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Pinus densata is the dominant forest-forming species in the southeastern Qinghai-Tibetan Plateau. Photo: Wei Zhao
The plant journal New Phytologist has selected a study led by Umeå University researcher Xiao-Ru Wang as its cover story in the October issue. The paper is about effects of landscapes and range expansion on population structure and local adaptation.
“Understanding the origin and distribution of genetic diversity across landscapes is critical for predicting the future of organisms in changing climates”, says Xiao-Ru Wang, professor at the Department of Ecology and Environmental sciences at Umeå University and associated group leader at UPSC.
The study addresses a fundamental question in landscape genetics: the relative roles of population history, geography and natural selection in shaping genetic diversity in wild populations.
In the study, Xiao-Ru and a Chinese research group analyzed diversity and population structure in the pine tree Pinus densata, a keystone species on the Qinghai-Tibetan Plateau. They mapped the genetic variation to geographical and climate variables across the distribution range to establish the contribution of geo- and eco-factors to the observed spatial genetic pattern. Based on this information, the study further simulated how its genetic legacy may limit the persistence of P. densata in future climates.
The results illustrate that significant adaptation to extreme environment, when coupled with reduced diversity as a result of past demographic history, constrains potential evolutionary response to climate change.
As the dominant forest-forming species in the southeastern Qinghai-Tibetan Plateau, the resilience of P. densata underlies regional ecosystem function. Qinghai-Tibetan Plateau is the largest plateau on earth and also the most vulnerable ecosystem. While the deep valleys and high mountain ridges of the Qinghai-Tibetan Plateau have helped to create a global biodiversity hotspot, these same features can constrain adaptive responses to climate change. This is a particular concern for organisms with limited dispersal ability.
“The strong signal of genomic vulnerability in P. densata may be representative for other plateau endemics. As we accumulate further examples, it will become possible to gain a more general understanding of how demography and landscape factors constrain or promote adaptation to novel and changing environments,” Prof. Xiao-Ru Wang explains.
The study was performed in close collaboration with Beijing Forestry University; the joint team has been working together on this study system for more than 20 years.
The original article
Zhao, W., et al: Effects of landscapes and range expansion on population structure and local adaptation. New Phytologist Volume 228, Issue 1, October 2020. Pages 330-3432020. https://doi.org/10.1111/nph.16619
More information about Xiao-Ru Wang's research
More information about evolutionary biology research at Umeå University
Text: Ingrid Söderbergh
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An international research team led by Colin Turnbull from Imperial College London and Karin Ljung from UPSC showed that cytokinin, a substance that regulates plant growth, can be sensed on the outside of the plant cell. For a long time, researchers were convinced that cytokinin is mainly perceived within the cell, initiating reactions to adjust the cell’s development. These new findings, that were published last week in the journal Nature Communications, will fuel a 20-year-old discussion.
Cytokinins have many different functions in the plant. They control root and shoot growth, autumn senescence, they regulate cell division and much more. Within the plant cell, cytokinins bind to cytokinin receptors and these proteins then initiate a reaction that leads to, for example, enhanced shoot growth. This was the common view so far. In the current publication, the research team found a proportion of cytokinin receptors also sitting on the surface of the cell and they showed that they are fully functional there.
“The discussion about cytokinin receptor localization started almost 20 years ago when the first receptor was discovered. The recent view was that the receptors were mainly localised in the endoplasmic reticulum, which is a membrane system located within the cell,” explains Ioanna Antoniadi, who is postdoc in Karin Ljung’s group and first author of the article. “However, it was never excluded that the receptors might also sit in the plasma membrane, the membrane surrounding the cell.”
Initially, the researchers wanted to identify which of the different existing cytokinin forms is the active one that regulates root growth and development. They isolated individual cells from the root of thale cress, measured the cytokinin contents within and were really surprised to find similar amounts of active cytokinins inside and outside of the cell.
“We were wondering what these active cytokinins are doing out there and if they could actually be perceived,” says Ioanna Antoniadi, who started this work as part of her PhD thesis in London in 2013. “We started a collaboration with Karel Doležal and his team from the Palacký University in Olomouc, Czech Republic, who developed an incredible tool to answer our question.”
The Czech group synthesized active cytokinin molecules and attached them to sepharose beads that were bigger in size than a plant cell. These bound cytokinins could not enter the plant cell but were still able to activate a cytokinin response in the cell.
During their latest experiments, the researchers got in touch with yet another research team that was coming to the same conclusions as them but used a completely different approach. They were able to publish their results at the same time in the same journal fuelling the ongoing discussion even more.
Left: Microscopic photo of isolated plant cells from Thale cress roots (protoplasts, small circles) next to sepharose beads with bound cytokinin molecules (big circles). The cell wall of the plant cells was removed with digesting proteins leaving only the cell surrounding plasma membrane. Right: Graphic illustrating the results of the Nature Communications article. The common view was that active cytokinin binds to cytokinin receptors that are located in the endoplasmic reticulum - a membrane system in the plant cell. The researchers showed that active cytokinins are available outside and inside of the plant cell and that cytokinin receptors are also located in the plasma membrane of the cell. They used active cytokinin molecules bound to sepharose beads that are bigger than the plant cell to prove that the receptors in the plasma membrane are fully functional and can also initiate a typical cytokinin response in the cell. (Figure: Ioanna Antoniadi)The article
Antoniadi I, Novák O, Gelová Z, Johnson A, Plíhal O, Simerský R, Mik V, Vain T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko J, Robert S, Friml J, Doležal K, Ljung K, Turnbull C. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communication 11, 4284 (2020).
https://doi.org/10.1038/s41467-020-17700-9
The corresponding article that was published at the same time:
Kubiasová K, Montesinos JC, Šamajová O, Nisler J, Mik V, Semerádová H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K, Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communication 11, 4285 (2020).
https://doi.org/10.1038/s41467-020-17949-0
For more information, please contact:
Ioanna Antoniadi
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences (SLU)
Email:
Karin Ljung
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences (SLU)
Email:
Phone: +46 (0)90 786 8355
https://www.upsc.se/karin_ljung
Colin Turnbull
Department of Life Sciences
Imperial College london
Email:
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Linghua Zhou (right) and her supervisor Rosario García Gil (left) after Linghua Zhou's PhD defence (Photo: Sonali Ranade)
Norway spruce is one of the industrially most important trees, also here in Sweden. Its generation time is with about 20 years relatively long making traditional breeding tedious. Linghua Zhou, PhD student in Rosario García Gil’s group, investigated the potential of different genomic-based breeding methods to assist in Norway spruce breeding. She showed that several of these new breeding methods have the potential to improve and speed up the breeding process of Norway spruce in future. Linghua Zhou successfully defended her PhD thesis at SLU on Friday last week, 28th of August.
Tree breeders look for individuals with the most favourable characteristics and use these then as parents in the next breeding cycle. Tree height, stem diameter, wood quality parameters and also resistance to fungi infection are traits the breeders are interested in. Genomic-based breeding methods try to relate such traits to the genetic information of the tree and use then the genetic information to select the best tree candidates for the breeding. Often this can speed up the breeding cycle because the genetic information can be analysed already in young trees when differences in a certain trait might not be seen yet on the tree.
“Genomic selection as one of genomic-based breeding method is applied almost routinely in animal and crop breeding, like for example for cattle, maize or wheat and also the breeding cycle of fast-growing trees like eucalypts and poplar could be shortened using these methods”, explains Linghua Zhou. “Another advantage is that the most interesting trees can be selected more accurately than with just traditional methods.”
Linghua Zhou and her colleagues firstly tried to identify marker regions in the DNA sequence that are determining how a certain trait is expressed in the tree. They focussed on different wood quality traits, like for example wood density and stiffness, but also looked for marker regions that determine the resistance to fungi. Their results showed that the genomic information of a tree partly determines which fungi species colonise the tree’s buds causing potentially a huge financial lost due to fungal infection.
“By genome-wide association study, another genomic-based breeding method, we successfully identified some genes associating with some traits we were interested in. However, they cannot describe the major variance that we see for the trait which means we cannot use them for breeding directly,” says Linghua Zhou. “That is why we moved from genome-wide association studies to genomic selection which uses the full genomic information instead of just certain DNA regions to predict the trait values of our population of trees.”
The main challenge Linghua Zhou and her colleagues faced during their analyses was the still low quality of the sequenced Norway spruce genome which limits the power of the genomic-based breeding methods. Also, the number of tree individuals that were analysed was partly too small to really use some of the methods to their full extent.
“Our results help to improve the understanding of genetic structure for some complex traits for Norway spruce. And even though genomic-based breeding has limited power at this state, I believe that it will be the trend in future for Norway spruce breeding,” concludes Linghua Zhou.
About the public defence:
The public defence took place on Friday, 28th of September at SLU Umeå. Faculty opponent was Marcio Resende from the Horticultural Sciences Department of the University of Florida, USA. Linghua Zhou's supervisor was María Rosario García Gil. The dissertation was live broadcasted on https://play.slu.se/.
Title of the thesis: Towards genomic-based breeding in Norway spruce
Link to the thesis: https://pub.epsilon.slu.se/17349/
For more information, please contact:
Linghua Zhou
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences
Email:
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Field site with transgenic hybrid aspen trees, taken 2017 (Photo: Marta Derba-Maceluch)
Researchers from the Swedish University of Agricultural Sciences and Umeå University have developed genetically modified hybrid aspen that have a higher energy yield for the production of biofuels. The trees have grown well in greenhouses, and were now tested for the first time under more stressful field conditions. Some of the modified trees were more susceptible to insect infestation but others grew very well also in the field. The results were published in the journal Frontiers in Plant Sciences.
Hybrid aspen, a crossing between European and American aspen, is one of Sweden's most productive tree species which grows better than the usual aspen. Rapidly growing deciduous trees are used as an important resource for energy supply, but some of the properties of woody cell walls limit the possibility to produce biofuels and "green" chemicals from it.
To use the energy stored in the wood, cellulose first needs to be digested by enzymes releasing sugars that are then converted into bioethanol by microorganisms. The problem is that the cell wall component xylan is often extensively acetylated in hardwoods like hybrid aspen making the cellulose of the wood less accessible and thus the bioethanol production less efficient.
Ewa Mellerowicz and her group at the Umeå Plant Science Centre have reduced the acetylation of xylan by modifying hybrid aspen transgenically. The transgenic trees performed well in greenhouse experiments and the cellulose in their wood was easier to digest by enzymes to release more sugars. 18 of these different transgenic hybrid lines have now been evaluated for the first time in field trials, where they are subjected to much greater stress coming from the environment.
“The field trial was performed in agreement with the Swedish and European rules for handling genetically modified plants,” says Ewa Mellerowicz, professor SLU. “The most important outcome of the study was that we could demonstrate that reduction of acetylation, when targeted to wood tissue is a viable strategy to improve hardwood for biorefinery.”
The researchers used different strategies to modify the acetylation of xylan. They either prevented that the acetylation of xylan takes place or they cleaved off the acetyl group with the help of fungal enzymes that were introduced in the tree, and the modification was either directed specifically to the wood or introduced to the whole tree.
Most of the tested hybrid aspen trees grew similar to non-modified control trees planted in the same field. However, the researchers could see that trees in which the genetic modification was limited to the wood performed better than trees in which the modification was active in the whole tree.
“The trial showed the importance of testing modified aspen trees under field conditions to follow up results from lab and greenhouse experiments. It is urgent to continue and develop the field-testing programs”, points out Ulf Johansson, experimental manager at the Unit for Field-based Forest Research at SLU. Marta Derba-Maceluch, first author of the article and researcher at UPSC adds: “Our study shows that early field testing can be worth more than investing in extensive greenhouse experimentations.”
Especially those trees in which the fungal gene was active in the whole plant suffered much more from insect attacks. These trees were growing slower than the controls and their leaves had an altered amount and composition of phenolic compounds, chemical compounds that are important for plants to defend themselves against insect attacks or other types of stress.
“Our study confirmed that cell wall acetylation may alter both, the composition and concentrations of phenolic compounds in hybrid aspen”, explains Benedicte R. Albrectsen, researcher in chemical ecology and plant defence dynamics at Umeå University. “However, the main finding to me is that reduced cell wall acetylation did not cause any outstanding general differences in growth and resistance to herbivores and pathogens when compared to the untransformed wild type.”
The field site, where the experiment was done, was located in Våxtorp in the south of Sweden. 636 trees were planted there in August 2014. In the coming four years, their growth and the damage by insects, fungi, frost or other environmental stresses was monitored regularly until the harvest in 2018. Currently, researchers from Umeå University, lead by Professor Leif Jönsson, evaluate the harvested samples to see if the cellulose is still easier to digest. The best improved trees will be further tested at a larger scale in a biorefinery in Örnsköldsvik.
The article
Derba-Maceluch Marta, Amini Fariba, Donev Evgeniy N., Pawar Prashant Mohan-Anupama, Michaud Lisa, Johansson Ulf, Albrectsen Benedicte R., Mellerowicz Ewa J. (2020). Cell Wall Acetylation in Hybrid Aspen Affects Field Performance, Foliar Phenolic Composition and Resistance to Biological Stress Factors in a Construct-Dependent Fashion. Frontiers in Plant Science 11: 651
https://doi.org/10.3389/fpls.2020.00651
For more information, please contact:
Ewa Mellerowicz
Professor
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences (SLU)
Email:
Phone: +46 (0)90 786 8367
https://www.upsc.se/ewa_mellerowicz
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Jean Claude Nzayisenga and his supervisor Anita Sellstedt after the defence (Photo: Anne Honsel)
Microalgae have a high potential for biodiesel production and in parallel benefit domestic sewage treatment. Jean Claude Nzayisenga, PhD student in Anita Sellstedt’s group at the Department of Plant Physiology, validated a method to rapidly analyse the lipid, carbohydrate and protein content of microalgae. He also tested different growth conditions that improve quality of algal biodiesel and in parallel treat sewage. He successfully defended his PhD thesis at Umeå University on Monday, 15th of June.
Microalgae are photosynthetic, fast growing single cell organisms that live mostly in water and produce high amounts of proteins, fatty acids and carbohydrates. To measure the amount of these compounds produced during the growth of microalgae, Jean Claude Nzayisenga and his colleagues coupled the optical method Fourier-transform infrared spectroscopy (FTIR) with the complex mathematical modelling method Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS). They demonstrated that the combination of the two methods is useful to monitor changes in fatty acid, carbohydrates and protein contents.
“FTIR was already shown to allow measuring fatty acid and carbohydrate contents of microalgae but used alone, it relied on the assumption that the protein content remains constant during cultivation, which may not always be true”, says Jean Claude Nzayisenga. “We compared our results with the ones gained by using other standard techniques and showed that FTIR is a useful method for monitoring changes of the biochemical composition in microalgae. As FTIR is a relatively fast method, it could be even applied on a daily basis to monitor a microalgae cultivation system.”
Jean Claude Nzayisenga worked with microalgae species that were isolated in Northern Sweden and are adjusted to the long winters with low temperatures and only a few hours of light. Some of these microalgae are able to grow even without light as long as an alternative carbon-source is given. Jean Claude Nzayisenga and his colleagues grew microalgae either with light and carbon dioxide to allow doing them photosynthesis, with light and glucose or glycerol as carbon source so that they were still able to make photosynthesis but not completely rely on it, or they grew them without light but with glucose or glycerol, so that they were fully depended on the external carbon source.
“When we grew microalgae without light but with glycerol as carbon source, we could see that the microalgae are able to produce high amounts of fatty acids and that the composition of these fatty acids looks promising for biodiesel production”, explains Jean Claude Nzayisenga. “We chose glycerol because it is a cheaper carbon source than glucose and it is a by-product of biodiesel production offering a more sustainable and cost-effective production circuit. In future, it would be interesting to test also other carbon sources that are produced as industrial by-products or come from food waste.”
In another experiment, Jean Claude Nzayisenga tested the effect of different light intensities on the production of fatty acids. Under high light intensity, the microalgae produced more fatty acids than under low light intensities and also here the composition of fatty acids looked promising for biodiesel production. The team around Jean Claude Nzayisenga took a closer look and analysed which biochemical changes were associated with the accumulation of fatty acids. When growing without light and with glycerol, fatty acids accumulated on the expense of carbohydrates, while under high light conditions the content of proteins decreased instead.
In most of his experiments, Jean Claude Nzayisenga used not just one microalgae strain but compared different strains and evaluated which strain has the best properties for biodiesel production under the respective growth conditions. He also analysed the capability of the microalgae strains to take up nutrients from municipal wastewater to see if they could benefit sewage treatment. All tested microalgae strains were able to take up most of the nitrogen and phosphor from the wastewater which are the main contaminants in municipal wastewater. This offers the possibility to use microalgae for the wastewater treatment and in parallel produce raw material for biodiesel production.
About the public defence:
The public defence took place on Monday, 15th of June at Umeå University. Faculty opponent was Professor Ashton Keith Cowan from the Institute for Environmental Biotechnology, Rhodes University, South Africa. Jean Claude Nzayisenga 's supervisor was Anita Sellstedt from the Department of Plant Physiology (UPSC). The dissertation was broadcasted via Zoom.
Title of the thesis: Autotrophic and heterotrophic culture of Nordic microalgae in wastewater for lipid production
Link to the thesis: https://www.diva-portal.org/smash/record.jsf?pid=diva2%3A1430620&dswid=1987
For more information, please contact:
Jean Claude Nzayisenga
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
Email:
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PhD Student Bastian Schiffthaler (Photo: Alena Aliashkevich)
Most plant and animal features arise from complex interactions of genes, proteins and metabolites. The identification and analysis of these complex genetic traits is very challenging, especially when the sequenced genomes are fragmented. Bastian Schiffthaler, PhD student in Nathanial Street’s group, improved the genome information from European aspen and developed bioinformatic tools that help to analyse complex genetic traits in plants. He has successfully defended his PhD thesis at Umeå University today, on the 12th of June.
For sequencing a genome, the DNA is normally cut into small pieces, the sequence is read and then bioinformatic software assembles the whole sequence information using overlapping regions of these small pieces in an iterative process that ideally yields full length chromosomes. For trees, which often have very complex genomes and most available genome assemblies are therefore not very contiguous. Bastian Schiffthaler worked on improving the contiguity of such genomes focussing on European aspen.
When Bastian Schiffthaler started, the genome sequence of European aspen was already quite good compared to for example Norway spruce. However, it was still fragmented which made it difficult to carry out analyses that depend on a highly contiguous assembly. Examples of this are the detection of DNA signatures that relate to traits via genome wide association, or studying evolutionary history by looking at large scale genomic rearrangements. “Our strategy included modern long read sequencing, polished with highly accurate short-read data and combined with an optical and a genetic map to further link the initially assembled scaffolds into fully assembled chromosomes. At close to 20,000 genetic markers, the genetic map is one of the most comprehensive ones created for any organism to date. This was an overwhelming mass of information that most of the commonly used free software programmes were not able to handle.”
Ordering markers on a genetic map is a classic application of the travelling salesman problem, which aims to find the shortest between a set of points or locations. To derive the perfect order for only sixty markers would take more calculations than are atoms in the universe, hence all software relies on approximations, but even those were too slow for a dataset of this size. To overcome this problem, Bastian Schiffthaler developed “BatchMap”, a software package that speeds up the computations required to find the order of genetic markers with the highest likelihood given their inheritance patterns.
“BatchMap” divides calculations into small batches, which are easy to compute and can run in parallel. This drastically decreased the calculation time and Bastian Schiffthaler could produce a dense map of genetic signatures on the European aspen chromosomes. Since the creation of BatchMap, it has now been adopted by other genome projects such as those assembling the Norway spruce or a strawberry genome, which comprises eight chromosome sets.
“We wanted to evaluate our improved assembly in the context of genome wide association studies to look for genes that are involved in the salicinoid metabolism. These metabolites are only available in Populus and Salix species and help to protect the plant against herbivores,” explains Bastian Schiffthaler. “When compared to previous attempts using the more fragmented assembly, we could see that our new genome version improved the analysis of this complex trait a lot and we were able to gain new insights into the evolution of the different Populus species.”
To identify genes that are controlling complex traits is very challenging. Bastian Schiffthaler and his colleagues studied leaf shape variation in European aspen, a complex trait that is inherited from the parents but still highly diverse between individuals. Their results show that leaf shape is controlled by a complex network of many different genes, but the individual gene often exerted only a minor influence on the final leaf shape.
Bastian Schiffthaler believes that it in order to better understand the workings of traits like leaf shape, an integrative approach, where traits are analysed at all stages that contribute to their emergence. He therefore developed “Seidr”, a toolkit to study the interactions of genes that are actively being made into protein within an organism. He hopes that integrating “Seidr” with other layers of data will enable scientists to better predict complex traits in the future.
About the public defence:
The public defence took place on Friday, 12th of June at Umeå University. The faculty opponent was Marek Mutwil from The School of Biological Sciences at Nanyang Technological University in Singapore, who participated remotely in the defence. Supervisor was Nathaniel Street. The defence was broadcasted live. Interested people could participate via Zoom.
Title of the thesis: Embracing the Data Flood – Integrating Diverse Data to Improve Phenotype Association Discovery in Forest Trees.
Link to the thesis in DIVA: http://umu.diva-portal.org/smash/record.jsf?pid=diva2%3A1429905&dswid=8163
For more information, please contact
Bastian Schiffthaler
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
Email:
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The Swedish Foundation for Strategic Research (SFF) approved last week four SSF Agenda 2030 Research (ARC) Centers on Future Advanced Technology for Sustainability. The project “Re-designing photosynthesis for future food security” with Åsa Strand from UPSC as main applicant was granted. Åsa Strand and her three co-applicants want to improve photosynthesis and apply CRISPR/Cas9 and other genetic modification techniques to increase crop productivity.
The world-wide crop production is stagnating while the population is growing which threatens food security. “Zero hunger” is defined as one of 17 Sustainable Development Goals that are addressed by the Agenda 2030. Åsa Strand and her co-applicants plan to target this goal by improving crop productivity through optimising the efficiency of photosynthesis. Because plants are only using a fraction of the light energy that they perceive, the researchers want to optimise the harvest of the light energy by plants and identify limiting steps during carbon fixation.
Åsa Strand’s co-applicants are Alexey Amunts from Stockholm University, Paul Hudson from the Royal Institute of Technology (KTH) and Alizée Malnoë who is like Åsa Strand working at the Department of Plant Physiology at Umeå University. All of them are internationally recognized and bring in different competences to the project. They will closely collaborate with the biotechnology company SweTree Technologies which will help them to test their engineering strategies in transformable crop species that are relevant to the Swedish agriculture.
The researchers will use cyanobacteria and Arabidopsis as two model systems in parallel. Cyanobacteria use the light energy much more efficiently compared to plants and also their carbon fixation rates are higher. The plant chloroplasts, the place where photosynthesis takes place, share the same ancestor as todays cyanobacteria. During evolution, photosynthesis in the chloroplast was adjusted to coordinate it with the more complex development and growth of plants – on the expense of the photosynthetic efficiency. The researchers hope that they can transfer knowledge from cyanobacteria to the chloroplasts of plants and maybe even re-introduce genes that were lost or modified in plants during evolution.
Their assumption is that photosynthesis in Cyanobacteria is adapted first and foremost to biomass formation. They think that the comparison between Cyanobacteria and plants will allow them to define the bottlenecks that restrict the light harvesting efficiency and limits the carbon fixation rate. Using multiple research lines and genetic engineering, they hope to break the bottlenecks and improve the efficiency of photosynthesis in plants and like this increase their productivity. Several initiatives are working internationally on improving biological photosynthetic efficiency using different approaches and the researchers hope to complement these efforts with their novel approach.
Four strategic areas have been identified by the Swedish Foundation for Strategic Research in the frame of their call for SSF-ARC Centers. These were “Future Nuclear Power”, “Plant Biotechnology including GMO and CRISPR/Cas9” which is the area that Åsa Strand applied for, “Hydrogen/Fuel Cells and Next Generation of Antibiotics and/or Actions to prevent pandemics”. In every strategic area, one application was granted. The four centers will share 200 million SEK.
The researchers plan to compare cyanobacteria and plant chloroplasts. Both have common ancestors, but their evolution separated about 1 billion years ago (1bya). The researchers want to transfer knowledge from the photosynthetic more efficient cyanobacteria to the plant chloroplast and like this improve crop productivity (Figure: Daria Chrobok, DC SciArt).Link to the Swedish press release from SSF:
https://strategiska.se/pressmeddelande/har-ar-de-ssf-arc-center-som-far-dela-pa-200-miljoner-kronor/
Information about the applicants:
Alexey Amunts
Associate Professor
Department of Biochemistry and Biophysics
Stockholm University
E-mail:
Phone: +46(0)8161003
https://www.su.se/english/profiles/aamun-1.219419
Paul Hudson
Associate Professor
Division of Systems Biology
KTH Royal Institute of Technology
E-mail:
Phone: +46 (0)70 783 95 07
https://www.kth.se/profile/huds
Alizée Malnoë
Assistant Professor
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
E-mail:
Phone: +46(0)907869314
https://www.upsc.se/alizee_malnoe
Åsa Strand
Professor
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
E-mail:
Phone: +46 (0)90 786 9314
https://www.upsc.se/asa_strand
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PhD student Chanaka Mannapperuma (photo: Lena Maria)
[2020-06-04] Chanaka Mannapperuma, PhD student in Nathaniel Street’s group at the Department of Plant Physiology and co-supervised by John Waterworth from the Department of Informatics, has developed bioinformatics tools that help biologists to analyse their complex genomics data. His aim was to create intuitive, easy to use tools that do not require specialized bioinformatics knowledge. He improved the design of the tools based on user experiences and general principals of the field of Human-computer interaction. Chanaka Mannapperuma will defend his PhD thesis at Umeå University on Thursday, 11th of June.
The topic of your PhD thesis is unusual for UPSC. What aroused your interest in this topic?
When I started at UPSC, there were not so many analysis tools available for Biologists to do their analysis easily. I have a computer science and interaction design education background, so this was a good opportunity to apply previous knowledge to make a database system and tools for Plant Biologists. Since most Biologists are not familiar with programming, they needed tools to analyse their data without learning to program themselves. I thought that this type of work is useful for UPSC and Stefan Jansson, Nathaniel Street, Andreas Sjödin and Simon Birve made me more interested and motivated to continue this work at the beginning.
How was it for you to do this type of work at UPSC?
I had a great companionship and pleasurable friendly working atmosphere at UPSC during my work. Most of my colleagues are plant biologists and they wanted to have a database system to store, filter and analyse their data. Thanks to my supervisor and his team, we managed to establish a web resource specialised for Biologists to make their research easier. I want to express my gratitude towards my colleagues and fellows at UPSC who offered constant support, availability and productive suggestions which were a determining factor for the success of my thesis.
Did it help that John Waterworth from the Department of Informatics, who is an expert in Human-computer interaction (HCI), was your second supervisor?
Yes, it was a great experience to work with John – already since I was a student in Human-computer interaction. He is an expert in this field as he has many years of experience as a psychologist. Being a psychologist, John has a good understanding and exceptional knowledge of human perception and cognitive behaviour. He was a great help to accomplish this work and thanks to John for this. Many more people from the Department of Informatics also contributed to this work. Anna Croon Fors, Karin Danielsson, Mikael Wiberg and Patrik Bjornfot are among others.
What is meant with Human-computer interaction?
The aim is to study how users interact with computer interfaces and how to use design principles, and visualization techniques to improve user interaction and make usable systems. HCI is a multidisciplinary field combining design, computer science, psychology, anthropology, sociology, ergonomics and others. This will help us to understand how we perceive different signals, process and interpret them using our cognitive abilities and evaluate the outcome. These are some of the main questions in HCI, and the entire design process helps us to make user-friendly tools.
Your thesis contains different aspects: programming, design and I guess a lot of communication with users. Which aspect did you like most?
Design, programming and user interaction are well connected. I am enjoying all three aspects and the entire design process, especially making useful tools for biologists that they can explore to gain biological insights. The design process starts with the prototype or the production tool of the previous version. To be specific, starting with the prototype, then apply design principles and visualisation techniques to reshape the tool and use heuristic evaluation methods to make usable tools with the help of user feedback. Users expect an interactively engaging and appealing experience in addition to the usable tool. Mere iteration of the design process will make better user-friendly and usable tools.
Was it difficult to get usable feedback from the users of your tools?
We used online surveys as our initial usability methods. However, we realised that although we have 1000 users that are using the PlantGenIE platform, very few of them were willing to answer the survey questions. But thanks to the technology, we had alternative usability methods such as web analytics to gain implicit user feedback. So, we could easily capture the user feedback.
I guess many biologists are very grateful for your work. Do you plan to continue working in this direction?
It was a pleasant experience, and I am enjoying work in this direction. I can also see the need for designing user centred tools that will help biologist to do their analysis much more easy. In addition to that, I have an excellent supervisor with a nice team. I am planning to continue working at UPSC and improving the resource for a while.
Chanaka Mannapperuma started to work at UPSC in 2010 as programmer with the task to develop an online tool to do a simple BLAST (Basic Local Alignment Search Tool) search for gene analyses as part of the PopGenIE website. This tool allows to compare a gene or protein sequences with a library of sequences and to identify similarities between the sequence of interest and library sequences. After four years working as programmer, he started his PhD and developed the primary tool further into an extended web resource with different functionalities for gene and genome analyses. The web resource can be found here: https://plantgenie.org/
Screenshot from the PlantGenIE sites About the public defence:
The public defence will take place on Thursday, 11th of June at Umeå University. Faculty opponent will be Marek Mutwil from The School of Biological Sciences, Nanyang Technological University, Singapore. Chanaka Mannapperuma's supervisors are Nathaniel Street from the Department of Plant Physiology (UPSC) and John Waterworth from the Department of Informatics. The dissertation will be live broadcasted via Zoom.
Title of the thesis: Human-computer interaction principles for developing web-based genomics resources
Link to the thesis:
http://umu.diva-portal.org/smash/record.jsf?pid=diva2%3A1426665&dswid=9080
Link to the Zoom live broadcast:
https://umu.zoom.us/j/62366789113?pwd=Mjc2N3RVWlhaOXlYODJsRjREVy9KUT09
Meeting ID: 623 6678 9113
Password: 878277
For more information, please contact:
Chanaka Mannapperuma
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
Email:
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Nathaniel Street (left) and Judith Lundberg-Felten (right) in an online Zoom meeting
Judith Lundberg-Felten and Nathaniel Street were recently appointed as docents at SLU and Umeå University, respectively. Both are working already for several years at UPSC, first as postdocs and now as group leaders. The appointment as docent is the next career step within the Swedish academic system. Here they are talking about their career, what is driving them and their future goals.
Did you always want to make an academic career?
Judith: I have enjoyed doing research in plant biology since my Master’s project. I love the analytical, scientific approach. This and my curiosity for science has motivated me to continue on the academic path.
Nathaniel: No, for me, that came late. I didn’t think properly about it until during my PhD. By then, I knew that I loved research enough to always want to do that.
What is your driving force?
Nathaniel: The world around me. I have always been fascinated by the fact that the largescale emerges from processes at the small scale and trees are an ultimate example of that for me. I love the ordered chaos of biology and the challenge of trying to understand that system. So, my biology interest is the major force but I also want to pass on that passion to others and to create an environment where people can explore and develop their own ideas, interests and skills.
Judith: As a group leader, I also want to empower young scientists on their road to discover the molecular processes happening inside plants and to understand how these fascinating and highly diverse organisms develop and function. I believe that one day, the knowledge that I create through my research team will foster creating innovative solutions for a future sustainable society.
Why did you come to UPSC?
Nathaniel: Trees. I love working on trees and Sweden loves trees. I visited UPSC during my PhD and loved working there. People at UPSC were passionate about tree genomics and that was inspiring. They were using the latest techniques and technologies – at the time cDNA microarrays – and that also appealed to the side of me that loves new technology. Microarrays really fuelled my love of working with largescale datasets and applying that also at larger scales out in the field.
Judith: I had worked on poplar trees during my PhD project in France and when I heard about UPSC, it seemed like a dream place for me to work at, both because of its scientific excellence and extraordinary infrastructure and, because of its ‘exotic’ Northern geographical location. Moving to Sweden and receiving a (rather unexpected) postdoc-opportunity at UPSC – this was like a dream come true for me as a young scientist.
What do you like about teaching?
Judith: I love to interact with students, to hear what they are curious about and to see them learn and grow in their reflections with every new piece of knowledge and skills they acquire. Also, I find teaching a very rewarding activity as the feedback that I receive from the students makes me reflect about myself and develop new skills. I see teaching as a continuous dialogue and opportunity for development for both students and teacher.
Nathaniel: Initially, I liked simply trying to pass on my own passion for the subject. Now, I also enjoy challenging and encouraging students to develop their own learning skills to become independent learners and thinkers.
What are your goals for the future?
Nathaniel: More of the same but better – both in the research and teaching or career development aspects of the job. I enjoy approaching research from a system-wide perspective, but this does not always provide concrete end results. Learning how to do this better is my major aim at the moment. In teaching, I want to continue exploring which teaching techniques provide the best learning and development opportunities for students and to evolve my courses accordingly. For my group, I want to create an environment that supports each person in identifying, developing and exploring their interest in biology. I want to make sure that their time in the group is providing them with the skills, output and opportunities they need to advance in their careers. I don’t want my own limitations to limit others.
Judith: I have used flipped classroom techniques in the past for my own lectures and want to develop that throughout my courses even more. I have students with varying background knowledge, and I see an advantage in having them learn the basics at their own pace through recorded lectures that integrate interactive moments such as quizzes. As teacher, I can focus then on interactive activities in the physical classroom such as case scenarios, problem-based learning, group exercises, discussions and so on. The students do not only learn to remember new material, but also to apply, compare, analyse and evaluate information. It is surprising not only for me but also for the students how much they learned through such discussions and interactive lectures and I would like to develop my teaching skills further to stimulate this type of learning.
Do you have some tips for young researchers?
Nathaniel: Be sure you know what inspires you about research and always remind yourself of that to let it drive you forward. There’s lots of important, practical advice about publishing papers and thinking strategically about the next move in your career. However, if you forget why you’re doing it then none of that practical advice really matters as you need that drive to provide the energy for those practical concerns. It’s good to remember that also other routes can lead you forward. If an opportunity arises that interests you but diverges from the model career path, don’t be blind by focusing only on strategic career advices.
Judith: Yes, I agree on that. I think it is very important to find out early during your career what you are passionate about, what you are good at and what makes you get out of bed in the morning with a smile on your face. Set yourself a goal and pave your unique path with patience and kindness for yourself. And remember: Doubt will kill more dreams than failure ever will. Believe in your dreams!
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Irena Fundová successfully defended her PhD thesis at SLU (photo: Sonali Ranade)
[2020-04-29] It is easy to measure the height or the stem diameter of a tree. But how can you get a clue about the quality of the wood without cutting down the tree? Irena Fundová, PhD student in Harry Wu’s group at UPSC, tested in her PhD thesis different methods to estimate the wood quality of Scots pine without harming the tree. Based on her results, she gives advices on the applicability of the tested methods and suggests a breeding strategy to improve growth, fibre and wood quality of Scots pine at the same time. Irena Fundová has successfully defended her PhD thesis on Friday, the 24th of April in P-O Bäckströms sal at SLU in Umeå.
What aroused your interest in your PhD project?
I wanted to continue with research on wood quality in forest trees that I started already at the University of British Columbia in Canada. I was particularly interested in applied research that would be as practical as possible for forestry and wood processing industries.
Did the fact that the PhD project was part of the industrial graduate school, that is a collaboration project between the UPSC Centre for Forest Biotechnology and its industrial partners, influence your decision?
Yes, it was important for me. I viewed it as a bridge between university science and industrial application. I hope that my thesis will be useful for my host company (Skogforsk).
What was most fascinating during your PhD?
I really enjoyed fieldwork. I travelled all over Sweden and visited many remote places. Sometimes we had to stay in a tent as there was no accommodation nearby. We met a lot of wildlife including a bear. I also had the opportunity to visit USA, Brazil and China and see their forest tree improvement programs. It was a great experience for me.
What was the most disappointing experience you had during your PhD?
The first year of my PhD was very difficult because I had no data. But then we shifted the direction a little bit, got enough funding through several research grants and my work started to progress.
What is the major outcome from your thesis? Can you provide practical information or tips for forestry and wood processing industries?
I tested the suitability of various methods for rapid and non destructive assessment of wood quality traits that are important for construction, pulp & paper and bioenergy industries. I concluded that 1- the resistograph, a tool based on drilling resistance, is suitable for non-destructive wood density assessment, 2- standing-tree acoustic velocity provides a good estimate of sawn-board stiffness and strength, 3- grain angle measured under bark of standing trees well predicts sawn-board twisting and crooking, and 4- Fourier transform infrared spectroscopy is suitable for non-destructive assessment of the chemical composition of wood in Scots pine. Furthermore, I evaluated the potential of growth and wood quality traits for simultaneous genetic improvement through recurrent selective breeding.
What are your plans for the future?
I have got several job offers (although none of them is from Sweden) but it is hard to make any plans during the current coronavirus pandemic. Before the situation clears off, I would like to process the tons of data I have generated during my studies that I could not include in my thesis.
Irena Fundová was student of the industrial graduate student Research School of Forest Genetics, Biotechnology and Breeding at UPSC. She performed her PhD studies in close collaboration with Skogforsk, the Forestry Research Institute of Sweden.
About the public defence:
The public defence took place on Friday, 24th of April at SLU Umeå. Faculty opponent was Philippe Rozenberg from the French National Research Institute for Agriculture, Food, and Environment (INRAE), Val de Loire, France. Irena Fundová's supervisor is Prof. Harry Xiaming Wu. The dissertation was live broadcasted on https://play.slu.se/.
Title of the thesis: Quantitative Genetics of Wood Quality Traits in Scots Pine
Link to the thesis: https://pub.epsilon.slu.se/16809/
For more information, please contact:
Irena Fundová
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences
Email:
One of Irena Fundová's trial plots - a Scots pine progeny test that is used for breeding (photo: Irena Fundová)
Irena Fundová measuring acoustic velocity on a standing Scots pine tree (photo: Tomáš Funda)
Scots pine logs in a sawmill (photo: Irena Fundová)
The final product - sawn boards from Scots pine (photo: Irena Fundová)