henrik and Moritz, Thomas and Jansson, Stefan and Trygg, Johan},
	month = oct,
	year = {2006},
	pages = {2554--2555},
}

Predictive metabolite profiling applying hierarchical multivariate curve resolution to GC-MS datas - A potential tool for multi-parametric diagnosis. Jonsson, P., Johansson, E. S., Wuolikainen, A., Lindberg, J., Schuppe-Koistinen, I., Kusano, M., Sjostrom, M., Trygg, J., Moritz, T., & Antti, H. Journal of Proteome Research, 5(6): 1407–1414. June 2006. Place: Washington Publisher: Amer Chemical Soc WOS:000237973400012
doi link bibtex abstract

@article{jonsson_predictive_2006,
	title = {Predictive metabolite profiling applying hierarchical multivariate curve resolution to {GC}-{MS} datas - {A} potential tool for multi-parametric diagnosis},
	volume = {5},
	issn = {1535-3893},
	doi = {10.1021/pr0600071},
	abstract = {A method for predictive metabolite profiling based on resolution of GC-MS data followed by multivariate data analysis is presented and applied to three different biofluid data sets (rat urine, aspen leaf extracts, and human blood plasma). Hierarchical multivariate curve resolution (H-MCR) was used to simultaneously resolve the GC-MS data into pure profiles, describing the relative metabolite concentrations between samples, for multivariate analysis. Here, we present an extension of the H-MCR method allowing treatment of independent samples according to processing parameters estimated from a set of training samples. Predictions or inclusion of the new samples, based on their metabolite profiles, into an existing model could then be carried out, which is a requirement for a working application within, e. g., clinical diagnosis. Apart from allowing treatment and prediction of independent samples the proposed method also reduces the time for the curve resolution process since only a subset of representative samples have to be processed while the remaining samples can be treated according to the obtained processing parameters. The time required for resolving the 30 training samples in the rat urine example was approximately 13 h, while the treatment of the 30 test samples according to the training parameters required only approximately 30 s per sample ( similar to 15 min in total). In addition, the presented results show that the suggested approach works for describing metabolic changes in different biofluids, indicating that this is a general approach for high-throughput predictive metabolite profiling, which could have important applications in areas such as plant functional genomics, drug toxicity, treatment efficacy and early disease diagnosis.},
	language = {English},
	number = {6},
	journal = {Journal of Proteome Research},
	author = {Jonsson, Par and Johansson, Elin Sjovik and Wuolikainen, Anna and Lindberg, Johan and Schuppe-Koistinen, Ina and Kusano, Miyako and Sjostrom, Michael and Trygg, Johan and Moritz, Thomas and Antti, Henrik},
	month = jun,
	year = {2006},
	note = {Place: Washington
Publisher: Amer Chemical Soc
WOS:000237973400012},
	keywords = {chemometrics, chromatography, clinical diagnosis, components, curve resolution, design, gc-ms, genomics, h-mcr, high-throughput, identifying differences, metabolic profiling, metabolomics, metabonomics, o-pls, projections, samples, strategy},
	pages = {1407--1414},
}

Regulation of flowering in the long-day grass Lolium temulentum by Gibberellins and the FLOWERING LOCUS T gene. King, R. W., Moritz, T., Evans, L. T., Martin, J., Andersen, C. H., Blundell, C., Kardailsky, I., & Chandler, P. M. Plant Physiology, 141(2): 498–507. June 2006. Place: Rockville Publisher: Amer Soc Plant Biologists WOS:000238168800025
doi link bibtex abstract

@article{king_regulation_2006,
	title = {Regulation of flowering in the long-day grass {Lolium} temulentum by {Gibberellins} and the {FLOWERING} {LOCUS} {T} gene},
	volume = {141},
	issn = {0032-0889},
	doi = {10/bc3fw3},
	abstract = {Seasonal control of flowering often involves leaf sensing of daylength coupled to time measurement and generation and transport of florigenic signals to the shoot apex. We show that transmitted signals in the grass Lolium temulentum may include gibberellins ( GAs) and the FLOWERING LOCUS T ( FT) gene. Within 2 h of starting a florally inductive long day ( LD), expression of a 20-oxidase GA biosynthetic gene increases in the leaf; its product, GA 20, then increases 5.7-fold versus short day; its substrate, GA 19, decreases equivalently; and a bioactive product, GA 5, increases 4-fold. A link between flowering, LD, GAs, and GA biosynthesis is shown in three ways: ( 1) applied GA 19 became florigenic on exposure to LD; ( 2) expression of LtGA20ox1, an important GA biosynthetic gene, increased in a florally effective LD involving incandescent lamps, but not with noninductive fluorescent lamps; and ( 3) paclobutrazol, an inhibitor of an early step of GA biosynthesis, blocked flowering, but only if applied before the LD. Expression studies of a 2-oxidase catabolic gene showed no changes favoring a GA increase. Thus, the early LD increase in leaf GA 5 biosynthesis, coupled with subsequent doubling in GA 5 content at the shoot apex, provides a substantial trail of evidence for GA 5 as a LD florigen. LD signaling may also involve transport of FT mRNA or protein because expression of LtFT and LtCONSTANS increased rapidly, substantially ({\textgreater} 80-fold for FT), and independently of GA. However, because a LD from fluorescent lamps induced LtFT expression but not flowering, the nature of the light response of FT requires clarification.},
	language = {English},
	number = {2},
	journal = {Plant Physiology},
	author = {King, Rod W. and Moritz, Thomas and Evans, Lloyd T. and Martin, Jerome and Andersen, Claus H. and Blundell, Cheryl and Kardailsky, Igor and Chandler, Peter M.},
	month = jun,
	year = {2006},
	note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000238168800025},
	keywords = {20-oxidase, biosynthesis, expression, in-vitro, inflorescence initiation, metabolism, molecular-cloning, photoperiod, shoot apices, stem   elongation},
	pages = {498--507},
}

Statistical multivariate metabolite profiling for aiding biomarker pattern detection and mechanistic interpretations in GC/MS based metabolomics. Pohjanen, E., Thysell, E., Lindberg, J., Schuppe-Koistinen, I., Moritz, T., Jonsson, P., & Antti, H. Metabolomics, 2(4): 257–268. December 2006.

Paper doi link bibtex abstract

@article{pohjanen_statistical_2006,
	title = {Statistical multivariate metabolite profiling for aiding biomarker pattern detection and mechanistic interpretations in {GC}/{MS} based metabolomics},
	volume = {2},
	issn = {1573-3890},
	url = {https://doi.org/10.1007/s11306-006-0032-4},
	doi = {10.1007/s11306-006-0032-4},
	abstract = {A strategy for robust and reliable mechanistic statistical modelling of metabolic responses in relation to drug induced toxicity is presented. The suggested approach addresses two cases commonly occurring within metabonomic toxicology studies, namely; 1) A pre-defined hypothesis about the biological mechanism exists and 2) No such hypothesis exists. GC/MS data from a liver toxicity study consisting of rat urine from control rats and rats exposed to a proprietary AstraZeneca compound were resolved by means of hierarchical multivariate curve resolution (H-MCR) generating 287 resolved chromatographic profiles with corresponding mass spectra. Filtering according to significance in relation to drug exposure rendered in 210 compound profiles, which were subjected to further statistical analysis following correction to account for the control variation over time. These dose related metabolite traces were then used as new observations in the subsequent analyses. For case 1, a multivariate approach, named Target Batch Analysis, based on OPLS regression was applied to correlate all metabolite traces to one or more key metabolites involved in the pre-defined hypothesis. For case 2, principal component analysis (PCA) was combined with hierarchical cluster analysis (HCA) to create a robust and interpretable framework for unbiased mechanistic screening. Both the Target Batch Analysis and the unbiased approach were cross-verified using the other method to ensure that the results did match in terms of detected metabolite traces. This was also the case, implying that this is a working concept for clustering of metabolites in relation to their toxicity induced dynamic profiles regardless if there is a pre-existing hypothesis or not. For each of the methods the detected metabolites were subjected to identification by means of data base comparison as well as verification in the raw data. The proposed strategy should be seen as a general approach for facilitating mechanistic modelling and interpretations in metabolomic studies.},
	language = {en},
	number = {4},
	urldate = {2021-06-11},
	journal = {Metabolomics},
	author = {Pohjanen, Elin and Thysell, Elin and Lindberg, Johan and Schuppe-Koistinen, Ina and Moritz, Thomas and Jonsson, Pär and Antti, Henrik},
	month = dec,
	year = {2006},
	pages = {257--268},
}

A strategy for robust and reliable mechanistic statistical modelling of metabolic responses in relation to drug induced toxicity is presented. The suggested approach addresses two cases commonly occurring within metabonomic toxicology studies, namely; 1) A pre-defined hypothesis about the biological mechanism exists and 2) No such hypothesis exists. GC/MS data from a liver toxicity study consisting of rat urine from control rats and rats exposed to a proprietary AstraZeneca compound were resolved by means of hierarchical multivariate curve resolution (H-MCR) generating 287 resolved chromatographic profiles with corresponding mass spectra. Filtering according to significance in relation to drug exposure rendered in 210 compound profiles, which were subjected to further statistical analysis following correction to account for the control variation over time. These dose related metabolite traces were then used as new observations in the subsequent analyses. For case 1, a multivariate approach, named Target Batch Analysis, based on OPLS regression was applied to correlate all metabolite traces to one or more key metabolites involved in the pre-defined hypothesis. For case 2, principal component analysis (PCA) was combined with hierarchical cluster analysis (HCA) to create a robust and interpretable framework for unbiased mechanistic screening. Both the Target Batch Analysis and the unbiased approach were cross-verified using the other method to ensure that the results did match in terms of detected metabolite traces. This was also the case, implying that this is a working concept for clustering of metabolites in relation to their toxicity induced dynamic profiles regardless if there is a pre-existing hypothesis or not. For each of the methods the detected metabolites were subjected to identification by means of data base comparison as well as verification in the raw data. The proposed strategy should be seen as a general approach for facilitating mechanistic modelling and interpretations in metabolomic studies.

Transitions in the functioning of the shoot apical meristem in birch (Betula pendula) involve ethylene. Ruonala, R., Rinne, P. L. H., Baghour, M., Moritz, T., Tuominen, H., & Kangasjarvi, J. Plant Journal, 46(4): 628–640. May 2006. Place: Hoboken Publisher: Wiley WOS:000237098000008
doi link bibtex abstract

@article{ruonala_transitions_2006,
	title = {Transitions in the functioning of the shoot apical meristem in birch ({Betula} pendula) involve ethylene},
	volume = {46},
	issn = {0960-7412},
	doi = {10/dmkh9w},
	abstract = {In many trees, a short photoperiod (SD) triggers substantial physiological adjustments necessary for over-wintering. We have used transgenic ethylene-insensitive birches (Betula pendula), which express the Arabidopsis ethylene receptor gene ETR1 carrying the dominant mutation etr1-1, to investigate the role of ethylene in SD-induced responses in the shoot apical meristem (SAM). Under SD, the ethylene-insensitive trees ceased elongation growth comparably to the wild-type. In contrast, the formation of terminal buds, which in trees is typically induced by SD, was abolished. However, although delayed, endo-dormancy did eventually develop in the ethylene-insensitive trees. This, together with the rapid resumption of growth in the ethylene-insensitive trees after transfer from non-permissive to permissive conditions suggests that ethylene facilitates the SD-induced terminal bud formation, as well as growth arrest. In addition, apical buds of the ethylene-insensitive birch did not accumulate abscisic acid (ABA) under SD, suggesting interaction between ethylene and ABA signalling in the bud. Alterations in SAM functioning were further exemplified by reduced apical dominance and early flowering in ethylene-insensitive birches. Gene expression analysis of shoot apices revealed that the ethylene-insensitive birch lacked the marked increase in expression of a beta-xylosidase gene typical to the SD-exposed wild-type. The ethylene-dependent beta-xylosidase gene expression is hypothesized to relate to modification of cell walls in terminal buds during SD-induced growth cessation. Our results suggest that ethylene is involved in terminal bud formation and in the timely suppression of SAM activity, not only in the shoot apex, but also in axillary and reproductive meristems.},
	language = {English},
	number = {4},
	journal = {Plant Journal},
	author = {Ruonala, R. and Rinne, P. L. H. and Baghour, M. and Moritz, T. and Tuominen, H. and Kangasjarvi, J.},
	month = may,
	year = {2006},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000237098000008},
	keywords = {abscisic-acid, apical dominance, arabidopsis-thaliana, beta-xylosidase gene, birch, bud dormancy, cell-wall metabolism, dormancy, ethylene, expression, flowering, freezing   tolerance, induction, lateral bud growth, response pathway, xylosidase},
	pages = {628--640},
}

2005 (5)

Extraction and GC/MS Analysis of the Human Blood Plasma Metabolome. A, J., Trygg, J., Gullberg, J., Johansson, A. I., Jonsson, P., Antti, H., Marklund, S. L., & Moritz, T. Analytical Chemistry, 77(24): 8086–8094. December 2005. Publisher: American Chemical Society

Extraction and GC/MS Analysis of the Human Blood Plasma Metabolome [link]

Paper doi link bibtex abstract

@article{a_extraction_2005,
	title = {Extraction and {GC}/{MS} {Analysis} of the {Human} {Blood} {Plasma} {Metabolome}},
	volume = {77},
	issn = {0003-2700},
	url = {https://doi.org/10.1021/ac051211v},
	doi = {10.1021/ac051211v},
	abstract = {Analysis of the entire set of low molecular weight compounds (LMC), the metabolome, could provide deeper insights into mechanisms of disease and novel markers for diagnosis. In the investigation, we developed an extraction and derivatization protocol, using experimental design theory (design of experiment), for analyzing the human blood plasma metabolome by GC/MS. The protocol was optimized by evaluating the data for more than 500 resolved peaks using multivariate statistical tools including principal component analysis and partial least-squares projections to latent structures (PLS). The performance of five organic solvents (methanol, ethanol, acetonitrile, acetone, chloroform), singly and in combination, was investigated to optimize the LMC extraction. PLS analysis demonstrated that methanol extraction was particularly efficient and highly reproducible. The extraction and derivatization conditions were also optimized. Quantitative data for 32 endogenous compounds showed good precision and linearity. In addition, the determined amounts of eight selected compounds agreed well with analyses by independent methods in accredited laboratories, and most of the compounds could be detected at absolute levels of ∼0.1 pmol injected, corresponding to plasma concentrations between 0.1 and 1 μM. The results suggest that the method could be usefully integrated into metabolomic studies for various purposes, e.g., for identifying biological markers related to diseases.},
	number = {24},
	urldate = {2021-06-11},
	journal = {Analytical Chemistry},
	author = {A, Jiye and Trygg, Johan and Gullberg, Jonas and Johansson, Annika I. and Jonsson, Pär and Antti, Henrik and Marklund, Stefan L. and Moritz, Thomas},
	month = dec,
	year = {2005},
	note = {Publisher: American Chemical Society},
	pages = {8086--8094},
}

Extraction, interpretation and validation of information for comparing samples in metabolic LC/MS data sets. Jonsson, P., Bruce, S. J., Moritz, T., Trygg, J., Sjöström, M., Plumb, R., Granger, J., Maibaum, E., Nicholson, J. K., Holmes, E., & Antti, H. Analyst, 130(5): 701–707. April 2005. Publisher: The Royal Society of Chemistry

Extraction, interpretation and validation of information for comparing samples in metabolic LC/MS data sets [link]

Paper doi link bibtex abstract

@article{jonsson_extraction_2005,
	title = {Extraction, interpretation and validation of information for comparing samples in metabolic {LC}/{MS} data sets},
	volume = {130},
	issn = {1364-5528},
	url = {https://pubs.rsc.org/en/content/articlelanding/2005/an/b501890k},
	doi = {10.1039/B501890K},
	abstract = {LC/MS is an analytical technique that, due to its high sensitivity, has become increasingly popular for the generation of metabolic signatures in biological samples and for the building of metabolic data bases. However, to be able to create robust and interpretable (transparent) multivariate models for the comparison of many samples, the data must fulfil certain specific criteria: (i) that each sample is characterized by the same number of variables, (ii) that each of these variables is represented across all observations, and (iii) that a variable in one sample has the same biological meaning or represents the same metabolite in all other samples. In addition, the obtained models must have the ability to make predictions of, e.g. related and independent samples characterized accordingly to the model samples. This method involves the construction of a representative data set, including automatic peak detection, alignment, setting of retention time windows, summing in the chromatographic dimension and data compression by means of alternating regression, where the relevant metabolic variation is retained for further modelling using multivariate analysis. This approach has the advantage of allowing the comparison of large numbers of samples based on their LC/MS metabolic profiles, but also of creating a means for the interpretation of the investigated biological system. This includes finding relevant systematic patterns among samples, identifying influential variables, verifying the findings in the raw data, and finally using the models for predictions. The presented strategy was here applied to a population study using urine samples from two cohorts, Shanxi (People’s Republic of China) and Honolulu (USA). The results showed that the evaluation of the extracted information data using partial least square discriminant analysis (PLS-DA) provided a robust, predictive and transparent model for the metabolic differences between the two populations. The presented findings suggest that this is a general approach for data handling, analysis, and evaluation of large metabolic LC/MS data sets.},
	language = {en},
	number = {5},
	urldate = {2021-06-11},
	journal = {Analyst},
	author = {Jonsson, Pär and Bruce, Stephen J. and Moritz, Thomas and Trygg, Johan and Sjöström, Michael and Plumb, Robert and Granger, Jennifer and Maibaum, Elaine and Nicholson, Jeremy K. and Holmes, Elaine and Antti, Henrik},
	month = apr,
	year = {2005},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {701--707},
}

LC/MS is an analytical technique that, due to its high sensitivity, has become increasingly popular for the generation of metabolic signatures in biological samples and for the building of metabolic data bases. However, to be able to create robust and interpretable (transparent) multivariate models for the comparison of many samples, the data must fulfil certain specific criteria: (i) that each sample is characterized by the same number of variables, (ii) that each of these variables is represented across all observations, and (iii) that a variable in one sample has the same biological meaning or represents the same metabolite in all other samples. In addition, the obtained models must have the ability to make predictions of, e.g. related and independent samples characterized accordingly to the model samples. This method involves the construction of a representative data set, including automatic peak detection, alignment, setting of retention time windows, summing in the chromatographic dimension and data compression by means of alternating regression, where the relevant metabolic variation is retained for further modelling using multivariate analysis. This approach has the advantage of allowing the comparison of large numbers of samples based on their LC/MS metabolic profiles, but also of creating a means for the interpretation of the investigated biological system. This includes finding relevant systematic patterns among samples, identifying influential variables, verifying the findings in the raw data, and finally using the models for predictions. The presented strategy was here applied to a population study using urine samples from two cohorts, Shanxi (People’s Republic of China) and Honolulu (USA). The results showed that the evaluation of the extracted information data using partial least square discriminant analysis (PLS-DA) provided a robust, predictive and transparent model for the metabolic differences between the two populations. The presented findings suggest that this is a general approach for data handling, analysis, and evaluation of large metabolic LC/MS data sets.

GC–MS libraries for the rapid identification of metabolites in complex biological samples. Schauer, N., Steinhauser, D., Strelkov, S., Schomburg, D., Allison, G., Moritz, T., Lundgren, K., Roessner-Tunali, U., Forbes, M. G., Willmitzer, L., Fernie, A. R., & Kopka, J. FEBS Letters, 579(6): 1332–1337. 2005.

GC–MS libraries for the rapid identification of metabolites in complex biological samples [link]

Paper doi link bibtex abstract

@article{schauer_gcms_2005,
	title = {{GC}–{MS} libraries for the rapid identification of metabolites in complex biological samples},
	volume = {579},
	issn = {1873-3468},
	url = {https://febs.onlinelibrary.wiley.com/doi/abs/10.1016/j.febslet.2005.01.029},
	doi = {10/fg7786},
	abstract = {Gas chromatography–mass spectrometry based metabolite profiling of biological samples is rapidly becoming one of the cornerstones of functional genomics and systems biology. Thus, the technology needs to be available to many laboratories and open exchange of information is required such as those achieved for transcript and protein data. The key-step in metabolite profiling is the unambiguous identification of metabolites in highly complex metabolite preparations with composite structure. Collections of mass spectra, which comprise frequently observed identified and non-identified metabolites, represent the most effective means to pool the identification efforts currently performed in many laboratories around the world. Here, we describe a platform for mass spectral and retention time index libraries that will enable this process (MSRI; www.csbdb.mpimp-golm.mpg.de/gmd.html). This resource should ameliorate many of the problems that each laboratory will face both for the initial establishment of metabolome analysis and for its maintenance at a constant sample throughput.},
	language = {en},
	number = {6},
	urldate = {2021-08-31},
	journal = {FEBS Letters},
	author = {Schauer, Nicolas and Steinhauser, Dirk and Strelkov, Sergej and Schomburg, Dietmar and Allison, Gordon and Moritz, Thomas and Lundgren, Krister and Roessner-Tunali, Ute and Forbes, Megan G. and Willmitzer, Lothar and Fernie, Alisdair R. and Kopka, Joachim},
	year = {2005},
	keywords = {GC, GC–MS, Gas chromatography–mass spectrometry, MS, MST, Mass spectral library, Metabolite profiling, Metabolomics, RI, Retention time index, TOF, gas chromatography, mass spectral metabolite tag, mass spectrometry, retention time index, time of flight},
	pages = {1332--1337},
}

High-Throughput Data Analysis for Detecting and Identifying Differences between Samples in GC/MS-Based Metabolomic Analyses. Jonsson, P., Johansson, A. I., Gullberg, J., Trygg, J., A, J., Grung, B., Marklund, S., Sjöström, M., Antti, H., & Moritz, T. Analytical Chemistry, 77(17): 5635–5642. September 2005. Publisher: American Chemical Society

High-Throughput Data Analysis for Detecting and Identifying Differences between Samples in GC/MS-Based Metabolomic Analyses [link]

Paper doi link bibtex abstract

@article{jonsson_high-throughput_2005,
	title = {High-{Throughput} {Data} {Analysis} for {Detecting} and {Identifying} {Differences} between {Samples} in {GC}/{MS}-{Based} {Metabolomic} {Analyses}},
	volume = {77},
	issn = {0003-2700},
	url = {https://doi.org/10.1021/ac050601e},
	doi = {10.1021/ac050601e},
	abstract = {In metabolomics, the objective is to identify differences in metabolite profiles between samples. A widely used tool in metabolomics investigations is gas chromatography−mass spectrometry (GC/MS). More than 400 compounds can be detected in a single analysis, if overlapping GC/MS peaks are deconvoluted. However, the deconvolution process is time-consuming and difficult to automate, and additional processing is needed in order to compare samples. Therefore, there is a need to improve and automate the data processing strategy for data generated in GC/MS-based metabolomics; if not, the processing step will be a major bottleneck for high-throughput analyses. Here we describe a new semiautomated strategy using a hierarchical multivariate curve resolution approach that processes all samples simultaneously. The presented strategy generates (after appropriate treatment, e.g., multivariate analysis) tables of all the detected metabolites that differ in relative concentrations between samples. The processing of 70 samples took similar time to that of the GC/TOFMS analyses of the samples. The strategy has been validated using two different sets of samples:  a complex mixture of standard compounds and Arabidopsis samples.},
	number = {17},
	urldate = {2021-06-11},
	journal = {Analytical Chemistry},
	author = {Jonsson, Pär and Johansson, Annika I. and Gullberg, Jonas and Trygg, Johan and A, Jiye and Grung, Bjørn and Marklund, Stefan and Sjöström, Michael and Antti, Henrik and Moritz, Thomas},
	month = sep,
	year = {2005},
	note = {Publisher: American Chemical Society},
	pages = {5635--5642},
}

Tissue-specific localization of gibberellins and expression of gibberellin-biosynthetic and signaling genes in wood-forming tissues in aspen. Israelsson, M., Sundberg, B., & Moritz, T. The Plant Journal, 44(3): 494–504. 2005. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2005.02547.x

Paper doi link bibtex abstract

@article{israelsson_tissue-specific_2005,
	title = {Tissue-specific localization of gibberellins and expression of gibberellin-biosynthetic and signaling genes in wood-forming tissues in aspen},
	volume = {44},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2005.02547.x},
	doi = {10/b9g6dq},
	abstract = {Bioactive gibberellins (GAs) are known regulators of shoot growth and development in plants. In an attempt to identify where GAs are formed, we have analyzed the expression patterns of six GA biosynthesis genes and two genes with predicted roles in GA signaling and responses in relation to measured levels of GAs. The analysis was based on tangential sections, giving tissue-specific resolution across the cambial region of aspen trees (Populus tremula). Gibberellin quantification by GC/MS-SRM showed that the bioactive GA1 and GA4 were predominantly located in the zone of expansion of xylem cells. Based on co-localization of the expression of the late GA biosynthesis gene GA 20-oxidase 1 and bioactive GAs, we suggest that de novo GA biosynthesis occurs in the expanding xylem. However, expression levels of the first committed GA biosynthesis enzyme, ent-copalyl diphosphate synthase, were high in the phloem, suggesting that a GA precursor(s) may be transported to the xylem. The expression of the GA signaling and response genes DELLA-like1 and GIP-like1 coincided well with sites of high bioactive GA levels. We therefore suggest that the main role of GA during wood formation is to regulate early stages of xylem differentiation, including cell elongation.},
	language = {en},
	number = {3},
	urldate = {2021-06-11},
	journal = {The Plant Journal},
	author = {Israelsson, Maria and Sundberg, Björn and Moritz, Thomas},
	year = {2005},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2005.02547.x},
	keywords = {DELLA, Populus, fiber, gibberellin-biosynthetic genes, gibberellins, wood formation},
	pages = {494--504},
}

2004 (8)

A Strategy for Identifying Differences in Large Series of Metabolomic Samples Analyzed by GC/MS. Jonsson, P., Gullberg, J., Nordström, A., Kusano, M., Kowalczyk, M., Sjöström, M., & Moritz, T. Analytical Chemistry, 76(6): 1738–1745. March 2004. Publisher: American Chemical Society

A Strategy for Identifying Differences in Large Series of Metabolomic Samples Analyzed by GC/MS [link]

Paper doi link bibtex abstract

@article{jonsson_strategy_2004,
	title = {A {Strategy} for {Identifying} {Differences} in {Large} {Series} of {Metabolomic} {Samples} {Analyzed} by {GC}/{MS}},
	volume = {76},
	issn = {0003-2700},
	url = {https://doi.org/10.1021/ac0352427},
	doi = {10/dm24rr},
	abstract = {In metabolomics, the purpose is to identify and quantify all the metabolites in a biological system. Combined gas chromatography and mass spectrometry (GC/MS) is one of the most commonly used techniques in metabolomics together with 1H NMR, and it has been shown that more than 300 compounds can be distinguished with GC/MS after deconvolution of overlapping peaks. To avoid having to deconvolute all analyzed samples prior to multivariate analysis of the data, we have developed a strategy for rapid comparison of nonprocessed MS data files. The method includes baseline correction, alignment, time window determinations, alternating regression, PLS-DA, and identification of retention time windows in the chromatograms that explain the differences between the samples. Use of alternating regression also gives interpretable loadings, which retain the information provided by m/z values that vary between the samples in each retention time window. The method has been applied to plant extracts derived from leaves of different developmental stages and plants subjected to small changes in day length. The data show that the new method can detect differences between the samples and that it gives results comparable to those obtained when deconvolution is applied prior to the multivariate analysis. We suggest that this method can be used for rapid comparison of large sets of GC/MS data, thereby applying time-consuming deconvolution only to parts of the chromatograms that contribute to explain the differences between the samples.},
	number = {6},
	urldate = {2021-06-30},
	journal = {Analytical Chemistry},
	author = {Jonsson, Pär and Gullberg, Jonas and Nordström, Anders and Kusano, Miyako and Kowalczyk, Mariusz and Sjöström, Michael and Moritz, Thomas},
	month = mar,
	year = {2004},
	note = {Publisher: American Chemical Society},
	pages = {1738--1745},
}

AtGA3ox2, a Key Gene Responsible for Bioactive Gibberellin Biosynthesis, Is Regulated during Embryogenesis by LEAFY COTYLEDON2 and FUSCA3 in Arabidopsis. Curaba, J., Moritz, T., Blervaque, R., Parcy, F., Raz, V., Herzog, M., & Vachon, G. Plant Physiology, 136(3): 3660–3669. November 2004.

Paper doi link bibtex abstract

@article{curaba_atga3ox2_2004,
	title = {{AtGA3ox2}, a {Key} {Gene} {Responsible} for {Bioactive} {Gibberellin} {Biosynthesis}, {Is} {Regulated} during {Embryogenesis} by {LEAFY} {COTYLEDON2} and {FUSCA3} in {Arabidopsis}},
	volume = {136},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.104.047266},
	doi = {10/d4dh37},
	abstract = {Embryonic regulators LEC2 (LEAFY COTYLEDON2) and FUS3 (FUSCA3) are involved in multiple aspects of Arabidopsis (Arabidopsis thaliana) seed development, including repression of leaf traits and premature germination and activation of seed storage protein genes. In this study, we show that gibberellin (GA) hormone biosynthesis is regulated by LEC2 and FUS3 pathways. The level of bioactive GAs is increased in immature seeds of lec2 and fus3 mutants relative to wild-type level. In addition, we show that the formation of ectopic trichome cells on lec2 and fus3 embryos is a GA-dependent process as in true leaves, suggesting that the GA pathway is misactivated in embryonic mutants. We next demonstrate that the GA-biosynthesis gene AtGA3ox2, which encodes the key enzyme AtGA3ox2 that catalyzes the conversion of inactive to bioactive GAs, is ectopically activated in embryos of the two mutants. Interestingly, both β-glucuronidase reporter gene expression and in situ hybridization indicate that FUS3 represses AtGA3ox2 expression mainly in epidermal cells of embryo axis, which is distinct from AtGA3ox2 pattern at germination. Finally, we show that the FUS3 protein physically interacts with two RY elements (CATGCATG) present in the AtGA3ox2 promoter. This work suggests that GA biosynthesis is directly controlled by embryonic regulators during Arabidopsis embryonic development.},
	number = {3},
	urldate = {2021-06-15},
	journal = {Plant Physiology},
	author = {Curaba, Julien and Moritz, Thomas and Blervaque, Renaud and Parcy, François and Raz, Vered and Herzog, Michel and Vachon, Gilles},
	month = nov,
	year = {2004},
	pages = {3660--3669},
}

Cloning and Overproduction of Gibberellin 3-Oxidase in Hybrid Aspen Trees. Effects on Gibberellin Homeostasis and Development. Israelsson, M., Mellerowicz, E., Chono, M., Gullberg, J., & Moritz, T. Plant Physiology, 135(1): 221–230. May 2004.

Cloning and Overproduction of Gibberellin 3-Oxidase in Hybrid Aspen Trees. Effects on Gibberellin Homeostasis and Development [link]

Paper doi link bibtex abstract

@article{israelsson_cloning_2004,
	title = {Cloning and {Overproduction} of {Gibberellin} 3-{Oxidase} in {Hybrid} {Aspen} {Trees}. {Effects} on {Gibberellin} {Homeostasis} and {Development}},
	volume = {135},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.104.038935},
	doi = {10/bpzz6v},
	abstract = {To broaden our understanding of gibberellin (GA) biosynthesis and the mechanism whereby GA homeostasis is maintained in plants, we have investigated the degree to which the enzyme GA 3-oxidase (GA3ox) limits the formation of bioactive GAs in elongating shoots of hybrid aspen (Populus tremula × Populus tremuloides). We describe the cloning of a hybrid aspen GA3ox and its functional characterization, which confirmed that it has 3β-hydroxylation activity and more efficiently converts GA9 to GA4 than GA20 to GA1. To complement previous studies, in which transgenic GA 20-oxidase (GA20ox) overexpressers were found to produce 20-fold higher bioactive GA levels and subsequently grew faster than wild-type plants, we overexpressed an Arabidopsis GA3ox in hybrid aspen. The generated GA3ox overexpresser lines had increased 3β-hydroxylation activity but exhibited no major changes in morphology. The nearly unaltered growth pattern was associated with relatively small changes in GA1 and GA4 levels, although tissue-dependent differences were observed. The absence of increases in bioactive GA levels did not appear to be due to feedback or feed-forward regulation of dioxygenase transcripts, according to semiquantitative reverse transcription polymerase chain reaction analysis of PttGA20ox1, PttGA3ox1, and two putative PttGA2ox genes. We conclude that 20-oxidation is the limiting step, rather than 3β-hydroxylation, in the formation of GA1 and GA4 in elongating shoots of hybrid aspen, and that ectopic GA3ox expression alone cannot increase the flux toward bioactive GAs. Finally, several lines of evidence now suggest that GA4 has a more pivotal role in the tree hybrid aspen than previously believed.},
	number = {1},
	urldate = {2021-06-15},
	journal = {Plant Physiology},
	author = {Israelsson, Maria and Mellerowicz, Ewa and Chono, Makiko and Gullberg, Jonas and Moritz, Thomas},
	month = may,
	year = {2004},
	pages = {221--230},
}

Derivatization for LC-Electrospray Ionization-MS: A Tool for Improving Reversed-Phase Separation and ESI Responses of Bases, Ribosides, and Intact Nucleotides. Nordström, A., Tarkowski, P., Tarkowska, D., Dolezal, K., Åstot, C., Sandberg, G., & Moritz, T. Analytical Chemistry, 76(10): 2869–2877. May 2004. Publisher: American Chemical Society

Paper doi link bibtex abstract

@article{nordstrom_derivatization_2004,
	title = {Derivatization for {LC}-{Electrospray} {Ionization}-{MS}:  {A} {Tool} for {Improving} {Reversed}-{Phase} {Separation} and {ESI} {Responses} of {Bases}, {Ribosides}, and {Intact} {Nucleotides}},
	volume = {76},
	issn = {0003-2700},
	shorttitle = {Derivatization for {LC}-{Electrospray} {Ionization}-{MS}},
	url = {https://doi.org/10.1021/ac0499017},
	doi = {10/b9ckbc},
	abstract = {We have developed a method for analyzing polar compounds by reversed-phase LC-ESI-MS following esterification of the analytes' free hydroxyl groups with propionyl or benzoyl acid anhydride. The method was applied to members of the plant hormone group cytokinins, which includes adenine bases, ribosides/glycosides, and nucleotides substituted at N-6 with an isoprenoid side chain, spanning a wide range of polarity. It was also used to analyze other compounds of biological importance, e.g., the nucleotides AMP, ADP, and ATP. The formation of more hydrophobic derivatives had a significant impact on two aspects of the analysis. The retention on a reversed-phase material was greatly increased without the use of any acetate/formate buffer or ion pairing reagent, and the ESI response was enhanced, due to the higher surface activities of the derivatives. Detection limits of propionylated cytokinins were in the high-attomole to low-femtomole range, an improvement by factors of 10−100 compared to previously reported figures. Using an automated SPE-based purification method, 12 endogenous cytokinins were quantified in extracts from 20- to 100-mg samples of leaves (from the plant Arabidopsis thaliana) with high accuracy and precision. Furthermore, the chromatographic properties of the benzoylated AMP, ADP, and ATP in the reversed-phase LC−MS system were much better in terms of retention, separation, and sensitivity than those of their underivatized counterparts, even without the use of any ion pairing reagent. Our data show that derivatization followed by LC-ESI-MS is an effective strategy for analyzing low molecular weight compounds, enabling compounds with a wide range of polarity to be determined in a single-injection LC−MS analysis.},
	number = {10},
	urldate = {2021-06-30},
	journal = {Analytical Chemistry},
	author = {Nordström, Anders and Tarkowski, Petr and Tarkowska, Danuse and Dolezal, Karel and Åstot, Crister and Sandberg, Göran and Moritz, Thomas},
	month = may,
	year = {2004},
	note = {Publisher: American Chemical Society},
	pages = {2869--2877},
}

Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry. Gullberg, J., Jonsson, P., Nordström, A., Sjöström, M., & Moritz, T. Analytical Biochemistry, 331(2): 283–295. August 2004.

Paper doi link bibtex abstract

@article{gullberg_design_2004,
	title = {Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of {Arabidopsis} thaliana samples in metabolomic studies with gas chromatography/mass spectrometry},
	volume = {331},
	issn = {0003-2697},
	shorttitle = {Design of experiments},
	url = {https://www.sciencedirect.com/science/article/pii/S0003269704003811},
	doi = {10/ftg6fz},
	abstract = {The usual aim in metabolomic studies is to quantify the entire metabolome of each of a series of biological samples. To do this for complex biological matrices, e.g., plant tissues, efficient and reproducible extraction protocols must be developed. However, derivatization protocols must also be developed if GC/MS (one of the mostly widely used analytical methods for metabolomics) is involved. The aim of this study was to investigate how different chemical and physical factors (extraction solvent, derivatization reagents, and temperature) affect the extraction and derivatization of the metabolome from leaves of the plant Arabidopsis thaliana. Using design of experiment procedures, variation was systematically introduced, and the effects of this variation were analyzed using regression models. The results show that this approach allows a reliable protocol for metabolomic analysis of Arabidopsis to be determined with a relatively limited number of experiments. Following two different investigations an extraction and derivatization protocol was chosen. Further, the reproducibility of the analysis of 66 endogenous compounds was investigated, and it was shown that both hydrophilic and lipophilic compounds were detected with high reproducibility.},
	language = {en},
	number = {2},
	urldate = {2021-06-30},
	journal = {Analytical Biochemistry},
	author = {Gullberg, Jonas and Jonsson, Pär and Nordström, Anders and Sjöström, Michael and Moritz, Thomas},
	month = aug,
	year = {2004},
	keywords = {Derivatization, Design of experiments, Extraction, Mass spectrometry, Metabolomics},
	pages = {283--295},
}

Gibberellins and the floral transition in Sinapis alba. Corbesier, L., Kustermans, G., Perilleux, C., Melzer, S., Moritz, T., Havelange, A., & Bernier, G. Physiologia Plantarum, 122(1): 152–158. September 2004. Place: Hoboken Publisher: Wiley WOS:000223589000018
doi link bibtex abstract

@article{corbesier_gibberellins_2004,
	title = {Gibberellins and the floral transition in {Sinapis} alba},
	volume = {122},
	issn = {0031-9317},
	doi = {10/fqn2j7},
	abstract = {The putative role of gibberellins in the transition to flowering was investigated in Sinapis alba, a caulescent long-day (LD) plant. It was observed that: (1) physiological doses of exogenous gibberellins (GA(1), GA(3), GA(9)) do not cause the floral shift of the meristem when applied to plants grown in short days but have some positive effect on the flowering response to a suboptimal LD; no inhibition was observed in any case; (2) GA-biosynthesis inhibitors (prohexadione-Ca and paclobutrazol) considerably inhibit stem growth but have some negative effect on flowering only when a suboptimal LD is given; and (3) the floral transition induced by one 22-h LD does not correlate with any detectable change in GA content of the apical bud, of the leaves, and of the phloem exudate reaching the apex. Taken together, these results suggest that GAs do not act as a major signal for photoperiodic flower induction in Sinapis.},
	language = {English},
	number = {1},
	journal = {Physiologia Plantarum},
	author = {Corbesier, L. and Kustermans, G. and Perilleux, C. and Melzer, S. and Moritz, T. and Havelange, A. and Bernier, G.},
	month = sep,
	year = {2004},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000223589000018},
	keywords = {arabidopsis-thaliana, biosynthesis, cytokinins, endogenous gibberellins, induction, localization, phloem, photoperiod, shoot, stem growth},
	pages = {152--158},
}

Global analysis of low-molecular-weight compounds in human plasma using GC/TOF-MS. Jiye, A., Trygg, J., Gullberg, J., Moritz, T., & Marklund, S. Drug Metabolism Reviews, 36: 246–246. August 2004. Place: Philadelphia Publisher: Taylor & Francis Inc WOS:000224023200489
link bibtex

@article{jiye_global_2004,
	title = {Global analysis of low-molecular-weight compounds in human plasma using {GC}/{TOF}-{MS}},
	volume = {36},
	issn = {0360-2532},
	language = {English},
	journal = {Drug Metabolism Reviews},
	author = {Jiye, A. and Trygg, J. and Gullberg, J. and Moritz, T. and Marklund, S.},
	month = aug,
	year = {2004},
	note = {Place: Philadelphia
Publisher: Taylor \& Francis Inc
WOS:000224023200489},
	pages = {246--246},
}

The Roles of Ethylene, Auxin, Abscisic Acid, and Gibberellin in the Hyponastic Growth of Submerged Rumex palustris Petioles. Cox, M. C., Benschop, J. J., Vreeburg, R. A., Wagemaker, C. A., Moritz, T., Peeters, A. J., & Voesenek, L. A. Plant Physiology, 136(2): 2948–2960. October 2004.

The Roles of Ethylene, Auxin, Abscisic Acid, and Gibberellin in the Hyponastic Growth of Submerged Rumex palustris Petioles [link]

Paper doi link bibtex abstract

@article{cox_roles_2004,
	title = {The {Roles} of {Ethylene}, {Auxin}, {Abscisic} {Acid}, and {Gibberellin} in the {Hyponastic} {Growth} of {Submerged} {Rumex} palustris {Petioles}},
	volume = {136},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.104.049197},
	doi = {10/bkt5tx},
	abstract = {Rumex palustris responds to complete submergence with upward movement of the younger petioles. This so-called hyponastic response, in combination with stimulated petiole elongation, brings the leaf blade above the water surface and restores contact with the atmosphere. We made a detailed study of this differential growth process, encompassing the complete range of the known signal transduction pathway: from the cellular localization of differential growth, to the hormonal regulation, and the possible involvement of a cell wall loosening protein (expansin) as a downstream target. We show that hyponastic growth is caused by differential cell elongation across the petiole base, with cells on the abaxial (lower) surface elongating faster than cells on the adaxial (upper) surface. Pharmacological studies and endogenous hormone measurements revealed that ethylene, auxin, abscisic acid (ABA), and gibberellin regulate different and sometimes overlapping stages of hyponastic growth. Initiation of hyponastic growth and (maintenance of) the maximum petiole angle are regulated by ethylene, ABA, and auxin, whereas the speed of the response is influenced by ethylene, ABA, and gibberellin. We found that a submergence-induced differential redistribution of endogenous indole-3-acetic acid in the petiole base could play a role in maintenance of the response, but not in the onset of hyponastic growth. Since submergence does not induce a differential expression of expansins across the petiole base, it is unlikely that this cell wall loosening protein is the downstream target for the hormones that regulate the differential cell elongation leading to submergence-induced hyponastic growth in R. palustris.},
	number = {2},
	urldate = {2021-06-15},
	journal = {Plant Physiology},
	author = {Cox, Marjolein C.H. and Benschop, Joris J. and Vreeburg, Robert A.M. and Wagemaker, Cornelis A.M. and Moritz, Thomas and Peeters, Anton J.M. and Voesenek, Laurentius A.C.J.},
	month = oct,
	year = {2004},
	pages = {2948--2960},
}

2003 (1)

Changes in gene expression in the wood-forming tissue of transgenic hybrid aspen with increased secondary growth. Israelsson, M., Eriksson, M. E., Hertzberg, M., Aspeborg, H., Nilsson, P., & Moritz, T. Plant Molecular Biology, 52(4): 893–903. July 2003.

Changes in gene expression in the wood-forming tissue of transgenic hybrid aspen with increased secondary growth [link]

Paper doi link bibtex abstract

@article{israelsson_changes_2003,
	title = {Changes in gene expression in the wood-forming tissue of transgenic hybrid aspen with increased secondary growth},
	volume = {52},
	issn = {1573-5028},
	url = {https://doi.org/10.1023/A:1025097410445},
	doi = {10/b7zwj2},
	abstract = {Transgenic lines of hybrid aspen with elevated levels of gibberellin (GA) show greatly increased numbers of xylem fibres and increases in xylem fibre length. These plants therefore provide excellent models for studying secondary growth. We have used cDNA microarry analysis to investigate how gene transcription in the developing xylem is affected by GA-induced growth. A recent investigation has shown that genes encoding lignin and cellulose biosynthetic enzymes, as well as a number of transcription factors and other potential regulators of xylogenesis, are under developmental-stage-specific transcriptional control. The present study shows that the highest transcript changes in our transgenic trees occurs in genes generally restricted to the early stages of xylogenesis, including cell division, early expansion and late expansion. The results reveal genes among those arrayed that are up-regulated with an increased xylem production, thus indicating key components in the production of wood.},
	language = {en},
	number = {4},
	urldate = {2022-03-11},
	journal = {Plant Molecular Biology},
	author = {Israelsson, Maria and Eriksson, Maria E. and Hertzberg, Magnus and Aspeborg, Henrik and Nilsson, Peter and Moritz, Thomas},
	month = jul,
	year = {2003},
	pages = {893--903},
}

2002 (3)

Daylength and spatial expression of a gibberellin 20-oxidase isolated from hybrid aspen (Populus tremula L. × P. tremuloides Michx.). Eriksson, M. E., & Moritz, T. Planta, 214(6): 920–930. April 2002.

Daylength and spatial expression of a gibberellin 20-oxidase isolated from hybrid aspen (Populus tremula L. × P. tremuloides Michx.) [link]

Paper doi link bibtex abstract 1 download

@article{eriksson_daylength_2002,
	title = {Daylength and spatial expression of a gibberellin 20-oxidase isolated from hybrid aspen ({Populus} tremula {L}. × {P}. tremuloides {Michx}.)},
	volume = {214},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s00425-001-0703-3},
	doi = {10/bn4z3p},
	abstract = {Physiologically active gibberellins (GAs) are key regulators of shoot growth in trees. To investigate this mechanism of GA-controlled growth in hybrid aspen, we cloned cDNAs encoding gibberellin 20-oxidase (GA 20-oxidase), a key, highly regulated enzyme in the biosynthesis of GAs. Clones were isolated from leaf and cambium cDNA libraries using probes generated by polymerase chain reaction, based on conserved domains of GA 20-oxidases. Upon expression in Escherichia coli, the GST-fusion protein was shown to oxidise GA12 as well as oxidising the 13-hydroxylated substrate GA53, successively to GA9 and GA20, respectively. The gene PttGA20ox1 was expressed in meristematic cells and growing tissues such as expanding internodes, leaves and roots. The expression was negatively regulated by both GA4 and overexpression of phytochrome A. RNA analysis also showed that the expression was down-regulated in late-expanding leaf tissue in response to short days (SDs). Actively growing tissues such as early elongating internodes, petioles and leaf blades had the highest levels of C19-GAs. Upon transfer to SDs an accumulation of GA19 was observed in early elongating internodes and leaf blades. The levels of C19-GAs were also to some extent changed upon transfer to SDs. The levels of GA20 were down-regulated in internodes, and those of GA1 were significantly reduced in early expanding leaf blades. In roots the metabolites GA19 and GA8 decreased upon shifts to SDs, while GA20 accumulated slightly. The down-regulation of GA 20-oxidase activity in response to SDs was further indicated by studies of [14C]GA12 metabolism in shoots, demonstrating that the substrate for GA 20-oxidase, [14C]GA53, accumulates in SDs.},
	language = {en},
	number = {6},
	urldate = {2021-10-19},
	journal = {Planta},
	author = {Eriksson, Maria E. and Moritz, Thomas},
	month = apr,
	year = {2002},
	pages = {920--930},
}

Independent Activation of Cold Acclimation by Low Temperature and Short Photoperiod in Hybrid Aspen. Welling, A., Moritz, T., Palva, E. T., & Junttila, O. Plant Physiology, 129(4): 1633–1641. August 2002.

Independent Activation of Cold Acclimation by Low Temperature and Short Photoperiod in Hybrid Aspen [link]

Paper doi link bibtex abstract

@article{welling_independent_2002,
	title = {Independent {Activation} of {Cold} {Acclimation} by {Low} {Temperature} and {Short} {Photoperiod} in {Hybrid} {Aspen}},
	volume = {129},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.003814},
	doi = {10/bwp2sf},
	abstract = {Temperate zone woody plants cold acclimate in response to both short daylength (SD) and low temperature (LT). We were able to show that these two environmental cues induce cold acclimation independently by comparing the wild type (WT) and the transgenic hybrid aspen (Populus tremula × Populus tremuloides Michx.) line 22 overexpressing the oat (Avena sativa) PHYTOCHROME A gene. Line 22 was not able to detect the SD and, consequently, did not stop growing in SD conditions. This resulted in an impaired freezing tolerance development under SD. In contrast, exposure to LT resulted in cold acclimation of line 22 to a degree comparable with the WT. In contrast to the WT, line 22 could not dehydrate the overwintering tissues or induce the production of dehydrins (DHN) under SD conditions. Furthermore, abscisic acid (ABA) content of the buds of line 22 were the same under SD and long daylength, whereas prolonged SD exposure decreased the ABA level in the WT. LT exposure resulted in a rapid accumulation of DHN in both the WT and line 22. Similarly, ABA content increased transiently in both the WT and line 22. Our results indicate that phytochrome A is involved in photoperiodic regulation of ABA and DHN levels, but at LT they are regulated by a different mechanism. Although SD and LT induce cold acclimation independently, ABA and DHN may play important roles in both modes of acclimation.},
	number = {4},
	urldate = {2021-10-19},
	journal = {Plant Physiology},
	author = {Welling, Annikki and Moritz, Thomas and Palva, E. Tapio and Junttila, Olavi},
	month = aug,
	year = {2002},
	pages = {1633--1641},
}

Molecular and physiological characterization of Arabidopsis GAI alleles obtained in targeted Ds-tagging experiments. Peng, J., Richards, D. E., Moritz, T., Ezura, H., Carol, P., & Harberd, N. P. Planta, 214(4): 591–596. February 2002.

Molecular and physiological characterization of Arabidopsis GAI alleles obtained in targeted Ds-tagging experiments [link]

Paper doi link bibtex abstract

@article{peng_molecular_2002,
	title = {Molecular and physiological characterization of {Arabidopsis} {GAI} alleles obtained in targeted {Ds}-tagging experiments},
	volume = {214},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s004250100643},
	doi = {10.1007/s004250100643},
	abstract = {Bioactive gibberellin (GA) is an essential regulator of vascular plant development. The GAI gene of Arabidopsis thaliana (L.) Heynh. encodes a product (GAI) that is involved in GA signalling. The dominant mutant gai allele encodes an altered product (gai) that confers reduced GA responses, dwarfism, and elevated endogenous GA levels. Recessive, presumed loss-of-function alleles of GAI confer normal height and resistance to the GA biosynthesis inhibitor paclobutrazol. One explanation for these observations is that GAI is a growth repressor whose activity is opposed by GA, whilst gai retains a constitutive repressor activity that is less affected by GA. Previously, we described gai-t6, a mutant allele which contains an insertion of a maize Ds transposable element into gai. Here we describe the molecular and physiological characterization of two further alleles (gai-t5, gai-t7) identified during the Ds mutagenesis experiment. These alleles confer paclobutrazol resistance and normal endogenous GA levels. Thus the phenotype conferred by gai-t5, gai-t6 and gai-t7 is not due to elevated GA levels, but is due to loss of gai, a constitutively active plant growth repressor.},
	language = {en},
	number = {4},
	urldate = {2021-10-19},
	journal = {Planta},
	author = {Peng, Jinrong and Richards, Donald E. and Moritz, Thomas and Ezura, Hiroshi and Carol, Pierre and Harberd, Nicholas P.},
	month = feb,
	year = {2002},
	pages = {591--596},
}

2001 (4)

Function and Dynamics of Auxin and Carbohydrates during Earlywood/Latewood Transition in Scots Pine1. Uggla, C., Magel, E., Moritz, T., & Sundberg, B. Plant Physiology, 125(4): 2029–2039. April 2001.

Function and Dynamics of Auxin and Carbohydrates during Earlywood/Latewood Transition in Scots Pine1 [link]

Paper doi link bibtex abstract

@article{uggla_function_2001,
	title = {Function and {Dynamics} of {Auxin} and {Carbohydrates} during {Earlywood}/{Latewood} {Transition} in {Scots} {Pine1}},
	volume = {125},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.125.4.2029},
	doi = {10/csvzgg},
	abstract = {In temperate regions the annual pattern of wood development is characterized by the formation of radially narrow and thick walled latewood cells. This takes place at the later part of the growing season when cambial cell division declines. To gain new insight into the regulation of this process, micro-analytical techniques were used to visualize the distribution of indole-3-acetic acid (IAA), soluble carbohydrates, and activities of sucrose (Suc)-metabolizing enzymes across the cambial region tissues in Scots pine (Pinus sylvestris). The total amount of IAA in the cambial region did not change with latewood initiation. But its radial distribution pattern was altered, resulting in an increased concentration in the cambial meristem and its recent derivatives. Thus, initiation of latewood formation and cessation of cambial cell division is not a consequence of decreased IAA concentrations in dividing and expanding cells. Rather, IAA most likely has a role in defining the altered developmental pattern associated with latewood formation. Carbohydrates and enzyme activities showed distinctive radial distribution patterns. Suc peaked in the phloem and decreased sharply to low levels across the cambial zone, whereas fructose and glucose reached their highest levels in the maturing tracheids. Suc synthase was the dominating Suc cleaving enzyme with a peak in the secondary wall-forming tracheids and in the phloem. Soluble acid invertase peaked in dividing and expanding cells. Suc-phosphate synthase had its highest activities in the phloem. Activities of cell wall bound invertase were low. The absence of major seasonal variations indicates that carbohydrate availability is not a trigger for latewood initiation. However, steep concentration gradients of the sugars suggest a role for sugar signaling in vascular development.},
	number = {4},
	urldate = {2021-11-02},
	journal = {Plant Physiology},
	author = {Uggla, Claes and Magel, Elisabeth and Moritz, Thomas and Sundberg, Björn},
	month = apr,
	year = {2001},
	pages = {2029--2039},
}

GAMYB-like Genes, Flowering, and Gibberellin Signaling in Arabidopsis. Gocal, G. F., Sheldon, C. C., Gubler, F., Moritz, T., Bagnall, D. J., MacMillan, C. P., Li, S. F., Parish, R. W., Dennis, E. S., Weigel, D., & King, R. W. Plant Physiology, 127(4): 1682–1693. December 2001.

GAMYB-like Genes, Flowering, and Gibberellin Signaling in Arabidopsis [link]

Paper link bibtex abstract

@article{gocal_gamyb-like_2001,
	title = {{GAMYB}-like {Genes}, {Flowering}, and {Gibberellin}  {Signaling} in {Arabidopsis}},
	volume = {127},
	issn = {0032-0889},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC133573/},
	abstract = {We have identified three Arabidopsis genes with GAMYB-like activity, AtMYB33, AtMYB65, and AtMYB101, which can substitute for barley (Hordeum vulgare) GAMYB in transactivating the barley α-amylase promoter. We have investigated the relationships between gibberellins (GAs), these GAMYB-like genes, and petiole elongation and flowering of Arabidopsis. Within 1 to 2 d of transferring plants from short- to long-day photoperiods, growth rate and erectness of petioles increased, and there were morphological changes at the shoot apex associated with the transition to flowering. These responses were accompanied by accumulation of GAs in the petioles (GA1 by 11-fold and GA4 by 3-fold), and an increase in expression of AtMYB33 at the shoot apex. Inhibition of GA biosynthesis using paclobutrazol blocked the petiole elongation induced by long days. Causality was suggested by the finding that, with GA treatment, plants flowered in short days, AtMYB33 expression increased at the shoot apex, and the petioles elongated and grew erect. That AtMYB33 may mediate a GA signaling role in flowering was supported by its ability to bind to a specific 8-bp sequence in the promoter of the floral meristem-identity gene, LEAFY, this same sequence being important in the GA response of the LEAFY promoter. One or more of these AtMYB genes may also play a role in the root tip during germination and, later, in stem tissue. These findings extend our earlier studies of GA signaling in the Gramineae to include a dicot species, Arabidopsis, and indicate that GAMYB-like genes may mediate GA signaling in growth and flowering responses.},
	number = {4},
	urldate = {2021-11-02},
	journal = {Plant Physiology},
	author = {Gocal, Gregory F.W. and Sheldon, Candice C. and Gubler, Frank and Moritz, Thomas and Bagnall, David J. and MacMillan, Colleen P. and Li, Song F. and Parish, Roger W. and Dennis, Elizabeth S. and Weigel, Detlef and King, Rod W.},
	month = dec,
	year = {2001},
	pmid = {11743113},
	pmcid = {PMC133573},
	pages = {1682--1693},
}

Gibberellins Are Not Required for Normal Stem Growth in Arabidopsis thaliana in the Absence of GAI and RGA. King, K. E, Moritz, T., & Harberd, N. P Genetics, 159(2): 767–776. October 2001.

Gibberellins Are Not Required for Normal Stem Growth in Arabidopsis thaliana in the Absence of GAI and RGA [link]

Paper doi link bibtex abstract

@article{king_gibberellins_2001,
	title = {Gibberellins {Are} {Not} {Required} for {Normal} {Stem} {Growth} in {Arabidopsis} thaliana in the {Absence} of {GAI} and {RGA}},
	volume = {159},
	issn = {1943-2631},
	url = {https://doi.org/10.1093/genetics/159.2.767},
	doi = {10/gn2mhv},
	abstract = {The growth of Arabidopsis thaliana is quantitatively regulated by the phytohormone gibberellin (GA) via two closely related nuclear GA-signaling components, GAI and RGA. Here we test the hypothesis that GAI and RGA function as “GA-derepressible repressors” of plant growth. One prediction of this hypothesis is that plants lacking GAI and RGA do not require GA for normal stem growth. Analysis of GA-deficient mutants lacking GAI and RGA confirms this prediction and suggests that in the absence of GAI and RGA, “growth” rather than “no growth” is the default state of plant stems. The function of the GA-signaling system is thus to act as a control system regulating the amount of this growth. We also demonstrate that the GA dose dependency of hypocotyl elongation is altered in mutants lacking GAI and RGA and propose that increments in GAI/RGA repressor function can explain the quantitative nature of GA responses.},
	number = {2},
	urldate = {2021-11-02},
	journal = {Genetics},
	author = {King, Kathryn E and Moritz, Thomas and Harberd, Nicholas P},
	month = oct,
	year = {2001},
	pages = {767--776},
}

Long-Day Induction of Flowering in Lolium temulentum Involves Sequential Increases in Specific Gibberellins at the Shoot Apex. King, R. W., Moritz, T., Evans, L. T., Junttila, O., & Herlt, A. J. Plant Physiology, 127(2): 624–632. October 2001.

Long-Day Induction of Flowering in Lolium temulentum Involves Sequential Increases in Specific Gibberellins at the Shoot Apex [link]

Paper link bibtex abstract

@article{king_long-day_2001,
	title = {Long-{Day} {Induction} of {Flowering} in {Lolium} temulentum {Involves} {Sequential} {Increases} in {Specific}  {Gibberellins} at the {Shoot} {Apex}},
	volume = {127},
	issn = {0032-0889},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC125097/},
	abstract = {One challenge for plant biology has been to identify floral stimuli at the shoot apex. Using sensitive and specific gas chromatography-mass spectrometry techniques, we have followed changes in gibberellins (GAs) at the shoot apex during long day (LD)-regulated induction of flowering in the grass Lolium temulentum. Two separate roles of GAs in flowering are indicated. First, within 8 h of an inductive LD, i.e. at the time of floral evocation, the GA5 content of the shoot apex doubled to about 120 ng g−1 dry weight. The concentration of applied GA5 required for floral induction of excised apices (R.W. King, C. Blundell, L.T. Evans [1993] Aust J Plant Physiol 20: 337–348) was similar to that in the shoot apex. Leaf-applied [2H4] GA5 was transported intact from the leaf to the shoot apex, flowering being proportional to the amount of GA5 imported. Thus, GA5 could be part of the LD stimulus for floral evocation of L. temulentum or, alternatively, its increase at the shoot apex could follow import of a primary floral stimulus. Later, during inflorescence differentiation and especially after exposure to additional LD, a second GA action was apparent. The content of GA1 and GA4 in the apex increased greatly, whereas GA5 decreased by up to 75\%. GA4 applied during inflorescence differentiation strongly promoted flowering and stem elongation, whereas it was ineffective for earlier floral evocation although it caused stem growth at all times of application. Thus, we conclude that GA1 and GA4 are secondary, late-acting LD stimuli for inflorescence differentiation in L. temulentum.},
	number = {2},
	urldate = {2021-11-02},
	journal = {Plant Physiology},
	author = {King, Rod W. and Moritz, Thomas and Evans, Lloyd T. and Junttila, Olavi and Herlt, Anthony J.},
	month = oct,
	year = {2001},
	pmid = {11598236},
	pmcid = {PMC125097},
	pages = {624--632},
}

2000 (4)

An alternative cytokinin biosynthesis pathway. Åstot, C., Dolezal, K., Nordström, A., Wang, Q., Kunkel, T., Moritz, T., Chua, N., & Sandberg, G. Proceedings of the National Academy of Sciences, 97(26): 14778–14783. December 2000. Publisher: National Academy of Sciences Section: Biological Sciences

An alternative cytokinin biosynthesis pathway [link]

Paper doi link bibtex abstract

@article{astot_alternative_2000,
	title = {An alternative cytokinin biosynthesis pathway},
	volume = {97},
	copyright = {Copyright © 2000, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/97/26/14778},
	doi = {10/dt77jp},
	abstract = {Studies of de novo cytokinin biosynthesis in isopentenyltransferase (ipt)-transformed Arabidopsis thaliana, involving in vivo deuterium labeling and mass spectrometry, showed that the biosynthetic rate of zeatinriboside-5′-monophosphate was around 66-fold higher than that of isopentenyladenosine-5′-monophosphate (iPMP), the proposed primary product of the Agrobacterium ipt. Double tracer analysis, using [2H6] isopentenyladenosine and deuterium oxide, provided evidence for an alternative, iPMP-independent, biosynthetic pathway for zeatin-type cytokinins, present in both ipt-expressing and wild-type Arabidopsis thaliana. Reduction of the biosynthetic flux in the alternative pathway by use of mevastatin, an inhibitor for 3-hydroxy-3-methylglutaryl CoA reductase, indicated a terpenoid origin for the side-chain precursor of the iPMP independent pathway.},
	language = {en},
	number = {26},
	urldate = {2021-11-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Åstot, Crister and Dolezal, Karel and Nordström, Anders and Wang, Qun and Kunkel, Tim and Moritz, Thomas and Chua, Nam-Hai and Sandberg, Göran},
	month = dec,
	year = {2000},
	pmid = {11114204},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	pages = {14778--14783},
}

Deuterium in vivo labelling of cytokinins in Arabidopsis thaliana analysed by capillary liquid chromatography/frit-fast atom bombardment mass spectrometry. Åstot, C., Dolezal, K., Moritz, T., & Sandberg, G. Journal of Mass Spectrometry, 35(1): 13–22. 2000. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/%28SICI%291096-9888%28200001%2935%3A1%3C13%3A%3AAID-JMS901%3E3.0.CO%3B2-I

Paper doi link bibtex abstract

@article{astot_deuterium_2000,
	title = {Deuterium in vivo labelling of cytokinins in {Arabidopsis} thaliana analysed by capillary liquid chromatography/frit-fast atom bombardment mass spectrometry},
	volume = {35},
	issn = {1096-9888},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291096-9888%28200001%2935%3A1%3C13%3A%3AAID-JMS901%3E3.0.CO%3B2-I},
	doi = {10.1002/(SICI)1096-9888(200001)35:1<13::AID-JMS901>3.0.CO;2-I},
	abstract = {A method was developed for analysing the biosynthetic rate of the cytokinin class of plant hormones. Transgenic, cytokinin-overproducing Arabidopsis thaliana plants were incubated in liquid culture media enriched with 30\% deuterium oxide, and incorporation into the different parts of the cytokinin molecule was analysed by capillary liquid chromatography/frit-fast atom bombardment mass spectrometry after precolumn propionylation. The sugar moieties of the cytokinins generally showed a high and independent incorporation, so the analysis in this study focused on the cytokinin base moieties. It was observed that during a 24 h incubation period almost all labelling was incorporated into the side-chain, rather than the adenine moiety. The incorporation dynamics of isopentenyladenosine-5′-monophosphate, zeatinriboside-5′-monophosphate (ZRMP) and zeatin-9-glucoside were investigated through analysis of the cytokinin base fragments in high-resolution selective ion monitoring mode. Using a fractional synthetic rate approach, the biosynthetic rate of ZRMP was determined to be 18 ng h−1 g−1 fresh weight, giving a turnover time of 25 h. A method for the mass isotopomer abundance analysis of the cytokinins in the zeatin family, based on selective reaction monitoring, was also developed to gain further sensitivity. Use of this technique showed that there was a higher level of enrichment in zeatin nucleotide than in the corresponding nucleoside, in agreement with the hypothesis that cytokinin nucleotides are primary products in this pathway. Copyright © 2000 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {1},
	urldate = {2021-11-08},
	journal = {Journal of Mass Spectrometry},
	author = {Åstot, Crister and Dolezal, Karel and Moritz, Thomas and Sandberg, Göran},
	year = {2000},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/\%28SICI\%291096-9888\%28200001\%2935\%3A1\%3C13\%3A\%3AAID-JMS901\%3E3.0.CO\%3B2-I},
	keywords = {Arabidopsis thaliana, cytokinin biosynthesis, fast atom bombardment, in vivo labelling, isotopomer},
	pages = {13--22},
}

Increased gibberellin biosynthesis in transgenic trees promotes growth, biomass production and xylem fiber length. Eriksson, M. E., Israelsson, M., Olsson, O., & Moritz, T. Nature Biotechnology, 18(7): 784–788. July 2000. Bandiera_abtest: a Cg_type: Nature Research Journals Number: 7 Primary_atype: Research Publisher: Nature Publishing Group

Increased gibberellin biosynthesis in transgenic trees promotes growth, biomass production and xylem fiber length [link]

Paper doi link bibtex abstract 2 downloads

@article{eriksson_increased_2000,
	title = {Increased gibberellin biosynthesis in transgenic trees promotes growth, biomass production and xylem fiber length},
	volume = {18},
	copyright = {2000 Nature America Inc.},
	issn = {1546-1696},
	url = {https://www.nature.com/articles/nbt0700_784},
	doi = {10.1038/77355},
	abstract = {In most tree-breeding programs worldwide, increasing the trees' growth rates and stem volumes and shortening their rotation times are important aims. Such trees would yield more biomass per unit area. Here we show that overexpressing a key regulatory gene in the biosynthesis of the plant hormone gibberellin (GA) in hybrid aspen (Populus tremula × P. tremuloides) improves growth rate and biomass. In addition, these transgenic trees have more numerous and longer xylem fibers than unmodified wild-type (wt) plants. Long fibers are desirable in the production of strong paper, but it has not as yet proved possible to influence this trait by traditional breeding techniques. We also show that GA has an antagonistic effect on root initiation, as the transgenic lines showed poorer rooting than the control plants when potted in soil. However, the negative effect on rooting efficiencies in the initial establishment of young plantlets in the growth chamber did not significantly affect root growth at later stages.},
	language = {en},
	number = {7},
	urldate = {2021-11-08},
	journal = {Nature Biotechnology},
	author = {Eriksson, Maria E. and Israelsson, Maria and Olsson, Olof and Moritz, Thomas},
	month = jul,
	year = {2000},
	note = {Bandiera\_abtest: a
Cg\_type: Nature Research Journals
Number: 7
Primary\_atype: Research
Publisher: Nature Publishing Group},
	keywords = {Agriculture, Bioinformatics, Biomedical Engineering/Biotechnology, Biomedicine, Biotechnology, Life Sciences, general},
	pages = {784--788},
}

Transgenic tobacco plants co-expressing Agrobacterium iaa and ipt genes have wild-type hormone levels but display both auxin- and cytokinin-overproducing phenotypes. Eklöf, S., Åstot, C., Sitbon, F., Moritz, T., Olsson, O., & Sandberg, G. The Plant Journal, 23(2): 279–284. 2000. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313x.2000.00762.x

Paper doi link bibtex abstract

@article{eklof_transgenic_2000,
	title = {Transgenic tobacco plants co-expressing {Agrobacterium} iaa and ipt genes have wild-type hormone levels but display both auxin- and cytokinin-overproducing phenotypes},
	volume = {23},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-313x.2000.00762.x},
	doi = {10/dkzdj3},
	abstract = {Transgenic tobacco lines simultaneously expressing the Agrobacterium iaaM, iaaH and ipt genes, obtained by crossing lines expressing ipt with lines expressing iaaM and iaaH, were used to study in planta interactions between auxin and cytokinins. All phenotypic traits of the respective parental lines characteristic of cytokinin and auxin overproduction were present in the cross. Indole-3-acetic acid (IAA) and combined zeatin riboside (ZR) and zeatin riboside-5′-monophosphate (ZRMP) contents were analysed by mass spectrometry in young, developing leaves from the cross, the parental lines and the wild type. Unexpectedly, hormone levels in the cross were very similar to wild-type levels. Thus IAA levels in the cross were much lower throughout vegetative development than in the parental IAA overproducing line, although expression of the bacterial IAA biosynthesis genes was not reduced. The results suggest that effects on apical dominance, adventitious root formation, leaf morphology and other traits commonly ± associated with IAA and cytokinin overproduction, and observed in the iaaËipt cross, cannot be explained solely by analysis of auxin and cytokinin contents in individual organs. As traits associated with both hormones are expressed in close spatial and temporal proximity, it is likely that cellular resolution of hormone contents is essential to explain physiological responses to auxins and cytokinins.},
	language = {en},
	number = {2},
	urldate = {2021-11-08},
	journal = {The Plant Journal},
	author = {Eklöf, Staffan and Åstot, Crister and Sitbon, Folke and Moritz, Thomas and Olsson, Olof and Sandberg, Göran},
	year = {2000},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313x.2000.00762.x},
	keywords = {IAA, Nicotiana tabacum, cytokinin, morphology, ratio hypothesis, transgenic plants},
	pages = {279--284},
}

1999 (3)

Dwarf (di)haploid pito mutants obtained from a tetraploid potato cultivar (Solanum tuberosum subsp. tuberosum) via anther culture are defective in gibberellin biosynthesis. Valkonen, J. P. T., Moritz, T., Watanabe, K. N., & Rokka, V. Plant Science, 149(1): 51–57. November 1999.

Paper doi link bibtex abstract

@article{valkonen_dwarf_1999,
	title = {Dwarf (di)haploid pito mutants obtained from a tetraploid potato cultivar ({Solanum} tuberosum subsp. tuberosum) via anther culture are defective in gibberellin biosynthesis},
	volume = {149},
	issn = {0168-9452},
	url = {https://www.sciencedirect.com/science/article/pii/S0168945299001417},
	doi = {10/b29hzp},
	abstract = {Nine dwarf (di)haploid lines (2n=2×=24) were obtained from the tetraploid (2n=4×=48), long day-adapted potato cultivar ‘Pito’ (Solanum tuberosum subsp. tuberosum) through anther culture. They grew slowly, had very short internodes, compact and ball-shaped appearance, and dark green leaves. Dwarfism was due to a recessive gene, designated pito. Endogenous gibberellin contents were measured in the leaves of dwarf and wild-type lines by gas chromatography linked to mass spectrometry (GC-MS). High amounts of GA19, GA20, GA29, GA1, and GA8 were detected in the wild-type plants, which indicated that the early 13-hydroxylation pathway was predominantly used for GA biosynthesis in S. t. subsp. tuberosum. Also GA53, GA15 and GA9 were detected but not quantified. Very low endogenous amounts of all analysed GAs were detected in the pito mutants, indicating a block at an early part of the GA biosynthesis pathway. The dwarf lines strongly and quickly responded to the exogenous application of low amounts (79 nM) of bioactive GA (GA3), which restored normal growth and confirmed that the pito dwarfs were synthesis mutants and not GA response mutants.},
	language = {en},
	number = {1},
	urldate = {2021-11-08},
	journal = {Plant Science},
	author = {Valkonen, Jari P. T. and Moritz, Thomas and Watanabe, Kazuo N. and Rokka, Veli-Matti},
	month = nov,
	year = {1999},
	keywords = {Dwarf, Gas chromatography mass spectrometry GC-MS, Gibberellin, Potato},
	pages = {51--57},
}

Extragenic Suppressors of the Arabidopsis gaiMutation Alter the Dose-Response Relationship of Diverse Gibberellin Responses1. Peng, J., Richards, D. E., Moritz, T., Caño-Delgado, A., & Harberd, N. P. Plant Physiology, 119(4): 1199–1208. April 1999.

Extragenic Suppressors of the Arabidopsis gaiMutation Alter the Dose-Response Relationship of Diverse Gibberellin Responses1 [link]

Paper doi link bibtex abstract

@article{peng_extragenic_1999,
	title = {Extragenic {Suppressors} of the {Arabidopsis} {gaiMutation} {Alter} the {Dose}-{Response} {Relationship} of {Diverse} {Gibberellin} {Responses1}},
	volume = {119},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.119.4.1199},
	doi = {10/bd2xj4},
	abstract = {Active gibberellins (GAs) are endogenous factors that regulate plant growth and development in a dose-dependent fashion. Mutant plants that are GA deficient, or exhibit reduced GA responses, display a characteristic dwarf phenotype. Extragenic suppressor analysis has resulted in the isolation of Arabidopsis mutations, which partially suppress the dwarf phenotype conferred by GA deficiency and reduced GA-response mutations. Here we describe detailed studies of the effects of two of these suppressors,spy-7 and gar2–1, on several different GA-responsive growth processes (seed germination, vegetative growth, stem elongation, chlorophyll accumulation, and flowering) and on the in planta amounts of active and inactive GA species. The results of these experiments show that spy-7 and gar2–1affect the GA dose-response relationship for a wide range of GA responses and suggest that all GA-regulated processes are controlled through a negatively acting GA-signaling pathway.},
	number = {4},
	urldate = {2021-11-08},
	journal = {Plant Physiology},
	author = {Peng, Jinrong and Richards, Donald E. and Moritz, Thomas and Caño-Delgado, Ana and Harberd, Nicholas P.},
	month = apr,
	year = {1999},
	pages = {1199--1208},
}

The Arabidopsis Dwarf Mutant shi Exhibits Reduced Gibberellin Responses Conferred by Overexpression of a New Putative Zinc Finger Protein. Fridborg, I., Kuusk, S., Moritz, T., & Sundberg, E. The Plant Cell, 11(6): 1019–1031. June 1999.

The Arabidopsis Dwarf Mutant shi Exhibits Reduced Gibberellin Responses Conferred by Overexpression of a New Putative Zinc Finger Protein [link]

Paper doi link bibtex abstract

@article{fridborg_arabidopsis_1999,
	title = {The {Arabidopsis} {Dwarf} {Mutant} shi {Exhibits} {Reduced} {Gibberellin} {Responses} {Conferred} by {Overexpression} of a {New} {Putative} {Zinc} {Finger} {Protein}},
	volume = {11},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.11.6.1019},
	doi = {10/cx9c78},
	abstract = {shi (for short internodes), a semidominant dwarfing mutation of Arabidopsis caused by a transposon insertion, confers a phenotype typical of mutants defective in the biosynthesis of gibberellin (GA). However, the application of GA does not correct the dwarf phenotype of shi plants, suggesting that shi is defective in the perception of or in the response to GA. In agreement with this observation, the level of active GAs was elevated in shi plants, which is the result expected when feedback control of GA biosynthesis is reduced. Cloning of the SHI gene revealed that in shi, the transposon is inserted into the untranslated leader so that a cauliflower mosaic virus 35S promoter in the transposon reads out toward the SHI open reading frame. This result, together with mRNA analysis, suggests that the phenotype of the shi mutant is a result of overexpression of the SHI open reading frame. The predicted amino acid sequence of SHI has acidic and glutamine-rich stretches and shows sequence similarity over a putative zinc finger region to three presumptive Arabidopsis proteins. This suggests that SHI may act as a negative regulator of GA responses through transcriptional control.},
	number = {6},
	urldate = {2021-11-08},
	journal = {The Plant Cell},
	author = {Fridborg, Ingela and Kuusk, Sandra and Moritz, Thomas and Sundberg, Eva},
	month = jun,
	year = {1999},
	pages = {1019--1031},
}

1997 (2)

Ectopic expression of oat phytochrome A in hybrid aspen changes critical daylength for growth and prevents cold acclimatization. Olsen, J. E., Junttila, O., Nilsen, J., Eriksson, M. E., Martinussen, I., Olsson, O., Sandberg, G., & Moritz, T. The Plant Journal, 12(6): 1339–1350. 1997. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313x.1997.12061339.x

Ectopic expression of oat phytochrome A in hybrid aspen changes critical daylength for growth and prevents cold acclimatization [link]

Paper doi link bibtex abstract

@article{olsen_ectopic_1997,
	title = {Ectopic expression of oat phytochrome {A} in hybrid aspen changes critical daylength for growth and prevents cold acclimatization},
	volume = {12},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-313x.1997.12061339.x},
	doi = {10/c5z6sf},
	abstract = {Survival of temperate-zone tree species under the normal summer-winter cycle is dependent on proper timing of apical growth cessation and cold acclimatization. This timing is primarily based on the perception of daylength, and through evolution many tree species have developed photoperiodic ecotypes which are closely adapted to the local light conditions. The longest photoperiod inducing growth cessation, the critical photoperiod, is inherited as a quantitative character. The phytochrome pigment family is the probable receptor of daylength, but the exact role of phytochrome and the physiological basis for the different responses between photoperiodic ecotypes are not known. This report shows for the first time that over-expression of the oat phytochrome A gene (PHYA) in a tree significantly changes the critical daylength and effectively prevents cold acclimatization. While the critical daylength for elongation growth in the wild-type of hybrid aspen (Populus tremula × tremuloides) was approximately 15 h, transgenic lines with a strong expression of the oat PHYA gene did not stop growing even under a photoperiod of 6 h. Quantitative analysis of gibberellins (GA) as well as indole-3-acetic acid (IAA) revealed that levels of these were not down-regulated under short days in the transgenic plants expressing high levels of oat PHYA, as in the wild-type. These results indicate that photoperiodic responses in trees might be regulated by the amount of PHYA gene expressed in the plants, and that the amount of phytochrome A (phyA) affects the metabolism of GAs and IAA.},
	language = {en},
	number = {6},
	urldate = {2022-03-11},
	journal = {The Plant Journal},
	author = {Olsen, Jorunn E. and Junttila, Olavi and Nilsen, Jarle and Eriksson, Maria E. and Martinussen, Inger and Olsson, Olof and Sandberg, Göran and Moritz, Thomas},
	year = {1997},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313x.1997.12061339.x},
	pages = {1339--1350},
}

Phytochrome Overexpression and Cold Hardiness in Transgenic Populus. Junttila, O., Olsen, J. E., Nilsen, J., Martinussen, I., Moritz, T., Eriksson, M., Olsson, O., & Sandberg, G. In Li, P. H., & Chen, T. H. H., editor(s), Plant Cold Hardiness: Molecular Biology, Biochemistry, and Physiology, pages 245–255. Springer US, Boston, MA, 1997.

Phytochrome Overexpression and Cold Hardiness in Transgenic Populus [link]

Paper doi link bibtex abstract

@incollection{junttila_phytochrome_1997,
	address = {Boston, MA},
	title = {Phytochrome {Overexpression} and {Cold} {Hardiness} in {Transgenic} {Populus}},
	isbn = {978-1-4899-0277-1},
	url = {https://doi.org/10.1007/978-1-4899-0277-1_22},
	abstract = {Photoperiodic effects on woody plants were reported already by Gardner and Allard in 1923 and comprehensive studies during the ’50s confirmed the role of photoperiod as an important environmental regulator of growth and growth cessation in many northern tree species (Nitsch, 1957; Wareing, 1956). In woody plants cessation of apical growth is a prerequisite for cold acclimation (Weiser, 1970) and photoperiod, as a factor controlling growth cessation, is therefore an important environmental signal for initiation of cold acclimation. In many cases a proper timing of acclimation and deacclimation, in respect to annual variation of temperature conditions, is more critical for winter survival than the maximum level of frost hardiness. Also in such coniferous species where cessation of apical growth is not controlled by photoperiod, short photoperiod is necessary for good cold acclimation, low temperature causes no or only a limited level of hardiness if combined with long day conditions (Schwarz, 1970; Aronsson, 1975; Christersson, 1978; Jonsson et al., 1981). Thus, photoperiod may have both an indirect, through induction of growth cessation, and a more direct influence on cold acclimation in woody plants.},
	language = {en},
	urldate = {2022-03-11},
	booktitle = {Plant {Cold} {Hardiness}: {Molecular} {Biology}, {Biochemistry}, and {Physiology}},
	publisher = {Springer US},
	author = {Junttila, O. and Olsen, J. E. and Nilsen, J. and Martinussen, I. and Moritz, T. and Eriksson, M. and Olsson, O. and Sandberg, G.},
	editor = {Li, Paul H. and Chen, Tony H. H.},
	year = {1997},
	doi = {10.1007/978-1-4899-0277-1_22},
	keywords = {Cold Acclimation, Cold Hardiness, Growth Cessation, Photoperiodic Response, Short Photoperiod},
	pages = {245--255},
}

1996 (1)

Expression of the Agrobacterium rhizogenes rolC Gene in a Deciduous Forest Tree Alters Growth and Development and Leads to Stem Fasciation. Nilsson, O., Moritz, T., Sundberg, B., Sandberg, G., & Olsson, O. Plant Physiology, 112(2): 493–502. October 1996.

Expression of the Agrobacterium rhizogenes rolC Gene in a Deciduous Forest Tree Alters Growth and Development and Leads to Stem Fasciation [link]

Paper doi link bibtex abstract

@article{nilsson_expression_1996,
	title = {Expression of the {Agrobacterium} rhizogenes {rolC} {Gene} in a {Deciduous} {Forest} {Tree} {Alters} {Growth} and {Development} and {Leads} to {Stem} {Fasciation}},
	volume = {112},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.112.2.493},
	doi = {10.1104/pp.112.2.493},
	abstract = {We have altered the growth and development of a deciduous forest tree by transforming hybrid aspen (Populus tremula x Populus tremuloides) with the Agrobacterium rhizogenes rolC gene expressed under the strong cauliflower mosaic virus 35S promoter. We demonstrate that the genetically manipulated perennial plants, after a period of dormancy, maintain the induced phenotypical changes during the second growing period. Furthermore, mass-spectrometrical quantifications of the free and conjugated forms of indole-3-acetic acid and cytokinins and several gibberellins on one transgenic line correlate the induced developmental alterations such as stem fasciation to changes in plant hormone metabolism. We also show that the presence of the RolC protein increases the levels of the free cytokinins, but not by a process involving hydrolysis of the inactive cytokinin conjugates.},
	number = {2},
	urldate = {2024-10-07},
	journal = {Plant Physiology},
	author = {Nilsson, O. and Moritz, T. and Sundberg, B. and Sandberg, G. and Olsson, O.},
	month = oct,
	year = {1996},
	pages = {493--502},
}

1993 (2)

Hormonal Characterization of Transgenic Tobacco Plants Expressing the rolC Gene of Agrobacterium rhizogenes TL-DNA. Nilsson, O., Moritz, T., Imbault, N., Sandberg, G., & Olsson, O. Plant Physiology, 102(2): 363–371. June 1993.

Hormonal Characterization of Transgenic Tobacco Plants Expressing the rolC Gene of Agrobacterium rhizogenes TL-DNA [link]

Paper doi link bibtex abstract

@article{nilsson_hormonal_1993,
	title = {Hormonal {Characterization} of {Transgenic} {Tobacco} {Plants} {Expressing} the {rolC} {Gene} of {Agrobacterium} rhizogenes {TL}-{DNA}},
	volume = {102},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.102.2.363},
	doi = {10.1104/pp.102.2.363},
	abstract = {Transgenic tobacco (Nicotiana tabacum L. cv Wisconsin 38) plants expressing the Agrobacterium rhizogenes rolC gene under the control of the cauliflower mosaic virus 35S RNA promoter were constructed. These plants displayed several morphological alterations reminiscent of changes in indole-3-acetic acid (IAA), cytokinin, and gibberellin (GA) content. However, investigations showed that neither the IAA pool size nor its rate of turnover were altered significantly in the rolC plants. The biggest difference between rolC and wild-type plants was in the concentrations of the cytokinin, isopentenyladenosine (iPA) and the gibberellin GA19. Radio-immunoassay and liquid chromatography-mass spectrometry measurements revealed a drastic reduction in rolC plants of iPA as well as in several other cytokinins tested, suggesting a possible reduction in the synthesis rate of cytokinins. Furthermore, gas chromatography-mass spectrometry quantifications of GA19 showed a 5- to 6-fold increase in rolC plants compared with wild-type plants, indicating a reduced activity of the GA19 oxidase, a proposed regulatory step in the gibberellin biosynthesis. Thus, we conclude that RolC activity in transgenic plants leads to major alterations in the metabolism of cytokinins and gibberellins.},
	number = {2},
	urldate = {2024-10-07},
	journal = {Plant Physiology},
	author = {Nilsson, O. and Moritz, T. and Imbault, N. and Sandberg, G. and Olsson, O.},
	month = jun,
	year = {1993},
	pages = {363--371},
}

Separation and identification of cytokinins using combined capillary liquid chromatography/mass spectrometry. Imbault, N., Moritz, T., Nilsson, O., Chen, H., Bollmark, M., & Sandberg, G. Biological Mass Spectrometry, 22(3): 201–210. 1993. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/bms.1200220310

Separation and identification of cytokinins using combined capillary liquid chromatography/mass spectrometry [link]

Paper doi link bibtex abstract

@article{imbault_separation_1993,
	title = {Separation and identification of cytokinins using combined capillary liquid chromatography/mass spectrometry},
	volume = {22},
	copyright = {Copyright © 1993 John Wiley \& Sons, Ltd.},
	issn = {1096-9888},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/bms.1200220310},
	doi = {10.1002/bms.1200220310},
	abstract = {Non-derivatized cytokinins were analysed by liquid chromatography/mass spectrometry (LC/MS). The effluent from a capillary reversed-phase high-performance liquid chromatography column was introduced into the ion source of a double-focusing mass spectrometer via a frit interface, and ions were generated by fast atom bombardment (FAB) with 1\% glycerol in the mobile phase acting as a matrix. Positive FAB spectra were obtained for base, riboside, ribotide and glucoside forms of cytokinins. The spectra were found to provide useful information for identification and structural elucidation of cytokinins. The LC/MS system was used to identify iso-pentenyladenosine in a purified extract from Norway spruce (Picea abies) needles. Quantitative analysis of iso-pentenyladenosine using (2H6)isopentenyladenosine as internal standard indicated levels of 1.2 ng g−1 fresh weight.},
	language = {en},
	number = {3},
	urldate = {2024-10-07},
	journal = {Biological Mass Spectrometry},
	author = {Imbault, Nadine and Moritz, Thomas and Nilsson, Ove and Chen, Hao-Jie and Bollmark, Marie and Sandberg, Göran},
	year = {1993},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/bms.1200220310},
	pages = {201--210},
}

Svenska

Research

Photo: Queena Xu

Light in excess of photosynthetic capacity can be damaging to cells constituents. Thus ways to protect against damage have evolved in photosynthetic organisms, including ways to minimize light absorption, detoxify reactive oxygen species generated by excess light, and dissipate excess absorbed light. Together, these processes are known as photoprotection.

For more information see also our lab website at https://malnoelab.com.

Despite the physiological importance of photoprotection, the molecular mechanisms that protect against light stress, especially those protecting against sustained light stress, remain largely unknown. In my group, we combine genetics, biochemistry, biophysics and physiology to elucidate the molecular mechanisms of photoprotection under sustained abiotic stress. Our research will provide insights into fundamental mechanisms of light energy capture, utilization and dissipation in plants.

Collage of four images showing Arabidopsis plants in a growth cabinet on the left and flurorescence images on the right

Arabidopsis plants and false-color images of chlorophyll fluorescence from Arabidopsis seedlings and Nicotiana leaf

Key Publications

Bru P, Steen CJ, Park S, Amstutz CL, Sylak-Glassman EJ, Leuenberger M, Lam L, Longoni F, Fleming GR, Niyogi KK and Malnoë A* (2021) Isolation of quenched light-harvesting complex II trimers from Arabidopsis leaves with sustained photoprotection (qH). bioRxiv: 2021.2007.2009.450705.
Yu, G, Pan, X, Hao, J, Shi, L, Zhang, Y, Wang, J, Xiao, Y, Yang, F, Lou, J, Chang, W, Malnoë, A* and Li, M* (2021) Structure of SOQ1 lumenal domains identifies potential disulfide exchange for negative regulation of photoprotection, qH. bioRxiv: 2021.2003.2016.435614
https://www.biorxiv.org/content/10.1101/2021.03.16.435614v1
Amstutz, C, Fristedt, R, Schultink, A, Merchant, S, Niyogi, KK, & Malnoë, A* (2020) An atypical short-chain dehydrogenase-reductase functions in the relaxation of photoprotective qH in Arabidopsis. Nat Plants 6:154–166
https://doi.org/10.1038/s41477-020-0591-9
Malnoë A (2018). Photoinhibition or photoprotection of photosynthesis? Update on the (newly termed) sustained quenching component qH. Environmental and Experimental Botany 154: 123-133
https://doi.org/10.1016/j.envexpbot.2018.05.005
Malnoë, A*, Schultink, A, Shahrasbi, S, Rumeau, D, Havaux, M, and Niyogi, KK* (2018). The Plastid Lipocalin LCNP is Required for Sustained Photoprotective Energy Dissipation in Arabidopsis. Plant Cell 30: 196-208
https://doi.org/10.1105/tpc.17.00536

CV A. Malnoë

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CV E. Stavrinidou

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Ecological genomics

Seed orchards and adaptability of production forests

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CV X.-R. Wang

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CV J. Leppälä

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CV T. Näsholm

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Wastewater reclamation and biomass generation by Nordic microalgae

Plant proteases

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CV C. Funk

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Utifrån min tidigare forskning om fotosyntes fokussera mitt arbete för närvarande på två nya inriktningar: Växtproteasernas funktion och Nordiska mikroalgernas potential för återvinning av avloppsvatten och produktion av biomassa.

Återvinning av avloppsvatten och produktion av biomassa med hjälp av nordiska mikroalger

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CV S. Björklund

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Ambient temperature & alternative pre-mRNA splicing

Regulation of flowering time & flower development

Trehalose 6 phosphate & SnRK1 signaling

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CV M. Schmid

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CV T. Moritz

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