Publications 2016

@article{young_structure_2016,
	title = {Structure of photosystem {II} and substrate binding at room temperature},
	volume = {540},
	copyright = {2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/nature20161},
	doi = {10.1038/nature20161},
	abstract = {The structures of three intermediate states of photosystem II, which is crucial for photosynthesis, have been solved at room temperature, shedding new light on this process.},
	language = {en},
	number = {7633},
	urldate = {2024-12-10},
	journal = {Nature},
	author = {Young, Iris D. and Ibrahim, Mohamed and Chatterjee, Ruchira and Gul, Sheraz and Fuller, Franklin D. and Koroidov, Sergey and Brewster, Aaron S. and Tran, Rosalie and Alonso-Mori, Roberto and Kroll, Thomas and Michels-Clark, Tara and Laksmono, Hartawan and Sierra, Raymond G. and Stan, Claudiu A. and Hussein, Rana and Zhang, Miao and Douthit, Lacey and Kubin, Markus and de Lichtenberg, Casper and Vo Pham, Long and Nilsson, Håkan and Cheah, Mun Hon and Shevela, Dmitriy and Saracini, Claudio and Bean, Mackenzie A. and Seuffert, Ina and Sokaras, Dimosthenis and Weng, Tsu-Chien and Pastor, Ernest and Weninger, Clemens and Fransson, Thomas and Lassalle, Louise and Bräuer, Philipp and Aller, Pierre and Docker, Peter T. and Andi, Babak and Orville, Allen M. and Glownia, James M. and Nelson, Silke and Sikorski, Marcin and Zhu, Diling and Hunter, Mark S. and Lane, Thomas J. and Aquila, Andy and Koglin, Jason E. and Robinson, Joseph and Liang, Mengning and Boutet, Sébastien and Lyubimov, Artem Y. and Uervirojnangkoorn, Monarin and Moriarty, Nigel W. and Liebschner, Dorothee and Afonine, Pavel V. and Waterman, David G. and Evans, Gwyndaf and Wernet, Philippe and Dobbek, Holger and Weis, William I. and Brunger, Axel T. and Zwart, Petrus H. and Adams, Paul D. and Zouni, Athina and Messinger, Johannes and Bergmann, Uwe and Sauter, Nicholas K. and Kern, Jan and Yachandra, Vittal K. and Yano, Junko},
	month = dec,
	year = {2016},
	note = {Publisher: Nature Publishing Group},
	keywords = {Bioenergetics, Biophysical chemistry, Nanocrystallography, Photosystem II},
	pages = {453--457},
}

The structures of three intermediate states of photosystem II, which is crucial for photosynthesis, have been solved at room temperature, shedding new light on this process.

@article{siggel_gernot_2016,
	title = {Gernot {Renger} (1937–2013): his life, {Max}-{Volmer} {Laboratory}, and photosynthesis research},
	volume = {129},
	issn = {1573-5079},
	shorttitle = {Gernot {Renger} (1937–2013)},
	url = {https://doi.org/10.1007/s11120-016-0280-8},
	doi = {10.1007/s11120-016-0280-8},
	abstract = {Gernot Renger (October 23, 1937–January 12, 2013), one of the leading biophysicists in the field of photosynthesis research, studied and worked at the Max-Volmer-Institute (MVI) of the Technische Universität Berlin, Germany, for more than 50 years, and thus witnessed the rise and decline of photosynthesis research at this institute, which at its prime was one of the leading centers in this field. We present a tribute to Gernot Renger’s work and life in the context of the history of photosynthesis research of that period, with special focus on the MVI. Gernot will be remembered for his thought-provoking questions and his boundless enthusiasm for science.},
	language = {en},
	number = {2},
	urldate = {2024-12-10},
	journal = {Photosynthesis Research},
	author = {Siggel, Ulrich and Schmitt, Franz-Josef and Messinger, Johannes},
	month = aug,
	year = {2016},
	keywords = {ADRY agent, Horst T. Witt, Max-Volmer-Institute, Mechanism of water splitting, Oxygen evolving complex, Photosystem II, Water oxidizing complex (WOC)},
	pages = {109--127},
}

Gernot Renger (October 23, 1937–January 12, 2013), one of the leading biophysicists in the field of photosynthesis research, studied and worked at the Max-Volmer-Institute (MVI) of the Technische Universität Berlin, Germany, for more than 50 years, and thus witnessed the rise and decline of photosynthesis research at this institute, which at its prime was one of the leading centers in this field. We present a tribute to Gernot Renger’s work and life in the context of the history of photosynthesis research of that period, with special focus on the MVI. Gernot will be remembered for his thought-provoking questions and his boundless enthusiasm for science.

@article{shevela_biogenesis_2016,
	title = {Biogenesis of water splitting by photosystem {II} during de-etiolation of barley ({Hordeum} vulgare {L}.)},
	volume = {39},
	copyright = {© 2016 John Wiley \& Sons Ltd},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.12719},
	doi = {10.1111/pce.12719},
	abstract = {Etioplasts lack thylakoid membranes and photosystem complexes. Light triggers differentiation of etioplasts into mature chloroplasts, and photosystem complexes assemble in parallel with thylakoid membrane development. Plastids isolated at various time points of de-etiolation are ideal to study the kinetic biogenesis of photosystem complexes during chloroplast development. Here, we investigated the chronology of photosystem II (PSII) biogenesis by monitoring assembly status of chlorophyll-binding protein complexes and development of water splitting via O2 production in plastids (etiochloroplasts) isolated during de-etiolation of barley (Hordeum vulgare L.). Assembly of PSII monomers, dimers and complexes binding outer light-harvesting antenna [PSII-light-harvesting complex II (LHCII) supercomplexes] was identified after 1, 2 and 4 h of de-etiolation, respectively. Water splitting was detected in parallel with assembly of PSII monomers, and its development correlated with an increase of bound Mn in the samples. After 4 h of de-etiolation, etiochloroplasts revealed the same water-splitting efficiency as mature chloroplasts. We conclude that the capability of PSII to split water during de-etiolation precedes assembly of the PSII-LHCII supercomplexes. Taken together, data show a rapid establishment of water-splitting activity during etioplast-to-chloroplast transition and emphasize that assembly of the functional water-splitting site of PSII is not the rate-limiting step in the formation of photoactive thylakoid membranes.},
	language = {en},
	number = {7},
	urldate = {2024-12-10},
	journal = {Plant, Cell \& Environment},
	author = {Shevela, Dmitriy and Arnold, Janine and Reisinger, Veronika and Berends, Hans-Martin and Kmiec, Karol and Koroidov, Sergey and Bue, Ann Kristin and Messinger, Johannes and Eichacker, Lutz A.},
	year = {2016},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.12719},
	keywords = {chloroplast biogenesis, oxygen evolution, oxygen-evolving complex, photosystem II assembly},
	pages = {1524--1536},
}

Etioplasts lack thylakoid membranes and photosystem complexes. Light triggers differentiation of etioplasts into mature chloroplasts, and photosystem complexes assemble in parallel with thylakoid membrane development. Plastids isolated at various time points of de-etiolation are ideal to study the kinetic biogenesis of photosystem complexes during chloroplast development. Here, we investigated the chronology of photosystem II (PSII) biogenesis by monitoring assembly status of chlorophyll-binding protein complexes and development of water splitting via O2 production in plastids (etiochloroplasts) isolated during de-etiolation of barley (Hordeum vulgare L.). Assembly of PSII monomers, dimers and complexes binding outer light-harvesting antenna [PSII-light-harvesting complex II (LHCII) supercomplexes] was identified after 1, 2 and 4 h of de-etiolation, respectively. Water splitting was detected in parallel with assembly of PSII monomers, and its development correlated with an increase of bound Mn in the samples. After 4 h of de-etiolation, etiochloroplasts revealed the same water-splitting efficiency as mature chloroplasts. We conclude that the capability of PSII to split water during de-etiolation precedes assembly of the PSII-LHCII supercomplexes. Taken together, data show a rapid establishment of water-splitting activity during etioplast-to-chloroplast transition and emphasize that assembly of the functional water-splitting site of PSII is not the rate-limiting step in the formation of photoactive thylakoid membranes.

@article{sharifi_toward_2016,
	title = {Toward a {Low}-{Cost} {Artificial} {Leaf}: {Driving} {Carbon}-{Based} and {Bifunctional} {Catalyst} {Electrodes} with {Solution}-{Processed} {Perovskite} {Photovoltaics}},
	volume = {6},
	copyright = {© 2016 The Authors. Published by WILEY-VCH Verlag GmbH \& Co. KGaA, Weinheim},
	issn = {1614-6840},
	shorttitle = {Toward a {Low}-{Cost} {Artificial} {Leaf}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/aenm.201600738},
	doi = {10.1002/aenm.201600738},
	abstract = {Molecular hydrogen can be generated renewably by water splitting with an “artificial-leaf device”, which essentially comprises two electrocatalyst electrodes immersed in water and powered by photovoltaics. Ideally, this device should operate efficiently and be fabricated with cost-efficient means using earth-abundant materials. Here, a lightweight electrocatalyst electrode, comprising large surface-area NiCo2O4 nanorods that are firmly anchored onto a carbon–paper current collector via a dense network of nitrogen-doped carbon nanotubes is presented. This electrocatalyst electrode is bifunctional in that it can efficiently operate as both anode and cathode in the same alkaline solution, as quantified by a delivered current density of 10 mA cm−2 at an overpotential of 400 mV for each of the oxygen and hydrogen evolution reactions. By driving two such identical electrodes with a solution-processed thin-film perovskite photovoltaic assembly, a wired artificial-leaf device is obtained that features a Faradaic H2 evolution efficiency of 100\%, and a solar-to-hydrogen conversion efficiency of 6.2\%. A detailed cost analysis is presented, which implies that the material-payback time of this device is of the order of 100 days.},
	language = {en},
	number = {20},
	urldate = {2024-12-10},
	journal = {Advanced Energy Materials},
	author = {Sharifi, Tiva and Larsen, Christian and Wang, Jia and Kwong, Wai Ling and Gracia-Espino, Eduardo and Mercier, Guillaume and Messinger, Johannes and Wågberg, Thomas and Edman, Ludvig},
	year = {2016},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/aenm.201600738},
	keywords = {artificial-leaf devices, bifunctional electrocatalyst, carbon paper, nitrogen-doped carbon nanotubes, perovskite photovoltaics},
	pages = {1600738},
}

Molecular hydrogen can be generated renewably by water splitting with an “artificial-leaf device”, which essentially comprises two electrocatalyst electrodes immersed in water and powered by photovoltaics. Ideally, this device should operate efficiently and be fabricated with cost-efficient means using earth-abundant materials. Here, a lightweight electrocatalyst electrode, comprising large surface-area NiCo2O4 nanorods that are firmly anchored onto a carbon–paper current collector via a dense network of nitrogen-doped carbon nanotubes is presented. This electrocatalyst electrode is bifunctional in that it can efficiently operate as both anode and cathode in the same alkaline solution, as quantified by a delivered current density of 10 mA cm−2 at an overpotential of 400 mV for each of the oxygen and hydrogen evolution reactions. By driving two such identical electrodes with a solution-processed thin-film perovskite photovoltaic assembly, a wired artificial-leaf device is obtained that features a Faradaic H2 evolution efficiency of 100%, and a solar-to-hydrogen conversion efficiency of 6.2%. A detailed cost analysis is presented, which implies that the material-payback time of this device is of the order of 100 days.

@article{sharifi_maghemite_2016,
	title = {Maghemite nanorods anchored on a {3D} nitrogen-doped carbon nanotubes substrate as scalable direct electrode for water oxidation},
	volume = {41},
	issn = {0360-3199},
	url = {https://www.sciencedirect.com/science/article/pii/S0360319915027433},
	doi = {10.1016/j.ijhydene.2015.11.165},
	abstract = {A hybrid catalyst 3D electrode for electrochemical water oxidation to molecular oxygen is presented. The electrode comprises needle shaped maghemite nanorods firmly anchored to nitrogen doped carbon nanotubes, which in turn are grown on a conducting carbon paper that acts as efficient current collector. In 0.1 M KOH this hybrid electrode reaches a current density of 1 mA/cm2 (geometric surface) at an overpotential of 362 mV performing high chronoamperometric stability. The electrochemical attributes point toward efficient catalytic processes at the surface of the maghemite nanorods, and demonstrate a very high surface area of the 3D electrode, as well as a firm anchoring of each active component enabling an efficient charge transport from the surface of the maghemite rods to the carbon paper current collector. The latter property also explains the good stability of our hybrid electrode compared to transition metal oxides deposited on conducting support such as fluorine doped tin oxide. These results introduce maghemite as efficient, stable and earth abundant oxygen evolution reaction catalyst, and provide insight into key issues for obtaining practical electrodes for oxygen evolution reaction, which are compatible with large scale production processes.},
	number = {1},
	urldate = {2024-12-10},
	journal = {International Journal of Hydrogen Energy},
	author = {Sharifi, Tiva and Kwong, Wai Ling and Berends, Hans-Martin and Larsen, Christian and Messinger, Johannes and Wågberg, Thomas},
	month = jan,
	year = {2016},
	keywords = {3D electrode, Hybrid catalyst, Maghemite, Nitrogen-doped carbon nanotubes, Water oxidation},
	pages = {69--78},
}

A hybrid catalyst 3D electrode for electrochemical water oxidation to molecular oxygen is presented. The electrode comprises needle shaped maghemite nanorods firmly anchored to nitrogen doped carbon nanotubes, which in turn are grown on a conducting carbon paper that acts as efficient current collector. In 0.1 M KOH this hybrid electrode reaches a current density of 1 mA/cm2 (geometric surface) at an overpotential of 362 mV performing high chronoamperometric stability. The electrochemical attributes point toward efficient catalytic processes at the surface of the maghemite nanorods, and demonstrate a very high surface area of the 3D electrode, as well as a firm anchoring of each active component enabling an efficient charge transport from the surface of the maghemite rods to the carbon paper current collector. The latter property also explains the good stability of our hybrid electrode compared to transition metal oxides deposited on conducting support such as fluorine doped tin oxide. These results introduce maghemite as efficient, stable and earth abundant oxygen evolution reaction catalyst, and provide insight into key issues for obtaining practical electrodes for oxygen evolution reaction, which are compatible with large scale production processes.

@article{sauter_no_2016,
	title = {No observable conformational changes in {PSII}},
	volume = {533},
	copyright = {2016 Springer Nature Limited},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/nature17983},
	doi = {10.1038/nature17983},
	language = {en},
	number = {7603},
	urldate = {2024-12-10},
	journal = {Nature},
	author = {Sauter, Nicholas K. and Echols, Nathaniel and Adams, Paul D. and Zwart, Petrus H. and Kern, Jan and Brewster, Aaron S. and Koroidov, Sergey and Alonso-Mori, Roberto and Zouni, Athina and Messinger, Johannes and Bergmann, Uwe and Yano, Junko and Yachandra, Vittal K.},
	month = may,
	year = {2016},
	note = {Publisher: Nature Publishing Group},
	keywords = {Photosystem II, X-ray crystallography},
	pages = {E1--E2},
}

@article{pham_probing_2016,
	title = {Probing {S}-state advancements and recombination pathways in photosystem {II} with a global fit program for flash-induced oxygen evolution pattern},
	volume = {1857},
	issn = {0005-2728},
	url = {https://www.sciencedirect.com/science/article/pii/S0005272816300603},
	doi = {10.1016/j.bbabio.2016.03.013},
	abstract = {The oxygen-evolving complex (OEC) in photosystem II catalyzes the oxidation of water to molecular oxygen. Four decades ago, measurements of flash-induced oxygen evolution have shown that the OEC steps through oxidation states S0, S1, S2, S3 and S4 before O2 is released and the S0 state is reformed. The light-induced transitions between these states involve misses and double hits. While it is widely accepted that the miss parameter is S state dependent and may be further modulated by the oxidation state of the acceptor side, the traditional way of analyzing each flash-induced oxygen evolution pattern (FIOP) individually did not allow using enough free parameters to thoroughly test this proposal. Furthermore, this approach does not allow assessing whether the presently known recombination processes in photosystem II fully explain all measured oxygen yields during Si state lifetime measurements. Here we present a global fit program that simultaneously fits all flash-induced oxygen yields of a standard FIOP (2Hz flash frequency) and of 11–18 FIOPs each obtained while probing the S0, S2 and S3 state lifetimes in spinach thylakoids at neutral pH. This comprehensive data treatment demonstrates the presence of a very slow phase of S2 decay, in addition to the commonly discussed fast and slow reduction of S2 by YD and QB−, respectively. Our data support previous suggestions that the S0→S1 and S1→S2 transitions involve low or no misses, while high misses occur in the S2→S3 or S3→S0 transitions.},
	number = {6},
	urldate = {2024-12-10},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Pham, Long Vo and Messinger, Johannes},
	month = jun,
	year = {2016},
	keywords = {Flash induced oxygen evolution pattern (FIOP), Kok model, Oxygen (O) evolution, Photosynthesis, Photosystem 2 (PSII), Water oxidation},
	pages = {848--859},
}

The oxygen-evolving complex (OEC) in photosystem II catalyzes the oxidation of water to molecular oxygen. Four decades ago, measurements of flash-induced oxygen evolution have shown that the OEC steps through oxidation states S0, S1, S2, S3 and S4 before O2 is released and the S0 state is reformed. The light-induced transitions between these states involve misses and double hits. While it is widely accepted that the miss parameter is S state dependent and may be further modulated by the oxidation state of the acceptor side, the traditional way of analyzing each flash-induced oxygen evolution pattern (FIOP) individually did not allow using enough free parameters to thoroughly test this proposal. Furthermore, this approach does not allow assessing whether the presently known recombination processes in photosystem II fully explain all measured oxygen yields during Si state lifetime measurements. Here we present a global fit program that simultaneously fits all flash-induced oxygen yields of a standard FIOP (2Hz flash frequency) and of 11–18 FIOPs each obtained while probing the S0, S2 and S3 state lifetimes in spinach thylakoids at neutral pH. This comprehensive data treatment demonstrates the presence of a very slow phase of S2 decay, in addition to the commonly discussed fast and slow reduction of S2 by YD and QB−, respectively. Our data support previous suggestions that the S0→S1 and S1→S2 transitions involve low or no misses, while high misses occur in the S2→S3 or S3→S0 transitions.

@article{nilsson_estimation_2016,
	title = {Estimation of the driving force for dioxygen formation in photosynthesis},
	volume = {1857},
	issn = {0005-2728},
	url = {https://www.sciencedirect.com/science/article/pii/S0005272815001991},
	doi = {10.1016/j.bbabio.2015.09.011},
	abstract = {Photosynthetic water oxidation to molecular oxygen is carried out by photosystem II (PSII) over a reaction cycle involving four photochemical steps that drive the oxygen-evolving complex through five redox states Si (i=0,…, 4). For understanding the catalytic strategy of biological water oxidation it is important to elucidate the energetic landscape of PSII and in particular that of the final S4→S0 transition. In this short-lived chemical step the four oxidizing equivalents accumulated in the preceding photochemical events are used up to form molecular oxygen, two protons are released and at least one substrate water molecule binds to the Mn4CaO5 cluster. In this study we probed the probability to form S4 from S0 and O2 by incubating YD-less PSII in the S0 state for 2–3days in the presence of 18O2 and H216O. The absence of any measurable 16,18O2 formation by water-exchange in the S4 state suggests that the S4 state is hardly ever populated. On the basis of a detailed analysis we determined that the equilibrium constant K of the S4→S0 transition is larger than 1.0×107 so that this step is highly exergonic. We argue that this finding is consistent with current knowledge of the energetics of the S0 to S4 reactions, and that the high exergonicity is required for the kinetic efficiency of PSII.},
	number = {1},
	urldate = {2024-12-10},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Nilsson, Håkan and Cournac, Laurent and Rappaport, Fabrice and Messinger, Johannes and Lavergne, Jérôme},
	month = jan,
	year = {2016},
	keywords = {Equilibrium constant for S→S transition, Oxygen-evolving complex (OEC), Photosystem II, Water-oxidizing complex (WOC)},
	pages = {23--33},
}

Photosynthetic water oxidation to molecular oxygen is carried out by photosystem II (PSII) over a reaction cycle involving four photochemical steps that drive the oxygen-evolving complex through five redox states Si (i=0,…, 4). For understanding the catalytic strategy of biological water oxidation it is important to elucidate the energetic landscape of PSII and in particular that of the final S4→S0 transition. In this short-lived chemical step the four oxidizing equivalents accumulated in the preceding photochemical events are used up to form molecular oxygen, two protons are released and at least one substrate water molecule binds to the Mn4CaO5 cluster. In this study we probed the probability to form S4 from S0 and O2 by incubating YD-less PSII in the S0 state for 2–3days in the presence of 18O2 and H216O. The absence of any measurable 16,18O2 formation by water-exchange in the S4 state suggests that the S4 state is hardly ever populated. On the basis of a detailed analysis we determined that the equilibrium constant K of the S4→S0 transition is larger than 1.0×107 so that this step is highly exergonic. We argue that this finding is consistent with current knowledge of the energetics of the S0 to S4 reactions, and that the high exergonicity is required for the kinetic efficiency of PSII.

@article{kwong_transparent_2016,
	title = {Transparent {Nanoparticulate} {FeOOH} {Improves} the {Performance} of a {WO3} {Photoanode} in a {Tandem} {Water}-{Splitting} {Device}},
	volume = {120},
	issn = {1932-7447},
	url = {https://doi.org/10.1021/acs.jpcc.6b02432},
	doi = {10.1021/acs.jpcc.6b02432},
	abstract = {Oxygen evolution catalysts (OEC) are often employed on the surface of photoactive, semiconducting photoanodes to boost their kinetics and stability during photoelectrochemical water oxidation. However, the necessity of using optically transparent OEC to avoid parasitic light absorption by the OEC under front-side illumination is often neglected. Here, we show that furnishing the surface of a WO3 photoanode with suitable loading of FeOOH as a transparent OEC improved the photocurrent density by 300\% at 1 V versus RHE and the initial photocurrent-to-O2 Faradaic efficiency from ∼70 to ∼100\%. The data from the photovoltammetry, electrochemical impedance, and gas evolution measurements show that these improvements were a combined result of reduced hole-transfer resistance for water oxidation, minimized surface recombination of charge carriers, and improved stability against photocorrosion of WO3. We demonstrate the utility of transparent FeOOH-coated WO3 in a solar-powered, tandem water-splitting device by combining it with a double-junction Si solar cell and a Ni–Mo hydrogen evolution catalyst. This device performed at a solar-to-hydrogen conversion efficiency of 1.8\% in near-neutral K2SO4 electrolyte.},
	number = {20},
	urldate = {2024-12-10},
	journal = {The Journal of Physical Chemistry C},
	author = {Kwong, Wai Ling and Lee, Cheng Choo and Messinger, Johannes},
	month = may,
	year = {2016},
	note = {Publisher: American Chemical Society},
	pages = {10941--10950},
}

Oxygen evolution catalysts (OEC) are often employed on the surface of photoactive, semiconducting photoanodes to boost their kinetics and stability during photoelectrochemical water oxidation. However, the necessity of using optically transparent OEC to avoid parasitic light absorption by the OEC under front-side illumination is often neglected. Here, we show that furnishing the surface of a WO3 photoanode with suitable loading of FeOOH as a transparent OEC improved the photocurrent density by 300% at 1 V versus RHE and the initial photocurrent-to-O2 Faradaic efficiency from ∼70 to ∼100%. The data from the photovoltammetry, electrochemical impedance, and gas evolution measurements show that these improvements were a combined result of reduced hole-transfer resistance for water oxidation, minimized surface recombination of charge carriers, and improved stability against photocorrosion of WO3. We demonstrate the utility of transparent FeOOH-coated WO3 in a solar-powered, tandem water-splitting device by combining it with a double-junction Si solar cell and a Ni–Mo hydrogen evolution catalyst. This device performed at a solar-to-hydrogen conversion efficiency of 1.8% in near-neutral K2SO4 electrolyte.

@article{alonso-mori_towards_2016,
	title = {Towards characterization of photo-excited electron transfer and catalysis in natural and artificial systems using {XFELs}},
	volume = {194},
	issn = {1364-5498},
	url = {https://pubs.rsc.org/en/content/articlelanding/2016/fd/c6fd00084c},
	doi = {10.1039/C6FD00084C},
	abstract = {The ultra-bright femtosecond X-ray pulses provided by X-ray Free Electron Lasers (XFELs) open capabilities for studying the structure and dynamics of a wide variety of biological and inorganic systems beyond what is possible at synchrotron sources. Although the structure and chemistry at the catalytic sites have been studied intensively in both biological and inorganic systems, a full understanding of the atomic-scale chemistry requires new approaches beyond the steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure at ambient conditions, while overcoming X-ray damage to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by using the intense and ultra-short femtosecond X-ray pulses from an XFEL, where sample is probed before it is damaged. We have developed methodology for simultaneously collecting X-ray diffraction data and X-ray emission spectra, using an energy dispersive spectrometer, at ambient conditions, and used this approach to study the room temperature structure and intermediate states of the photosynthetic water oxidizing metallo-protein, photosystem II. Moreover, we have also used this setup to simultaneously collect the X-ray emission spectra from multiple metals to follow the ultrafast dynamics of light-induced charge transfer between multiple metal sites. A Mn–Ti containing system was studied at an XFEL to demonstrate the efficacy and potential of this method.},
	language = {en},
	number = {0},
	urldate = {2024-12-10},
	journal = {Faraday Discussions},
	author = {Alonso-Mori, R. and Asa, K. and Bergmann, U. and Brewster, A. S. and Chatterjee, R. and Cooper, J. K. and Frei, H. M. and Fuller, F. D. and Goggins, E. and Gul, S. and Fukuzawa, H. and Iablonskyi, D. and Ibrahim, M. and Katayama, T. and Kroll, T. and Kumagai, Y. and McClure, B. A. and Messinger, J. and Motomura, K. and Nagaya, K. and Nishiyama, T. and Saracini, C. and Sato, Y. and Sauter, N. K. and Sokaras, D. and Takanashi, T. and Togashi, T. and Ueda, K. and Weare, W. W. and Weng, T.-C. and Yabashi, M. and Yachandra, V. K. and Young, I. D. and Zouni, A. and Kern, J. F. and Yano, J.},
	month = dec,
	year = {2016},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {621--638},
}

The ultra-bright femtosecond X-ray pulses provided by X-ray Free Electron Lasers (XFELs) open capabilities for studying the structure and dynamics of a wide variety of biological and inorganic systems beyond what is possible at synchrotron sources. Although the structure and chemistry at the catalytic sites have been studied intensively in both biological and inorganic systems, a full understanding of the atomic-scale chemistry requires new approaches beyond the steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure at ambient conditions, while overcoming X-ray damage to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by using the intense and ultra-short femtosecond X-ray pulses from an XFEL, where sample is probed before it is damaged. We have developed methodology for simultaneously collecting X-ray diffraction data and X-ray emission spectra, using an energy dispersive spectrometer, at ambient conditions, and used this approach to study the room temperature structure and intermediate states of the photosynthetic water oxidizing metallo-protein, photosystem II. Moreover, we have also used this setup to simultaneously collect the X-ray emission spectra from multiple metals to follow the ultrafast dynamics of light-induced charge transfer between multiple metal sites. A Mn–Ti containing system was studied at an XFEL to demonstrate the efficacy and potential of this method.

@incollection{manzoor_avenues_2016,
	title = {Avenues for improving drought tolerance in crops by {ABA} regulation},
	copyright = {© 2016 John Wiley \& Sons, Ltd.},
	isbn = {978-1-119-05445-0},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119054450.ch13},
	abstract = {Crop productivity is greatly reduced due to abiotic stresses including drought stress. Naturally occurring drought stress tolerant plants have evolved some adaptations to cope with drought stress. Based on drought adaptive responses in wild or crop plants, plant scientists are pursuing efforts to develop crop tolerance against drought stress using heritable traits that contribute in drought tolerance through conventional or advanced molecular techniques. Among these drought tolerance traits, organic compatible solutes, antioxidant compounds, and plant growth regulators are of great significance. Among various plant growth regulators, abscisic acid (ABA) is known to regulate environmental stress responses in plants by affecting transpirational water loss, stomatal closure, photosynthesis, water use efficiency, seed development and maturation, leaf senescence and cell membrane protection, and so on. The degree of biosynthesis and accumulation of ABA in a crop cultivar is a possible indicator of drought tolerance. Drought stress-regulated ABA biosynthesis depends on a key enzyme, 9-cis-epoxycarotenoid dioxygenase (NCED) involved in ABA biosynthesis. NCED3 and/or its corresponding orthologs could be valuable targets for improving drought tolerance in crops. In all ABA-dependent physiological and developmental processes, regulation of ABA signaling is central to develop drought tolerance in plants. A number of drought tolerance related functional and regulatory genes that are regulated by ABA have been discovered, of which bZIP transcription factors (TFs), ABI5, AREB/ABFs, SnRK2-AREB/ABF, and WRKY are of key importance. However, impact of these genes in developing drought tolerance is confounded in some cases because drought tolerance mechanism is very complex and varies with plant developmental stage. In addition, an ABA-independent pathway for drought tolerance also exists in plants, which causes further complexity in understanding the mechanisms of drought tolerance. Finding missing links in sensing and response components of ABA signaling cascades using a wide range of high-throughput analytical techniques for measuring metabolites, proteins, and transcripts in plant tissues will pave new avenues for studying stress resistance in crops.},
	language = {en},
	urldate = {2024-08-30},
	booktitle = {Water {Stress} and {Crop} {Plants}},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Manzoor, Hamid and Athar, Habib-ur-Rehman and Rasul, Sumaira and Kanwal, Tehseen and Anjam, Muhammad Shahzad and Qureshi, Muhammad Kamran and Bashir, Nahidah and Zafar, Zafar Ullah and Ali, Muhammad and Ashraf, Muhammad},
	year = {2016},
	doi = {10.1002/9781119054450.ch13},
	note = {Section: 13
\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119054450.ch13},
	keywords = {NCED3, abscisic acid, crop improvement, hormones, osmotic stress, photosynthesis, signal transduction},
	pages = {177--193},
}

Crop productivity is greatly reduced due to abiotic stresses including drought stress. Naturally occurring drought stress tolerant plants have evolved some adaptations to cope with drought stress. Based on drought adaptive responses in wild or crop plants, plant scientists are pursuing efforts to develop crop tolerance against drought stress using heritable traits that contribute in drought tolerance through conventional or advanced molecular techniques. Among these drought tolerance traits, organic compatible solutes, antioxidant compounds, and plant growth regulators are of great significance. Among various plant growth regulators, abscisic acid (ABA) is known to regulate environmental stress responses in plants by affecting transpirational water loss, stomatal closure, photosynthesis, water use efficiency, seed development and maturation, leaf senescence and cell membrane protection, and so on. The degree of biosynthesis and accumulation of ABA in a crop cultivar is a possible indicator of drought tolerance. Drought stress-regulated ABA biosynthesis depends on a key enzyme, 9-cis-epoxycarotenoid dioxygenase (NCED) involved in ABA biosynthesis. NCED3 and/or its corresponding orthologs could be valuable targets for improving drought tolerance in crops. In all ABA-dependent physiological and developmental processes, regulation of ABA signaling is central to develop drought tolerance in plants. A number of drought tolerance related functional and regulatory genes that are regulated by ABA have been discovered, of which bZIP transcription factors (TFs), ABI5, AREB/ABFs, SnRK2-AREB/ABF, and WRKY are of key importance. However, impact of these genes in developing drought tolerance is confounded in some cases because drought tolerance mechanism is very complex and varies with plant developmental stage. In addition, an ABA-independent pathway for drought tolerance also exists in plants, which causes further complexity in understanding the mechanisms of drought tolerance. Finding missing links in sensing and response components of ABA signaling cascades using a wide range of high-throughput analytical techniques for measuring metabolites, proteins, and transcripts in plant tissues will pave new avenues for studying stress resistance in crops.

@article{anjam_improved_2016,
	title = {An improved procedure for isolation of high-quality {RNA} from nematode-infected {Arabidopsis} roots through laser capture microdissection},
	volume = {12},
	issn = {1746-4811},
	url = {https://doi.org/10.1186/s13007-016-0123-9},
	doi = {10.1186/s13007-016-0123-9},
	abstract = {Cyst nematodes are biotrophs that form specialized feeding structures in the roots of host plants, which consist of a syncytial fusion of hypertrophied cells. The formation of syncytium is accompanied by profound transcriptional changes and active metabolism in infected tissues. The challenge in gene expression studies for syncytium has always been the isolation of pure syncytial material and subsequent extraction of intact RNA. Root fragments containing syncytium had been used for microarray analyses. However, the inclusion of neighbouring cells dilutes the syncytium-specific mRNA population. Micro-sectioning coupled with laser capture microdissection (LCM) offers an opportunity for the isolation of feeding sites from heterogeneous cell populations. But recovery of intact RNA from syncytium dissected by LCM is complicated due to extended steps of fixation, tissue preparation, embedding and sectioning.},
	number = {1},
	urldate = {2024-08-30},
	journal = {Plant Methods},
	author = {Anjam, Muhammad Shahzad and Ludwig, Yvonne and Hochholdinger, Frank and Miyaura, Chisato and Inada, Masaki and Siddique, Shahid and Grundler, Florian M. W.},
	month = apr,
	year = {2016},
	keywords = {Arabidopsis, Cyst nematode, LCM, Nematode, RNA degradation, Root, Syncytium},
	pages = {25},
}

Cyst nematodes are biotrophs that form specialized feeding structures in the roots of host plants, which consist of a syncytial fusion of hypertrophied cells. The formation of syncytium is accompanied by profound transcriptional changes and active metabolism in infected tissues. The challenge in gene expression studies for syncytium has always been the isolation of pure syncytial material and subsequent extraction of intact RNA. Root fragments containing syncytium had been used for microarray analyses. However, the inclusion of neighbouring cells dilutes the syncytium-specific mRNA population. Micro-sectioning coupled with laser capture microdissection (LCM) offers an opportunity for the isolation of feeding sites from heterogeneous cell populations. But recovery of intact RNA from syncytium dissected by LCM is complicated due to extended steps of fixation, tissue preparation, embedding and sectioning.

@article{pandey_virus-induced_2016,
	title = {Virus-induced gene silencing ({VIGS})-mediated functional characterization of two genes involved in lignocellulosic secondary cell wall formation},
	volume = {35},
	issn = {1432-203X},
	url = {https://doi.org/10.1007/s00299-016-2039-2},
	doi = {10.1007/s00299-016-2039-2},
	abstract = {Functional characterization of two tobacco genes, one involved in xylan synthesis and the other, a positive regulator of secondary cell wall formation, is reported.},
	language = {en},
	number = {11},
	urldate = {2023-11-14},
	journal = {Plant Cell Reports},
	author = {Pandey, Shashank K. and Nookaraju, Akula and Fujino, Takeshi and Pattathil, Sivakumar and Joshi, Chandrashekhar P.},
	month = nov,
	year = {2016},
	keywords = {Bioethanol production, Saccharification, Secondary cell wall (SCW), Transcriptional regulation, Virus-induced gene silencing (VIGS), Xylan synthesis},
	pages = {2353--2367},
}

Functional characterization of two tobacco genes, one involved in xylan synthesis and the other, a positive regulator of secondary cell wall formation, is reported.

@article{kim_expression_2016,
	title = {Expression and {Protein} {Interaction} {Analyses} {Reveal} {Combinatorial} {Interactions} of {LBD} {Transcription} {Factors} {During} {Arabidopsis} {Pollen} {Development}},
	volume = {57},
	issn = {0032-0781},
	url = {https://doi.org/10.1093/pcp/pcw145},
	doi = {10.1093/pcp/pcw145},
	abstract = {LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factor gene family members play key roles in diverse aspects of plant development. LBD10 and LBD27 have been shown to be essential for pollen development in Arabidopsis thaliana. From the previous RNA sequencing (RNA-Seq) data set of Arabidopsis pollen, we identified the mRNAs of LBD22, LBD25 and LBD36 in addition to LBD10 and LBD27 in Arabidopsis pollen. Here we conducted expression and cellular analysis using GFP:GUS (green fluorescent protein:β-glucuronidase) reporter gene and subcellular localization assays using LBD:GFP fusion proteins expressed under the control of their own promoters in Arabidopsis. We found that these LBD proteins display spatially and temporally distinct and overlapping expression patterns during pollen development. Bimolecular fluorescence complementation and GST (glutathione S-transferase) pull-down assays demonstrated that protein–protein interactions occur among the LBDs exhibiting overlapping expression during pollen development. We further showed that LBD10, LBD22, LBD25, LBD27 and LBD36 interact with each other to form heterodimers, which are localized to the nucleus in Arabidopsis protoplasts. Taken together, these results suggest that combinatorial interactions among LBD proteins may be important for their function in pollen development in Arabidopsis.},
	number = {11},
	urldate = {2023-11-14},
	journal = {Plant and Cell Physiology},
	author = {Kim, Mirim and Kim, Min-Jung and Pandey, Shashank and Kim, Jungmook},
	month = nov,
	year = {2016},
	pages = {2291--2299},
}

LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factor gene family members play key roles in diverse aspects of plant development. LBD10 and LBD27 have been shown to be essential for pollen development in Arabidopsis thaliana. From the previous RNA sequencing (RNA-Seq) data set of Arabidopsis pollen, we identified the mRNAs of LBD22, LBD25 and LBD36 in addition to LBD10 and LBD27 in Arabidopsis pollen. Here we conducted expression and cellular analysis using GFP:GUS (green fluorescent protein:β-glucuronidase) reporter gene and subcellular localization assays using LBD:GFP fusion proteins expressed under the control of their own promoters in Arabidopsis. We found that these LBD proteins display spatially and temporally distinct and overlapping expression patterns during pollen development. Bimolecular fluorescence complementation and GST (glutathione S-transferase) pull-down assays demonstrated that protein–protein interactions occur among the LBDs exhibiting overlapping expression during pollen development. We further showed that LBD10, LBD22, LBD25, LBD27 and LBD36 interact with each other to form heterodimers, which are localized to the nucleus in Arabidopsis protoplasts. Taken together, these results suggest that combinatorial interactions among LBD proteins may be important for their function in pollen development in Arabidopsis.

@article{xu_germination_2016,
	title = {Germination and early seedling growth of {Pinus} densata {Mast}. provenances},
	volume = {27},
	issn = {1993-0607},
	url = {https://doi.org/10.1007/s11676-015-0186-x},
	doi = {10.1007/s11676-015-0186-x},
	abstract = {We studied seed germination and early seedling growth of Pinus densata to explore the range of variability within the species and to inform afforestation practices. Phenotypes were evaluated at a forest tree nursery under conditions that support Pinus yunnanensis, one of the presumed parental species of P. densata. Seeds were collected from 20 open-pollinated trees within each of eight autochthonous populations representing the natural distribution of P. densata in China to assess variation in germination traits and early seedling growth, and to examine the relationships among these traits. Results showed that seeds from all populations germinated and seedlings established successfully. There were significant differences among populations in 13 of 14 traits evaluated. Seed germination and early seedling growth were strongly related to seed size and seed weight. Bigger seeds germinated earlier and faster than small seeds, and seedling size was positively correlated with seed size. Some germination traits were strongly and significantly correlated with climatic variables associated with the provenance of the studied populations. Based on these observations, we conclude there were large, significant, and biologically important differences among P. densata populations in seed germination and seedling growth traits. The observed variability probably reflects a high degree of adaptive differentiation among populations that is likely to be relevant for future afforestation.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Journal of Forestry Research},
	author = {Xu, Yulan and Cai, Nianhui and He, Bin and Zhang, Ruili and Zhao, Wei and Mao, Jianfeng and Duan, Anan and Li, Yue and Woeste, Keith},
	month = apr,
	year = {2016},
	keywords = {Afforestation, Conifer, Gaoshan pine, Provenance, Seed germination, Seed size, Seedling vigor},
	pages = {283--294},
}

We studied seed germination and early seedling growth of Pinus densata to explore the range of variability within the species and to inform afforestation practices. Phenotypes were evaluated at a forest tree nursery under conditions that support Pinus yunnanensis, one of the presumed parental species of P. densata. Seeds were collected from 20 open-pollinated trees within each of eight autochthonous populations representing the natural distribution of P. densata in China to assess variation in germination traits and early seedling growth, and to examine the relationships among these traits. Results showed that seeds from all populations germinated and seedlings established successfully. There were significant differences among populations in 13 of 14 traits evaluated. Seed germination and early seedling growth were strongly related to seed size and seed weight. Bigger seeds germinated earlier and faster than small seeds, and seedling size was positively correlated with seed size. Some germination traits were strongly and significantly correlated with climatic variables associated with the provenance of the studied populations. Based on these observations, we conclude there were large, significant, and biologically important differences among P. densata populations in seed germination and seedling growth traits. The observed variability probably reflects a high degree of adaptive differentiation among populations that is likely to be relevant for future afforestation.

@article{jin_genetic_2016,
	title = {Genetic evaluation of the breeding population of a valuable reforestation conifer {Platycladus} orientalis ({Cupressaceae})},
	volume = {6},
	copyright = {2016 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/srep34821},
	doi = {10.1038/srep34821},
	abstract = {Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average He = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Scientific Reports},
	author = {Jin, Yuqing and Ma, Yongpeng and Wang, Shun and Hu, Xian-Ge and Huang, Li-Sha and Li, Yue and Wang, Xiao-Ru and Mao, Jian-Feng},
	month = oct,
	year = {2016},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Forestry, Plant breeding},
	pages = {34821},
}

Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average He = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.

@article{huang_genetic_2016,
	title = {Genetic structure of needle morphological and anatomical traits of {Pinus} yunnanensis},
	volume = {27},
	issn = {1993-0607},
	url = {https://doi.org/10.1007/s11676-015-0133-x},
	doi = {10.1007/s11676-015-0133-x},
	abstract = {Pinus yunnanensis Franch. is an particular conifer tree species in Yunnan–Guizhou plateau in southwest China. The morphological and anatomical traits of needles are important to evaluate geographic variation and population dynamics of conifer species. Seedlings from seven populations of P. yunnanensis were analyzed, looking at 22 morphological and anatomical needle traits. The results showed that variations among and within populations were significantly different for all traits and the variance components within populations were generally higher than that among populations in the most tested needle traits. The proportions of three-needle fascicle were significantly different among populations. The traits related to needle size in both morphology and anatomy were positive with latitude and negative with annual temperature and precipitation. Ratio indices, including mesophyll area/vascular bundle area, mesophyll area/resin canals area, vascular bundle area/resin canals area and mesophyll area/(resin canals area and vascular bundle area), were negatively correlated with elevation and positively correlated with the annual mean temperature, showing some fitness feature for the populations. Needle traits were more significantly correlated with longitude than with other four environmental factors. Needle length was significantly correlated with almost all environmental factors. First four principal components accounted for 81.596 \% of the variation with eigenvalues {\textgreater}1; the differences among populations were mainly dependent on needle width, stomatal density, section areas of vascular bundle, total resin canals, and mesophyll, as well as area ratio traits. Seven populations were divided into three categories by Euclidean distance. Variations in needle traits among the populations have shown systematic microevolution in terms of geographic impact on P. yunnanensis. This study would provide empirical data to characterize adaptation and genetic variation of P. yunnanensis, which would be helpful for management of genetic resources and reasonable utilization of them in future.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Journal of Forestry Research},
	author = {Huang, Yujie and Mao, Jianfeng and Chen, Zhiqiang and Meng, Jingxiang and Xu, Yulan and Duan, Anan and Li, Yue},
	month = feb,
	year = {2016},
	keywords = {Genetic structure, Geographic population, Morphological and anatomical traits, Needle, Pinus yunnanensis},
	pages = {13--25},
}

Pinus yunnanensis Franch. is an particular conifer tree species in Yunnan–Guizhou plateau in southwest China. The morphological and anatomical traits of needles are important to evaluate geographic variation and population dynamics of conifer species. Seedlings from seven populations of P. yunnanensis were analyzed, looking at 22 morphological and anatomical needle traits. The results showed that variations among and within populations were significantly different for all traits and the variance components within populations were generally higher than that among populations in the most tested needle traits. The proportions of three-needle fascicle were significantly different among populations. The traits related to needle size in both morphology and anatomy were positive with latitude and negative with annual temperature and precipitation. Ratio indices, including mesophyll area/vascular bundle area, mesophyll area/resin canals area, vascular bundle area/resin canals area and mesophyll area/(resin canals area and vascular bundle area), were negatively correlated with elevation and positively correlated with the annual mean temperature, showing some fitness feature for the populations. Needle traits were more significantly correlated with longitude than with other four environmental factors. Needle length was significantly correlated with almost all environmental factors. First four principal components accounted for 81.596 % of the variation with eigenvalues \textgreater1; the differences among populations were mainly dependent on needle width, stomatal density, section areas of vascular bundle, total resin canals, and mesophyll, as well as area ratio traits. Seven populations were divided into three categories by Euclidean distance. Variations in needle traits among the populations have shown systematic microevolution in terms of geographic impact on P. yunnanensis. This study would provide empirical data to characterize adaptation and genetic variation of P. yunnanensis, which would be helpful for management of genetic resources and reasonable utilization of them in future.

@article{hu_global_2016,
	title = {Global transcriptome analysis of {Sabina} chinensis ({Cupressaceae}), a valuable reforestation conifer},
	volume = {36},
	issn = {1572-9788},
	url = {https://doi.org/10.1007/s11032-016-0526-3},
	doi = {10.1007/s11032-016-0526-3},
	abstract = {Sabina chinensis has broad distribution in China and is widely used in the reforestation and as an urban tree. The species is frost resistant and grows well on contaminated soils and is becoming valuable for soil remediation and protection against air pollution. Breeding programs aimed at exploiting the species’ unique properties were handicapped by the lack of basic genetic information. Here, we established a transcriptomic profiling study from five different tissues using RNA-Seq to gain insight on the functional genes and the development of molecular markers for breeding and conservation purposes. In total 90,382,108 high-quality sequence reads ({\textasciitilde}9.0 bp) were obtained, and 116,814 unigenes (≥200 nt) were assembled. Of which, 45,026 and 15,589 unigenes were mapped to the Nr and KOG databases, 31,288 (26.78 \%) and 17,596 (15.06 \%) were annotated to GO and KEGG database, respectively. Additionally, 28,843 (24.68 \%) and 43,033 (36.84 \%) S. chinensis unigenes were aligned to the Pinus taeda draft genome and PLAZA2.5 database, respectively. A total of 4570 simple sequence repeat (SSR) motifs were identified in the unigenes. Furthermore, we obtained 6 (12.5 \%) polymorphic and 21 (43.75 \%) monomorphic loci in the verification of 48 randomly selected SSR loci. This study represents the first transcriptome data of S. chinensis and confirms that the transcriptome assembly data of S. chinensis are a useful resource for EST-SSR loci development. The substantial number of transcripts obtained will aid our understanding of the species adaptation mechanisms and provide valuable genomic information for conservation and breeding applications.},
	language = {en},
	number = {7},
	urldate = {2023-04-27},
	journal = {Molecular Breeding},
	author = {Hu, Xian-Ge and Liu, Hui and Zhang, Jia-Qing and Sun, Yan-Qiang and Jin, YuQing and Zhao, Wei and El-Kassaby, Yousry A. and Wang, Xiao-Ru and Mao, Jian-Feng},
	month = jul,
	year = {2016},
	keywords = {De novo assembly, EST-SSR, Gene discovery, RNA-Seq, Sabina chinensis},
	pages = {99},
}

Sabina chinensis has broad distribution in China and is widely used in the reforestation and as an urban tree. The species is frost resistant and grows well on contaminated soils and is becoming valuable for soil remediation and protection against air pollution. Breeding programs aimed at exploiting the species’ unique properties were handicapped by the lack of basic genetic information. Here, we established a transcriptomic profiling study from five different tissues using RNA-Seq to gain insight on the functional genes and the development of molecular markers for breeding and conservation purposes. In total 90,382,108 high-quality sequence reads (~9.0 bp) were obtained, and 116,814 unigenes (≥200 nt) were assembled. Of which, 45,026 and 15,589 unigenes were mapped to the Nr and KOG databases, 31,288 (26.78 %) and 17,596 (15.06 %) were annotated to GO and KEGG database, respectively. Additionally, 28,843 (24.68 %) and 43,033 (36.84 %) S. chinensis unigenes were aligned to the Pinus taeda draft genome and PLAZA2.5 database, respectively. A total of 4570 simple sequence repeat (SSR) motifs were identified in the unigenes. Furthermore, we obtained 6 (12.5 %) polymorphic and 21 (43.75 %) monomorphic loci in the verification of 48 randomly selected SSR loci. This study represents the first transcriptome data of S. chinensis and confirms that the transcriptome assembly data of S. chinensis are a useful resource for EST-SSR loci development. The substantial number of transcripts obtained will aid our understanding of the species adaptation mechanisms and provide valuable genomic information for conservation and breeding applications.

@article{hu_novo_2016,
	title = {De {Novo} {Transcriptome} {Assembly} and {Characterization} for the {Widespread} and {Stress}-{Tolerant} {Conifer} {Platycladus} orientalis},
	volume = {11},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0148985},
	doi = {10.1371/journal.pone.0148985},
	abstract = {Platycladus orientalis, of the family Cupressaceae, is a widespread conifer throughout China and is extensively used for ecological reforestation, horticulture, and in medicine. Transcriptome assemblies are required for this ecologically important conifer for understanding genes underpinning adaptation and complex traits for breeding programs. To enrich the species’ genomic resources, a de novo transcriptome sequencing was performed using Illumina paired-end sequencing. In total, 104,073,506 high quality sequence reads (approximately 10.3 Gbp) were obtained, which were assembled into 228,948 transcripts and 148,867 unigenes that were longer than 200 nt. Quality assessment using CEGMA showed that the transcriptomes obtained were mostly complete for highly conserved core eukaryotic genes. Based on similarity searches with known proteins, 62,938 (42.28\% of all unigenes), 42,158 (28.32\%), and 23,179 (15.57\%) had homologs in the Nr, GO, and KOG databases, 25,625 (17.21\%) unigenes were mapped to 322 pathways by BLASTX comparison against the KEGG database and 1,941 unigenes involved in environmental signaling and stress response were identified. We also identified 43 putative terpene synthase (TPS) functional genes loci and compared them with TPSs from other species. Additionally, 5,296 simple sequence repeats (SSRs) were identified in 4,715 unigenes, which were assigned to 142 motif types. This is the first report of a complete transcriptome analysis of P. orientalis. These resources provide a foundation for further studies of adaptation mechanisms and molecular-based breeding programs.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {PLOS ONE},
	author = {Hu, Xian-Ge and Liu, Hui and Jin, YuQing and Sun, Yan-Qiang and Li, Yue and Zhao, Wei and El-Kassaby, Yousry A. and Wang, Xiao-Ru and Mao, Jian-Feng},
	month = feb,
	year = {2016},
	note = {Publisher: Public Library of Science},
	keywords = {Genome annotation, Genomic databases, Genomics, Microsatellite loci, Pines, RNA sequencing, Terpenes, Transcriptome analysis},
	pages = {e0148985},
}

Platycladus orientalis, of the family Cupressaceae, is a widespread conifer throughout China and is extensively used for ecological reforestation, horticulture, and in medicine. Transcriptome assemblies are required for this ecologically important conifer for understanding genes underpinning adaptation and complex traits for breeding programs. To enrich the species’ genomic resources, a de novo transcriptome sequencing was performed using Illumina paired-end sequencing. In total, 104,073,506 high quality sequence reads (approximately 10.3 Gbp) were obtained, which were assembled into 228,948 transcripts and 148,867 unigenes that were longer than 200 nt. Quality assessment using CEGMA showed that the transcriptomes obtained were mostly complete for highly conserved core eukaryotic genes. Based on similarity searches with known proteins, 62,938 (42.28% of all unigenes), 42,158 (28.32%), and 23,179 (15.57%) had homologs in the Nr, GO, and KOG databases, 25,625 (17.21%) unigenes were mapped to 322 pathways by BLASTX comparison against the KEGG database and 1,941 unigenes involved in environmental signaling and stress response were identified. We also identified 43 putative terpene synthase (TPS) functional genes loci and compared them with TPSs from other species. Additionally, 5,296 simple sequence repeats (SSRs) were identified in 4,715 unigenes, which were assigned to 142 motif types. This is the first report of a complete transcriptome analysis of P. orientalis. These resources provide a foundation for further studies of adaptation mechanisms and molecular-based breeding programs.

@article{merelo_regulation_2016,
	title = {Regulation of {MIR165}/166 by class {II} and class {III} homeodomain leucine zipper proteins establishes leaf polarity},
	volume = {113},
	url = {https://www.pnas.org/doi/10.1073/pnas.1516110113},
	doi = {10.1073/pnas.1516110113},
	abstract = {A defining feature of plant leaves is their flattened shape. This shape depends on an antagonism between the genes that specify adaxial (top) and abaxial (bottom) tissue identity; however, the molecular nature of this antagonism remains poorly understood. Class III homeodomain leucine zipper (HD-ZIP) transcription factors are key mediators in the regulation of adaxial–abaxial patterning. Their expression is restricted adaxially during early development by the abaxially expressed microRNA (MIR)165/166, yet the mechanism that restricts MIR165/166 expression to abaxial leaf tissues remains unknown. Here, we show that class III and class II HD-ZIP proteins act together to repress MIR165/166 via a conserved cis-element in their promoters. Organ morphology and tissue patterning in plants, therefore, depend on a bidirectional repressive circuit involving a set of miRNAs and its targets.},
	number = {42},
	urldate = {2022-11-30},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Merelo, Paz and Ram, Hathi and Pia Caggiano, Monica and Ohno, Carolyn and Ott, Felix and Straub, Daniel and Graeff, Moritz and Cho, Seok Keun and Yang, Seong Wook and Wenkel, Stephan and Heisler, Marcus G.},
	month = oct,
	year = {2016},
	pages = {11973--11978},
}

A defining feature of plant leaves is their flattened shape. This shape depends on an antagonism between the genes that specify adaxial (top) and abaxial (bottom) tissue identity; however, the molecular nature of this antagonism remains poorly understood. Class III homeodomain leucine zipper (HD-ZIP) transcription factors are key mediators in the regulation of adaxial–abaxial patterning. Their expression is restricted adaxially during early development by the abaxially expressed microRNA (MIR)165/166, yet the mechanism that restricts MIR165/166 expression to abaxial leaf tissues remains unknown. Here, we show that class III and class II HD-ZIP proteins act together to repress MIR165/166 via a conserved cis-element in their promoters. Organ morphology and tissue patterning in plants, therefore, depend on a bidirectional repressive circuit involving a set of miRNAs and its targets.

@article{graeff_microprotein-mediated_2016,
	title = {{MicroProtein}-{Mediated} {Recruitment} of {CONSTANS} into a {TOPLESS} {Trimeric} {Complex} {Represses} {Flowering} in {Arabidopsis}},
	volume = {12},
	issn = {1553-7404},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005959},
	doi = {10.1371/journal.pgen.1005959},
	abstract = {MicroProteins are short, single domain proteins that act by sequestering larger, multi-domain proteins into non-functional complexes. MicroProteins have been identified in plants and animals, where they are mostly involved in the regulation of developmental processes. Here we show that two Arabidopsis thaliana microProteins, miP1a and miP1b, physically interact with CONSTANS (CO) a potent regulator of flowering time. The miP1a/b-type microProteins evolved in dicotyledonous plants and have an additional carboxy-terminal PF(V/L)FL motif. This motif enables miP1a/b microProteins to interact with TOPLESS/TOPLESS-RELATED (TPL/TPR) proteins. Interaction of CO with miP1a/b/TPL causes late flowering due to a failure in the induction of FLOWERING LOCUS T (FT) expression under inductive long day conditions. Both miP1a and miP1b are expressed in vascular tissue, where CO and FT are active. Genetically, miP1a/b act upstream of CO thus our findings unravel a novel layer of flowering time regulation via microProtein-inhibition.},
	language = {en},
	number = {3},
	urldate = {2022-11-30},
	journal = {PLOS Genetics},
	author = {Graeff, Moritz and Straub, Daniel and Eguen, Tenai and Dolde, Ulla and Rodrigues, Vandasue and Brandt, Ronny and Wenkel, Stephan},
	month = mar,
	year = {2016},
	keywords = {Arabidopsis thaliana, Flowering plants, Gene expression, Genetically modified plants, Leaves, Protein domains, Transcription factors, Yeast},
	pages = {e1005959},
}

MicroProteins are short, single domain proteins that act by sequestering larger, multi-domain proteins into non-functional complexes. MicroProteins have been identified in plants and animals, where they are mostly involved in the regulation of developmental processes. Here we show that two Arabidopsis thaliana microProteins, miP1a and miP1b, physically interact with CONSTANS (CO) a potent regulator of flowering time. The miP1a/b-type microProteins evolved in dicotyledonous plants and have an additional carboxy-terminal PF(V/L)FL motif. This motif enables miP1a/b microProteins to interact with TOPLESS/TOPLESS-RELATED (TPL/TPR) proteins. Interaction of CO with miP1a/b/TPL causes late flowering due to a failure in the induction of FLOWERING LOCUS T (FT) expression under inductive long day conditions. Both miP1a and miP1b are expressed in vascular tissue, where CO and FT are active. Genetically, miP1a/b act upstream of CO thus our findings unravel a novel layer of flowering time regulation via microProtein-inhibition.

@article{marhavy_targeted_2016,
	title = {Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation},
	volume = {30},
	issn = {0890-9369, 1549-5477},
	url = {http://genesdev.cshlp.org/lookup/doi/10.1101/gad.276964.115},
	doi = {10.1101/gad.276964.115},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Genes \& Development},
	author = {Marhavý, Peter and Montesinos, Juan Carlos and Abuzeineh, Anas and Van Damme, Daniel and Vermeer, Joop E.M. and Duclercq, Jerôme and Rakusová, Hana and Nováková, Petra and Friml, Jiři and Geldner, Niko and Benková, Eva},
	month = feb,
	year = {2016},
	keywords = {auxin, lateral root organogenesis, mechanical forces, meristem proliferation activity},
	pages = {471--483},
}

@article{wang_natural_2016,
	title = {Natural {Selection} and {Recombination} {Rate} {Variation} {Shape} {Nucleotide} {Polymorphism} {Across} the {Genomes} of {Three} {Related} {Populus} {Species}},
	volume = {202},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/202/3/1185/5930198},
	doi = {10.1534/genetics.115.183152},
	abstract = {Abstract
            A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Genetics},
	author = {Wang, Jing and Street, Nathaniel R and Scofield, Douglas G and Ingvarsson, Pär K},
	month = mar,
	year = {2016},
	pages = {1185--1200},
}

Abstract A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.

@article{galletti_developing_2016,
	title = {Developing a ‘thick skin’: a paradoxical role for mechanical tension in maintaining epidermal integrity?},
	volume = {143},
	issn = {0950-1991},
	shorttitle = {Developing a ‘thick skin’},
	url = {https://doi.org/10.1242/dev.132837},
	doi = {10.1242/dev.132837},
	abstract = {Plant aerial epidermal tissues, like animal epithelia, act as load-bearing layers and hence play pivotal roles in development. The presence of tension in the epidermis has morphogenetic implications for organ shapes but it also constantly threatens the integrity of this tissue. Here, we explore the multi-scale relationship between tension and cell adhesion in the plant epidermis, and we examine how tensile stress perception may act as a regulatory input to preserve epidermal tissue integrity and thus normal morphogenesis. From this, we identify parallels between plant epidermal and animal epithelial tissues and highlight a list of unexplored questions for future research.},
	number = {18},
	urldate = {2021-10-14},
	journal = {Development},
	author = {Galletti, Roberta and Verger, Stéphane and Hamant, Olivier and Ingram, Gwyneth C.},
	month = sep,
	year = {2016},
	pages = {3249--3258},
}

Plant aerial epidermal tissues, like animal epithelia, act as load-bearing layers and hence play pivotal roles in development. The presence of tension in the epidermis has morphogenetic implications for organ shapes but it also constantly threatens the integrity of this tissue. Here, we explore the multi-scale relationship between tension and cell adhesion in the plant epidermis, and we examine how tensile stress perception may act as a regulatory input to preserve epidermal tissue integrity and thus normal morphogenesis. From this, we identify parallels between plant epidermal and animal epithelial tissues and highlight a list of unexplored questions for future research.

@incollection{john_wiley__sons_ltd_plant_2016,
	address = {Chichester, UK},
	title = {Plant {Circadian} {Rhythms}},
	isbn = {978-0-470-01590-2 978-0-470-01617-6},
	url = {http://doi.wiley.com/10.1002/9780470015902.a0020113.pub2},
	language = {en},
	urldate = {2021-06-07},
	booktitle = {{eLS}},
	publisher = {John Wiley \& Sons, Ltd},
	author = {McWatters, Harriet G and Eriksson, Maria E.},
	editor = {{John Wiley \& Sons Ltd}},
	month = may,
	year = {2016},
	doi = {10.1002/9780470015902.a0020113.pub2},
	pages = {1--10},
}

@article{cruz-santos_role_2016,
	title = {The {Role} of {microRNAs} in {Animal} {Cell} {Reprogramming}},
	volume = {25},
	issn = {1547-3287, 1557-8534},
	url = {https://www.liebertpub.com/doi/10.1089/scd.2015.0359},
	doi = {10/f3rw7p},
	language = {en},
	number = {14},
	urldate = {2021-06-07},
	journal = {Stem Cells and Development},
	author = {Cruz-Santos, María Concepción and Aragón-Raygoza, Alejandro and Espinal-Centeno, Annie and Arteaga-Vázquez, Mario and Cruz-Hernández, Andrés and Bakó, Laszlo and Cruz-Ramírez, Alfredo},
	month = jul,
	year = {2016},
	pages = {1035--1049},
}

@article{klocko_ft_2016,
	title = {{FT} overexpression induces precocious flowering and normal reproductive development in {Eucalyptus}},
	volume = {14},
	copyright = {© 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley \& Sons Ltd},
	issn = {1467-7652},
	url = {https://www.onlinelibrary.wiley.com/doi/abs/10.1111/pbi.12431},
	doi = {10/f78rxh},
	abstract = {Eucalyptus trees are among the most important species for industrial forestry worldwide. However, as with most forest trees, flowering does not begin for one to several years after planting which can limit the rate of conventional and molecular breeding. To speed flowering, we transformed a Eucalyptus grandis × urophylla hybrid (SP7) with a variety of constructs that enable overexpression of FLOWERING LOCUS T (FT). We found that FT expression led to very early flowering, with events showing floral buds within 1–5 months of transplanting to the glasshouse. The most rapid flowering was observed when the cauliflower mosaic virus 35S promoter was used to drive the Arabidopsis thaliana FT gene (AtFT). Early flowering was also observed with AtFT overexpression from a 409S ubiquitin promoter and under heat induction conditions with Populus trichocarpa FT1 (PtFT1) under control of a heat-shock promoter. Early flowering trees grew robustly, but exhibited a highly branched phenotype compared to the strong apical dominance of nonflowering transgenic and control trees. AtFT-induced flowers were morphologically normal and produced viable pollen grains and viable self- and cross-pollinated seeds. Many self-seedlings inherited AtFT and flowered early. FT overexpression-induced flowering in Eucalyptus may be a valuable means for accelerating breeding and genetic studies as the transgene can be easily segregated away in progeny, restoring normal growth and form.},
	language = {en},
	number = {2},
	urldate = {2021-06-21},
	journal = {Plant Biotechnology Journal},
	author = {Klocko, Amy L. and Ma, Cathleen and Robertson, Sarah and Esfandiari, Elahe and Nilsson, Ove and Strauss, Steven H.},
	year = {2016},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.12431},
	keywords = {Eucalypts, Flowering Locus T, breeding, forest biotechnology, genetic engineering, transgenic},
	pages = {808--819},
}

Eucalyptus trees are among the most important species for industrial forestry worldwide. However, as with most forest trees, flowering does not begin for one to several years after planting which can limit the rate of conventional and molecular breeding. To speed flowering, we transformed a Eucalyptus grandis × urophylla hybrid (SP7) with a variety of constructs that enable overexpression of FLOWERING LOCUS T (FT). We found that FT expression led to very early flowering, with events showing floral buds within 1–5 months of transplanting to the glasshouse. The most rapid flowering was observed when the cauliflower mosaic virus 35S promoter was used to drive the Arabidopsis thaliana FT gene (AtFT). Early flowering was also observed with AtFT overexpression from a 409S ubiquitin promoter and under heat induction conditions with Populus trichocarpa FT1 (PtFT1) under control of a heat-shock promoter. Early flowering trees grew robustly, but exhibited a highly branched phenotype compared to the strong apical dominance of nonflowering transgenic and control trees. AtFT-induced flowers were morphologically normal and produced viable pollen grains and viable self- and cross-pollinated seeds. Many self-seedlings inherited AtFT and flowered early. FT overexpression-induced flowering in Eucalyptus may be a valuable means for accelerating breeding and genetic studies as the transgene can be easily segregated away in progeny, restoring normal growth and form.

@article{bennett_connective_2016,
	title = {Connective {Auxin} {Transport} in the {Shoot} {Facilitates} {Communication} between {Shoot} {Apices}},
	volume = {14},
	issn = {1545-7885},
	url = {https://dx.plos.org/10.1371/journal.pbio.1002446},
	doi = {10/f3t29d},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {PLOS Biology},
	author = {Bennett, Tom and Hines, Geneviève and van Rongen, Martin and Waldie, Tanya and Sawchuk, Megan G. and Scarpella, Enrico and Ljung, Karin and Leyser, Ottoline},
	editor = {Reed, Jason},
	month = apr,
	year = {2016},
	pages = {e1002446},
}

@article{gardestrom_origin_2016,
	title = {The origin of cytosolic {ATP} in photosynthetic cells},
	volume = {157},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12455},
	doi = {10/f3rscd},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Gardeström, Per and Igamberdiev, Abir U.},
	month = jul,
	year = {2016},
	pages = {367--379},
}

@article{lien_atlantic_2016,
	title = {The {Atlantic} salmon genome provides insights into rediploidization},
	volume = {533},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature17164},
	doi = {10/f3rv45},
	abstract = {Abstract
            
              The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (
              Salmo salar
              ), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.},
	language = {en},
	number = {7602},
	urldate = {2021-06-07},
	journal = {Nature},
	author = {Lien, Sigbjørn and Koop, Ben F. and Sandve, Simen R. and Miller, Jason R. and Kent, Matthew P. and Nome, Torfinn and Hvidsten, Torgeir R. and Leong, Jong S. and Minkley, David R. and Zimin, Aleksey and Grammes, Fabian and Grove, Harald and Gjuvsland, Arne and Walenz, Brian and Hermansen, Russell A. and von Schalburg, Kris and Rondeau, Eric B. and Di Genova, Alex and Samy, Jeevan K. A. and Olav Vik, Jon and Vigeland, Magnus D. and Caler, Lis and Grimholt, Unni and Jentoft, Sissel and Inge Våge, Dag and de Jong, Pieter and Moen, Thomas and Baranski, Matthew and Palti, Yniv and Smith, Douglas R. and Yorke, James A. and Nederbragt, Alexander J. and Tooming-Klunderud, Ave and Jakobsen, Kjetill S. and Jiang, Xuanting and Fan, Dingding and Hu, Yan and Liberles, David A. and Vidal, Rodrigo and Iturra, Patricia and Jones, Steven J. M. and Jonassen, Inge and Maass, Alejandro and Omholt, Stig W. and Davidson, William S.},
	month = may,
	year = {2016},
	pages = {200--205},
}

Abstract The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon ( Salmo salar ), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.

@article{smakowska_lack_2016,
	title = {Lack of {FTSH4} {Protease} {Affects} {Protein} {Carbonylation}, {Mitochondrial} {Morphology}, and {Phospholipid} {Content} in {Mitochondria} of {Arabidopsis}: {New} {Insights} into a {Complex} {Interplay}},
	volume = {171},
	issn = {0032-0889, 1532-2548},
	shorttitle = {Lack of {FTSH4} {Protease} {Affects} {Protein} {Carbonylation}, {Mitochondrial} {Morphology}, and {Phospholipid} {Content} in {Mitochondria} of {Arabidopsis}},
	url = {https://academic.oup.com/plphys/article/171/4/2516-2535/6115245},
	doi = {10/f3r2fs},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Smakowska, Elwira and Skibior-Blaszczyk, Renata and Czarna, Malgorzata and Kolodziejczak, Marta and Kwasniak-Owczarek, Malgorzata and Parys, Katarzyna and Funk, Christiane and Janska, Hanna},
	month = aug,
	year = {2016},
	pages = {2516--2535},
}

@article{schiffthaler_training_2016,
	title = {Training in {High}-{Throughput} {Sequencing}: {Common} {Guidelines} to {Enable} {Material} {Sharing}, {Dissemination}, and {Reusability}},
	volume = {12},
	issn = {1553-7358},
	shorttitle = {Training in {High}-{Throughput} {Sequencing}},
	url = {https://dx.plos.org/10.1371/journal.pcbi.1004937},
	doi = {10/f3sd3h},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {PLOS Computational Biology},
	author = {Schiffthaler, Bastian and Kostadima, Myrto and {NGS Trainer Consortium} and Delhomme, Nicolas and Rustici, Gabriella},
	editor = {Ouellette, Francis},
	month = jun,
	year = {2016},
	pages = {e1004937},
}

@article{von_sydow_psby_2016,
	title = {The {PsbY} protein of {Arabidopsis} {Photosystem} {II} is important for the redox control of cytochrome b 559},
	volume = {1857},
	issn = {00052728},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272816305369},
	doi = {10/f3rzx4},
	language = {en},
	number = {9},
	urldate = {2021-06-07},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {von Sydow, Lotta and Schwenkert, Serena and Meurer, Jörg and Funk, Christiane and Mamedov, Fikret and Schröder, Wolfgang P.},
	month = sep,
	year = {2016},
	pages = {1524--1533},
}

@article{hermansen_extracting_2016,
	title = {Extracting functional trends from whole genome duplication events using comparative genomics},
	volume = {18},
	issn = {1480-9222, 1480-9222},
	url = {http://biologicalproceduresonline.biomedcentral.com/articles/10.1186/s12575-016-0041-2},
	doi = {10/f3r25q},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Biological Procedures Online},
	author = {Hermansen, Russell A. and Hvidsten, Torgeir R. and Sandve, Simen Rød and Liberles, David A.},
	month = dec,
	year = {2016},
	pages = {11},
}

@article{noren_circadian_2016,
	title = {Circadian and {Plastid} {Signaling} {Pathways} {Are} {Integrated} to {Ensure} {Correct} {Expression} of the {CBF} and {COR} {Genes} during {Photoperiodic} {Growth}},
	volume = {171},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.16.00374},
	doi = {10/f3rvjv},
	abstract = {The circadian clock synchronizes a wide range of biological processes with the day/night cycle, and correct circadian regulation is essential for photosynthetic activity and plant growth. We describe here a mechanism where a plastid signal converges with the circadian clock to fine-tune the regulation of nuclear gene expression in Arabidopsis (Arabidopsis thaliana). Diurnal oscillations of tetrapyrrole levels in the chloroplasts contribute to the regulation of the nucleus-encoded transcription factors C-REPEAT BINDING FACTORS (CBFs). The plastid signal triggered by tetrapyrrole accumulation inhibits the activity of cytosolic HEAT SHOCK PROTEIN90 and, as a consequence, the maturation and stability of the clock component ZEITLUPE (ZTL). ZTL negatively regulates the transcription factor LONG HYPOCOTYL5 (HY5) and PSEUDO-RESPONSE REGULATOR5 (PRR5). Thus, low levels of ZTL result in a HY5- and PRR5-mediated repression of CBF3 and PRR5-mediated repression of CBF1 and CBF2 expression. The plastid signal thereby contributes to the rhythm of CBF expression and the downstream COLD RESPONSIVE expression during day/night cycles. These findings provide insight into how plastid signals converge with, and impact upon, the activity of well-defined clock components involved in circadian regulation.},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Norén, Louise and Kindgren, Peter and Stachula, Paulina and Rühl, Mark and Eriksson, Maria E. and Hurry, Vaughan and Strand, Åsa},
	month = jun,
	year = {2016},
	pages = {1392--1406},
}

The circadian clock synchronizes a wide range of biological processes with the day/night cycle, and correct circadian regulation is essential for photosynthetic activity and plant growth. We describe here a mechanism where a plastid signal converges with the circadian clock to fine-tune the regulation of nuclear gene expression in Arabidopsis (Arabidopsis thaliana). Diurnal oscillations of tetrapyrrole levels in the chloroplasts contribute to the regulation of the nucleus-encoded transcription factors C-REPEAT BINDING FACTORS (CBFs). The plastid signal triggered by tetrapyrrole accumulation inhibits the activity of cytosolic HEAT SHOCK PROTEIN90 and, as a consequence, the maturation and stability of the clock component ZEITLUPE (ZTL). ZTL negatively regulates the transcription factor LONG HYPOCOTYL5 (HY5) and PSEUDO-RESPONSE REGULATOR5 (PRR5). Thus, low levels of ZTL result in a HY5- and PRR5-mediated repression of CBF3 and PRR5-mediated repression of CBF1 and CBF2 expression. The plastid signal thereby contributes to the rhythm of CBF expression and the downstream COLD RESPONSIVE expression during day/night cycles. These findings provide insight into how plastid signals converge with, and impact upon, the activity of well-defined clock components involved in circadian regulation.

@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},
}

@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.

@article{zheng_local_2016,
	title = {Local auxin metabolism regulates environment-induced hypocotyl elongation},
	volume = {2},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/nplants201625},
	doi = {10/f3t37r},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Zheng, Zuyu and Guo, Yongxia and Novák, Ondřej and Chen, William and Ljung, Karin and Noel, Joseph P. and Chory, Joanne},
	month = apr,
	year = {2016},
	pages = {16025},
}

@article{dejonghe_mitochondrial_2016,
	title = {Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification},
	volume = {7},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms11710},
	doi = {10/f3r3j2},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Dejonghe, Wim and Kuenen, Sabine and Mylle, Evelien and Vasileva, Mina and Keech, Olivier and Viotti, Corrado and Swerts, Jef and Fendrych, Matyáš and Ortiz-Morea, Fausto Andres and Mishev, Kiril and Delang, Simon and Scholl, Stefan and Zarza, Xavier and Heilmann, Mareike and Kourelis, Jiorgos and Kasprowicz, Jaroslaw and Nguyen, Le Son Long and Drozdzecki, Andrzej and Van Houtte, Isabelle and Szatmári, Anna-Mária and Majda, Mateusz and Baisa, Gary and Bednarek, Sebastian York and Robert, Stéphanie and Audenaert, Dominique and Testerink, Christa and Munnik, Teun and Van Damme, Daniël and Heilmann, Ingo and Schumacher, Karin and Winne, Johan and Friml, Jiří and Verstreken, Patrik and Russinova, Eugenia},
	month = sep,
	year = {2016},
	pages = {11710},
}

@article{cheregi_insights_2016,
	title = {Insights into the {Cyanobacterial} {Deg}/{HtrA} {Proteases}},
	volume = {7},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2016.00694/full},
	doi = {10/f3rrmt},
	abstract = {Proteins are the main machinery for all living processes in a cell; they provide structural elements, regulate biochemical reactions as enzymes, and are the interface to the outside as receptors and transporters. Like any other machinery proteins have to be assembled correctly and need maintenance after damage, e.g. caused by changes in environmental conditions, genetic mutations, and limitations in the availability of cofactors. Proteases and chaperones help in repair, assembly, and folding of damaged and misfolded protein complexes cost-effective, with low energy investment compared with neo-synthesis. Despite their importance for viability, the specific biological role of most proteases in vivo is largely unknown. Deg/HtrA proteases, a family of serine-type ATP-independent proteases, have been shown in higher plants to be involved in the degradation of the Photosystem II reaction center protein D1. The objective of this review is to highlight the structure and function of their cyanobacterial orthologues. Homology modeling was used to find specific features of the Deg/HtrA proteases of Synechocystis sp. PCC 6803. Based on the available data concerning their location and their physiological substrates we conclude that these Deg proteases not only have important housekeeping and chaperone functions within the cell, but also are needed for remodeling the cell exterior.},
	language = {English},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Cheregi, Otilia and Wagner, Raik and Funk, Christiane},
	year = {2016},
	note = {Publisher: Frontiers},
	keywords = {Chaperone, Cyanobacteria, PSII degradation, Serine Proteases, cell surface, phylogeny, secretion},
}

Proteins are the main machinery for all living processes in a cell; they provide structural elements, regulate biochemical reactions as enzymes, and are the interface to the outside as receptors and transporters. Like any other machinery proteins have to be assembled correctly and need maintenance after damage, e.g. caused by changes in environmental conditions, genetic mutations, and limitations in the availability of cofactors. Proteases and chaperones help in repair, assembly, and folding of damaged and misfolded protein complexes cost-effective, with low energy investment compared with neo-synthesis. Despite their importance for viability, the specific biological role of most proteases in vivo is largely unknown. Deg/HtrA proteases, a family of serine-type ATP-independent proteases, have been shown in higher plants to be involved in the degradation of the Photosystem II reaction center protein D1. The objective of this review is to highlight the structure and function of their cyanobacterial orthologues. Homology modeling was used to find specific features of the Deg/HtrA proteases of Synechocystis sp. PCC 6803. Based on the available data concerning their location and their physiological substrates we conclude that these Deg proteases not only have important housekeeping and chaperone functions within the cell, but also are needed for remodeling the cell exterior.

@article{immanen_cytokinin_2016,
	title = {Cytokinin and {Auxin} {Display} {Distinct} but {Interconnected} {Distribution} and {Signaling} {Profiles} to {Stimulate} {Cambial} {Activity}},
	volume = {26},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982216305504},
	doi = {10/f82nd5},
	language = {en},
	number = {15},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Immanen, Juha and Nieminen, Kaisa and Smolander, Olli-Pekka and Kojima, Mikiko and Alonso Serra, Juan and Koskinen, Patrik and Zhang, Jing and Elo, Annakaisa and Mähönen, Ari Pekka and Street, Nathaniel and Bhalerao, Rishikesh P. and Paulin, Lars and Auvinen, Petri and Sakakibara, Hitoshi and Helariutta, Ykä},
	month = aug,
	year = {2016},
	pages = {1990--1997},
}

@article{procko_epidermis_2016,
	title = {The epidermis coordinates auxin-induced stem growth in response to shade},
	volume = {30},
	issn = {0890-9369, 1549-5477},
	url = {http://genesdev.cshlp.org/lookup/doi/10.1101/gad.283234.116},
	doi = {10/f3t2tn},
	language = {en},
	number = {13},
	urldate = {2021-06-07},
	journal = {Genes \& Development},
	author = {Procko, Carl and Burko, Yogev and Jaillais, Yvon and Ljung, Karin and Long, Jeff A. and Chory, Joanne},
	month = jul,
	year = {2016},
	pages = {1529--1541},
}

@article{eyer_24-d_2016,
	title = {2,4-{D} and {IAA} {Amino} {Acid} {Conjugates} {Show} {Distinct} {Metabolism} in {Arabidopsis}},
	volume = {11},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0159269},
	doi = {10/gbpkvw},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Eyer, Luděk and Vain, Thomas and Pařízková, Barbora and Oklestkova, Jana and Barbez, Elke and Kozubíková, Hana and Pospíšil, Tomáš and Wierzbicka, Roksana and Kleine-Vehn, Jürgen and Fránek, Milan and Strnad, Miroslav and Robert, Stéphanie and Novak, Ondrej},
	editor = {Rahman, Abidur},
	month = jul,
	year = {2016},
	pages = {e0159269},
}

@article{wagner_deletion_2016,
	title = {Deletion of {FtsH11} protease has impact on chloroplast structure and function in \textit{{Arabidopsis} thaliana} when grown under continuous light: {Impact} of {FtsH11} in \textit{{Arabidopsis} thaliana}},
	volume = {39},
	issn = {01407791},
	shorttitle = {Deletion of {FtsH11} protease has impact on chloroplast structure and function in \textit{{Arabidopsis} thaliana} when grown under continuous light},
	url = {http://doi.wiley.com/10.1111/pce.12808},
	doi = {10/f3rwgc},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Wagner, Raik and von Sydow, Lotta and Aigner, Harald and Netotea, Sergiu and Brugière, Sabine and Sjögren, Lars and Ferro, Myriam and Clarke, Adrian and Funk, Christiane},
	month = nov,
	year = {2016},
	pages = {2530--2544},
}

@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},
}

@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},
}

@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},
}

@article{verger_cell_2016,
	title = {Cell adhesion in plants is under the control of putative {O}-fucosyltransferases},
	volume = {143},
	issn = {0950-1991},
	url = {https://doi.org/10.1242/dev.132308},
	doi = {10/f9n5bb},
	abstract = {Cell-to-cell adhesion in plants is mediated by the cell wall and the presence of a pectin-rich middle lamella. However, we know very little about how the plant actually controls and maintains cell adhesion during growth and development and how it deals with the dynamic cell wall remodeling that takes place. Here we investigate the molecular mechanisms that control cell adhesion in plants. We carried out a genetic suppressor screen and a genetic analysis of cell adhesion-defective Arabidopsis thaliana mutants. We identified a genetic suppressor of a cell adhesion defect affecting a putative O-fucosyltransferase. Furthermore, we show that the state of cell adhesion is not directly linked with pectin content in the cell wall but instead is associated with altered pectin-related signaling. Our results suggest that cell adhesion is under the control of a feedback signal from the state of the pectin in the cell wall. Such a mechanism could be necessary for the control and maintenance of cell adhesion during growth and development.},
	number = {14},
	urldate = {2021-06-07},
	journal = {Development},
	author = {Verger, Stéphane and Chabout, Salem and Gineau, Emilie and Mouille, Grégory},
	month = jul,
	year = {2016},
	pages = {2536--2540},
}

Cell-to-cell adhesion in plants is mediated by the cell wall and the presence of a pectin-rich middle lamella. However, we know very little about how the plant actually controls and maintains cell adhesion during growth and development and how it deals with the dynamic cell wall remodeling that takes place. Here we investigate the molecular mechanisms that control cell adhesion in plants. We carried out a genetic suppressor screen and a genetic analysis of cell adhesion-defective Arabidopsis thaliana mutants. We identified a genetic suppressor of a cell adhesion defect affecting a putative O-fucosyltransferase. Furthermore, we show that the state of cell adhesion is not directly linked with pectin content in the cell wall but instead is associated with altered pectin-related signaling. Our results suggest that cell adhesion is under the control of a feedback signal from the state of the pectin in the cell wall. Such a mechanism could be necessary for the control and maintenance of cell adhesion during growth and development.

@article{pacheco-villalobos_effects_2016,
	title = {The {Effects} of {High} {Steady} {State} {Auxin} {Levels} on {Root} {Cell} {Elongation} in {Brachypodium}},
	volume = {28},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/28/5/1009-1024/6098461},
	doi = {10/bhng},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Pacheco-Villalobos, David and Díaz-Moreno, Sara M. and van der Schuren, Alja and Tamaki, Takayuki and Kang, Yeon Hee and Gujas, Bojan and Novak, Ondrej and Jaspert, Nina and Li, Zhenni and Wolf, Sebastian and Oecking, Claudia and Ljung, Karin and Bulone, Vincent and Hardtke, Christian S.},
	month = may,
	year = {2016},
	pages = {1009--1024},
}

@article{peviani_phylogeny_2016,
	title = {The phylogeny of {C}/{S1} {bZIP} transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of {S1} transcripts},
	volume = {6},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/srep30444},
	doi = {10/f3sc79},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Peviani, Alessia and Lastdrager, Jeroen and Hanson, Johannes and Snel, Berend},
	month = jul,
	year = {2016},
	pages = {30444},
}

@article{nukarinen_quantitative_2016,
	title = {Quantitative phosphoproteomics reveals the role of the {AMPK} plant ortholog {SnRK1} as a metabolic master regulator under energy deprivation},
	volume = {6},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/srep31697},
	doi = {10/f3rwtq},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Nukarinen, Ella and Nägele, Thomas and Pedrotti, Lorenzo and Wurzinger, Bernhard and Mair, Andrea and Landgraf, Ramona and Börnke, Frederik and Hanson, Johannes and Teige, Markus and Baena-Gonzalez, Elena and Dröge-Laser, Wolfgang and Weckwerth, Wolfram},
	month = aug,
	year = {2016},
	pages = {31697},
}

@article{kudahettige_nilsson_adaptability_2016,
	title = {Adaptability of {Trametes} versicolor to the lignocellulosic inhibitors furfural, {HMF}, phenol and levulinic acid during ethanol fermentation},
	volume = {90},
	issn = {09619534},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0961953416300927},
	doi = {10/f3pk4h},
	language = {en},
	urldate = {2021-06-07},
	journal = {Biomass and Bioenergy},
	author = {Kudahettige Nilsson, Rasika L. and Holmgren, Marie and Madavi, Batol and Nilsson, Robert T. and Sellstedt, Anita},
	month = jul,
	year = {2016},
	pages = {95--100},
}

@article{ingvarsson_towards_2016,
	title = {Towards integration of population and comparative genomics in forest trees},
	volume = {212},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14153},
	doi = {10/f3tpmx},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Ingvarsson, Pär K. and Hvidsten, Torgeir R. and Street, Nathaniel R.},
	month = oct,
	year = {2016},
	pages = {338--344},
}

@article{maaroufi_chronic_2016,
	title = {Chronic {Nitrogen} {Deposition} {Has} a {Minor} {Effect} on the {Quantity} and {Quality} of {Aboveground} {Litter} in a {Boreal} {Forest}},
	volume = {11},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0162086},
	doi = {10/f3tbg7},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Maaroufi, Nadia I. and Nordin, Annika and Palmqvist, Kristin and Gundale, Michael J.},
	editor = {BassiriRad, Hormoz},
	month = aug,
	year = {2016},
	pages = {e0162086},
}

@article{porco_dioxygenase-encoding_2016,
	title = {Dioxygenase-encoding \textit{{AtDAO1}} gene controls {IAA} oxidation and homeostasis in \textit{{Arabidopsis}}},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1604375113},
	doi = {10/f3t58q},
	abstract = {Auxin represents a key signal in plants, regulating almost every aspect of their growth and development. Major breakthroughs have been made dissecting the molecular basis of auxin transport, perception, and response. In contrast, how plants control the metabolism and homeostasis of the major form of auxin in plants, indole-3-acetic acid (IAA), remains unclear. In this paper, we initially describe the function of the
              Arabidopsis thaliana
              gene
              DIOXYGENASE FOR AUXIN OXIDATION 1
              (
              AtDAO1
              ). Transcriptional and translational reporter lines revealed that
              AtDAO1
              encodes a highly root-expressed, cytoplasmically localized IAA oxidase. Stable isotope-labeled IAA feeding studies of loss and gain of function
              AtDAO1
              lines showed that this oxidase represents the major regulator of auxin degradation to 2-oxoindole-3-acetic acid (oxIAA) in
              Arabidopsis
              . Surprisingly,
              AtDAO1
              loss and gain of function lines exhibited relatively subtle auxin-related phenotypes, such as altered root hair length. Metabolite profiling of mutant lines revealed that disrupting
              AtDAO1
              regulation resulted in major changes in steady-state levels of oxIAA and IAA conjugates but not IAA. Hence, IAA conjugation and catabolism seem to regulate auxin levels in
              Arabidopsis
              in a highly redundant manner. We observed that transcripts of
              AtDOA1
              IAA oxidase and
              GH3
              IAA-conjugating enzymes are auxin-inducible, providing a molecular basis for their observed functional redundancy. We conclude that the
              AtDAO1
              gene plays a key role regulating auxin homeostasis in
              Arabidopsis
              , acting in concert with
              GH3
              genes, to maintain auxin concentration at optimal levels for plant growth and development.},
	language = {en},
	number = {39},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Porco, Silvana and Pěnčík, Aleš and Rashed, Afaf and Voß, Ute and Casanova-Sáez, Rubén and Bishopp, Anthony and Golebiowska, Agata and Bhosale, Rahul and Swarup, Ranjan and Swarup, Kamal and Peňáková, Pavlína and Novák, Ondřej and Staswick, Paul and Hedden, Peter and Phillips, Andrew L. and Vissenberg, Kris and Bennett, Malcolm J. and Ljung, Karin},
	month = sep,
	year = {2016},
	pages = {11016--11021},
}

Auxin represents a key signal in plants, regulating almost every aspect of their growth and development. Major breakthroughs have been made dissecting the molecular basis of auxin transport, perception, and response. In contrast, how plants control the metabolism and homeostasis of the major form of auxin in plants, indole-3-acetic acid (IAA), remains unclear. In this paper, we initially describe the function of the Arabidopsis thaliana gene DIOXYGENASE FOR AUXIN OXIDATION 1 ( AtDAO1 ). Transcriptional and translational reporter lines revealed that AtDAO1 encodes a highly root-expressed, cytoplasmically localized IAA oxidase. Stable isotope-labeled IAA feeding studies of loss and gain of function AtDAO1 lines showed that this oxidase represents the major regulator of auxin degradation to 2-oxoindole-3-acetic acid (oxIAA) in Arabidopsis . Surprisingly, AtDAO1 loss and gain of function lines exhibited relatively subtle auxin-related phenotypes, such as altered root hair length. Metabolite profiling of mutant lines revealed that disrupting AtDAO1 regulation resulted in major changes in steady-state levels of oxIAA and IAA conjugates but not IAA. Hence, IAA conjugation and catabolism seem to regulate auxin levels in Arabidopsis in a highly redundant manner. We observed that transcripts of AtDOA1 IAA oxidase and GH3 IAA-conjugating enzymes are auxin-inducible, providing a molecular basis for their observed functional redundancy. We conclude that the AtDAO1 gene plays a key role regulating auxin homeostasis in Arabidopsis , acting in concert with GH3 genes, to maintain auxin concentration at optimal levels for plant growth and development.

@article{van_aken_mitochondrial_2016,
	title = {Mitochondrial and {Chloroplast} {Stress} {Responses} {Are} {Modulated} in {Distinct} {Touch} and {Chemical} {Inhibition} {Phases}},
	volume = {171},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/171/3/2150-2165/6115508},
	doi = {10/f3rznf},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Van Aken, Olivier and De Clercq, Inge and Ivanova, Aneta and Law, Simon R. and Van Breusegem, Frank and Millar, A. Harvey and Whelan, James},
	month = jul,
	year = {2016},
	pages = {2150--2165},
}

@article{mellor_dynamic_2016,
	title = {Dynamic regulation of auxin oxidase and conjugating enzymes \textit{{AtDAO1}} and \textit{{GH3}} modulates auxin homeostasis},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1604458113},
	doi = {10/f3t6ch},
	abstract = {The hormone auxin is a key regulator of plant growth and development, and great progress has been made understanding auxin transport and signaling. Here, we show that auxin metabolism and homeostasis are also regulated in a complex manner. The principal auxin degradation pathways in
              Arabidopsis
              include oxidation by
              Arabidopsis thaliana
              gene
              DIOXYGENASE FOR AUXIN OXIDATION 1/2
              (AtDAO1/2) and conjugation by Gretchen Hagen3s (GH3s). Metabolic profiling of
              dao1-1
              root tissues revealed a 50\% decrease in the oxidation product 2-oxoindole-3-acetic acid (oxIAA) and increases in the conjugated forms indole-3-acetic acid aspartic acid (IAA-Asp) and indole-3-acetic acid glutamic acid (IAA-Glu) of 438- and 240-fold, respectively, whereas auxin remains close to the WT. By fitting parameter values to a mathematical model of these metabolic pathways, we show that, in addition to reduced oxidation, both auxin biosynthesis and conjugation are increased in
              dao1-1
              . Transcripts of
              AtDAO1
              and
              GH3
              genes increase in response to auxin over different timescales and concentration ranges. Including this regulation of
              AtDAO1
              and
              GH3
              in an extended model reveals that auxin oxidation is more important for auxin homoeostasis at lower hormone concentrations, whereas auxin conjugation is most significant at high auxin levels. Finally, embedding our homeostasis model in a multicellular simulation to assess the spatial effect of the
              dao1-1
              mutant shows that auxin increases in outer root tissues in agreement with the
              dao1-1
              mutant root hair phenotype. We conclude that auxin homeostasis is dependent on
              AtDAO1
              , acting in concert with
              GH3
              , to maintain auxin at optimal levels for plant growth and development.},
	language = {en},
	number = {39},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Mellor, Nathan and Band, Leah R. and Pěnčík, Aleš and Novák, Ondřej and Rashed, Afaf and Holman, Tara and Wilson, Michael H. and Voß, Ute and Bishopp, Anthony and King, John R. and Ljung, Karin and Bennett, Malcolm J. and Owen, Markus R.},
	month = sep,
	year = {2016},
	pages = {11022--11027},
}

The hormone auxin is a key regulator of plant growth and development, and great progress has been made understanding auxin transport and signaling. Here, we show that auxin metabolism and homeostasis are also regulated in a complex manner. The principal auxin degradation pathways in Arabidopsis include oxidation by Arabidopsis thaliana gene DIOXYGENASE FOR AUXIN OXIDATION 1/2 (AtDAO1/2) and conjugation by Gretchen Hagen3s (GH3s). Metabolic profiling of dao1-1 root tissues revealed a 50% decrease in the oxidation product 2-oxoindole-3-acetic acid (oxIAA) and increases in the conjugated forms indole-3-acetic acid aspartic acid (IAA-Asp) and indole-3-acetic acid glutamic acid (IAA-Glu) of 438- and 240-fold, respectively, whereas auxin remains close to the WT. By fitting parameter values to a mathematical model of these metabolic pathways, we show that, in addition to reduced oxidation, both auxin biosynthesis and conjugation are increased in dao1-1 . Transcripts of AtDAO1 and GH3 genes increase in response to auxin over different timescales and concentration ranges. Including this regulation of AtDAO1 and GH3 in an extended model reveals that auxin oxidation is more important for auxin homoeostasis at lower hormone concentrations, whereas auxin conjugation is most significant at high auxin levels. Finally, embedding our homeostasis model in a multicellular simulation to assess the spatial effect of the dao1-1 mutant shows that auxin increases in outer root tissues in agreement with the dao1-1 mutant root hair phenotype. We conclude that auxin homeostasis is dependent on AtDAO1 , acting in concert with GH3 , to maintain auxin at optimal levels for plant growth and development.

@article{liebsch_darkinduced_2016,
	title = {Dark‐induced leaf senescence: new insights into a complex light‐dependent regulatory pathway},
	volume = {212},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Dark‐induced leaf senescence},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14217},
	doi = {10/f3trh7},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Liebsch, Daniela and Keech, Olivier},
	month = nov,
	year = {2016},
	pages = {563--570},
}

@article{wattelet-boyer_enrichment_2016,
	title = {Enrichment of hydroxylated {C24}- and {C26}-acyl-chain sphingolipids mediates {PIN2} apical sorting at trans-{Golgi} network subdomains},
	volume = {7},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms12788},
	doi = {10/ghtbhj},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Wattelet-Boyer, Valérie and Brocard, Lysiane and Jonsson, Kristoffer and Esnay, Nicolas and Joubès, Jérôme and Domergue, Frédéric and Mongrand, Sébastien and Raikhel, Natasha and Bhalerao, Rishikesh P. and Moreau, Patrick and Boutté, Yohann},
	month = nov,
	year = {2016},
	pages = {12788},
}

@article{johnsson_cambial_2016,
	title = {Cambial stem cells and their niche},
	volume = {252},
	issn = {01689452},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0168945216302862},
	doi = {10/gjcnkm},
	language = {en},
	urldate = {2021-06-07},
	journal = {Plant Science},
	author = {Johnsson, Christoffer and Fischer, Urs},
	month = nov,
	year = {2016},
	pages = {239--245},
}

@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},
}

@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},
}

@article{soler_woody-preferential_2016,
	title = {The {Woody}-{Preferential} {Gene} {EgMYB88} {Regulates} the {Biosynthesis} of {Phenylpropanoid}-{Derived} {Compounds} in {Wood}},
	volume = {7},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/Article/10.3389/fpls.2016.01422/abstract},
	doi = {10/f3tcr7},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Soler, Marçal and Plasencia, Anna and Lepikson-Neto, Jorge and Camargo, Eduardo L. O. and Dupas, Annabelle and Ladouce, Nathalie and Pesquet, Edouard and Mounet, Fabien and Larbat, Romain and Grima-Pettenati, Jacqueline},
	month = sep,
	year = {2016},
}

@article{krupinski_model_2016,
	title = {A {Model} {Analysis} of {Mechanisms} for {Radial} {Microtubular} {Patterns} at {Root} {Hair} {Initiation} {Sites}},
	volume = {7},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/article/10.3389/fpls.2016.01560/full},
	doi = {10/f3t5jz},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Krupinski, Pawel and Bozorg, Behruz and Larsson, André and Pietra, Stefano and Grebe, Markus and Jönsson, Henrik},
	month = oct,
	year = {2016},
}

@article{czaban_direct_2016,
	title = {Direct acquisition of organic {N} by white clover even in the presence of inorganic {N}},
	volume = {407},
	issn = {0032-079X, 1573-5036},
	url = {http://link.springer.com/10.1007/s11104-016-2896-z},
	doi = {10/f3tc8b},
	language = {en},
	number = {1-2},
	urldate = {2021-06-07},
	journal = {Plant and Soil},
	author = {Czaban, Weronika and Jämtgård, Sandra and Näsholm, Torgny and Rasmussen, Jim and Nicolaisen, Mogens and Fomsgaard, Inge S.},
	month = oct,
	year = {2016},
	pages = {91--107},
}

@article{mao_framework_2016,
	title = {A {Framework} for {Lateral} {Membrane} {Trafficking} and {Polar} {Tethering} of the {PEN3} {ATP}-{Binding} {Cassette} {Transporter}},
	volume = {172},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/172/4/2245-2260/6115810},
	doi = {10/f3vhhs},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Mao, Hailiang and Nakamura, Moritaka and Viotti, Corrado and Grebe, Markus},
	month = dec,
	year = {2016},
	pages = {2245--2260},
}

@article{chen_method_2016,
	title = {Method for accurate fiber length determination from increment cores for large-scale population analyses in {Norway} spruce},
	volume = {70},
	issn = {1437-434X, 0018-3830},
	url = {https://www.degruyter.com/document/doi/10.1515/hf-2015-0138/html},
	doi = {10/f3rwht},
	abstract = {Abstract
            
              Fiber (tracheid) length is an important trait targeted for genetic and silvicultural improvement. Such studies require large-scale non-destructive sampling, and accurate length determination. The standard procedure for non-destructive sampling is to collect increment cores, singularize their cells by maceration, measure them with optical analyzer and apply various corrections to suppress influence of non-fiber particles and cut fibers, as fibers are cut by the corer. The recently developed expectation-maximization method (EM) not only addresses the problem of non-fibers and cut fibers, but also corrects for the sampling bias. Here, the performance of the EM method has been evaluated by comparing it with length-weighing and squared length-weighing, both implemented in fiber analyzers, and with microscopy data for intact fibers, corrected for sampling bias, as the reference. This was done for 12-mm increment cores from 16 Norway spruce (
              Picea abies
              (L.) Karst) trees on fibers from rings 8–11 (counted from pith), representing juvenile wood of interest in breeding programs. The EM-estimates provided mean-fiber-lengths with bias of only +2.7\% and low scatter. Length-weighing and length
              2
              -weighing gave biases of -7.3\% and +9.3\%, respectively, and larger scatter. The suggested EM approach constitutes a more accurate non-destructive method for fiber length (FL) determination, expected to be applicable also to other conifers.},
	number = {9},
	urldate = {2021-06-07},
	journal = {Holzforschung},
	author = {Chen, Zhi-Qiang and Abramowicz, Konrad and Raczkowski, Rafal and Ganea, Stefana and Wu, Harry X. and Lundqvist, Sven-Olof and Mörling, Tommy and de Luna, Sara Sjöstedt and García Gil, María Rosario and Mellerowicz, Ewa J.},
	month = sep,
	year = {2016},
	pages = {829--838},
}

Abstract Fiber (tracheid) length is an important trait targeted for genetic and silvicultural improvement. Such studies require large-scale non-destructive sampling, and accurate length determination. The standard procedure for non-destructive sampling is to collect increment cores, singularize their cells by maceration, measure them with optical analyzer and apply various corrections to suppress influence of non-fiber particles and cut fibers, as fibers are cut by the corer. The recently developed expectation-maximization method (EM) not only addresses the problem of non-fibers and cut fibers, but also corrects for the sampling bias. Here, the performance of the EM method has been evaluated by comparing it with length-weighing and squared length-weighing, both implemented in fiber analyzers, and with microscopy data for intact fibers, corrected for sampling bias, as the reference. This was done for 12-mm increment cores from 16 Norway spruce ( Picea abies (L.) Karst) trees on fibers from rings 8–11 (counted from pith), representing juvenile wood of interest in breeding programs. The EM-estimates provided mean-fiber-lengths with bias of only +2.7% and low scatter. Length-weighing and length 2 -weighing gave biases of -7.3% and +9.3%, respectively, and larger scatter. The suggested EM approach constitutes a more accurate non-destructive method for fiber length (FL) determination, expected to be applicable also to other conifers.

@article{li_characterization_2016,
	title = {Characterization of a novel β-barrel protein ({AtOM47}) from the mitochondrial outer membrane of \textit{{Arabidopsis} thaliana}},
	volume = {67},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erw366},
	doi = {10/f9c9wf},
	language = {en},
	number = {21},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Li, Lu and Kubiszewski-Jakubiak, Szymon and Radomiljac, Jordan and Wang, Yan and Law, Simon R. and Keech, Olivier and Narsai, Reena and Berkowitz, Oliver and Duncan, Owen and Murcha, Monika W. and Whelan, James},
	month = nov,
	year = {2016},
	pages = {6061--6075},
}

@article{hasselquist_greater_2016,
	title = {Greater carbon allocation to mycorrhizal fungi reduces tree nitrogen uptake in a boreal forest},
	volume = {97},
	issn = {0012-9658 (Print) 0012-9658 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/27220217},
	doi = {10.1890/15-1222.1},
	abstract = {The central role that ectomycorrhizal (EM) symbioses play in the structure and function of boreal forests pivots around the common assumption that carbon (C) and nitrogen (N) are exchanged at rates favorable for plant growth. However, this may not always be the case. It has been hypothesized that the benefits mycorrhizal fungi convey to their host plants strongly depends upon the availability of C and N, both of which are rapidly changing as a result of intensified human land use and climate change. Using large-scale shading and N addition treatments, we assessed the independent and interactive effects of changes in C and N supply on the transfer of N in intact EM associations with -15 yr. old Scots pine trees. To assess the dynamics of N transfer in EM symbioses, we added trace amounts of highly enriched 5NO3(-) label to the EM-dominated mor-layer and followed the fate of the 15N label in tree foliage, fungal chitin on EM root tips, and EM sporocarps. Despite no change in leaf biomass, shading resulted in reduced tree C uptake, ca. 40\% lower fungal biomass on EM root tips, and greater 15N label in tree foliage compared to unshaded control plots, where more 15N label was found in fungal biomass on EM colonized root tips. Short-term addition of N shifted the incorporation of 15N label from EM fungi to tree foliage, despite no significant changes in below-ground tree C allocation to EM fungi. Contrary to the common assumption that C and N are exchanged at rates favorable for plant growth, our results show for the first time that under N-limited conditions greater C allocation to EM fungi in the field results in reduced, not increased, N transfer to host trees. Moreover, given the ubiquitous nature of mycorrhizal symbioses, our results stress the need to incorporate mycorrhizal dynamics into process-based ecosystem models to better predict forest C and N cycles in light of global climate change.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Ecology},
	author = {Hasselquist, N. J. and Metcalfe, D. B. and Inselsbacher, E. and Stangl, Z. and Oren, R. and Nasholm, T. and Hogberg, P.},
	month = apr,
	year = {2016},
	note = {Edition: 2016/05/26},
	keywords = {*Forests, Carbon/*metabolism, Mycorrhizae/*physiology, Nitrogen/*metabolism, Pinus sylvestris/*microbiology/physiology, Symbiosis, Trees/*microbiology/physiology},
	pages = {1012--22},
}

The central role that ectomycorrhizal (EM) symbioses play in the structure and function of boreal forests pivots around the common assumption that carbon (C) and nitrogen (N) are exchanged at rates favorable for plant growth. However, this may not always be the case. It has been hypothesized that the benefits mycorrhizal fungi convey to their host plants strongly depends upon the availability of C and N, both of which are rapidly changing as a result of intensified human land use and climate change. Using large-scale shading and N addition treatments, we assessed the independent and interactive effects of changes in C and N supply on the transfer of N in intact EM associations with -15 yr. old Scots pine trees. To assess the dynamics of N transfer in EM symbioses, we added trace amounts of highly enriched 5NO3(-) label to the EM-dominated mor-layer and followed the fate of the 15N label in tree foliage, fungal chitin on EM root tips, and EM sporocarps. Despite no change in leaf biomass, shading resulted in reduced tree C uptake, ca. 40% lower fungal biomass on EM root tips, and greater 15N label in tree foliage compared to unshaded control plots, where more 15N label was found in fungal biomass on EM colonized root tips. Short-term addition of N shifted the incorporation of 15N label from EM fungi to tree foliage, despite no significant changes in below-ground tree C allocation to EM fungi. Contrary to the common assumption that C and N are exchanged at rates favorable for plant growth, our results show for the first time that under N-limited conditions greater C allocation to EM fungi in the field results in reduced, not increased, N transfer to host trees. Moreover, given the ubiquitous nature of mycorrhizal symbioses, our results stress the need to incorporate mycorrhizal dynamics into process-based ecosystem models to better predict forest C and N cycles in light of global climate change.

@article{van_de_wouwer_chemical_2016,
	title = {Chemical {Genetics} {Uncovers} {Novel} {Inhibitors} of {Lignification}, {Including} \textit{p} -{Iodobenzoic} {Acid} {Targeting} {CINNAMATE}-4-{HYDROXYLASE}},
	volume = {172},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/172/1/198-220/6115558},
	doi = {10.1104/pp.16.00430},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Van de Wouwer, Dorien and Vanholme, Ruben and Decou, Raphaël and Goeminne, Geert and Audenaert, Dominique and Nguyen, Long and Höfer, René and Pesquet, Edouard and Vanholme, Bartel and Boerjan, Wout},
	month = sep,
	year = {2016},
	pages = {198--220},
}

@article{miguel_short-root-like_2016,
	title = {The {SHORT}-{ROOT}-like gene {PtSHR2B} is involved in {Populus} phellogen activity},
	volume = {67},
	issn = {1460-2431},
	doi = {10.1093/jxb/erv547},
	abstract = {SHORT-ROOT (SHR) is a GRAS transcription factor first characterized for its role in the specification of the stem cell niche and radial patterning in Arabidopsis thaliana (At) roots. Three SHR-like genes have been identified in Populus trichocarpa (Pt). PtSHR1 shares high similarity with AtSHR over the entire length of the coding sequence. The two other Populus SHR-like genes, PtSHR2A and PtSHR2B, are shorter in their 5' ends when compared with AtSHR. Unlike PtSHR1, that is expressed throughout the cambial zone of greenhouse-grown Populus trees, PtSHR2Bprom:uidA expression was detected in the phellogen. Additionally, PtSHR1 and PtSHR2B expression patterns markedly differ in the shoot apex and roots of in vitro plants. Transgenic hybrid aspen expressing PtSHR2B under the 35S constitutive promoter showed overall reduced tree growth while the proportion of bark increased relative to the wood. Reverse transcription-quantitative PCR (RT-qPCR) revealed increased transcript levels of cytokinin metabolism and response-related genes in the transgenic plants consistent with an increase of total cytokinin levels. This was confirmed by cytokinin quantification by LC-MS/MS. Our results indicate that PtSHR2B appears to function in the phellogen and therefore in the regulation of phellem and periderm formation, possibly acting through modulation of cytokinin homeostasis. Furthermore, this work points to a functional diversification of SHR after the divergence of the Populus and Arabidopsis lineages. This finding may contribute to selection and breeding strategies of cork oak in which, unlike Populus, the phellogen is active throughout the entire tree lifespan, being at the basis of a highly profitable cork industry.},
	language = {eng},
	number = {5},
	journal = {Journal of Experimental Botany},
	author = {Miguel, Andreia and Milhinhos, Ana and Novák, Ondřej and Jones, Brian and Miguel, Célia M.},
	month = mar,
	year = {2016},
	pmid = {26709311},
	keywords = {Cambium, Cytokinin, Cytokinins, Gene Expression Regulation, Plant, Genes, Plant, Hybridization, Genetic, Phenotype, Plant Proteins, Plant Stems, Plants, Genetically Modified, Populus, Populus tremula×Populus tremuloides, Promoter Regions, Genetic, SHORT-ROOT., Trees, Wood, lateral meristem, phellogen, secondary growth},
	pages = {1545--1555},
}

SHORT-ROOT (SHR) is a GRAS transcription factor first characterized for its role in the specification of the stem cell niche and radial patterning in Arabidopsis thaliana (At) roots. Three SHR-like genes have been identified in Populus trichocarpa (Pt). PtSHR1 shares high similarity with AtSHR over the entire length of the coding sequence. The two other Populus SHR-like genes, PtSHR2A and PtSHR2B, are shorter in their 5' ends when compared with AtSHR. Unlike PtSHR1, that is expressed throughout the cambial zone of greenhouse-grown Populus trees, PtSHR2Bprom:uidA expression was detected in the phellogen. Additionally, PtSHR1 and PtSHR2B expression patterns markedly differ in the shoot apex and roots of in vitro plants. Transgenic hybrid aspen expressing PtSHR2B under the 35S constitutive promoter showed overall reduced tree growth while the proportion of bark increased relative to the wood. Reverse transcription-quantitative PCR (RT-qPCR) revealed increased transcript levels of cytokinin metabolism and response-related genes in the transgenic plants consistent with an increase of total cytokinin levels. This was confirmed by cytokinin quantification by LC-MS/MS. Our results indicate that PtSHR2B appears to function in the phellogen and therefore in the regulation of phellem and periderm formation, possibly acting through modulation of cytokinin homeostasis. Furthermore, this work points to a functional diversification of SHR after the divergence of the Populus and Arabidopsis lineages. This finding may contribute to selection and breeding strategies of cork oak in which, unlike Populus, the phellogen is active throughout the entire tree lifespan, being at the basis of a highly profitable cork industry.

@article{gerber_highthroughput_2016,
	title = {High‐throughput microanalysis of large lignocellulosic sample sets by pyrolysis‐gas chromatography/mass spectrometry},
	volume = {156},
	issn = {0031-9317, 1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ppl.12397},
	doi = {10.1111/ppl.12397},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Gerber, Lorenz and Öhman, David and Kumar, Manoj and Ranocha, Philippe and Goffner, Deborah and Sundberg, Björn},
	month = feb,
	year = {2016},
	pages = {127--138},
}

@article{engineer_co_2016,
	title = {{CO} 2 {Sensing} and {CO} 2 {Regulation} of {Stomatal} {Conductance}: {Advances} and {Open} {Questions}},
	volume = {21},
	issn = {13601385},
	shorttitle = {{CO} 2 {Sensing} and {CO} 2 {Regulation} of {Stomatal} {Conductance}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138515002290},
	doi = {10.1016/j.tplants.2015.08.014},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Trends in Plant Science},
	author = {Engineer, Cawas B. and Hashimoto-Sugimoto, Mimi and Negi, Juntaro and Israelsson-Nordström, Maria and Azoulay-Shemer, Tamar and Rappel, Wouter-Jan and Iba, Koh and Schroeder, Julian I.},
	month = jan,
	year = {2016},
	pages = {16--30},
}

@article{shaikhali_redox_2016,
	title = {Redox regulation of the {MED28} and {MED32} mediator subunits is important for development and senescence},
	volume = {253},
	issn = {0033-183X, 1615-6102},
	url = {http://link.springer.com/10.1007/s00709-015-0853-y},
	doi = {10.1007/s00709-015-0853-y},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Protoplasma},
	author = {Shaikhali, Jehad and Davoine, Céline and Björklund, Stefan and Wingsle, Gunnar},
	month = may,
	year = {2016},
	pages = {957--963},
}

@article{pawar_expression_2016,
	title = {Expression of fungal acetyl xylan esterase in \textit{{Arabidopsis} thaliana} improves saccharification of stem lignocellulose},
	volume = {14},
	issn = {14677644},
	url = {http://doi.wiley.com/10.1111/pbi.12393},
	doi = {10.1111/pbi.12393},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Biotechnology Journal},
	author = {Pawar, Prashant Mohan-Anupama and Derba-Maceluch, Marta and Chong, Sun-Li and Gómez, Leonardo D. and Miedes, Eva and Banasiak, Alicja and Ratke, Christine and Gaertner, Cyril and Mouille, Grégory and McQueen-Mason, Simon J. and Molina, Antonio and Sellstedt, Anita and Tenkanen, Maija and Mellerowicz, Ewa J.},
	month = jan,
	year = {2016},
	pages = {387--397},
}

@article{hall_estimation_2016,
	title = {Estimation of number and size of {QTL} effects in forest tree traits},
	volume = {12},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-016-1073-0},
	doi = {10.1007/s11295-016-1073-0},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Tree Genetics \& Genomes},
	author = {Hall, David and Hallingbäck, Henrik R. and Wu, Harry X.},
	month = dec,
	year = {2016},
	pages = {110},
}

@article{steenackers_allelochemical_2016,
	title = {The allelochemical {MDCA} inhibits lignification and affects auxin homeostasis},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/172/2/874-888/6115977},
	doi = {10.1104/pp.15.01972},
	language = {en},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Steenackers, Ward Jan and Cesarino, Igor and Klíma, Petr and Quareshy, Mussa and Vanholme, Ruben and Corneillie, Sander and Kumpf, Robert P. and Van de Wouwer, Dorien and Ljung, Karin and Goeminne, Geert and Novak, Ondrej and Zažímalová, Eva and Napier, Richard M. and Boerjan, Wout A and Vanholme, Bartel},
	month = aug,
	year = {2016},
	pages = {pp.01972.2015},
}

@article{santuari_plethora_2016,
	title = {The {PLETHORA} {Gene} {Regulatory} {Network} {Guides} {Growth} and {Cell} {Differentiation} in {Arabidopsis} {Roots}},
	volume = {28},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/28/12/2937-2951/6098272},
	doi = {10.1105/tpc.16.00656},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Santuari, Luca and Sanchez-Perez, Gabino F. and Luijten, Marijn and Rutjens, Bas and Terpstra, Inez and Berke, Lidija and Gorte, Maartje and Prasad, Kalika and Bao, Dongping and Timmermans-Hereijgers, Johanna L.P.M. and Maeo, Kenichiro and Nakamura, Kenzo and Shimotohno, Akie and Pencik, Ales and Novak, Ondrej and Ljung, Karin and van Heesch, Sebastiaan and de Bruijn, Ewart and Cuppen, Edwin and Willemsen, Viola and Mähönen, Ari Pekka and Lukowitz, Wolfgang and Snel, Berend and de Ridder, Dick and Scheres, Ben and Heidstra, Renze},
	month = dec,
	year = {2016},
	pages = {2937--2951},
}

@article{zulfugarov_enhanced_2016,
	title = {Enhanced resistance of {PsbS}-deficient rice ({Oryza} sativa {L}.) to fungal and bacterial pathogens},
	volume = {59},
	issn = {1226-9239, 1867-0725},
	url = {http://link.springer.com/10.1007/s12374-016-0068-6},
	doi = {10.1007/s12374-016-0068-6},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Journal of Plant Biology},
	author = {Zulfugarov, Ismayil S. and Tovuu, Altanzaya and Kim, Chi-Yeol and Xuan Vo, Kieu Thi and Ko, Soo Yeon and Hall, Michael and Seok, Hye-Yeon and Kim, Yeon-Ki and Skogstrom, Oscar and Moon, Yong-Hwan and Jansson, Stefan and Jeon, Jong-Seong and Lee, Choon-Hwan},
	month = dec,
	year = {2016},
	pages = {616--626},
}

@article{cheregi_antibiotic_2016,
	title = {Antibiotic {Disc} {Assay} for {Synechocystis} sp. {PCC6803}},
	volume = {6},
	issn = {2331-8325},
	url = {https://bio-protocol.org/e2071},
	doi = {10.21769/BioProtoc.2071},
	language = {en},
	number = {24},
	urldate = {2021-06-07},
	journal = {BIO-PROTOCOL},
	author = {Cheregi, Otilia and Funk, Christiane},
	year = {2016},
}

@article{chen_genetic_2016,
	title = {Genetic analysis of fiber dimensions and their correlation with stem diameter and solid-wood properties in {Norway} spruce},
	volume = {12},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-016-1065-0},
	doi = {10.1007/s11295-016-1065-0},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Tree Genetics \& Genomes},
	author = {Chen, Zhi-Qiang and Karlsson, Bo and Mörling, Tommy and Olsson, Lars and Mellerowicz, Ewa J. and Wu, Harry X. and Lundqvist, Sven-Olof and Gil, María Rosario García},
	month = dec,
	year = {2016},
	pages = {123},
}

@article{ausin_dna_2016,
	title = {{DNA} methylome of the 20-gigabase {Norway} spruce genome},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1618019113},
	doi = {10.1073/pnas.1618019113},
	abstract = {DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce (
              Picea abies
              ) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.},
	language = {en},
	number = {50},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Ausin, Israel and Feng, Suhua and Yu, Chaowei and Liu, Wanlu and Kuo, Hsuan Yu and Jacobsen, Elise L. and Zhai, Jixian and Gallego-Bartolome, Javier and Wang, Lin and Egertsdotter, Ulrika and Street, Nathaniel R. and Jacobsen, Steven E. and Wang, Haifeng},
	month = dec,
	year = {2016},
	pages = {E8106--E8113},
}

DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce ( Picea abies ) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.

@article{nordstrom_impacts_2016,
	title = {Impacts of global climate change mitigation scenarios on forests and harvesting in {Sweden}},
	volume = {46},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2016-0122},
	doi = {10.1139/cjfr-2016-0122},
	abstract = {Under climate change, the importance of biomass resources is likely to increase and new approaches are needed to analyze future material and energy use of biomass globally and locally. Using Sweden as an example, we present an approach that combines global and national land-use and forest models to analyze impacts of climate change mitigation ambitions on forest management and harvesting in a specific country. National forest impact analyses in Sweden have traditionally focused on supply potential with little reference to international market developments. In this study, we use the global greenhouse gas concentration scenarios from the Intergovernmental Panel for Climate Change to estimate global biomass demand and assess potential implications on harvesting and biodiversity in Sweden. The results show that the short-term demand for wood is close to the full harvesting potential in Sweden in all scenarios. Under high bioenergy demand, harvest levels are projected to stay high over a longer time and particularly impact the harvest levels of pulpwood. The area of old forest in the managed landscape may decrease. This study highlights the importance of global scenarios when discussing national-level analysis and pinpoints trade-offs that policy making in Sweden may need to tackle in the near future.},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Nordström, Eva-Maria and Forsell, Nicklas and Lundström, Anders and Korosuo, Anu and Bergh, Johan and Havlík, Petr and Kraxner, Florian and Frank, Stefan and Fricko, Oliver and Lundmark, Tomas and Nordin, Annika},
	month = dec,
	year = {2016},
	pages = {1427--1438},
}

Under climate change, the importance of biomass resources is likely to increase and new approaches are needed to analyze future material and energy use of biomass globally and locally. Using Sweden as an example, we present an approach that combines global and national land-use and forest models to analyze impacts of climate change mitigation ambitions on forest management and harvesting in a specific country. National forest impact analyses in Sweden have traditionally focused on supply potential with little reference to international market developments. In this study, we use the global greenhouse gas concentration scenarios from the Intergovernmental Panel for Climate Change to estimate global biomass demand and assess potential implications on harvesting and biodiversity in Sweden. The results show that the short-term demand for wood is close to the full harvesting potential in Sweden in all scenarios. Under high bioenergy demand, harvest levels are projected to stay high over a longer time and particularly impact the harvest levels of pulpwood. The area of old forest in the managed landscape may decrease. This study highlights the importance of global scenarios when discussing national-level analysis and pinpoints trade-offs that policy making in Sweden may need to tackle in the near future.

@article{from_effects_2016,
	title = {Effects of simulated long-term {N} deposition on \textit{{Picea} abies} and \textit{{Pinus} sylvestris} growth in boreal forest},
	volume = {46},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2016-0201},
	doi = {10.1139/cjfr-2016-0201},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {From, F. and Lundmark, T. and Mörling, T. and Pommerening, A. and Nordin, A.},
	month = nov,
	year = {2016},
	pages = {1396--1403},
}

@article{decker_aspen_2016,
	title = {Aspen phenylpropanoid genes’ expression levels correlate with genets’ tannin richness and vary both in responses to soil nitrogen and associations with phenolic profiles},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpw118},
	doi = {10.1093/treephys/tpw118},
	language = {en},
	urldate = {2021-06-07},
	journal = {Tree Physiology},
	author = {Decker, Vicki H.G. and Bandau, Franziska and Gundale, Michael J. and Cole, Christopher T. and Albrectsen, Benedicte R.},
	editor = {Tsai, Chung-Jui},
	month = dec,
	year = {2016},
	pages = {treephys;tpw118v1},
}

@article{zheng_inheritance_2016,
	title = {Inheritance of growth and survival in two 9-year-old, open-pollinated progenies of an advanced breeding population of {Chinese} firs in southeastern {China}},
	volume = {27},
	issn = {1007-662X, 1993-0607},
	url = {http://link.springer.com/10.1007/s11676-016-0250-1},
	doi = {10.1007/s11676-016-0250-1},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Journal of Forestry Research},
	author = {Zheng, Renhua and Hong, Zhou and Su, Shunde and Bian, Liming and Xiao, Hui and Shi, Jisen and Wu, Harry X.},
	month = oct,
	year = {2016},
	pages = {1067--1075},
}

@article{dobrenel_arabidopsis_2016,
	title = {The {Arabidopsis} {TOR} {Kinase} {Specifically} {Regulates} the {Expression} of {Nuclear} {Genes} {Coding} for {Plastidic} {Ribosomal} {Proteins} and the {Phosphorylation} of the {Cytosolic} {Ribosomal} {Protein} {S6}},
	volume = {7},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/article/10.3389/fpls.2016.01611/full},
	doi = {10.3389/fpls.2016.01611},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Dobrenel, Thomas and Mancera-Martínez, Eder and Forzani, Céline and Azzopardi, Marianne and Davanture, Marlène and Moreau, Manon and Schepetilnikov, Mikhail and Chicher, Johana and Langella, Olivier and Zivy, Michel and Robaglia, Christophe and Ryabova, Lyubov A. and Hanson, Johannes and Meyer, Christian},
	month = nov,
	year = {2016},
}

@article{hoenicka_low_2016,
	title = {Low temperatures are required to induce the development of fertile flowers in transgenic male and female early flowering poplar ( \textit{{Populus} tremula} {L}.)},
	volume = {36},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpw015},
	doi = {10.1093/treephys/tpw015},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Tree Physiology},
	author = {Hoenicka, Hans and Lehnhardt, Denise and Briones, Valentina and Nilsson, Ove and Fladung, Matthias},
	editor = {Schnitzler, Jörg-Peter},
	month = may,
	year = {2016},
	pages = {667--677},
}

@article{krzeslowska_pectinous_2016,
	title = {Pectinous cell wall thickenings formation – {A} common defense strategy of plants to cope with {Pb}},
	volume = {214},
	issn = {02697491},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0269749116302858},
	doi = {10.1016/j.envpol.2016.04.019},
	language = {en},
	urldate = {2021-06-07},
	journal = {Environmental Pollution},
	author = {Krzesłowska, Magdalena and Rabęda, Irena and Basińska, Aneta and Lewandowski, Michał and Mellerowicz, Ewa J. and Napieralska, Anna and Samardakiewicz, Sławomir and Woźny, Adam},
	month = jul,
	year = {2016},
	pages = {354--361},
}

@article{fernandez-moreno_efficient_2016,
	title = {An efficient method for medium throughput screening of cuticular wax composition in different plant species},
	volume = {12},
	issn = {1573-3882, 1573-3890},
	url = {http://link.springer.com/10.1007/s11306-016-0982-0},
	doi = {10.1007/s11306-016-0982-0},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Metabolomics},
	author = {Fernandez-Moreno, Josefina-Patricia and Malitsky, Sergey and Lashbrooke, Justin and Biswal, Ajaya Kumar and Racovita, Radu C. and Mellerowicz, Ewa J. and Jetter, Reinhard and Orzaez, Diego and Aharoni, Asaph and Granell, Antonio},
	month = apr,
	year = {2016},
	pages = {73},
}

@article{hodges_perspectives_2016,
	title = {Perspectives for a better understanding of the metabolic integration of photorespiration within a complex plant primary metabolism network},
	volume = {67},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erw145},
	doi = {10.1093/jxb/erw145},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Hodges, Michael and Dellero, Younès and Keech, Olivier and Betti, Marco and Raghavendra, Agepati S. and Sage, Rowan and Zhu, Xin-Guang and Allen, Doug K. and Weber, Andreas P.M.},
	month = may,
	year = {2016},
	pages = {3015--3026},
}

@article{pullman_fraser_2016,
	title = {Fraser fir somatic embryogenesis: high frequency initiation, maintenance, embryo development, germination and cryopreservation},
	volume = {47},
	issn = {0169-4286, 1573-5095},
	shorttitle = {Fraser fir somatic embryogenesis},
	url = {http://link.springer.com/10.1007/s11056-016-9525-9},
	doi = {10.1007/s11056-016-9525-9},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Forests},
	author = {Pullman, Gerald S. and Olson, Katie and Fischer, Taylor and Egertsdotter, Ulrika and Frampton, John and Bucalo, Kylie},
	month = may,
	year = {2016},
	pages = {453--480},
}

@article{plochinger_functional_2016,
	title = {Functional {Update} of the {Auxiliary} {Proteins} {PsbW}, {PsbY}, {HCF136}, {PsbN}, {TerC} and {ALB3} in {Maintenance} and {Assembly} of {PSII}},
	volume = {7},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/Article/10.3389/fpls.2016.00423/abstract},
	doi = {10.3389/fpls.2016.00423},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Plöchinger, Magdalena and Schwenkert, Serena and von Sydow, Lotta and Schröder, Wolfgang P. and Meurer, Jörg},
	month = apr,
	year = {2016},
}

@article{wu_performance_2016,
	title = {Performance of {Seven} {Tree} {Breeding} {Strategies} {Under} {Conditions} of {Inbreeding} {Depression}},
	volume = {6},
	issn = {2160-1836},
	url = {https://academic.oup.com/g3journal/article/6/3/529/6027276},
	doi = {10.1534/g3.115.025767},
	abstract = {Abstract
            In the domestication and breeding of tree species that suffer from inbreeding depression (ID), the long-term performance of different breeding strategies is poorly known. Therefore, seven tree breeding strategies including single population, subline, selfing, and nucleus breeding were simulated using a multi-locus model with additive, partial, and complete dominance allele effects, and with intermediate, U-shaped, and major allele distributions. The strategies were compared for genetic gain, inbreeding accumulation, capacity to show ID, the frequencies and fixations of unfavorable alleles, and genetic variances in breeding and production populations. Measured by genetic gain of production population, the nucleus breeding and the single breeding population with mass selection strategies were equal or superior to subline and single breeding population with within-family selection strategies in all simulated scenarios, in spite of their higher inbreeding coefficients. Inbreeding and cross-breeding effectively decreased ID and could in some scenarios produce genetic gains during the first few generations. However, in all scenarios, considerable fixation of unfavorable alleles rendered the purging performance of selfing and cross-breeding strategies ineffective, and resulted in substantial inferiority in comparison to the other strategies in the long-term.},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Wu, Harry X and Hallingbäck, Henrik R and Sánchez, Leopoldo},
	month = mar,
	year = {2016},
	pages = {529--540},
}

Abstract In the domestication and breeding of tree species that suffer from inbreeding depression (ID), the long-term performance of different breeding strategies is poorly known. Therefore, seven tree breeding strategies including single population, subline, selfing, and nucleus breeding were simulated using a multi-locus model with additive, partial, and complete dominance allele effects, and with intermediate, U-shaped, and major allele distributions. The strategies were compared for genetic gain, inbreeding accumulation, capacity to show ID, the frequencies and fixations of unfavorable alleles, and genetic variances in breeding and production populations. Measured by genetic gain of production population, the nucleus breeding and the single breeding population with mass selection strategies were equal or superior to subline and single breeding population with within-family selection strategies in all simulated scenarios, in spite of their higher inbreeding coefficients. Inbreeding and cross-breeding effectively decreased ID and could in some scenarios produce genetic gains during the first few generations. However, in all scenarios, considerable fixation of unfavorable alleles rendered the purging performance of selfing and cross-breeding strategies ineffective, and resulted in substantial inferiority in comparison to the other strategies in the long-term.

@article{custers_eu_2016,
	title = {{EU} {Regulations} {Impede} {Market} {Introduction} of {GM} {Forest} {Trees}},
	volume = {21},
	issn = {13601385},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138516000315},
	doi = {10.1016/j.tplants.2016.01.015},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Trends in Plant Science},
	author = {Custers, René and Bartsch, Detlef and Fladung, Matthias and Nilsson, Ove and Pilate, Gilles and Sweet, Jeremy and Boerjan, Wout},
	month = apr,
	year = {2016},
	pages = {283--285},
}

@article{betti_manipulating_2016,
	title = {Manipulating photorespiration to increase plant productivity: recent advances and perspectives for crop improvement},
	volume = {67},
	issn = {0022-0957, 1460-2431},
	shorttitle = {Manipulating photorespiration to increase plant productivity},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erw076},
	doi = {10.1093/jxb/erw076},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Betti, Marco and Bauwe, Hermann and Busch, Florian A. and Fernie, Alisdair R. and Keech, Olivier and Levey, Myles and Ort, Donald R. and Parry, Martin A. J. and Sage, Rowan and Timm, Stefan and Walker, Berkley and Weber, Andreas P. M.},
	month = may,
	year = {2016},
	pages = {2977--2988},
}

@article{heskel_convergence_2016,
	title = {Convergence in the temperature response of leaf respiration across biomes and plant functional types},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1520282113},
	doi = {10.1073/pnas.1520282113},
	abstract = {Plant respiration constitutes a massive carbon flux to the atmosphere, and a major control on the evolution of the global carbon cycle. It therefore has the potential to modulate levels of climate change due to the human burning of fossil fuels. Neither current physiological nor terrestrial biosphere models adequately describe its short-term temperature response, and even minor differences in the shape of the response curve can significantly impact estimates of ecosystem carbon release and/or storage. Given this, it is critical to establish whether there are predictable patterns in the shape of the respiration–temperature response curve, and thus in the intrinsic temperature sensitivity of respiration across the globe. Analyzing measurements in a comprehensive database for 231 species spanning 7 biomes, we demonstrate that temperature-dependent increases in leaf respiration do not follow a commonly used exponential function. Instead, we find a decelerating function as leaves warm, reflecting a declining sensitivity to higher temperatures that is remarkably uniform across all biomes and plant functional types. Such convergence in the temperature sensitivity of leaf respiration suggests that there are universally applicable controls on the temperature response of plant energy metabolism, such that a single new function can predict the temperature dependence of leaf respiration for global vegetation. This simple function enables straightforward description of plant respiration in the land-surface components of coupled earth system models. Our cross-biome analyses shows significant implications for such fluxes in cold climates, generally projecting lower values compared with previous estimates.},
	language = {en},
	number = {14},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Heskel, Mary A. and O’Sullivan, Odhran S. and Reich, Peter B. and Tjoelker, Mark G. and Weerasinghe, Lasantha K. and Penillard, Aurore and Egerton, John J. G. and Creek, Danielle and Bloomfield, Keith J. and Xiang, Jen and Sinca, Felipe and Stangl, Zsofia R. and Martinez-de la Torre, Alberto and Griffin, Kevin L. and Huntingford, Chris and Hurry, Vaughan and Meir, Patrick and Turnbull, Matthew H. and Atkin, Owen K.},
	month = apr,
	year = {2016},
	pages = {3832--3837},
}

Plant respiration constitutes a massive carbon flux to the atmosphere, and a major control on the evolution of the global carbon cycle. It therefore has the potential to modulate levels of climate change due to the human burning of fossil fuels. Neither current physiological nor terrestrial biosphere models adequately describe its short-term temperature response, and even minor differences in the shape of the response curve can significantly impact estimates of ecosystem carbon release and/or storage. Given this, it is critical to establish whether there are predictable patterns in the shape of the respiration–temperature response curve, and thus in the intrinsic temperature sensitivity of respiration across the globe. Analyzing measurements in a comprehensive database for 231 species spanning 7 biomes, we demonstrate that temperature-dependent increases in leaf respiration do not follow a commonly used exponential function. Instead, we find a decelerating function as leaves warm, reflecting a declining sensitivity to higher temperatures that is remarkably uniform across all biomes and plant functional types. Such convergence in the temperature sensitivity of leaf respiration suggests that there are universally applicable controls on the temperature response of plant energy metabolism, such that a single new function can predict the temperature dependence of leaf respiration for global vegetation. This simple function enables straightforward description of plant respiration in the land-surface components of coupled earth system models. Our cross-biome analyses shows significant implications for such fluxes in cold climates, generally projecting lower values compared with previous estimates.

@article{scott_whole_2016,
	title = {Whole genome duplication in coast redwood ( \textit{{Sequoia} sempervirens} ) and its implications for explaining the rarity of polyploidy in conifers},
	volume = {211},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.13930},
	doi = {10.1111/nph.13930},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Scott, Alison Dawn and Stenz, Noah W. M. and Ingvarsson, Pär K. and Baum, David A.},
	month = jul,
	year = {2016},
	pages = {186--193},
}

@article{besya_intrinsic_2016,
	title = {Intrinsic phenotypic stability of a bi-stable auto regulatory gene},
	volume = {6},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/srep22951},
	doi = {10.1038/srep22951},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Besya, Azim-Berdy and Grönlund, Andreas},
	month = sep,
	year = {2016},
	pages = {22951},
}

@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},
}

@article{dobrenel_tor_2016,
	title = {{TOR} {Signaling} and {Nutrient} {Sensing}},
	volume = {67},
	issn = {1543-5008, 1545-2123},
	url = {http://www.annualreviews.org/doi/10.1146/annurev-arplant-043014-114648},
	doi = {10.1146/annurev-arplant-043014-114648},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Annual Review of Plant Biology},
	author = {Dobrenel, Thomas and Caldana, Camila and Hanson, Johannes and Robaglia, Christophe and Vincentz, Michel and Veit, Bruce and Meyer, Christian},
	month = apr,
	year = {2016},
	pages = {261--285},
}

@article{oyewole_soil_2016,
	title = {Soil diffusive fluxes constitute the bottleneck to tree nitrogen nutrition in a {Scots} pine forest},
	volume = {399},
	issn = {0032-079X, 1573-5036},
	url = {http://link.springer.com/10.1007/s11104-015-2680-5},
	doi = {10.1007/s11104-015-2680-5},
	language = {en},
	number = {1-2},
	urldate = {2021-06-07},
	journal = {Plant and Soil},
	author = {Oyewole, Olusegun Ayodeji and Jämtgård, Sandra and Gruffman, Linda and Inselsbacher, Erich and Näsholm, Torgny},
	month = feb,
	year = {2016},
	pages = {109--120},
}

@article{hall_precision_2016,
	title = {Precision {Automation} of {Cell} {Type} {Classification} and {Sub}-{Cellular} {Fluorescence} {Quantification} from {Laser} {Scanning} {Confocal} {Images}},
	volume = {7},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/Article/10.3389/fpls.2016.00119/abstract},
	doi = {10.3389/fpls.2016.00119},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Hall, Hardy C. and Fakhrzadeh, Azadeh and Luengo Hendriks, Cris L. and Fischer, Urs},
	month = feb,
	year = {2016},
}

@article{wang_inactivation_2016,
	title = {Inactivation of {Mitochondrial} {Complex} {I} {Induces} the {Expression} of a {Twin} {Cysteine} {Protein} that {Targets} and {Affects} {Cytosolic}, {Chloroplastidic} and {Mitochondrial} {Function}},
	volume = {9},
	issn = {16742052},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1674205216000113},
	doi = {10.1016/j.molp.2016.01.009},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Molecular Plant},
	author = {Wang, Yan and Lyu, Wenhui and Berkowitz, Oliver and Radomiljac, Jordan D. and Law, Simon R. and Murcha, Monika W. and Carrie, Chris and Teixeira, Pedro F. and Kmiec, Beata and Duncan, Owen and Van Aken, Olivier and Narsai, Reena and Glaser, Elzbieta and Huang, Shaobai and Roessner, Ute and Millar, A. Harvey and Whelan, James},
	month = may,
	year = {2016},
	pages = {696--710},
}

@article{staubert_increased_2016,
	title = {Increased lanosterol turnover: a metabolic burden for daunorubicin-resistant leukemia cells},
	volume = {33},
	issn = {1357-0560, 1559-131X},
	shorttitle = {Increased lanosterol turnover},
	url = {http://link.springer.com/10.1007/s12032-015-0717-5},
	doi = {10.1007/s12032-015-0717-5},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Medical Oncology},
	author = {Stäubert, Claudia and Krakowsky, Rosanna and Bhuiyan, Hasanuzzaman and Witek, Barbara and Lindahl, Anna and Broom, Oliver and Nordström, Anders},
	month = jan,
	year = {2016},
	pages = {6},
}

@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},
}

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.

@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},
}

@article{roberge_socio-ecological_2016,
	title = {Socio-ecological implications of modifying rotation lengths in forestry},
	volume = {45},
	issn = {0044-7447, 1654-7209},
	url = {http://link.springer.com/10.1007/s13280-015-0747-4},
	doi = {10.1007/s13280-015-0747-4},
	language = {en},
	number = {S2},
	urldate = {2021-06-07},
	journal = {Ambio},
	author = {Roberge, Jean-Michel and Laudon, Hjalmar and Björkman, Christer and Ranius, Thomas and Sandström, Camilla and Felton, Adam and Sténs, Anna and Nordin, Annika and Granström, Anders and Widemo, Fredrik and Bergh, Johan and Sonesson, Johan and Stenlid, Jan and Lundmark, Tomas},
	month = feb,
	year = {2016},
	pages = {109--123},
}

@article{jiskrova_extra-_2016,
	title = {Extra- and intracellular distribution of cytokinins in the leaves of monocots and dicots},
	volume = {33},
	issn = {18716784},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1871678416000029},
	doi = {10.1016/j.nbt.2015.12.010},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {New Biotechnology},
	author = {Jiskrová, Eva and Novák, Ondřej and Pospíšilová, Hana and Holubová, Katarína and Karády, Michal and Galuszka, Petr and Robert, Stéphanie and Frébort, Ivo},
	month = sep,
	year = {2016},
	pages = {735--742},
}

@article{laudon_role_2016,
	title = {The role of biogeochemical hotspots, landscape heterogeneity, and hydrological connectivity for minimizing forestry effects on water quality},
	volume = {45},
	issn = {0044-7447, 1654-7209},
	url = {http://link.springer.com/10.1007/s13280-015-0751-8},
	doi = {10.1007/s13280-015-0751-8},
	language = {en},
	number = {S2},
	urldate = {2021-06-07},
	journal = {Ambio},
	author = {Laudon, Hjalmar and Kuglerová, Lenka and Sponseller, Ryan A. and Futter, Martyn and Nordin, Annika and Bishop, Kevin and Lundmark, Tomas and Egnell, Gustaf and Ågren, Anneli M.},
	month = feb,
	year = {2016},
	pages = {152--162},
}

@article{sponseller_nitrogen_2016,
	title = {Nitrogen dynamics in managed boreal forests: {Recent} advances and future research directions},
	volume = {45},
	issn = {0044-7447, 1654-7209},
	shorttitle = {Nitrogen dynamics in managed boreal forests},
	url = {http://link.springer.com/10.1007/s13280-015-0755-4},
	doi = {10.1007/s13280-015-0755-4},
	language = {en},
	number = {S2},
	urldate = {2021-06-07},
	journal = {Ambio},
	author = {Sponseller, Ryan A. and Gundale, Michael J. and Futter, Martyn and Ring, Eva and Nordin, Annika and Näsholm, Torgny and Laudon, Hjalmar},
	month = feb,
	year = {2016},
	pages = {175--187},
}

@article{lundmark_comparison_2016,
	title = {Comparison of carbon balances between continuous-cover and clear-cut forestry in {Sweden}},
	volume = {45},
	issn = {0044-7447, 1654-7209},
	url = {http://link.springer.com/10.1007/s13280-015-0756-3},
	doi = {10.1007/s13280-015-0756-3},
	language = {en},
	number = {S2},
	urldate = {2021-06-07},
	journal = {Ambio},
	author = {Lundmark, Tomas and Bergh, Johan and Nordin, Annika and Fahlvik, Nils and Poudel, Bishnu Chandra},
	month = feb,
	year = {2016},
	pages = {203--213},
}

@article{ding_molecular_2016,
	title = {Molecular regulation of phenology in trees — because the seasons they are a-changin’},
	volume = {29},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526615001831},
	doi = {10.1016/j.pbi.2015.11.007},
	language = {en},
	urldate = {2021-06-07},
	journal = {Current Opinion in Plant Biology},
	author = {Ding, Jihua and Nilsson, Ove},
	month = feb,
	year = {2016},
	pages = {73--79},
}

@article{pedmale_cryptochromes_2016,
	title = {Cryptochromes {Interact} {Directly} with {PIFs} to {Control} {Plant} {Growth} in {Limiting} {Blue} {Light}},
	volume = {164},
	issn = {00928674},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0092867415016426},
	doi = {10.1016/j.cell.2015.12.018},
	language = {en},
	number = {1-2},
	urldate = {2021-06-07},
	journal = {Cell},
	author = {Pedmale, Ullas V. and Huang, Shao-shan Carol and Zander, Mark and Cole, Benjamin J. and Hetzel, Jonathan and Ljung, Karin and Reis, Pedro A.B. and Sridevi, Priya and Nito, Kazumasa and Nery, Joseph R. and Ecker, Joseph R. and Chory, Joanne},
	month = jan,
	year = {2016},
	pages = {233--245},
}

@article{dekkers_arabidopsis_2016,
	title = {The {Arabidopsis} \textit{{DELAY} {OF} {GERMINATION} 1} gene affects \textit{{ABSCISIC} {ACID} {INSENSITIVE} 5 ({ABI5})} expression and genetically interacts with \textit{{ABI3}} during {Arabidopsis} seed development},
	volume = {85},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.13118},
	doi = {10.1111/tpj.13118},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Dekkers, Bas J.W. and He, Hanzi and Hanson, Johannes and Willems, Leo A.J. and Jamar, Diaan C.L. and Cueff, Gwendal and Rajjou, Loïc and Hilhorst, Henk W.M. and Bentsink, Leónie},
	month = feb,
	year = {2016},
	pages = {451--465},
}

@article{he_effects_2016,
	title = {Effects of {Parental} {Temperature} and {Nitrate} on {Seed} {Performance} are {Reflected} by {Partly} {Overlapping} {Genetic} and {Metabolic} {Pathways}},
	volume = {57},
	issn = {0032-0781, 1471-9053},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcv207},
	doi = {10.1093/pcp/pcv207},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant and Cell Physiology},
	author = {He, Hanzi and Willems, Leo A. J. and Batushansky, Albert and Fait, Aaron and Hanson, Johannes and Nijveen, Harm and Hilhorst, Henk W.M. and Bentsink, Leónie},
	month = mar,
	year = {2016},
	pages = {473--487},
}

@article{missailidis_serum_2016,
	title = {Serum {Trimethylamine}-{N}-{Oxide} {Is} {Strongly} {Related} to {Renal} {Function} and {Predicts} {Outcome} in {Chronic} {Kidney} {Disease}},
	volume = {11},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0141738},
	doi = {10.1371/journal.pone.0141738},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Missailidis, Catharina and Hällqvist, Jenny and Qureshi, Abdel Rashid and Barany, Peter and Heimbürger, Olof and Lindholm, Bengt and Stenvinkel, Peter and Bergman, Peter},
	editor = {Burdmann, Emmanuel A},
	month = jan,
	year = {2016},
	pages = {e0141738},
}

@article{escamez_metacaspase9_2016,
	title = {{METACASPASE9} modulates autophagy to confine cell death to the target cells during \textit{{Arabidopsis}} vascular xylem differentiation},
	volume = {5},
	issn = {2046-6390},
	url = {https://journals.biologists.com/bio/article/5/2/122/643/METACASPASE9-modulates-autophagy-to-confine-cell},
	doi = {10.1242/bio.015529},
	abstract = {ABSTRACT
            We uncovered that the level of autophagy in plant cells undergoing programmed cell death determines the fate of the surrounding cells. Our approach consisted of using Arabidopsis thaliana cell cultures capable of differentiating into two different cell types: vascular tracheary elements (TEs) that undergo programmed cell death (PCD) and protoplast autolysis, and parenchymatic non-TEs that remain alive. The TE cell type displayed higher levels of autophagy when expression of the TE-specific METACASPASE9 (MC9) was reduced using RNAi (MC9-RNAi). Misregulation of autophagy in the MC9-RNAi TEs coincided with ectopic death of the non-TEs, implying the existence of an autophagy-dependent intercellular signalling from within the TEs towards the non-TEs. Viability of the non-TEs was restored when AUTOPHAGY2 (ATG2) was downregulated specifically in MC9-RNAi TEs, demonstrating the importance of autophagy in the spatial confinement of cell death. Our results suggest that other eukaryotic cells undergoing PCD might also need to tightly regulate their level of autophagy to avoid detrimental consequences for the surrounding cells.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Biology Open},
	author = {Escamez, Sacha and André, Domenique and Zhang, Bo and Bollhöner, Benjamin and Pesquet, Edouard and Tuominen, Hannele},
	month = feb,
	year = {2016},
	pages = {122--129},
}

ABSTRACT We uncovered that the level of autophagy in plant cells undergoing programmed cell death determines the fate of the surrounding cells. Our approach consisted of using Arabidopsis thaliana cell cultures capable of differentiating into two different cell types: vascular tracheary elements (TEs) that undergo programmed cell death (PCD) and protoplast autolysis, and parenchymatic non-TEs that remain alive. The TE cell type displayed higher levels of autophagy when expression of the TE-specific METACASPASE9 (MC9) was reduced using RNAi (MC9-RNAi). Misregulation of autophagy in the MC9-RNAi TEs coincided with ectopic death of the non-TEs, implying the existence of an autophagy-dependent intercellular signalling from within the TEs towards the non-TEs. Viability of the non-TEs was restored when AUTOPHAGY2 (ATG2) was downregulated specifically in MC9-RNAi TEs, demonstrating the importance of autophagy in the spatial confinement of cell death. Our results suggest that other eukaryotic cells undergoing PCD might also need to tightly regulate their level of autophagy to avoid detrimental consequences for the surrounding cells.

@article{bernhardsson_present_2016,
	title = {Present genetic structure is congruent with the common origin of distant {Scots} pine populations in its {Romanian} distribution},
	volume = {361},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378112715006052},
	doi = {10.1016/j.foreco.2015.10.047},
	language = {en},
	urldate = {2021-06-07},
	journal = {Forest Ecology and Management},
	author = {Bernhardsson, C. and Floran, V. and Ganea, S.L. and García-Gil, M.R.},
	month = feb,
	year = {2016},
	pages = {131--143},
}

@article{ranade_non-functional_2016,
	title = {Non-functional plastid ndh gene fragments are present in the nuclear genome of {Norway} spruce ({Picea} abies {L}. {Karsch}): insights from in silico analysis of nuclear and organellar genomes},
	volume = {291},
	issn = {1617-4615, 1617-4623},
	shorttitle = {Non-functional plastid ndh gene fragments are present in the nuclear genome of {Norway} spruce ({Picea} abies {L}. {Karsch})},
	url = {http://link.springer.com/10.1007/s00438-015-1159-7},
	doi = {10.1007/s00438-015-1159-7},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Molecular Genetics and Genomics},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario and Rosselló, Josep A.},
	month = apr,
	year = {2016},
	pages = {935--941},
}

@article{ranade_application_2016,
	title = {Application of monochromatic blue light during germination and hypocotyl development improves outplanted {Scots} pine ({Pinus} sylvestris {L}.) trees performance},
	volume = {361},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S037811271500657X},
	doi = {10.1016/j.foreco.2015.11.034},
	language = {en},
	urldate = {2021-06-07},
	journal = {Forest Ecology and Management},
	author = {Ranade, Sonali Sachin and García Gil, M.R.},
	month = feb,
	year = {2016},
	pages = {368--374},
}

@article{baral_exploring_2016,
	title = {Exploring exocytosis using chemical genomics},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1522317113},
	doi = {10.1073/pnas.1522317113},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Baral, Anirban and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2016},
	pages = {14--16},
}

@article{tibiletti_deletion_2016,
	title = {Deletion of the gene family of small chlorophyll-binding proteins ({ScpABCDE}) offsets {C}/{N} homeostasis in {Synechocystis} {PCC} 6803},
	volume = {1857},
	issn = {00052728},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272815002431},
	doi = {10.1016/j.bbabio.2015.11.011},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Tibiletti, Tania and Hernández-Prieto, Miguel A. and Matthijs, Hans C.P. and Niyogi, Krishna K. and Funk, Christiane},
	month = apr,
	year = {2016},
	pages = {396--407},
}

@incollection{caillaud_ratiometric_2016,
	address = {New York, NY},
	title = {Ratiometric {Fluorescence} {Live} {Imaging} {Analysis} of {Membrane} {Lipid} {Order} in {Arabidopsis} {Mitotic} {Cells} {Using} a {Lipid} {Order}-{Sensitive} {Probe}},
	volume = {1370},
	isbn = {9781493931415 9781493931422},
	url = {http://link.springer.com/10.1007/978-1-4939-3142-2_17},
	urldate = {2021-06-07},
	booktitle = {Plant {Cell} {Division}},
	publisher = {Springer New York},
	author = {Gerbeau-Pissot, Patricia and Der, Christophe and Grebe, Markus and Stanislas, Thomas},
	editor = {Caillaud, Marie-Cécile},
	year = {2016},
	doi = {10.1007/978-1-4939-3142-2_17},
	pages = {227--239},
}

@article{ricroch_challenges_2016,
	title = {Challenges facing {European} agriculture and possible biotechnological solutions},
	volume = {36},
	issn = {0738-8551, 1549-7801},
	url = {https://www.tandfonline.com/doi/full/10.3109/07388551.2015.1055707},
	doi = {10.3109/07388551.2015.1055707},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Critical Reviews in Biotechnology},
	author = {Ricroch, Agnès and Harwood, Wendy and Svobodová, Zdeňka and Sági, László and Hundleby, Penelope and Badea, Elena Marcela and Rosca, Ioan and Cruz, Gabriela and Salema Fevereiro, Manuel Pedro and Marfà Riera, Victoria and Jansson, Stefan and Morandini, Piero and Bojinov, Bojin and Cetiner, Selim and Custers, René and Schrader, Uwe and Jacobsen, Hans-Joerg and Martin-Laffon, Jacqueline and Boisron, Audrey and Kuntz, Marcel},
	month = sep,
	year = {2016},
	pages = {875--883},
}

@article{funda_mating_2016,
	title = {Mating dynamics of {Scots} pine in isolation tents},
	volume = {12},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-016-1074-z},
	doi = {10.1007/s11295-016-1074-z},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Tree Genetics \& Genomes},
	author = {Funda, Tomas and Wennström, Ulfstand and Almqvist, Curt and Andersson Gull, Bengt and Wang, Xiao-Ru},
	month = dec,
	year = {2016},
	pages = {112},
}

@article{bugala_characterization_2016,
	title = {Characterization of newly identified {DnaA} and {DnaB} proteins from {Acetobacter}},
	volume = {167},
	issn = {09232508},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0923250816300730},
	doi = {10.1016/j.resmic.2016.06.010},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Research in Microbiology},
	author = {Bugala, Juraj and Cimová, Viera and Grones, Peter and Grones, Jozef},
	month = oct,
	year = {2016},
	pages = {655--668},
}