Publications 2011

@article{messinger_photosynthetic_2011,
	title = {Photosynthetic {O2} {Evolution}},
	url = {https://books.rsc.org/books/edited-volume/1811/chapter/2135927/Photosynthetic-O2-Evolution},
	doi = {10.1039/9781849733038-00163},
	abstract = {Oxygen evolution by photosynthetic water oxidation has shaped life on planet Earth. This unique biological reaction may provide important clues for develop},
	language = {en},
	urldate = {2024-12-10},
	journal = {Molecular Solar Fuels RSC},
	author = {Messinger, Johannes and Noguchi, Takumi and Yano, Junko},
	month = dec,
	year = {2011},
	pages = {302--314},
}

Oxygen evolution by photosynthetic water oxidation has shaped life on planet Earth. This unique biological reaction may provide important clues for develop

@incollection{cahen_principles_2011,
	address = {Cambridge},
	title = {Principles of photosynthesis},
	isbn = {978-1-107-00023-0},
	url = {https://www.cambridge.org/core/books/fundamentals-of-materials-for-energy-and-environmental-sustainability/principles-of-photosynthesis/E498F19B0D9D77EEC9B92A3B12DF5C9B},
	abstract = {FocusPhotosynthesis is the biological process that converts sunlight into chemical energy. It provides the basis for life on Earth and is the ultimate source of all fossil fuels and of the oxygen we breathe. The primary light reactions occur with high quantum yield and drive free-energy-demanding chemical reactions with unsurpassed efficiency. Coupling of photosynthesis to hydrogenases allows some organisms to evolve H2. Research into understanding and applying the molecular details and reaction mechanisms of the involved catalysts is well under way.SynopsisLife needs free energy. On our planet this free energy is mostly provided by the Sun. The sunlight is captured and converted into chemical energy by a process known as photosynthesis (from Greek, photo, “light,” and synthesis, “putting together”). This process occurs in plants and many bacteria. The “big bang” of evolution was the development of oxygenic photosynthesis. In this process sunlight is employed to split the abundant water into the molecular oxygen we breathe. The protons and electrons gained are employed by the organism within complex reaction sequences to reduce CO2 to carbohydrates. The widespread availability of the electron source water allowed oxygenic organisms to spread and diversify rapidly. The O2 produced was initially toxic for most species, but those which learned to cope with the emerging oxygen-rich atmosphere were able to gain additional energy by “burning” organic matter.},
	urldate = {2024-12-10},
	booktitle = {Fundamentals of {Materials} for {Energy} and {Environmental} {Sustainability}},
	publisher = {Cambridge University Press},
	author = {Messinger, Johannes and Shevela, Dmitriy},
	editor = {Cahen, David and Ginley, David S.},
	year = {2011},
	doi = {10.1017/CBO9780511718786.028},
	pages = {302--314},
}

FocusPhotosynthesis is the biological process that converts sunlight into chemical energy. It provides the basis for life on Earth and is the ultimate source of all fossil fuels and of the oxygen we breathe. The primary light reactions occur with high quantum yield and drive free-energy-demanding chemical reactions with unsurpassed efficiency. Coupling of photosynthesis to hydrogenases allows some organisms to evolve H2. Research into understanding and applying the molecular details and reaction mechanisms of the involved catalysts is well under way.SynopsisLife needs free energy. On our planet this free energy is mostly provided by the Sun. The sunlight is captured and converted into chemical energy by a process known as photosynthesis (from Greek, photo, “light,” and synthesis, “putting together”). This process occurs in plants and many bacteria. The “big bang” of evolution was the development of oxygenic photosynthesis. In this process sunlight is employed to split the abundant water into the molecular oxygen we breathe. The protons and electrons gained are employed by the organism within complex reaction sequences to reduce CO2 to carbohydrates. The widespread availability of the electron source water allowed oxygenic organisms to spread and diversify rapidly. The O2 produced was initially toxic for most species, but those which learned to cope with the emerging oxygen-rich atmosphere were able to gain additional energy by “burning” organic matter.

@article{su_electronic_2011,
	title = {The electronic structures of the \textit{{S}}2 states of the oxygen-evolving complexes of photosystem {II} in plants and cyanobacteria in the presence and absence of methanol},
	volume = {1807},
	issn = {0005-2728},
	url = {https://www.sciencedirect.com/science/article/pii/S0005272811000533},
	doi = {10.1016/j.bbabio.2011.03.002},
	abstract = {The electronic properties of the Mn4OxCa cluster in the S2 state of the oxygen-evolving complex (OEC) were studied using X- and Q-band EPR and Q-band 55Mn-ENDOR using photosystem II preparations isolated from the thermophilic cyanobacterium T. elongatus and higher plants (spinach). The data presented here show that there is very little difference between the two species. Specifically it is shown that: (i) only small changes are seen in the fitted isotropic hyperfine values, suggesting that there is no significant difference in the overall spin distribution (electronic coupling scheme) between the two species; (ii) the inferred fine-structure tensor of the only MnIII ion in the cluster is of the same magnitude and geometry for both species types, suggesting that the MnIII ion has the same coordination sphere in both sample preparations; and (iii) the data from both species are consistent with only one structural model available in the literature, namely the Siegbahn structure [Siegbahn, P. E. M. Accounts Chem. Res. 2009, 42, 1871–1880, Pantazis, D. A. et al., Phys. Chem. Chem. Phys. 2009, 11, 6788–6798]. These measurements were made in the presence of methanol because it confers favorable magnetic relaxation properties to the cluster that facilitate pulse-EPR techniques. In the absence of methanol the separation of the ground state and the first excited state of the spin system is smaller. For cyanobacteria this effect is minor but in plant PS II it leads to a break-down of the ST=½ spin model of the S2 state. This suggests that the methanol–OEC interaction is species dependent. It is proposed that the effect of small organic solvents on the electronic structure of the cluster is to change the coupling between the outer Mn (MnA) and the other three Mn ions that form the trimeric part of the cluster (MnB, MnC, MnD), by perturbing the linking bis-μ-oxo bridge. The flexibility of this bridging unit is discussed with regard to the mechanism of O-O bond formation.},
	number = {7},
	urldate = {2024-12-10},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Su, Ji-Hu and Cox, Nicholas and Ames, William and Pantazis, Dimitrios A. and Rapatskiy, Leonid and Lohmiller, Thomas and Kulik, Leonid V. and Dorlet, Pierre and Rutherford, A. William and Neese, Frank and Boussac, Alain and Lubitz, Wolfgang and Messinger, Johannes},
	month = jul,
	year = {2011},
	keywords = {EPR, Methanol, Mn-ENDOR, MnOCa cluster, OEC, Orbach process, Photosystem II, Raman process, Spin Hamiltonian},
	pages = {829--840},
}

The electronic properties of the Mn4OxCa cluster in the S2 state of the oxygen-evolving complex (OEC) were studied using X- and Q-band EPR and Q-band 55Mn-ENDOR using photosystem II preparations isolated from the thermophilic cyanobacterium T. elongatus and higher plants (spinach). The data presented here show that there is very little difference between the two species. Specifically it is shown that: (i) only small changes are seen in the fitted isotropic hyperfine values, suggesting that there is no significant difference in the overall spin distribution (electronic coupling scheme) between the two species; (ii) the inferred fine-structure tensor of the only MnIII ion in the cluster is of the same magnitude and geometry for both species types, suggesting that the MnIII ion has the same coordination sphere in both sample preparations; and (iii) the data from both species are consistent with only one structural model available in the literature, namely the Siegbahn structure [Siegbahn, P. E. M. Accounts Chem. Res. 2009, 42, 1871–1880, Pantazis, D. A. et al., Phys. Chem. Chem. Phys. 2009, 11, 6788–6798]. These measurements were made in the presence of methanol because it confers favorable magnetic relaxation properties to the cluster that facilitate pulse-EPR techniques. In the absence of methanol the separation of the ground state and the first excited state of the spin system is smaller. For cyanobacteria this effect is minor but in plant PS II it leads to a break-down of the ST=½ spin model of the S2 state. This suggests that the methanol–OEC interaction is species dependent. It is proposed that the effect of small organic solvents on the electronic structure of the cluster is to change the coupling between the outer Mn (MnA) and the other three Mn ions that form the trimeric part of the cluster (MnB, MnC, MnD), by perturbing the linking bis-μ-oxo bridge. The flexibility of this bridging unit is discussed with regard to the mechanism of O-O bond formation.

@article{shevela_calcium_2011,
	title = {Calcium {Manganese} {Oxides} as {Oxygen} {Evolution} {Catalysts}: {O2} {Formation} {Pathways} {Indicated} by {18O}-{Labelling} {Studies}},
	volume = {17},
	copyright = {Copyright © 2011 WILEY-VCH Verlag GmbH \& Co. KGaA, Weinheim},
	issn = {1521-3765},
	shorttitle = {Calcium {Manganese} {Oxides} as {Oxygen} {Evolution} {Catalysts}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/chem.201002548},
	doi = {10.1002/chem.201002548},
	abstract = {Oxygen evolution catalysed by calcium manganese and manganese-only oxides was studied in 18O-enriched water. Using membrane-inlet mass spectrometry, we monitored the formation of the different O2 isotopologues 16O2, 16O18O and 18O2 in such reactions simultaneously with good time resolution. From the analysis of the data, we conclude that entirely different pathways of dioxygen formation catalysis exist for reactions involving hydrogen peroxide (H2O2), hydrogen persulfate (HSO5−) or single-electron oxidants such as CeIV and [RuIII(bipy)3]3+. Like the studied oxide catalysts, the active sites of manganese catalase and the oxygen-evolving complex (OEC) of photosystem II (PSII) consist of μ-oxido manganese or μ-oxido calcium manganese sites. The studied processes show very similar 18O-labelling behaviour to the natural enzymes and are therefore interesting model systems for in vivo oxygen formation by manganese metalloenzymes such as PSII.},
	language = {en},
	number = {19},
	urldate = {2024-12-10},
	journal = {Chemistry – A European Journal},
	author = {Shevela, Dmitriy and Koroidov, Sergey and Najafpour, M. Mahdi and Messinger, Johannes and Kurz, Philipp},
	year = {2011},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/chem.201002548},
	keywords = {heterogeneous catalysis, isotopic labelling, manganese, mass spectrometry, water splitting},
	pages = {5415--5423},
}

Oxygen evolution catalysed by calcium manganese and manganese-only oxides was studied in 18O-enriched water. Using membrane-inlet mass spectrometry, we monitored the formation of the different O2 isotopologues 16O2, 16O18O and 18O2 in such reactions simultaneously with good time resolution. From the analysis of the data, we conclude that entirely different pathways of dioxygen formation catalysis exist for reactions involving hydrogen peroxide (H2O2), hydrogen persulfate (HSO5−) or single-electron oxidants such as CeIV and [RuIII(bipy)3]3+. Like the studied oxide catalysts, the active sites of manganese catalase and the oxygen-evolving complex (OEC) of photosystem II (PSII) consist of μ-oxido manganese or μ-oxido calcium manganese sites. The studied processes show very similar 18O-labelling behaviour to the natural enzymes and are therefore interesting model systems for in vivo oxygen formation by manganese metalloenzymes such as PSII.

@article{cox_effect_2011,
	title = {Effect of {Ca2}+/{Sr2}+ {Substitution} on the {Electronic} {Structure} of the {Oxygen}-{Evolving} {Complex} of {Photosystem} {II}: {A} {Combined} {Multifrequency} {EPR}, {55Mn}-{ENDOR}, and {DFT} {Study} of the {S2} {State}},
	volume = {133},
	issn = {0002-7863},
	shorttitle = {Effect of {Ca2}+/{Sr2}+ {Substitution} on the {Electronic} {Structure} of the {Oxygen}-{Evolving} {Complex} of {Photosystem} {II}},
	url = {https://doi.org/10.1021/ja110145v},
	doi = {10.1021/ja110145v},
	abstract = {The electronic structures of the native Mn4OxCa cluster and the biosynthetically substituted Mn4OxSr cluster of the oxygen evolving complex (OEC) of photosystem II (PSII) core complexes isolated from Thermosynechococcus elongatus, poised in the S2 state, were studied by X- and Q-band CW-EPR and by pulsed Q-band 55Mn-ENDOR spectroscopy. Both wild type and tyrosine D less mutants grown photoautotrophically in either CaCl2 or SrCl2 containing media were measured. The obtained CW-EPR spectra of the S2 state displayed the characteristic, clearly noticeable differences in the hyperfine pattern of the multiline EPR signal [Boussac et al. J. Biol. Chem.2004, 279, 22809−22819]. In sharp contrast, the manganese (55Mn) ENDOR spectra of the Ca and Sr forms of the OEC were remarkably similar. Multifrequency simulations of the X- and Q-band CW-EPR and 55Mn-pulsed ENDOR spectra using the Spin Hamiltonian formalism were performed to investigate this surprising result. It is shown that (i) all four manganese ions contribute to the 55Mn-ENDOR spectra; (ii) only small changes are seen in the fitted isotropic hyperfine values for the Ca2+ and Sr2+ containing OEC, suggesting that there is no change in the overall spin distribution (electronic coupling scheme) upon Ca2+/Sr2+ substitution; (iii) the changes in the CW-EPR hyperfine pattern can be explained by a small decrease in the anisotropy of at least two hyperfine tensors. It is proposed that modifications at the Ca2+ site may modulate the fine structure tensor of the MnIII ion. DFT calculations support the above conclusions. Our data analysis also provides strong support for the notion that in the S2 state the coordination of the MnIII ion is square-pyramidal (5-coordinate) or octahedral (6-coordinate) with tetragonal elongation. In addition, it is shown that only one of the currently published OEC models, the Siegbahn structure [Siegbahn, P. E. M. Acc. Chem. Res.2009, 42, 1871−1880, Pantazis, D. A. et al. Phys. Chem. Chem. Phys.2009, 11, 6788−6798], is consistent with all data presented here. These results provide important information for the structure of the OEC and the water-splitting mechanism. In particular, the 5-coordinate MnIII is a potential site for substrate ‘water’ (H2O, OH−) binding. Its location within the cuboidal structural unit, as opposed to the external ‘dangler’ position, may have important consequences for the mechanism of O−O bond formation.},
	number = {10},
	urldate = {2024-12-10},
	journal = {Journal of the American Chemical Society},
	author = {Cox, Nicholas and Rapatskiy, Leonid and Su, Ji-Hu and Pantazis, Dimitrios A. and Sugiura, Miwa and Kulik, Leonid and Dorlet, Pierre and Rutherford, A. William and Neese, Frank and Boussac, Alain and Lubitz, Wolfgang and Messinger, Johannes},
	month = mar,
	year = {2011},
	note = {Publisher: American Chemical Society},
	pages = {3635--3648},
}

The electronic structures of the native Mn4OxCa cluster and the biosynthetically substituted Mn4OxSr cluster of the oxygen evolving complex (OEC) of photosystem II (PSII) core complexes isolated from Thermosynechococcus elongatus, poised in the S2 state, were studied by X- and Q-band CW-EPR and by pulsed Q-band 55Mn-ENDOR spectroscopy. Both wild type and tyrosine D less mutants grown photoautotrophically in either CaCl2 or SrCl2 containing media were measured. The obtained CW-EPR spectra of the S2 state displayed the characteristic, clearly noticeable differences in the hyperfine pattern of the multiline EPR signal [Boussac et al. J. Biol. Chem.2004, 279, 22809−22819]. In sharp contrast, the manganese (55Mn) ENDOR spectra of the Ca and Sr forms of the OEC were remarkably similar. Multifrequency simulations of the X- and Q-band CW-EPR and 55Mn-pulsed ENDOR spectra using the Spin Hamiltonian formalism were performed to investigate this surprising result. It is shown that (i) all four manganese ions contribute to the 55Mn-ENDOR spectra; (ii) only small changes are seen in the fitted isotropic hyperfine values for the Ca2+ and Sr2+ containing OEC, suggesting that there is no change in the overall spin distribution (electronic coupling scheme) upon Ca2+/Sr2+ substitution; (iii) the changes in the CW-EPR hyperfine pattern can be explained by a small decrease in the anisotropy of at least two hyperfine tensors. It is proposed that modifications at the Ca2+ site may modulate the fine structure tensor of the MnIII ion. DFT calculations support the above conclusions. Our data analysis also provides strong support for the notion that in the S2 state the coordination of the MnIII ion is square-pyramidal (5-coordinate) or octahedral (6-coordinate) with tetragonal elongation. In addition, it is shown that only one of the currently published OEC models, the Siegbahn structure [Siegbahn, P. E. M. Acc. Chem. Res.2009, 42, 1871−1880, Pantazis, D. A. et al. Phys. Chem. Chem. Phys.2009, 11, 6788−6798], is consistent with all data presented here. These results provide important information for the structure of the OEC and the water-splitting mechanism. In particular, the 5-coordinate MnIII is a potential site for substrate ‘water’ (H2O, OH−) binding. Its location within the cuboidal structural unit, as opposed to the external ‘dangler’ position, may have important consequences for the mechanism of O−O bond formation.

@article{cox_electronic_2011,
	title = {Electronic {Structure} of a {Weakly} {Antiferromagnetically} {Coupled} {MnIIMnIII} {Model} {Relevant} to {Manganese} {Proteins}: {A} {Combined} {EPR}, {55Mn}-{ENDOR}, and {DFT} {Study}},
	volume = {50},
	issn = {0020-1669},
	shorttitle = {Electronic {Structure} of a {Weakly} {Antiferromagnetically} {Coupled} {MnIIMnIII} {Model} {Relevant} to {Manganese} {Proteins}},
	url = {https://doi.org/10.1021/ic200767e},
	doi = {10.1021/ic200767e},
	abstract = {An analysis of the electronic structure of the [MnIIMnIII(μ-OH)-(μ-piv)2(Me3tacn)2](ClO4)2 (PivOH) complex is reported. It displays features that include: (i) a ground 1/2 spin state; (ii) a small exchange (J) coupling between the two Mn ions; (iii) a mono-μ-hydroxo bridge, bis-μ-carboxylato motif; and (iv) a strongly coupled, terminally bound N ligand to the MnIII. All of these features are observed in structural models of the oxygen evolving complex (OEC). Multifrequency electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) measurements were performed on this complex, and the resultant spectra simulated using the Spin Hamiltonian formalism. The strong field dependence of the 55Mn-ENDOR constrains the 55Mn hyperfine tensors such that a unique solution for the electronic structure can be deduced. Large hyperfine anisotropy is required to reproduce the EPR/ENDOR spectra for both the MnII and MnIII ions. The large effective hyperfine tensor anisotropy of the MnII, a d5 ion which usually exhibits small anisotropy, is interpreted within a formalism in which the fine structure tensor of the MnIII ion strongly perturbs the zero-field energy levels of the MnIIMnIII complex. An estimate of the fine structure parameter (d) for the MnIII of −4 cm–1 was made, by assuming the intrinsic anisotropy of the MnII ion is small. The magnitude of the fine structure and intrinsic (onsite) hyperfine tensor of the MnIII is consistent with the known coordination environment of the MnIII ion as seen from its crystal structure. Broken symmetry density functional theory (DFT) calculations were performed on the crystal structure geometry. DFT values for both the isotropic and the anisotropic components of the onsite (intrinsic) hyperfine tensors match those inferred from the EPR/ENDOR simulations described above, to within 5\%. This study demonstrates that DFT calculations provide reliable estimates for spectroscopic observables of mixed valence Mn complexes, even in the limit where the description of a well isolated S = 1/2 ground state begins to break down.},
	number = {17},
	urldate = {2024-12-10},
	journal = {Inorganic Chemistry},
	author = {Cox, Nicholas and Ames, William and Epel, Boris and Kulik, Leonid V. and Rapatskiy, Leonid and Neese, Frank and Messinger, Johannes and Wieghardt, Karl and Lubitz, Wolfgang},
	month = sep,
	year = {2011},
	note = {Publisher: American Chemical Society},
	pages = {8238--8251},
}

An analysis of the electronic structure of the [MnIIMnIII(μ-OH)-(μ-piv)2(Me3tacn)2](ClO4)2 (PivOH) complex is reported. It displays features that include: (i) a ground 1/2 spin state; (ii) a small exchange (J) coupling between the two Mn ions; (iii) a mono-μ-hydroxo bridge, bis-μ-carboxylato motif; and (iv) a strongly coupled, terminally bound N ligand to the MnIII. All of these features are observed in structural models of the oxygen evolving complex (OEC). Multifrequency electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) measurements were performed on this complex, and the resultant spectra simulated using the Spin Hamiltonian formalism. The strong field dependence of the 55Mn-ENDOR constrains the 55Mn hyperfine tensors such that a unique solution for the electronic structure can be deduced. Large hyperfine anisotropy is required to reproduce the EPR/ENDOR spectra for both the MnII and MnIII ions. The large effective hyperfine tensor anisotropy of the MnII, a d5 ion which usually exhibits small anisotropy, is interpreted within a formalism in which the fine structure tensor of the MnIII ion strongly perturbs the zero-field energy levels of the MnIIMnIII complex. An estimate of the fine structure parameter (d) for the MnIII of −4 cm–1 was made, by assuming the intrinsic anisotropy of the MnII ion is small. The magnitude of the fine structure and intrinsic (onsite) hyperfine tensor of the MnIII is consistent with the known coordination environment of the MnIII ion as seen from its crystal structure. Broken symmetry density functional theory (DFT) calculations were performed on the crystal structure geometry. DFT values for both the isotropic and the anisotropic components of the onsite (intrinsic) hyperfine tensors match those inferred from the EPR/ENDOR simulations described above, to within 5%. This study demonstrates that DFT calculations provide reliable estimates for spectroscopic observables of mixed valence Mn complexes, even in the limit where the description of a well isolated S = 1/2 ground state begins to break down.

@article{ames_theoretical_2011,
	title = {Theoretical {Evaluation} of {Structural} {Models} of the {S2} {State} in the {Oxygen} {Evolving} {Complex} of {Photosystem} {II}: {Protonation} {States} and {Magnetic} {Interactions}},
	volume = {133},
	issn = {0002-7863},
	shorttitle = {Theoretical {Evaluation} of {Structural} {Models} of the {S2} {State} in the {Oxygen} {Evolving} {Complex} of {Photosystem} {II}},
	url = {https://doi.org/10.1021/ja2041805},
	doi = {10.1021/ja2041805},
	abstract = {Protonation states of water ligands and oxo bridges are intimately involved in tuning the electronic structures and oxidation potentials of the oxygen evolving complex (OEC) in Photosystem II, steering the mechanistic pathway, which involves at least five redox state intermediates Sn (n = 0–4) resulting in the oxidation of water to molecular oxygen. Although protons are practically invisible in protein crystallography, their effects on the electronic structure and magnetic properties of metal active sites can be probed using spectroscopy. With the twin purpose of aiding the interpretation of the complex electron paramagnetic resonance (EPR) spectroscopic data of the OEC and of improving the view of the cluster at the atomic level, a complete set of protonation configurations for the S2 state of the OEC were investigated, and their distinctive effects on magnetic properties of the cluster were evaluated. The most recent X-ray structure of Photosystem II at 1.9 Å resolution was used and refined to obtain the optimum structure for the Mn4O5Ca core within the protein pocket. Employing this model, a set of 26 structures was constructed that tested various protonation scenarios of the water ligands and oxo bridges. Our results suggest that one of the two water molecules that are proposed to coordinate the outer Mn ion (MnA) of the cluster is deprotonated in the S2 state, as this leads to optimal experimental agreement, reproducing the correct ground state spin multiplicity (S = 1/2), spin expectation values, and EXAFS-derived metal–metal distances. Deprotonation of Ca2+-bound water molecules is strongly disfavored in the S2 state, but dissociation of one of the two water ligands appears to be facile. The computed isotropic hyperfine couplings presented here allow distinctions between models to be made and call into question the assumption that the largest coupling is always attributable to MnIII. The present results impose limits for the total charge and the proton configuration of the OEC in the S2 state, with implications for the cascade of events in the Kok cycle and for the water splitting mechanism.},
	number = {49},
	urldate = {2024-12-10},
	journal = {Journal of the American Chemical Society},
	author = {Ames, William and Pantazis, Dimitrios A. and Krewald, Vera and Cox, Nicholas and Messinger, Johannes and Lubitz, Wolfgang and Neese, Frank},
	month = dec,
	year = {2011},
	note = {Publisher: American Chemical Society},
	pages = {19743--19757},
}

Protonation states of water ligands and oxo bridges are intimately involved in tuning the electronic structures and oxidation potentials of the oxygen evolving complex (OEC) in Photosystem II, steering the mechanistic pathway, which involves at least five redox state intermediates Sn (n = 0–4) resulting in the oxidation of water to molecular oxygen. Although protons are practically invisible in protein crystallography, their effects on the electronic structure and magnetic properties of metal active sites can be probed using spectroscopy. With the twin purpose of aiding the interpretation of the complex electron paramagnetic resonance (EPR) spectroscopic data of the OEC and of improving the view of the cluster at the atomic level, a complete set of protonation configurations for the S2 state of the OEC were investigated, and their distinctive effects on magnetic properties of the cluster were evaluated. The most recent X-ray structure of Photosystem II at 1.9 Å resolution was used and refined to obtain the optimum structure for the Mn4O5Ca core within the protein pocket. Employing this model, a set of 26 structures was constructed that tested various protonation scenarios of the water ligands and oxo bridges. Our results suggest that one of the two water molecules that are proposed to coordinate the outer Mn ion (MnA) of the cluster is deprotonated in the S2 state, as this leads to optimal experimental agreement, reproducing the correct ground state spin multiplicity (S = 1/2), spin expectation values, and EXAFS-derived metal–metal distances. Deprotonation of Ca2+-bound water molecules is strongly disfavored in the S2 state, but dissociation of one of the two water ligands appears to be facile. The computed isotropic hyperfine couplings presented here allow distinctions between models to be made and call into question the assumption that the largest coupling is always attributable to MnIII. The present results impose limits for the total charge and the proton configuration of the OEC in the S2 state, with implications for the cascade of events in the Kok cycle and for the water splitting mechanism.

@article{su_probing_2011,
	title = {Probing {Mode} and {Site} of {Substrate} {Water} {Binding} to the {Oxygen}-{Evolving} {Complex} in the {S2} {State} of {Photosystem} {II} by {17O}-{HYSCORE} {Spectroscopy}},
	volume = {133},
	issn = {0002-7863},
	url = {https://doi.org/10.1021/ja205377n},
	doi = {10.1021/ja205377n},
	number = {31},
	urldate = {2024-11-29},
	journal = {Journal of the American Chemical Society},
	author = {Su, Ji-Hu and Lubitz, Wolfgang and Messinger, Johannes},
	month = aug,
	year = {2011},
	note = {Publisher: American Chemical Society},
	pages = {12317--12317},
}

@incollection{gonzalez-martinez_patterns_2011,
	title = {Patterns of {Nucleotide} {Diversity} and {Association} {Mapping}},
	isbn = {978-0-429-06593-4},
	abstract = {Understanding the molecular basis of adaptive traits is a major interest in conservation and population genetics. In commercial species, such as several conifers, it is also interesting for operational breeding. In this chapter, we provide a state-of-the-art view on candidate gene research, from general estimates of nucleotide diversity and recombination to new-generation neutrality tests and association genetics methodologies. Levels of nucleotide diversity in conifers are substantial, although lower than expected given their life-history traits. In addition, linkage disequilibrium seems to decay rapidly in this group of species, at least within genes that are not submitted to natural selection. These two facts makes genetic association studies appealing in conifers, as significant associations may correspond to the actual causal polymorphisms. Population genomic methods also seem appropriate in conifers, in particular for those species with accused population genetic structure and strong response to environmental gradients. New-generation neutrality tests, outlier loci detection methods and genotype/phenotype association studies have revealed various candidate genes and single nucleotide polymorphisms underlying different adaptive phenotypes, despite potential confounding effects of demographical and historical processes. Finally, perspectives about future genomic research in conifers are provided, including its application for conservation and breeding.},
	booktitle = {Genetics, {Genomics} and {Breeding} of {Conifers}},
	publisher = {CRC Press},
	author = {González-Martínez, S. C. and Dillon, S. and Garnier-Géré, P. H. and Krutovsky, K. V. and Alía, R. and Burgarella, C. and Eckert, A. J. and García-Gil, M. R. and Grivet, D. and Heuertz, M.},
	year = {2011},
	note = {Num Pages: 36},
}

Understanding the molecular basis of adaptive traits is a major interest in conservation and population genetics. In commercial species, such as several conifers, it is also interesting for operational breeding. In this chapter, we provide a state-of-the-art view on candidate gene research, from general estimates of nucleotide diversity and recombination to new-generation neutrality tests and association genetics methodologies. Levels of nucleotide diversity in conifers are substantial, although lower than expected given their life-history traits. In addition, linkage disequilibrium seems to decay rapidly in this group of species, at least within genes that are not submitted to natural selection. These two facts makes genetic association studies appealing in conifers, as significant associations may correspond to the actual causal polymorphisms. Population genomic methods also seem appropriate in conifers, in particular for those species with accused population genetic structure and strong response to environmental gradients. New-generation neutrality tests, outlier loci detection methods and genotype/phenotype association studies have revealed various candidate genes and single nucleotide polymorphisms underlying different adaptive phenotypes, despite potential confounding effects of demographical and historical processes. Finally, perspectives about future genomic research in conifers are provided, including its application for conservation and breeding.

@article{benlloch_integrating_2011,
	title = {Integrating long-day flowering signals: a {LEAFY} binding site is essential for proper photoperiodic activation of {APETALA1}},
	volume = {67},
	copyright = {© 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd},
	issn = {1365-313X},
	shorttitle = {Integrating long-day flowering signals},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2011.04660.x},
	doi = {10.1111/j.1365-313X.2011.04660.x},
	abstract = {The transition to flowering in Arabidopsis is characterized by the sharp and localized upregulation of APETALA1 (AP1) transcription in the newly formed floral primordia. Both the flower meristem-identity gene LEAFY (LFY) and the photoperiod pathway involving the FLOWERING LOCUS T (FT) and FD genes contribute to this upregulation. These pathways have been proposed to act independently but their respective contributions and mode of interaction have remained elusive. To address these questions, we studied the AP1 regulatory region. Combining in vitro and in vivo approaches, we identified which of the three putative LFY binding sites present in the AP1 promoter is essential for its activation by LFY. Interestingly, we found that this site is also important for the correct photoperiodic-dependent upregulation of AP1. In contrast, a previously proposed putative FD-binding site appears dispensable and unable to bind FD and we found no evidence for FD binding to other sites in the AP1 promoter, suggesting that the FT/FD-dependent activation of AP1 might be indirect. Altogether, our data give new insight into the interaction between the FT and LFY pathways in the upregulation of AP1 transcription under long-day conditions.},
	language = {en},
	number = {6},
	urldate = {2024-10-07},
	journal = {The Plant Journal},
	author = {Benlloch, Reyes and Kim, Min Chul and Sayou, Camille and Thévenon, Emmanuel and Parcy, Francois and Nilsson, Ove},
	year = {2011},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2011.04660.x},
	keywords = {APETALA1, FLOWERING LOCUS D, FLOWERING LOCUS T, LEAFY, floral induction, photoperiod},
	pages = {1094--1102},
}

The transition to flowering in Arabidopsis is characterized by the sharp and localized upregulation of APETALA1 (AP1) transcription in the newly formed floral primordia. Both the flower meristem-identity gene LEAFY (LFY) and the photoperiod pathway involving the FLOWERING LOCUS T (FT) and FD genes contribute to this upregulation. These pathways have been proposed to act independently but their respective contributions and mode of interaction have remained elusive. To address these questions, we studied the AP1 regulatory region. Combining in vitro and in vivo approaches, we identified which of the three putative LFY binding sites present in the AP1 promoter is essential for its activation by LFY. Interestingly, we found that this site is also important for the correct photoperiodic-dependent upregulation of AP1. In contrast, a previously proposed putative FD-binding site appears dispensable and unable to bind FD and we found no evidence for FD binding to other sites in the AP1 promoter, suggesting that the FT/FD-dependent activation of AP1 might be indirect. Altogether, our data give new insight into the interaction between the FT and LFY pathways in the upregulation of AP1 transcription under long-day conditions.

@article{pandey_update_2011,
	title = {An {Update} on {Biotechnological} {Approaches} for {Improving} {Abiotic} {Stress} {Tolerance} in {Tomato}},
	volume = {51},
	copyright = {Copyright © by the Crop Science Society of America, Inc.},
	issn = {1435-0653},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.2135/cropsci2010.10.0579},
	doi = {10.2135/cropsci2010.10.0579},
	abstract = {Tomato (Solanum lycopersicum L.) is the second most important vegetable crop in the world after potato (Solanum tuberosum L.), and its productivity is influenced by different abiotic stresses. Though cultivated tomato is moderately tolerant to various abiotic stresses, the crop losses due to unfavorable environmental conditions can be unpredictably severe. So far, several efforts have been made to improve abiotic stress tolerance in cultivated tomato through cultural practices, breeding techniques, and biotechnological approaches. Introgression of abiotic stress tolerance to cultivated tomato from more tolerant wild relatives through classical breeding has been attempted with limited success. However, genetic engineering based on the introgression of genes that are known to be involved in stress response and putative stress tolerance could provide powerful tools for improving abiotic stress tolerance in tomato coupled with the growing knowledge of stress physiology. The present review summarizes the current status and future directions on the use of biotechnological approaches to improve abiotic stress tolerance in tomato.},
	language = {en},
	number = {6},
	urldate = {2023-11-14},
	journal = {Crop Science},
	author = {Pandey, Shashank K. and Nookaraju, Akula and Upadhyaya, Chandrama P. and Gururani, Mayank A. and Venkatesh, Jelli and Kim, Doo-Hwan and Park, Se Won},
	year = {2011},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.2135/cropsci2010.10.0579},
	pages = {2303--2324},
}

Tomato (Solanum lycopersicum L.) is the second most important vegetable crop in the world after potato (Solanum tuberosum L.), and its productivity is influenced by different abiotic stresses. Though cultivated tomato is moderately tolerant to various abiotic stresses, the crop losses due to unfavorable environmental conditions can be unpredictably severe. So far, several efforts have been made to improve abiotic stress tolerance in cultivated tomato through cultural practices, breeding techniques, and biotechnological approaches. Introgression of abiotic stress tolerance to cultivated tomato from more tolerant wild relatives through classical breeding has been attempted with limited success. However, genetic engineering based on the introgression of genes that are known to be involved in stress response and putative stress tolerance could provide powerful tools for improving abiotic stress tolerance in tomato coupled with the growing knowledge of stress physiology. The present review summarizes the current status and future directions on the use of biotechnological approaches to improve abiotic stress tolerance in tomato.

@article{liu_geographic_2011,
	title = {Geographic {Isolation} between the {Homoploid} {Hybrid} {Pinus} densata and {Its} {Parental} {Pinus} yunnanensis},
	volume = {33},
	issn = {2096-2703},
	url = {https://journal.kib.ac.cn/EN/10.3724/SP.J.1143.2011.10227},
	doi = {10.3724/SP.J.1143.2011.10227},
	abstract = {In order to elucidate the geographic isolation mechanisms between the ...},
	language = {en},
	number = {3},
	urldate = {2023-04-27},
	journal = {Plant Diversity and Resources},
	author = {Liu, Yong-Liang and Mao, Jian-Feng and Wang, Xiao-Ru and Li, Yue},
	month = jun,
	year = {2011},
	keywords = {⚠️ Invalid DOI},
	pages = {269},
}

In order to elucidate the geographic isolation mechanisms between the ...

@article{wang_colonization_2011,
	title = {Colonization of the {Tibetan} {Plateau} by the homoploid hybrid pine {Pinus} densata},
	volume = {20},
	issn = {1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2011.05157.x},
	doi = {10.1111/j.1365-294X.2011.05157.x},
	abstract = {Pinus densata is an intriguingly successful homoploid hybrid species that occupies vast areas of the southeastern Tibetan Plateau in which neither of its parental species are present, but the colonization processes involved are poorly understood. To shed light on how this species colonized and became established on the plateau, we surveyed paternally inherited chloroplast (cp) and maternally inherited mitochondrial (mt) DNA variation within and among 54 populations of P. densata and its putative parental species throughout their respective ranges. Strong spatial genetic structure of both cp and mtDNA were detected in P. densata populations. Mitotypes specific to P. densata were likely generated by complex recombination events. A putative ancestral hybrid zone in the northeastern periphery of P. densata was identified, and we propose that the species then colonized the plateau by migrating westwards. Along the colonization route, consecutive bottlenecks and surfing of rare alleles caused a significant reduction in genetic diversity and strong population differentiation. The direction and intensity of introgression from parental species varied among geographic regions. In western parts of its range, the species seems to have been isolated from seed and pollen flow from its parent species for a long time. The observed spatial distribution of genetic diversity in P. densata also appears to reflect the persistence of this species on the plateau during the last glaciation. Our results indicate that both ancient and contemporary population dynamics have contributed to the spatial distribution of genetic diversity in P. densata, which accordingly reflects its evolutionary history.},
	language = {en},
	number = {18},
	urldate = {2023-04-27},
	journal = {Molecular Ecology},
	author = {Wang, Baosheng and Mao, Jian-Feng and Gao, Jie and Zhao, Wei and Wang, Xiao-Ru},
	year = {2011},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-294X.2011.05157.x},
	keywords = {bottleneck, colonization history, hybrid speciation, mtDNA recombination, population structure},
	pages = {3796--3811},
}

Pinus densata is an intriguingly successful homoploid hybrid species that occupies vast areas of the southeastern Tibetan Plateau in which neither of its parental species are present, but the colonization processes involved are poorly understood. To shed light on how this species colonized and became established on the plateau, we surveyed paternally inherited chloroplast (cp) and maternally inherited mitochondrial (mt) DNA variation within and among 54 populations of P. densata and its putative parental species throughout their respective ranges. Strong spatial genetic structure of both cp and mtDNA were detected in P. densata populations. Mitotypes specific to P. densata were likely generated by complex recombination events. A putative ancestral hybrid zone in the northeastern periphery of P. densata was identified, and we propose that the species then colonized the plateau by migrating westwards. Along the colonization route, consecutive bottlenecks and surfing of rare alleles caused a significant reduction in genetic diversity and strong population differentiation. The direction and intensity of introgression from parental species varied among geographic regions. In western parts of its range, the species seems to have been isolated from seed and pollen flow from its parent species for a long time. The observed spatial distribution of genetic diversity in P. densata also appears to reflect the persistence of this species on the plateau during the last glaciation. Our results indicate that both ancient and contemporary population dynamics have contributed to the spatial distribution of genetic diversity in P. densata, which accordingly reflects its evolutionary history.

@article{mao_distinct_2011,
	title = {Distinct {Niche} {Divergence} {Characterizes} the {Homoploid} {Hybrid} {Speciation} of {Pinus} densata on the {Tibetan} {Plateau}.},
	volume = {177},
	issn = {0003-0147},
	url = {https://www.journals.uchicago.edu/doi/10.1086/658905},
	doi = {10.1086/658905},
	abstract = {Ecological divergence and selection for novel adaptations to new habitats have been theoretically proposed to play important roles in promoting homoploid hybrid speciation (HHS). The successful establishment of Pinus densata on the Tibetan Plateau is one of the few known examples of HHS. In this study, we carried out extensive field expeditions to obtain representative coverage of occurrence sites of P. densata and its two putative parents. We then applied a series of geographic information system–based analyses to define the patterns of environmental variation within and among the three pine species, to remove potentially confounding effects of spatial autocorrelation in the environmental data due to allopatric ranges, and to build species distribution models. All results consistently indicated that the ecological preferences of P. densata and its parental species have diverged, and they identified candidate ecological factors associated with habitat-specific adaptation. Projections from niche modeling indicated that P. densata could extend across a vast range along the parallel valley systems of the southeastern Tibetan Plateau. Our findings provide evidence of a distinct niche shift in P. densata and support the hypothesis that local adaptation and geographic isolation help maintain and reinforce between-species differences and reproductive isolation in the species complex.},
	number = {4},
	urldate = {2023-04-27},
	journal = {The American Naturalist},
	author = {Mao, Jian-Feng and Wang, Xiao-Ru},
	month = apr,
	year = {2011},
	note = {Publisher: The University of Chicago Press},
	keywords = {ecological differentiation, hybrid speciation, local adaptation, reproductive isolation},
	pages = {424--439},
}

Ecological divergence and selection for novel adaptations to new habitats have been theoretically proposed to play important roles in promoting homoploid hybrid speciation (HHS). The successful establishment of Pinus densata on the Tibetan Plateau is one of the few known examples of HHS. In this study, we carried out extensive field expeditions to obtain representative coverage of occurrence sites of P. densata and its two putative parents. We then applied a series of geographic information system–based analyses to define the patterns of environmental variation within and among the three pine species, to remove potentially confounding effects of spatial autocorrelation in the environmental data due to allopatric ranges, and to build species distribution models. All results consistently indicated that the ecological preferences of P. densata and its parental species have diverged, and they identified candidate ecological factors associated with habitat-specific adaptation. Projections from niche modeling indicated that P. densata could extend across a vast range along the parallel valley systems of the southeastern Tibetan Plateau. Our findings provide evidence of a distinct niche shift in P. densata and support the hypothesis that local adaptation and geographic isolation help maintain and reinforce between-species differences and reproductive isolation in the species complex.

@article{staudt_regulation_2011,
	title = {Regulation of protein function by ‘{microProteins}’},
	volume = {12},
	issn = {1469-221X},
	url = {https://www.embopress.org/doi/full/10.1038/embor.2010.196},
	doi = {10.1038/embor.2010.196},
	abstract = {Many proteins achieve their function by acting as part of multi-protein complexes. The formation of these complexes is highly regulated and mediated through domains of protein?protein interaction. Disruption of a complex or of the ability of the proteins to form homodimers, heterodimers or multimers can have severe consequences for cellular function. In this context, the formation of dimers and multimers can be perturbed by proteins referred to here as ?microProteins?. These disruptive protein species contain the protein-interaction domains of bona fide interaction partners, but lack the functional domains required for the activation of, for example, transcription or DNA binding. MicroProteins thus behave as post-translational regulators by forming homotypic dimers with their targets, and act through the dominant?negative suppression of protein complex function. Although the first microProtein was identified more than two decades ago, the recent discovery and characterization of three further small protein species in plants emphasizes their importance. The studies discussed in this review demonstrate that the action of microProteins is general and that it has evolved in both the animal and the plant kingdoms.},
	number = {1},
	urldate = {2022-11-30},
	journal = {EMBO reports},
	author = {Staudt, Annica-Carolin and Wenkel, Stephan},
	month = jan,
	year = {2011},
	keywords = {Id-like proteins, homotypic interactions, protein–protein interaction, transcription factors},
	pages = {35--42},
}

Many proteins achieve their function by acting as part of multi-protein complexes. The formation of these complexes is highly regulated and mediated through domains of protein?protein interaction. Disruption of a complex or of the ability of the proteins to form homodimers, heterodimers or multimers can have severe consequences for cellular function. In this context, the formation of dimers and multimers can be perturbed by proteins referred to here as ?microProteins?. These disruptive protein species contain the protein-interaction domains of bona fide interaction partners, but lack the functional domains required for the activation of, for example, transcription or DNA binding. MicroProteins thus behave as post-translational regulators by forming homotypic dimers with their targets, and act through the dominant?negative suppression of protein complex function. Although the first microProtein was identified more than two decades ago, the recent discovery and characterization of three further small protein species in plants emphasizes their importance. The studies discussed in this review demonstrate that the action of microProteins is general and that it has evolved in both the animal and the plant kingdoms.

@article{malnoe_photosynthetic_2011,
	title = {Photosynthetic growth despite a broken {Q}-cycle},
	volume = {2},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms1299},
	doi = {10/fh7dj9},
	abstract = {Central in respiration or photosynthesis, the cytochrome bc1 and b6f complexes are regarded as functionally similar quinol oxidoreductases. They both catalyse a redox loop, the Q-cycle, which couples electron and proton transfer. This loop involves a bifurcated electron transfer step considered as being mechanistically mandatory, making the Q-cycle indispensable for growth. Attempts to falsify this paradigm in the case of cytochrome bc1 have failed. The rapid proteolytic degradation of b6f complexes bearing mutations aimed at hindering the Q-cycle has precluded so far the experimental assessment of this model in the photosynthetic chain. Here we combine mutations in Chlamydomonas that inactivate the redox loop but preserve high accumulation levels of b6f complexes. The oxidoreductase activity of these crippled complexes is sufficient to sustain photosynthetic growth, which demonstrates that the Q-cycle is dispensable for oxygenic photosynthesis.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Nature Communications},
	author = {Malnoë, Alizée and Wollman, Francis-André and de Vitry, Catherine and Rappaport, Fabrice},
	month = sep,
	year = {2011},
	pages = {301},
}

Central in respiration or photosynthesis, the cytochrome bc1 and b6f complexes are regarded as functionally similar quinol oxidoreductases. They both catalyse a redox loop, the Q-cycle, which couples electron and proton transfer. This loop involves a bifurcated electron transfer step considered as being mechanistically mandatory, making the Q-cycle indispensable for growth. Attempts to falsify this paradigm in the case of cytochrome bc1 have failed. The rapid proteolytic degradation of b6f complexes bearing mutations aimed at hindering the Q-cycle has precluded so far the experimental assessment of this model in the photosynthetic chain. Here we combine mutations in Chlamydomonas that inactivate the redox loop but preserve high accumulation levels of b6f complexes. The oxidoreductase activity of these crippled complexes is sufficient to sustain photosynthetic growth, which demonstrates that the Q-cycle is dispensable for oxygenic photosynthesis.

@article{keech_conserved_2011,
	title = {The conserved mobility of mitochondria during leaf senescence reflects differential regulation of the cytoskeletal components in {Arabidopsis} thaliana},
	volume = {6},
	issn = {null},
	url = {https://doi.org/10.4161/psb.6.1.14307},
	doi = {10/bzzb2q},
	abstract = {Leaf senescence is an organized process, which requires fine tuning between nuclear gene expression, activity of proteases and the maintenance of primary metabolism. Recently, we reported that leaf senescence was accompanied by an early degradation of the microtubule cytoskeleton in Arabidopsis thaliana. As the cytoskeleton is essential for cell stability, vesicle shuttling and organelle mobility, it might be asked how the regulation of these cell functions occurs with such drastic modifications of the cytoskeleton. Based on confocal laser microscopy observations and a micro-array analysis, the following addendum shows that mitochondrial mobility is conserved until the late stages of leaf senescence and provides evidences that the actin-cytoskeleton is maintained longer than the microtubule network. This conservation of actin-filaments is discussed with regards to energy metabolism as well as calcium signaling during programmed cell death.},
	number = {1},
	urldate = {2021-06-10},
	journal = {Plant Signaling \& Behavior},
	author = {Keech, Olivier},
	month = jan,
	year = {2011},
	pages = {147--150},
}

Leaf senescence is an organized process, which requires fine tuning between nuclear gene expression, activity of proteases and the maintenance of primary metabolism. Recently, we reported that leaf senescence was accompanied by an early degradation of the microtubule cytoskeleton in Arabidopsis thaliana. As the cytoskeleton is essential for cell stability, vesicle shuttling and organelle mobility, it might be asked how the regulation of these cell functions occurs with such drastic modifications of the cytoskeleton. Based on confocal laser microscopy observations and a micro-array analysis, the following addendum shows that mitochondrial mobility is conserved until the late stages of leaf senescence and provides evidences that the actin-cytoskeleton is maintained longer than the microtubule network. This conservation of actin-filaments is discussed with regards to energy metabolism as well as calcium signaling during programmed cell death.

@article{stepanova_arabidopsis_2011,
	title = {The {Arabidopsis} {YUCCA1} {Flavin} {Monooxygenase} {Functions} in the {Indole}-3-{Pyruvic} {Acid} {Branch} of {Auxin} {Biosynthesis}},
	volume = {23},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/23/11/3961/6097553},
	doi = {10/fpsm3j},
	abstract = {Abstract
            The effects of auxins on plant growth and development have been known for more than 100 years, yet our understanding of how plants synthesize this essential plant hormone is still fragmentary at best. Gene loss- and gain-of-function studies have conclusively implicated three gene families, CYTOCHROME P450 79B2/B3 (CYP79B2/B3), YUCCA (YUC), and TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1/TRYPTOPHAN AMINOTRANSFERASE-RELATED (TAA1/TAR), in the production of this hormone in the reference plant Arabidopsis thaliana. Each of these three gene families is believed to represent independent routes of auxin biosynthesis. Using a combination of pharmacological, genetic, and biochemical approaches, we examined the possible relationships between the auxin biosynthetic pathways defined by these three gene families. Our findings clearly indicate that TAA1/TARs and YUCs function in a common linear biosynthetic pathway that is genetically distinct from the CYP79B2/B3 route. In the redefined TAA1-YUC auxin biosynthetic pathway, TAA1/TARs are required for the production of indole-3-pyruvic acid (IPyA) from Trp, whereas YUCs are likely to function downstream. These results, together with the extensive genetic analysis of four pyruvate decarboxylases, the putative downstream components of the TAA1 pathway, strongly suggest that the enzymatic reactions involved in indole-3-acetic acid (IAA) production via IPyA are different than those previously postulated, and a new and testable model for how IAA is produced in plants is needed.},
	language = {en},
	number = {11},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Stepanova, Anna N. and Yun, Jeonga and Robles, Linda M. and Novak, Ondrej and He, Wenrong and Guo, Hongwei and Ljung, Karin and Alonso, Jose M.},
	month = nov,
	year = {2011},
	pages = {3961--3973},
}

Abstract The effects of auxins on plant growth and development have been known for more than 100 years, yet our understanding of how plants synthesize this essential plant hormone is still fragmentary at best. Gene loss- and gain-of-function studies have conclusively implicated three gene families, CYTOCHROME P450 79B2/B3 (CYP79B2/B3), YUCCA (YUC), and TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1/TRYPTOPHAN AMINOTRANSFERASE-RELATED (TAA1/TAR), in the production of this hormone in the reference plant Arabidopsis thaliana. Each of these three gene families is believed to represent independent routes of auxin biosynthesis. Using a combination of pharmacological, genetic, and biochemical approaches, we examined the possible relationships between the auxin biosynthetic pathways defined by these three gene families. Our findings clearly indicate that TAA1/TARs and YUCs function in a common linear biosynthetic pathway that is genetically distinct from the CYP79B2/B3 route. In the redefined TAA1-YUC auxin biosynthetic pathway, TAA1/TARs are required for the production of indole-3-pyruvic acid (IPyA) from Trp, whereas YUCs are likely to function downstream. These results, together with the extensive genetic analysis of four pyruvate decarboxylases, the putative downstream components of the TAA1 pathway, strongly suggest that the enzymatic reactions involved in indole-3-acetic acid (IAA) production via IPyA are different than those previously postulated, and a new and testable model for how IAA is produced in plants is needed.

@article{kindgren_novel_2011,
	title = {A novel proteomic approach reveals a role for {Mg}-protoporphyrin {IX} in response to oxidative stress},
	volume = {141},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1399-3054.2010.01440.x},
	doi = {10/d2cw82},
	abstract = {The presence of genes encoding organellar proteins in different cellular compartments necessitates a tight coordination of expression by the different genomes of the eukaryotic cell. This coordination of gene expression is achieved by organelle-to-nucleus communication. Stress-induced perturbations of the tetrapyrrole pathway trigger large changes in nuclear gene expression. In order to investigate whether the tetrapyrrole Mg-ProtoIX itself is an important part of plastid-to-nucleus communication, we used an affinity column containing Mg-ProtoIX covalently linked to an Affi-Gel matrix. The proteins that bound to Mg-ProtoIX were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis combined with nano liquid chromatography–mass spectrometry (MS)/MS. Thus, we present a novel proteomic approach to address the mechanisms involved in cellular signaling and we identified interactions between Mg-ProtoIX and a large number of proteins associated with oxidative stress responses. Our approach revealed an interaction between Mg-ProtoIX and the heat shock protein 90-type protein, HSP81-2 suggesting that a regulatory complex including HSP90 proteins and tetrapyrroles controlling gene expression is evolutionarily conserved between yeast and plants. In addition, our list of putative Mg-ProtoIX-binding proteins demonstrated that binding of tetrapyrroles does not depend on a specific amino acid motif but possibly on a specific fold of the protein.},
	language = {en},
	number = {4},
	urldate = {2021-09-02},
	journal = {Physiologia Plantarum},
	author = {Kindgren, Peter and Eriksson, Mats-Jerry and Benedict, Catherine and Mohapatra, Anasuya and Gough, Simon P. and Hansson, Mats and Kieselbach, Thomas and Strand, Åsa},
	year = {2011},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1399-3054.2010.01440.x},
	pages = {310--320},
}

The presence of genes encoding organellar proteins in different cellular compartments necessitates a tight coordination of expression by the different genomes of the eukaryotic cell. This coordination of gene expression is achieved by organelle-to-nucleus communication. Stress-induced perturbations of the tetrapyrrole pathway trigger large changes in nuclear gene expression. In order to investigate whether the tetrapyrrole Mg-ProtoIX itself is an important part of plastid-to-nucleus communication, we used an affinity column containing Mg-ProtoIX covalently linked to an Affi-Gel matrix. The proteins that bound to Mg-ProtoIX were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis combined with nano liquid chromatography–mass spectrometry (MS)/MS. Thus, we present a novel proteomic approach to address the mechanisms involved in cellular signaling and we identified interactions between Mg-ProtoIX and a large number of proteins associated with oxidative stress responses. Our approach revealed an interaction between Mg-ProtoIX and the heat shock protein 90-type protein, HSP81-2 suggesting that a regulatory complex including HSP90 proteins and tetrapyrroles controlling gene expression is evolutionarily conserved between yeast and plants. In addition, our list of putative Mg-ProtoIX-binding proteins demonstrated that binding of tetrapyrroles does not depend on a specific amino acid motif but possibly on a specific fold of the protein.

@article{ashelford_full_2011,
	title = {Full genome re-sequencing reveals a novel circadian clock mutation in {Arabidopsis}},
	volume = {12},
	issn = {1465-6906},
	url = {http://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-3-r28},
	doi = {10/dzpfvk},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Genome Biology},
	author = {Ashelford, Kevin and Eriksson, Maria E. and Allen, Christopher M and D'Amore, Rosalinda and Johansson, Mikael and Gould, Peter and Kay, Suzanne and Millar, Andrew J and Hall, Neil and Hall, Anthony},
	year = {2011},
	pages = {R28},
}

@article{eriksson_plant_2011,
	title = {Plant cell responses to cold are all about timing},
	volume = {14},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526611001282},
	doi = {10/bwjm2f},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Current Opinion in Plant Biology},
	author = {Eriksson, Maria E. and Webb, Alex AR},
	month = dec,
	year = {2011},
	pages = {731--737},
}

@article{baba_activity-dormancy_2011,
	title = {Activity-dormancy transition in the cambial meristem involves stage-specific modulation of auxin response in hybrid aspen},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1011506108},
	doi = {10/d34mx2},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Baba, K. and Karlberg, A. and Schmidt, J. and Schrader, J. and Hvidsten, T. R. and Bakó, L. and Bhalerao, Rishikesh P.},
	month = feb,
	year = {2011},
	pages = {3418--3423},
}

@article{gendre_conserved_2011,
	title = {Conserved {Arabidopsis} {ECHIDNA} protein mediates trans-{Golgi}-network trafficking and cell elongation},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1018371108},
	doi = {10/b6k65m},
	language = {en},
	number = {19},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Gendre, D. and Oh, J. and Boutte, Y. and Best, J. G. and Samuels, L. and Nilsson, R. and Uemura, T. and Marchant, A. and Bennett, M. J. and Grebe, M. and Bhalerao, Rishikesh P.},
	month = may,
	year = {2011},
	pages = {8048--8053},
}

@article{abraham_immunodetection_2011,
	title = {Immunodetection of retinoblastoma-related protein and its phosphorylated form in interphase and mitotic alfalfa cells},
	volume = {62},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erq413},
	doi = {10/dz5rcb},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Abraham, E. and Miskolczi, P. and Ayaydin, F. and Yu, P. and Kotogany, E. and Bakó, L. and Otvos, K. and Horvath, G. V. and Dudits, D.},
	month = mar,
	year = {2011},
	pages = {2155--2168},
}

@article{buren_importance_2011,
	title = {Importance of {Post}-{Translational} {Modifications} for {Functionality} of a {Chloroplast}-{Localized} {Carbonic} {Anhydrase} ({CAH1}) in {Arabidopsis} thaliana},
	volume = {6},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0021021},
	doi = {10/bdgdgk},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Burén, Stefan and Ortega-Villasante, Cristina and Blanco-Rivero, Amaya and Martínez-Bernardini, Andrea and Shutova, Tatiana and Shevela, Dmitriy and Messinger, Johannes and Bakó, Laszlo and Villarejo, Arsenio and Samuelsson, Göran},
	editor = {Bassham, Diane},
	month = jun,
	year = {2011},
	pages = {e21021},
}

@article{karlberg_short_2011,
	title = {Short {Day}–{Mediated} {Cessation} of {Growth} {Requires} the {Downregulation} of {AINTEGUMENTALIKE1} {Transcription} {Factor} in {Hybrid} {Aspen}},
	volume = {7},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1002361},
	doi = {10/dx44wg},
	language = {en},
	number = {11},
	urldate = {2021-06-08},
	journal = {PLoS Genetics},
	author = {Karlberg, Anna and Bakó, Laszlo and Bhalerao, Rishikesh P.},
	editor = {Sederoff, Ronald R.},
	month = nov,
	year = {2011},
	pages = {e1002361},
}

@article{ivkovic_developing_2011,
	title = {Developing breeding objectives for radiata pine structural wood production. {II}. {Sensitivity} analyses},
	url = {https://cdnsciencepub.com/doi/abs/10.1139/x06-162},
	doi = {10/bgc8d8},
	abstract = {In a companion paper we describe a bioeconomic model of a production system for radiata pine (Pinus radiata D. Don) structural timber and estimated economic weights for four breeding-objective trai...},
	language = {en},
	urldate = {2021-06-11},
	journal = {Canadian Journal of Forest Research},
	author = {Ivković, Milo and Wu, Harry X. and McRae, Tony A. and Matheson, Colin A.},
	month = feb,
	year = {2011},
	note = {Publisher: NRC Research Press Ottawa, Canada},
}

In a companion paper we describe a bioeconomic model of a production system for radiata pine (Pinus radiata D. Don) structural timber and estimated economic weights for four breeding-objective trai...

@article{li_efficiency_2011,
	title = {Efficiency of early selection for rotation-aged growth and wood density traits in {Pinus} radiata},
	url = {https://cdnsciencepub.com/doi/abs/10.1139/x05-134},
	doi = {10/dmm4gk},
	abstract = {A total of 1097 cross-sectional wood disks from breast height were sampled from two rotation-aged (27 and 31 years from planting) genetic trials of radiata pine (Pinus radiata D. Don) in Australia ...},
	language = {en},
	urldate = {2021-06-11},
	journal = {Canadian Journal of Forest Research},
	author = {Li, Li and Wu, Harry X.},
	month = feb,
	year = {2011},
	note = {Publisher: NRC Research Press Ottawa, Canada},
}

A total of 1097 cross-sectional wood disks from breast height were sampled from two rotation-aged (27 and 31 years from planting) genetic trials of radiata pine (Pinus radiata D. Don) in Australia ...

@article{kvaalen_somatic_2011,
	title = {Somatic embryogenesis for plant production of {Abies} lasiocarpa},
	url = {https://cdnsciencepub.com/doi/abs/10.1139/x05-035},
	doi = {10/fqvm8p},
	abstract = {Seeds of Abies lasiocarpa (Hook.) Nutt. (subalpine fir) were dissected, and the different parts were analyzed for elemental composition. The data were used to design a novel growth medium for initi...},
	language = {en},
	urldate = {2021-06-11},
	journal = {Canadian Journal of Forest Research},
	author = {Kvaalen, Harald and Daehlen, Ola Gram and Rognstad, Anne Tove and Grønstad, Borgny and Egertsdotter, Ulrika},
	month = feb,
	year = {2011},
	note = {Publisher: NRC Research Press Ottawa, Canada},
}

Seeds of Abies lasiocarpa (Hook.) Nutt. (subalpine fir) were dissected, and the different parts were analyzed for elemental composition. The data were used to design a novel growth medium for initi...

@article{ivkovic_developing_2011,
	title = {Developing breeding objectives for radiata pine structural wood production. {I}. {Bioeconomic} model and economic weights},
	url = {https://cdnsciencepub.com/doi/abs/10.1139/x06-161},
	doi = {10/df85c3},
	abstract = {Economic breeding objectives were developed for production of radiata pine (Pinus radiata D. Don) structural timber in Australia. Production systems of eight companies, including plantation growers...},
	language = {en},
	urldate = {2021-06-11},
	journal = {Canadian Journal of Forest Research},
	author = {Ivković, Milo and Wu, Harry X. and McRae, Tony A. and Powell, Mike B.},
	month = feb,
	year = {2011},
	note = {Publisher: NRC Research Press Ottawa, Canada},
}

Economic breeding objectives were developed for production of radiata pine (Pinus radiata D. Don) structural timber in Australia. Production systems of eight companies, including plantation growers...

@article{gapare_inheritance_2011,
	title = {Inheritance of spiral grain in the juvenile core of {Pinus} radiata},
	url = {https://cdnsciencepub.com/doi/abs/10.1139/x06-202},
	doi = {10/c2hfh2},
	abstract = {Spiral grain is the angular arrangement of fibres in a tangential plane with reference to the pith or vertical tree axis. Spiral grain angles exceeding 5° can cause wood to twist, which may result ...},
	language = {en},
	urldate = {2021-06-10},
	journal = {Canadian Journal of Forest Research},
	author = {Gapare, Washington and Hathorn, Adrian and Kain, Dominic and Matheson, Colin and Wu, Harry},
	month = dec,
	year = {2011},
	note = {Publisher: NRC Research Press Ottawa, Canada},
}

Spiral grain is the angular arrangement of fibres in a tangential plane with reference to the pith or vertical tree axis. Spiral grain angles exceeding 5° can cause wood to twist, which may result ...

@article{gapare_performance_2011,
	title = {Performance differences among ex situ native-provenance collections of {Pinus} radiata {D}. {Don}. 1: potential for infusion into breeding populations in {Australia} and {New} {Zealand}},
	volume = {7},
	issn = {1614-2942, 1614-2950},
	shorttitle = {Performance differences among ex situ native-provenance collections of {Pinus} radiata {D}. {Don}. 1},
	url = {http://link.springer.com/10.1007/s11295-010-0343-5},
	doi = {10/cjz6bv},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Gapare, Washington J. and Baltunis, Brian S. and Ivković, Miloš and Low, Charlie B. and Jefferson, Paul and Wu, Harry X.},
	month = apr,
	year = {2011},
	pages = {409--419},
}

@article{grebe_unveiling_2011,
	title = {Unveiling the {Casparian} strip},
	volume = {473},
	copyright = {2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/473294a},
	doi = {10/cq36hm},
	abstract = {The Casparian strip in plant roots is a diffusion barrier that directs water and solutes from the soil to the water-conducting tissues. Proteins involved in making the strip have at long last been identified. See Letter p.380},
	language = {en},
	number = {7347},
	urldate = {2021-06-08},
	journal = {Nature},
	author = {Grebe, Markus},
	month = may,
	year = {2011},
	note = {Number: 7347
Publisher: Nature Publishing Group},
	pages = {294--295},
}

The Casparian strip in plant roots is a diffusion barrier that directs water and solutes from the soil to the water-conducting tissues. Proteins involved in making the strip have at long last been identified. See Letter p.380

@article{kumaraswamy_mass_2011,
	title = {Mass {Spectrometry} {Based} {Metabolomics} to {Identify} {Potential} {Biomarkers} for {Resistance} in {Barley} against {Fusarium} {Head} {Blight} ({Fusarium} graminearum)},
	volume = {37},
	issn = {1573-1561},
	url = {https://doi.org/10.1007/s10886-011-9989-1},
	doi = {10/b4954n},
	abstract = {Resistance in Triticeae to fusarium head blight (FHB) is quantitatively inherited. Metabolomics as a tool was used to better understand the mechanisms of resistance and to identify potential FHB resistance biomarker metabolites in barley. Five FHB-resistant two-row barley genotypes (CIho 4196, Zhedar-1, Zhedar-2, Fredrickson, and Harbin-2r) and one FHB-susceptible genotype (CH 9520–30) were each inoculated with either pathogen-suspension or mock-solution. Disease severity, quantified as the proportion of spikelets diseased, varied among genotypes, being the greatest in CH 9520–30. Spikelets were sampled, metabolites extracted with aqueous methanol, and analyzed using an LC-ESI-LTQ-Orbitrap system. A pair wise, resistant vs. susceptible, t-test identified 1774 significant treatment peaks. Canonical discriminant analysis of peak abundance allowed the genotypes to be sorted into three clusters: (i) CH9520-30, (ii) Harbin-2r, (iii) the remaining four genotypes. The t-test was further used to identify resistance-related (RR) and pathogenesis-related (PR) metabolites. The pathogen-produced virulence factor deoxynivalenol (DON), and its detoxification product, DON-3-O-glucoside (D3G) were designated as resistance indicator (RI) metabolites. Metabolites (RR, PR, or RI) occurring in at least two resistant genotypes, showing a two-fold or greater abundance in resistant vs. susceptible lines, and also known to have plant defense functions were selected as potential FHB resistance biomarker metabolites. These included phenylalanine, p-coumaric acid, jasmonate, linolenic acid, total DON produced (TDP), and the proportion of DON converted to D3G (PDC). Total DON was the lowest in CIho 4196, while PDC was the highest in Zhedar-2. The application of RR, PR, and RI metabolites as potential biomarkers to enhance resistance is discussed.},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Journal of Chemical Ecology},
	author = {Kumaraswamy, Kenchappa G. and Kushalappa, Ajjamada C. and Choo, Thin M. and Dion, Yves and Rioux, Sylvie},
	month = aug,
	year = {2011},
	pages = {846--856},
}

Resistance in Triticeae to fusarium head blight (FHB) is quantitatively inherited. Metabolomics as a tool was used to better understand the mechanisms of resistance and to identify potential FHB resistance biomarker metabolites in barley. Five FHB-resistant two-row barley genotypes (CIho 4196, Zhedar-1, Zhedar-2, Fredrickson, and Harbin-2r) and one FHB-susceptible genotype (CH 9520–30) were each inoculated with either pathogen-suspension or mock-solution. Disease severity, quantified as the proportion of spikelets diseased, varied among genotypes, being the greatest in CH 9520–30. Spikelets were sampled, metabolites extracted with aqueous methanol, and analyzed using an LC-ESI-LTQ-Orbitrap system. A pair wise, resistant vs. susceptible, t-test identified 1774 significant treatment peaks. Canonical discriminant analysis of peak abundance allowed the genotypes to be sorted into three clusters: (i) CH9520-30, (ii) Harbin-2r, (iii) the remaining four genotypes. The t-test was further used to identify resistance-related (RR) and pathogenesis-related (PR) metabolites. The pathogen-produced virulence factor deoxynivalenol (DON), and its detoxification product, DON-3-O-glucoside (D3G) were designated as resistance indicator (RI) metabolites. Metabolites (RR, PR, or RI) occurring in at least two resistant genotypes, showing a two-fold or greater abundance in resistant vs. susceptible lines, and also known to have plant defense functions were selected as potential FHB resistance biomarker metabolites. These included phenylalanine, p-coumaric acid, jasmonate, linolenic acid, total DON produced (TDP), and the proportion of DON converted to D3G (PDC). Total DON was the lowest in CIho 4196, while PDC was the highest in Zhedar-2. The application of RR, PR, and RI metabolites as potential biomarkers to enhance resistance is discussed.

@article{nishikubo_xyloglucan_2011,
	title = {Xyloglucan \textit{endo} -{Transglycosylase}-{Mediated} {Xyloglucan} {Rearrangements} in {Developing} {Wood} of {Hybrid} {Aspen}},
	volume = {155},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/155/1/399/6111559},
	doi = {10/fswhm6},
	abstract = {Abstract
            Xyloglucan endo-transglycosylases (XETs) encoded by xyloglucan endo-transglycosylases/hydrolase (XTH) genes modify the xyloglucan-cellulose framework of plant cell walls, thereby regulating their expansion and strength. To evaluate the importance of XET in wood development, we studied xyloglucan dynamics and XTH gene expression in developing wood and modified XET activity in hybrid aspen (Populus tremula × tremuloides) by overexpressing PtxtXET16-34. We show that developmental modifications during xylem differentiation include changes from loosely to tightly bound forms of xyloglucan and increases in the abundance of fucosylated xyloglucan epitope recognized by the CCRC-M1 antibody. We found that at least 16 Populus  XTH genes, all likely encoding XETs, are expressed in developing wood. Five genes were highly and ubiquitously expressed, whereas PtxtXET16-34 was expressed more weakly but specifically in developing wood. Transgenic up-regulation of XET activity induced changes in cell wall xyloglucan, but its effects were dependent on developmental stage. For instance, XET overexpression increased abundance of the CCRC-M1 epitope in cambial cells and xylem cells in early stages of differentiation but not in mature xylem. Correspondingly, an increase in tightly bound xyloglucan content was observed in primary-walled xylem but a decrease was seen in secondary-walled xylem. Thus, in young xylem cells, XET activity limits xyloglucan incorporation into the tightly bound wall network but removes it from cell walls in older cells. XET overexpression promoted vessel element growth but not fiber expansion. We suggest that the amount of nascent xyloglucan relative to XET is an important determinant of whether XET strengthens or loosens the cell wall.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Nishikubo, Nobuyuki and Takahashi, Junko and Roos, Alexandra A. and Derba-Maceluch, Marta and Piens, Kathleen and Brumer, Harry and Teeri, Tuula T. and Stålbrand, Henrik and Mellerowicz, Ewa J.},
	month = jan,
	year = {2011},
	pages = {399--413},
}

Abstract Xyloglucan endo-transglycosylases (XETs) encoded by xyloglucan endo-transglycosylases/hydrolase (XTH) genes modify the xyloglucan-cellulose framework of plant cell walls, thereby regulating their expansion and strength. To evaluate the importance of XET in wood development, we studied xyloglucan dynamics and XTH gene expression in developing wood and modified XET activity in hybrid aspen (Populus tremula × tremuloides) by overexpressing PtxtXET16-34. We show that developmental modifications during xylem differentiation include changes from loosely to tightly bound forms of xyloglucan and increases in the abundance of fucosylated xyloglucan epitope recognized by the CCRC-M1 antibody. We found that at least 16 Populus  XTH genes, all likely encoding XETs, are expressed in developing wood. Five genes were highly and ubiquitously expressed, whereas PtxtXET16-34 was expressed more weakly but specifically in developing wood. Transgenic up-regulation of XET activity induced changes in cell wall xyloglucan, but its effects were dependent on developmental stage. For instance, XET overexpression increased abundance of the CCRC-M1 epitope in cambial cells and xylem cells in early stages of differentiation but not in mature xylem. Correspondingly, an increase in tightly bound xyloglucan content was observed in primary-walled xylem but a decrease was seen in secondary-walled xylem. Thus, in young xylem cells, XET activity limits xyloglucan incorporation into the tightly bound wall network but removes it from cell walls in older cells. XET overexpression promoted vessel element growth but not fiber expansion. We suggest that the amount of nascent xyloglucan relative to XET is an important determinant of whether XET strengthens or loosens the cell wall.

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

Background/Aim The changes in the cerebrospinal fluid (CSF) metabolome associated with the fatal neurodegenerative disease amyotrophic lateral sclerosis (ALS) are poorly understood and earlier smaller studies have shown conflicting results. The metabolomic methodology is suitable for screening large cohorts of samples. Global metabolomics can be used for detecting changes of metabolite concentrations in samples of fluids such as CSF. Methodology Using gas chromatography coupled to mass spectrometry (GC/TOFMS) and multivariate statistical modeling, we simultaneously studied the metabolome signature of ∼120 small metabolites in the CSF of patients with ALS, stratified according to hereditary disposition and clinical subtypes of ALS in relation to controls. Principal Findings The study is the first to report data validated over two sub-sets of ALS vs. control patients for a large set of metabolites analyzed by GC/TOFMS. We find that patients with sporadic amyotrophic lateral sclerosis (SALS) have a heterogeneous metabolite signature in the cerebrospinal fluid, in some patients being almost identical to controls. However, familial amyotrophic lateral sclerosis (FALS) without superoxide dismutase-1 gene (SOD1) mutation is less heterogeneous than SALS. The metabolome of the cerebrospinal fluid of 17 ALS patients with a SOD1 gene mutation was found to form a separate homogeneous group. Analysis of metabolites revealed that glutamate and glutamine were reduced, in particular in patients with a familial predisposition. There are significant differences in the metabolite profile and composition among patients with FALS, SALS and patients carrying a mutation in the SOD1 gene suggesting that the neurodegenerative process in different subtypes of ALS may be partially dissimilar. Conclusions/Significance Patients with a genetic predisposition to amyotrophic lateral sclerosis have a more distinct and homogeneous signature than patients with a sporadic disease.

@article{fries_density_2011,
	title = {Density and wood biomass development in whole-tree analyses of {Scots} pine, and aspects on heritability estimates},
	volume = {60},
	doi = {10/gjcmrn},
	abstract = {Twelve trees in a 36 year old full-sib progeny plantation, testing a part of the Scots pine breeding population, were analysed for wood density and the width of the earlywood and latewood sections in each annual ring. Wood samples (stem discs) were taken with 1 m intervals along the stem and the analyses covered thus the whole stem. Based on these data, the biomass of the earlywood and latewood of each annual ring in each 1 meter stem section was estimated. Latewood density increased from pith to bark while it decreased from stem base to top. Earlywood density was of similar size both radially and vertically. The biomass in each annual ring increased until around ring number 10 from pith for both wood types. For earlywood it then decreased while it remained quite constant for latewood. Latewood biomass decreased more rapidly towards the top of the tree than earlywood biomass. Heritabilities for earlywood and latewood in each annual ring at breast height (estimated in the same material in a previous study) were related to the corresponding biomasses to indirectly estimate overall heritability for wood density valid for the whole stem. The analyses indicate that the decrease in heritability for latewood density and increase for earlywood density, from the pith to bark, is compensated by the increase in latewood biomass in relation to earlywood biomass. Thus, the heritability of the latewood density and earlywood density seems to have the same influence on the overall heritability for density in the whole stem.},
	journal = {Silvae Genetica},
	author = {Fries, Anders and Mörling, Tommy},
	month = jun,
	year = {2011},
	pages = {224--232},
}

Twelve trees in a 36 year old full-sib progeny plantation, testing a part of the Scots pine breeding population, were analysed for wood density and the width of the earlywood and latewood sections in each annual ring. Wood samples (stem discs) were taken with 1 m intervals along the stem and the analyses covered thus the whole stem. Based on these data, the biomass of the earlywood and latewood of each annual ring in each 1 meter stem section was estimated. Latewood density increased from pith to bark while it decreased from stem base to top. Earlywood density was of similar size both radially and vertically. The biomass in each annual ring increased until around ring number 10 from pith for both wood types. For earlywood it then decreased while it remained quite constant for latewood. Latewood biomass decreased more rapidly towards the top of the tree than earlywood biomass. Heritabilities for earlywood and latewood in each annual ring at breast height (estimated in the same material in a previous study) were related to the corresponding biomasses to indirectly estimate overall heritability for wood density valid for the whole stem. The analyses indicate that the decrease in heritability for latewood density and increase for earlywood density, from the pith to bark, is compensated by the increase in latewood biomass in relation to earlywood biomass. Thus, the heritability of the latewood density and earlywood density seems to have the same influence on the overall heritability for density in the whole stem.

@article{agusti_strigolactone_2011,
	title = {Strigolactone signaling is required for auxin-dependent stimulation of secondary growth in plants},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/108/50/20242},
	doi = {10/fhvk7k},
	abstract = {Long distance cell-to-cell communication is critical for the development of multicellular organisms. In this respect, plants are especially demanding as they constantly integrate environmental inputs to adjust growth processes to different conditions. One example is thickening of shoots and roots, also designated as secondary growth. Secondary growth is mediated by the vascular cambium, a stem cell-like tissue whose cell-proliferating activity is regulated over a long distance by the plant hormone auxin. How auxin signaling is integrated at the level of cambium cells and how cambium activity is coordinated with other growth processes are largely unknown. Here, we provide physiological, genetic, and pharmacological evidence that strigolactones (SLs), a group of plant hormones recently described to be involved in the repression of shoot branching, positively regulate cambial activity and that this function is conserved among species. We show that SL signaling in the vascular cambium itself is sufficient for cambium stimulation and that it interacts strongly with the auxin signaling pathway. Our results provide a model of how auxin-based long-distance signaling is translated into cambium activity and suggest that SLs act as general modulators of plant growth forms linking the control of shoot branching with the thickening of stems and roots.},
	language = {en},
	number = {50},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Agusti, Javier and Herold, Silvia and Schwarz, Martina and Sanchez, Pablo and Ljung, Karin and Dun, Elizabeth A. and Brewer, Philip B. and Beveridge, Christine A. and Sieberer, Tobias and Sehr, Eva M. and Greb, Thomas},
	month = dec,
	year = {2011},
	pmid = {22123958},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {MORE AXILLARY BRANCHES, meristem, wood production},
	pages = {20242--20247},
}

Long distance cell-to-cell communication is critical for the development of multicellular organisms. In this respect, plants are especially demanding as they constantly integrate environmental inputs to adjust growth processes to different conditions. One example is thickening of shoots and roots, also designated as secondary growth. Secondary growth is mediated by the vascular cambium, a stem cell-like tissue whose cell-proliferating activity is regulated over a long distance by the plant hormone auxin. How auxin signaling is integrated at the level of cambium cells and how cambium activity is coordinated with other growth processes are largely unknown. Here, we provide physiological, genetic, and pharmacological evidence that strigolactones (SLs), a group of plant hormones recently described to be involved in the repression of shoot branching, positively regulate cambial activity and that this function is conserved among species. We show that SL signaling in the vascular cambium itself is sufficient for cambium stimulation and that it interacts strongly with the auxin signaling pathway. Our results provide a model of how auxin-based long-distance signaling is translated into cambium activity and suggest that SLs act as general modulators of plant growth forms linking the control of shoot branching with the thickening of stems and roots.

@article{pacurar_agrobacterium_2011,
	title = {Agrobacterium tumefaciens: {From} crown gall tumors to genetic transformation},
	volume = {76},
	issn = {08855765},
	shorttitle = {Agrobacterium tumefaciens},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0885576511000580},
	doi = {10/drwscf},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Physiological and Molecular Plant Pathology},
	author = {Păcurar, Daniel I. and Thordal-Christensen, Hans and Păcurar, Monica L. and Pamfil, Doru and Botez, Constantin and Bellini, Catherine},
	month = aug,
	year = {2011},
	pages = {76--81},
}

@article{huang_structural_2011,
	title = {Structural {Studies} of β-{Carbonic} {Anhydrase} from the {Green} {Alga} {Coccomyxa}: {Inhibitor} {Complexes} with {Anions} and {Acetazolamide}},
	volume = {6},
	issn = {1932-6203},
	shorttitle = {Structural {Studies} of β-{Carbonic} {Anhydrase} from the {Green} {Alga} {Coccomyxa}},
	url = {https://dx.plos.org/10.1371/journal.pone.0028458},
	doi = {10/ddjswd},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Huang, Shenghua and Hainzl, Tobias and Grundström, Christin and Forsman, Cecilia and Samuelsson, Göran and Sauer-Eriksson, A. Elisabeth},
	editor = {Hofmann, Andreas},
	month = dec,
	year = {2011},
	pages = {e28458},
}

@article{wang_reduced_2011,
	title = {Reduced {Expression} of the {SHORT}-{ROOT} {Gene} {Increases} the {Rates} of {Growth} and {Development} in {Hybrid} {Poplar} and {Arabidopsis}},
	volume = {6},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0028878},
	doi = {10/cx2jsh},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Wang, Jiehua and Andersson-Gunnerås, Sara and Gaboreanu, Ioana and Hertzberg, Magnus and Tucker, Matthew R. and Zheng, Bo and Leśniewska, Joanna and Mellerowicz, Ewa J. and Laux, Thomas and Sandberg, Göran and Jones, Brian},
	editor = {Schönbach, Christian},
	month = dec,
	year = {2011},
	pages = {e28878},
}

@article{lara-chavez_initiation_2011,
	title = {Initiation of somatic embryogenesis from immature zygotic embryos of {Oocarpa} pine ({Pinus} oocarpa {Schiede} ex {Schlectendal})},
	volume = {31},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpr126},
	doi = {10/fjp4pt},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {Tree Physiology},
	author = {Lara-Chavez, A. and Flinn, B. S. and Egertsdotter, U.},
	month = dec,
	year = {2011},
	pages = {1422--1422},
}

@article{onskog_classification_2011,
	title = {Classification of microarrays; synergistic effects between normalization, gene selection and machine learning},
	volume = {12},
	issn = {1471-2105},
	url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-390},
	doi = {10/d6gjdv},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Bioinformatics},
	author = {Önskog, Jenny and Freyhult, Eva and Landfors, Mattias and Rydén, Patrik and Hvidsten, Torgeir R},
	year = {2011},
	pages = {390},
}

@article{marhavy_cytokinin_2011,
	title = {Cytokinin {Modulates} {Endocytic} {Trafficking} of {PIN1} {Auxin} {Efflux} {Carrier} to {Control} {Plant} {Organogenesis}},
	volume = {21},
	issn = {15345807},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580711003522},
	doi = {10/bz65s4},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Developmental Cell},
	author = {Marhavý, Peter and Bielach, Agnieszka and Abas, Lindy and Abuzeineh, Anas and Duclercq, Jerome and Tanaka, Hirokazu and Pařezová, Markéta and Petrášek, Jan and Friml, Jiří and Kleine-Vehn, Jürgen and Benková, Eva},
	month = oct,
	year = {2011},
	pages = {796--804},
}

@article{bian_genetic_2011,
	title = {Genetic variation between and within \textit{ex-situ} native-provenance collections of \textit{{Pinus} radiata} {D}. {Don} planted in {Australia} and {New} {Zealand}},
	volume = {60},
	issn = {2509-8934},
	url = {https://www.sciendo.com/article/10.1515/sg-2011-0036},
	doi = {10/gjcmm5},
	abstract = {Abstract
            
              A total of 1226 increment cores were sampled from two provenance trials of
              Pinus radiata
              D. Don planted in New Zealand (Kaingaroa) and Australia (Kangaroovale), to study variation and inheritance of wood density in selections from three mainland California natural populations: Año Nuevo, Monterey and Cambria. The study represents a back-to-back comparison of the same provenance and family material on contrasting sites between New Zealand and Australia. Monterey was significantly different to Año Nuevo and Cambria at Kaingaroa (
              p
              {\textless}0.05), and had slightly higher density, whereas all provenances were almost identical and not significantly different at Kangaroovale. However, there were significant differences for wood density at family level for Año Nuevo and Cambria at Kangaroovale. No significant provenance or family differences were detected for core length at either site. The estimates of heritability for wood density were all above 0.50 and generally higher at Kaingaroa than at Kangaroovale. Estimates of additive genetic correlations between wood density and core length were imprecise. Genotype × site interactions for density appeared minor (estimated type-B genetic correlation= 0.70) despite substantial differences in rainfall and soils. The similarity of Cambria to Año Nuevo for density is an interesting result because the genetic base of the present Australian and New Zealand plantations has been shown to be from Año Nuevo and Monterey. Infusion of Cambria material would increase the overall genetic base of the radiata pine breeding programs, with potential long-term benefits, despite the often disappointing growth performance of material collected from Cambria.},
	language = {en},
	number = {1-6},
	urldate = {2021-06-08},
	journal = {Silvae Genetica},
	author = {Bian, L. and Gapare, W. J. and Ivković, M. and Jefferson, P. and Wu, H. X.},
	month = dec,
	year = {2011},
	pages = {276--285},
}

Abstract A total of 1226 increment cores were sampled from two provenance trials of Pinus radiata D. Don planted in New Zealand (Kaingaroa) and Australia (Kangaroovale), to study variation and inheritance of wood density in selections from three mainland California natural populations: Año Nuevo, Monterey and Cambria. The study represents a back-to-back comparison of the same provenance and family material on contrasting sites between New Zealand and Australia. Monterey was significantly different to Año Nuevo and Cambria at Kaingaroa ( p \textless0.05), and had slightly higher density, whereas all provenances were almost identical and not significantly different at Kangaroovale. However, there were significant differences for wood density at family level for Año Nuevo and Cambria at Kangaroovale. No significant provenance or family differences were detected for core length at either site. The estimates of heritability for wood density were all above 0.50 and generally higher at Kaingaroa than at Kangaroovale. Estimates of additive genetic correlations between wood density and core length were imprecise. Genotype × site interactions for density appeared minor (estimated type-B genetic correlation= 0.70) despite substantial differences in rainfall and soils. The similarity of Cambria to Año Nuevo for density is an interesting result because the genetic base of the present Australian and New Zealand plantations has been shown to be from Año Nuevo and Monterey. Infusion of Cambria material would increase the overall genetic base of the radiata pine breeding programs, with potential long-term benefits, despite the often disappointing growth performance of material collected from Cambria.

@article{drakakaki_clusters_2011,
	title = {Clusters of bioactive compounds target dynamic endomembrane networks in vivo},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/108/43/17850},
	doi = {10/bf5jvk},
	abstract = {Endomembrane trafficking relies on the coordination of a highly complex, dynamic network of intracellular vesicles. Understanding the network will require a dissection of cargo and vesicle dynamics at the cellular level in vivo. This is also a key to establishing a link between vesicular networks and their functional roles in development. We used a high-content intracellular screen to discover small molecules targeting endomembrane trafficking in vivo in a complex eukaryote, Arabidopsis thaliana. Tens of thousands of molecules were prescreened and a selected subset was interrogated against a panel of plasma membrane (PM) and other endomembrane compartment markers to identify molecules that altered vesicle trafficking. The extensive image dataset was transformed by a flexible algorithm into a marker-by-phenotype-by-treatment time matrix and revealed groups of molecules that induced similar subcellular fingerprints (clusters). This matrix provides a platform for a systems view of trafficking. Molecules from distinct clusters presented avenues and enabled an entry point to dissect recycling at the PM, vacuolar sorting, and cell-plate maturation. Bioactivity in human cells indicated the value of the approach to identifying small molecules that are active in diverse organisms for biology and drug discovery.},
	language = {en},
	number = {43},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Drakakaki, Georgia and Robert, Stéphanie and Szatmari, Anna-Maria and Brown, Michelle Q. and Nagawa, Shingo and Damme, Daniel Van and Leonard, Marilyn and Yang, Zhenbiao and Girke, Thomas and Schmid, Sandra L. and Russinova, Eugenia and Friml, Jiří and Raikhel, Natasha V. and Hicks, Glenn R.},
	month = oct,
	year = {2011},
	pmid = {22006339},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {chemical genomics, endosidin, endosome, high content screen},
	pages = {17850--17855},
}

Endomembrane trafficking relies on the coordination of a highly complex, dynamic network of intracellular vesicles. Understanding the network will require a dissection of cargo and vesicle dynamics at the cellular level in vivo. This is also a key to establishing a link between vesicular networks and their functional roles in development. We used a high-content intracellular screen to discover small molecules targeting endomembrane trafficking in vivo in a complex eukaryote, Arabidopsis thaliana. Tens of thousands of molecules were prescreened and a selected subset was interrogated against a panel of plasma membrane (PM) and other endomembrane compartment markers to identify molecules that altered vesicle trafficking. The extensive image dataset was transformed by a flexible algorithm into a marker-by-phenotype-by-treatment time matrix and revealed groups of molecules that induced similar subcellular fingerprints (clusters). This matrix provides a platform for a systems view of trafficking. Molecules from distinct clusters presented avenues and enabled an entry point to dissect recycling at the PM, vacuolar sorting, and cell-plate maturation. Bioactivity in human cells indicated the value of the approach to identifying small molecules that are active in diverse organisms for biology and drug discovery.

@article{li_transcriptome_2011,
	title = {Transcriptome profiling of {Pinus} radiata juvenile wood with contrasting stiffness identifies putative candidate genes involved in microfibril orientation and cell wall mechanics},
	volume = {12},
	issn = {1471-2164},
	url = {http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-480},
	doi = {10/cg5tp5},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Genomics},
	author = {Li, Xinguo and Wu, Harry X and Southerton, Simon G},
	month = dec,
	year = {2011},
	pages = {480},
}

@article{mishra_expression_2011,
	title = {Expression, purification, crystallization and preliminary {X}-ray crystallographic studies of alkyl hydroperoxide reductase ({AhpC}) from the cyanobacterium \textit{{Anabaena}} sp. {PCC} 7120},
	volume = {67},
	issn = {1744-3091},
	url = {http://scripts.iucr.org/cgi-bin/paper?S1744309111025747},
	doi = {10/djxscc},
	number = {10},
	urldate = {2021-06-08},
	journal = {Acta Crystallographica Section F Structural Biology and Crystallization Communications},
	author = {Mishra, Yogesh and Hall, Michael and Chaurasia, Neha and Rai, Lal Chand and Jansson, Stefan and Schröder, Wolfgang P. and Sauer, Uwe H.},
	month = oct,
	year = {2011},
	pages = {1203--1206},
}

@article{kleinevehn_recycling_2011,
	title = {Recycling, clustering, and endocytosis jointly maintain {PIN} auxin carrier polarity at the plasma membrane},
	volume = {7},
	issn = {1744-4292, 1744-4292},
	url = {https://onlinelibrary.wiley.com/doi/10.1038/msb.2011.72},
	doi = {10/d9hncd},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Molecular Systems Biology},
	author = {Kleine‐Vehn, Jürgen and Wabnik, Krzysztof and Martinière, Alexandre and Łangowski, Łukasz and Willig, Katrin and Naramoto, Satoshi and Leitner, Johannes and Tanaka, Hirokazu and Jakobs, Stefan and Robert, Stéphanie and Luschnig, Christian and Govaerts, Willy and W Hell, Stefan and Runions, John and Friml, Jiří},
	month = jan,
	year = {2011},
	pages = {540},
}

@article{kleczkowski_common_2011,
	title = {A common structural blueprint for plant {UDP}-sugar-producing pyrophosphorylases},
	volume = {439},
	issn = {0264-6021, 1470-8728},
	url = {https://portlandpress.com/biochemj/article/439/3/375/45641/A-common-structural-blueprint-for-plant},
	doi = {10/dm53gk},
	abstract = {Plant pyrophosphorylases that are capable of producing UDP-sugars, key precursors for glycosylation reactions, include UDP-glucose pyrophosphorylases (A- and B-type), UDP-sugar pyrophosphorylase and UDP-N-acetylglucosamine pyrophosphorylase. Although not sharing significant homology at the amino acid sequence level, the proteins share a common structural blueprint. Their structures are characterized by the presence of the Rossmann fold in the central (catalytic) domain linked to enzyme-specific N-terminal and C-terminal domains, which may play regulatory functions. Molecular mobility between these domains plays an important role in substrate binding and catalysis. Evolutionary relationships and the role of (de)oligomerization as a regulatory mechanism are discussed.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Biochemical Journal},
	author = {Kleczkowski, Leszek A. and Geisler, Matt and Fitzek, Elisabeth and Wilczynska, Malgorzata},
	month = nov,
	year = {2011},
	pages = {375--381},
}

Plant pyrophosphorylases that are capable of producing UDP-sugars, key precursors for glycosylation reactions, include UDP-glucose pyrophosphorylases (A- and B-type), UDP-sugar pyrophosphorylase and UDP-N-acetylglucosamine pyrophosphorylase. Although not sharing significant homology at the amino acid sequence level, the proteins share a common structural blueprint. Their structures are characterized by the presence of the Rossmann fold in the central (catalytic) domain linked to enzyme-specific N-terminal and C-terminal domains, which may play regulatory functions. Molecular mobility between these domains plays an important role in substrate binding and catalysis. Evolutionary relationships and the role of (de)oligomerization as a regulatory mechanism are discussed.

@article{lundberg_crystal_2011,
	title = {Crystal structure of the {TL29} protein from {Arabidopsis} thaliana: {An} {APX} homolog without peroxidase activity},
	volume = {176},
	issn = {10478477},
	shorttitle = {Crystal structure of the {TL29} protein from {Arabidopsis} thaliana},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1047847711001973},
	doi = {10/d9g2fv},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Journal of Structural Biology},
	author = {Lundberg, Erik and Storm, Patrik and Schröder, Wolfgang P. and Funk, Christiane},
	month = oct,
	year = {2011},
	pages = {24--31},
}

@incollection{jarvis_preparation_2011,
	address = {Totowa, NJ},
	title = {Preparation of {Stroma}, {Thylakoid} {Membrane}, and {Lumen} {Fractions} from {Arabidopsis} thaliana {Chloroplasts} for {Proteomic} {Analysis}},
	volume = {775},
	isbn = {978-1-61779-236-6 978-1-61779-237-3},
	url = {http://link.springer.com/10.1007/978-1-61779-237-3_11},
	urldate = {2021-06-08},
	booktitle = {Chloroplast {Research} in {Arabidopsis}},
	publisher = {Humana Press},
	author = {Hall, Michael and Mishra, Yogesh and Schröder, Wolfgang P.},
	editor = {Jarvis, R. Paul},
	year = {2011},
	doi = {10.1007/978-1-61779-237-3_11},
	note = {Series Title: Methods in Molecular Biology},
	pages = {207--222},
}

@article{bernhardsson_molecular_2011,
	title = {Molecular {Population} {Genetics} of {Elicitor}-{Induced} {Resistance} {Genes} in {European} {Aspen} ({Populus} tremula {L}., {Salicaceae})},
	volume = {6},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0024867},
	doi = {10/chthqd},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Bernhardsson, Carolina and Ingvarsson, Pär K.},
	editor = {Ortiz-Barrientos, Daniel},
	month = sep,
	year = {2011},
	pages = {e24867},
}

@article{floran_organelle_2011,
	title = {Organelle {Genetic} {Diversity} and {Phylogeography} of {Scots} {Pine} ({Pinus} sylvestris {L}.)},
	volume = {39},
	doi = {10/gg32mz},
	abstract = {The paper reviews the present knowledge of Scots pine (Pinus sylvestris L.) diversity, historical and geographical distribution, based on mitochondrial and chloroplast DNA data. The observed differences in the estimates of genetic differentiation between different types of genomes suggest that both pollen and seed contribute significantly to gene flow within species. Organelles' diversity represents an important criterion which could be later applied in planning for future forest management and breeding through a better understanding of adaptation strategies of different Scots pine haplotypes. This analysis would provide valuable references when facing current day problems with climate change, species adaptation, and loss of forest with negative effects on biodiversity. Research on organelles' diversity could lead to important practical applications in areas such as traceability and eco-certification of forest products, and the identification of plant populations for conservation. Based on the results from earlier investigations, Scots pine in Europe can be divided into at least three evolutionary units (Spain, northern/central Europe and northern Fennoscandia), each with a different origin after glaciations. However, it must be emphasized that these interpretations are preliminary and further mitochondrial and chloroplast DNA data need to be analyzed in conjunction with evidence from pollen and fossil analysis.},
	journal = {Notulae Botanicae Horti Agrobotanici Cluj-Napoca},
	author = {Floran, Valentina and Sestras, Radu and Garcia Gil, Rosario},
	month = may,
	year = {2011},
	pages = {317--322},
}

The paper reviews the present knowledge of Scots pine (Pinus sylvestris L.) diversity, historical and geographical distribution, based on mitochondrial and chloroplast DNA data. The observed differences in the estimates of genetic differentiation between different types of genomes suggest that both pollen and seed contribute significantly to gene flow within species. Organelles' diversity represents an important criterion which could be later applied in planning for future forest management and breeding through a better understanding of adaptation strategies of different Scots pine haplotypes. This analysis would provide valuable references when facing current day problems with climate change, species adaptation, and loss of forest with negative effects on biodiversity. Research on organelles' diversity could lead to important practical applications in areas such as traceability and eco-certification of forest products, and the identification of plant populations for conservation. Based on the results from earlier investigations, Scots pine in Europe can be divided into at least three evolutionary units (Spain, northern/central Europe and northern Fennoscandia), each with a different origin after glaciations. However, it must be emphasized that these interpretations are preliminary and further mitochondrial and chloroplast DNA data need to be analyzed in conjunction with evidence from pollen and fossil analysis.

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

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

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

@article{igamberdiev_magnesium_2011,
	title = {Magnesium and cell energetics in plants under anoxia},
	volume = {437},
	issn = {0264-6021, 1470-8728},
	url = {https://portlandpress.com/biochemj/article/437/3/373/45860/Magnesium-and-cell-energetics-in-plants-under},
	doi = {10/b5db7d},
	abstract = {Stress conditions (e.g. anoxia) frequently result in a decrease of [ATP] and in an increase of [ADP] and [AMP], with a concomitant increase of [Mg2+] and other cations, e.g. Ca2+. The elevation of [Mg2+] is linked to the shift in the apparent equilibrium of adenylate kinase. As a result, enzymes that use Mg2+ as a cofactor are activated, Ca2+ activates calcium-dependent signalling pathways, and PPi can serve as an alternative energy source in its active form of MgPPi or Mg2PPi. Under anoxic conditions in plants, an important source of PPi may come as a result of combined reactions of PK (pyruvate kinase) and PPDK (pyruvate, phosphate dikinase). The PPi formed in the PPDK/PK cycle ignites glycolysis in conditions of low [ATP] by involving PPi-dependent reactions. This saves ATP and makes metabolism under stress conditions more energy efficient.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Biochemical Journal},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = aug,
	year = {2011},
	pages = {373--379},
}

Stress conditions (e.g. anoxia) frequently result in a decrease of [ATP] and in an increase of [ADP] and [AMP], with a concomitant increase of [Mg2+] and other cations, e.g. Ca2+. The elevation of [Mg2+] is linked to the shift in the apparent equilibrium of adenylate kinase. As a result, enzymes that use Mg2+ as a cofactor are activated, Ca2+ activates calcium-dependent signalling pathways, and PPi can serve as an alternative energy source in its active form of MgPPi or Mg2PPi. Under anoxic conditions in plants, an important source of PPi may come as a result of combined reactions of PK (pyruvate kinase) and PPDK (pyruvate, phosphate dikinase). The PPi formed in the PPDK/PK cycle ignites glycolysis in conditions of low [ATP] by involving PPi-dependent reactions. This saves ATP and makes metabolism under stress conditions more energy efficient.

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

@article{saavedra_pipks_2011,
	title = {{PIPKs} are essential for rhizoid elongation and caulonemal cell development in the moss {Physcomitrella} patens: {Physiological} role of {PpPIPKs}},
	volume = {67},
	issn = {09607412},
	shorttitle = {{PIPKs} are essential for rhizoid elongation and caulonemal cell development in the moss {Physcomitrella} patens},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2011.04623.x},
	doi = {10/c2ncv5},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Saavedra, Laura and Balbi, Virginia and Lerche, Jennifer and Mikami, Koji and Heilmann, Ingo and Sommarin, Marianne},
	month = aug,
	year = {2011},
	pages = {635--647},
}

@article{gundale_bryophytes_2011,
	title = {Bryophytes attenuate anthropogenic nitrogen inputs in boreal forests: {BRYOPHYTES} {ATTENUATE} {NITROGEN} {DEPOSITION}},
	volume = {17},
	issn = {13541013},
	shorttitle = {Bryophytes attenuate anthropogenic nitrogen inputs in boreal forests},
	url = {http://doi.wiley.com/10.1111/j.1365-2486.2011.02407.x},
	doi = {10/b8mkq2},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Global Change Biology},
	author = {Gundale, Michael J. and Deluca, Thomas H. and Nordin, Annika},
	month = aug,
	year = {2011},
	pages = {2743--2753},
}

@article{granlund_clustering_2011,
	title = {Clustering of {MS} spectra for improved protein identification rate and screening for protein variants and modifications by {MALDI}-{MS}/{MS}},
	volume = {74},
	issn = {18743919},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1874391911001503},
	doi = {10/cmvvfc},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Journal of Proteomics},
	author = {Granlund, Irene and Kieselbach, Thomas and Alm, Rikard and Schröder, Wolfgang P. and Emanuelsson, Cecilia},
	month = aug,
	year = {2011},
	pages = {1190--1200},
}

@article{aden_extraordinary_2011,
	title = {Extraordinary μs–ms backbone dynamics in {Arabidopsis} thaliana peroxiredoxin {Q}},
	volume = {1814},
	issn = {15709639},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1570963911002068},
	doi = {10/c5xcjf},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics},
	author = {Ådén, Jörgen and Wallgren, Marcus and Storm, Patrik and Weise, Christoph F. and Christiansen, Alexander and Schröder, Wolfgang P. and Funk, Christiane and Wolf-Watz, Magnus},
	month = dec,
	year = {2011},
	pages = {1880--1890},
}

@article{pop_auxin_2011,
	title = {Auxin {Control} in the {Formation} of {Adventitious} {Roots}},
	volume = {39},
	doi = {10/gc8s37},
	abstract = {Adventitious rooting is a complex process and a key step in the vegetative propagation of economically important woody, horticultural and agricultural species, playing an important role in the successful production of elite clones. The formation of adventitious roots is a quantitative genetic trait regulated by both environmental and endogenous factors. Among phytohormones, auxin plays an essential role in regulating roots development and it has been shown to be intimately involved in the process of adventitious rooting. Great progress has been made in elucidating the auxin-induced genes and auxin signaling pathway, especially in auxin response Aux/IAA and Auxin Response Factor gene families. Although some important aspects of adventitious and lateral rooting signaling have been revealed, the intricate signaling network remains poorly understood. This review summarizes some of the current knowledge on the physiological aspects of adventitious root formation and highlights the recent progress made in the identification of putative molecular players involved in the control of adventitious rooting. Despite much has been discovered regarding the effects and regulation of auxins on plant growth since the Darwin experiments, there is much that remains unknown.},
	journal = {Notulae Botanicae Horti Agrobotanici Cluj-Napoca},
	author = {Pop, Tiberia and Pamfil, Doru and Bellini, Catherine},
	month = jun,
	year = {2011},
	pages = {307--316},
}

Adventitious rooting is a complex process and a key step in the vegetative propagation of economically important woody, horticultural and agricultural species, playing an important role in the successful production of elite clones. The formation of adventitious roots is a quantitative genetic trait regulated by both environmental and endogenous factors. Among phytohormones, auxin plays an essential role in regulating roots development and it has been shown to be intimately involved in the process of adventitious rooting. Great progress has been made in elucidating the auxin-induced genes and auxin signaling pathway, especially in auxin response Aux/IAA and Auxin Response Factor gene families. Although some important aspects of adventitious and lateral rooting signaling have been revealed, the intricate signaling network remains poorly understood. This review summarizes some of the current knowledge on the physiological aspects of adventitious root formation and highlights the recent progress made in the identification of putative molecular players involved in the control of adventitious rooting. Despite much has been discovered regarding the effects and regulation of auxins on plant growth since the Darwin experiments, there is much that remains unknown.

@article{shitov_carbonic_2011,
	title = {A carbonic anhydrase inhibitor induces bicarbonate-reversible suppression of electron transfer in pea photosystem 2 membrane fragments},
	volume = {104},
	issn = {10111344},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1011134411000935},
	doi = {10/cjmg4d},
	language = {en},
	number = {1-2},
	urldate = {2021-06-08},
	journal = {Journal of Photochemistry and Photobiology B: Biology},
	author = {Shitov, A.V. and Zharmukhamedov, S.K. and Shutova, T.V. and Allakhverdiev, S.I. and Samuelsson, G. and Klimov, V.V.},
	month = jul,
	year = {2011},
	pages = {366--371},
}

@article{barberon_monoubiquitin-dependent_2011,
	title = {Monoubiquitin-dependent endocytosis of the {IRON}-{REGULATED} {TRANSPORTER} 1 ({IRT1}) transporter controls iron uptake in plants},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1100659108},
	doi = {10/dw2prg},
	language = {en},
	number = {32},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Barberon, Marie and Zelazny, Enric and Robert, Stéphanie and Conéjéro, Geneviève and Curie, Cathy and Friml, Jìří and Vert, Grégory},
	month = aug,
	year = {2011},
	pages = {E450--E458},
}

@article{aksmann_mechanism_2011,
	title = {The mechanism of anthracene interaction with photosynthetic apparatus: {A} study using intact cells, thylakoid membranes and {PS} {II} complexes isolated from {Chlamydomonas} reinhardtii},
	volume = {104},
	issn = {0166445X},
	shorttitle = {The mechanism of anthracene interaction with photosynthetic apparatus},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0166445X11001226},
	doi = {10/ffzwwr},
	language = {en},
	number = {3-4},
	urldate = {2021-06-08},
	journal = {Aquatic Toxicology},
	author = {Aksmann, Anna and Shutova, Tatiana and Samuelsson, Göran and Tukaj, Zbigniew},
	month = aug,
	year = {2011},
	pages = {205--210},
}

@article{olsson_ultra-structural_2011,
	title = {Ultra-structural organisation of cell wall polymers in normal and tension wood of aspen revealed by polarisation {FTIR} microspectroscopy},
	volume = {233},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-011-1384-1},
	doi = {10/bvrsnj},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Planta},
	author = {Olsson, Anne-Mari and Bjurhager, Ingela and Gerber, Lorenz and Sundberg, Björn and Salmén, Lennart},
	month = jun,
	year = {2011},
	pages = {1277--1286},
}

@article{inselsbacher_potential_2011,
	title = {The potential of microdialysis to monitor organic and inorganic nitrogen compounds in soil},
	volume = {43},
	issn = {00380717},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0038071711001167},
	doi = {10/b7vf8p},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Soil Biology and Biochemistry},
	author = {Inselsbacher, Erich and Öhlund, Jonas and Jämtgård, Sandra and Huss-Danell, Kerstin and Näsholm, Torgny},
	month = jun,
	year = {2011},
	pages = {1321--1332},
}

@article{funk_high_2011,
	title = {High light stress and the one-helix {LHC}-like proteins of the cryptophyte {Guillardia} theta},
	volume = {1807},
	issn = {00052728},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272811000624},
	doi = {10/brwtzt},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Funk, Christiane and Alami, Meriem and Tibiletti, Tania and Green, Beverley R.},
	month = jul,
	year = {2011},
	pages = {841--846},
}

@article{gorzsas_cell-specific_2011,
	title = {Cell-specific chemotyping and multivariate imaging by combined {FT}-{IR} microspectroscopy and orthogonal projections to latent structures ({OPLS}) analysis reveals the chemical landscape of secondary xylem: {The} chemical landscape of secondary xylem},
	volume = {66},
	issn = {09607412},
	shorttitle = {Cell-specific chemotyping and multivariate imaging by combined {FT}-{IR} microspectroscopy and orthogonal projections to latent structures ({OPLS}) analysis reveals the chemical landscape of secondary xylem},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2011.04542.x},
	doi = {10/cr7zsk},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Gorzsás, András and Stenlund, Hans and Persson, Per and Trygg, Johan and Sundberg, Björn},
	month = jun,
	year = {2011},
	pages = {903--914},
}

@article{li_transcriptome_2011,
	title = {Transcriptome profiling of wood maturation in {Pinus} radiata identifies differentially expressed genes with implications in juvenile and mature wood variation},
	volume = {487},
	issn = {03781119},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378111911003659},
	doi = {10/dc32cg},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Gene},
	author = {Li, Xinguo and Wu, Harry X. and Southerton, Simon G.},
	month = nov,
	year = {2011},
	pages = {62--71},
}

@article{pesquet_mechanisms_2011,
	title = {Mechanisms for shaping, orienting, positioning and patterning plant secondary cell walls},
	volume = {6},
	doi = {10/fqj787},
	abstract = {Xylem vessels are cells that develop a specifically ornamented secondary cell wall to ensure their vascular function, conferring both structural strength and impermeability. Further plasticity is given to these vascular cells by a range of different patterns described by their secondary cell walls that-as for the growth of all plant organs-are developmentally regulated. Microtubules and their associated proteins, named MAPs, are essential to define the shape, the orientation, the position and the overall pattern of these secondary cell walls. Key actors in this process are the land-plant specific MAP70 proteins which not only allow the secondary cell wall to be positioned at the cell cortex but also determine the overall pattern described by xylem vessel secondary cell walls.},
	journal = {Plant signaling \& behavior},
	author = {Pesquet, Edouard and Korolev, Andrey and Calder, Grant and Lloyd, Clive},
	month = jun,
	year = {2011},
	pages = {843--9},
}

Xylem vessels are cells that develop a specifically ornamented secondary cell wall to ensure their vascular function, conferring both structural strength and impermeability. Further plasticity is given to these vascular cells by a range of different patterns described by their secondary cell walls that-as for the growth of all plant organs-are developmentally regulated. Microtubules and their associated proteins, named MAPs, are essential to define the shape, the orientation, the position and the overall pattern of these secondary cell walls. Key actors in this process are the land-plant specific MAP70 proteins which not only allow the secondary cell wall to be positioned at the cell cortex but also determine the overall pattern described by xylem vessel secondary cell walls.

@article{jones_auxin_2011,
	title = {Auxin and cytokinin regulate each other’s levels via a metabolic feedback loop},
	volume = {6},
	issn = {1559-2324},
	url = {http://www.tandfonline.com/doi/abs/10.4161/psb.6.6.15323},
	doi = {10/bdn8kg},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Plant Signaling \& Behavior},
	author = {Jones, Brian and Ljung, Karin},
	month = jun,
	year = {2011},
	pages = {901--904},
}

@article{zhang_arabidopsis_2011,
	title = {Arabidopsis as a model for wood formation},
	volume = {22},
	issn = {09581669},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0958166910002260},
	doi = {10/bp3824},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Current Opinion in Biotechnology},
	author = {Zhang, Jing and Elo, Annakaisa and Helariutta, Ykä},
	month = apr,
	year = {2011},
	pages = {293--299},
}

@article{kitakura_clathrin_2011,
	title = {Clathrin {Mediates} {Endocytosis} and {Polar} {Distribution} of {PIN} {Auxin} {Transporters} in \textit{{Arabidopsis}}},
	volume = {23},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/23/5/1920/6097062},
	doi = {10/bdwh3s},
	abstract = {Abstract
            Endocytosis is a crucial mechanism by which eukaryotic cells internalize extracellular and plasma membrane material, and it is required for a multitude of cellular and developmental processes in unicellular and multicellular organisms. In animals and yeast, the best characterized pathway for endocytosis depends on the function of the vesicle coat protein clathrin. Clathrin-mediated endocytosis has recently been demonstrated also in plant cells, but its physiological and developmental roles remain unclear. Here, we assessed the roles of the clathrin-mediated mechanism of endocytosis in plants by genetic means. We interfered with clathrin heavy chain (CHC) function through mutants and dominant-negative approaches in Arabidopsis thaliana and established tools to manipulate clathrin function in a cell type–specific manner. The chc2 single mutants and dominant-negative CHC1 (HUB) transgenic lines were defective in bulk endocytosis as well as in internalization of prominent plasma membrane proteins. Interference with clathrin-mediated endocytosis led to defects in constitutive endocytic recycling of PIN auxin transporters and their polar distribution in embryos and roots. Consistent with this, these lines had altered auxin distribution patterns and associated auxin transport-related phenotypes, such as aberrant embryo patterning, imperfect cotyledon specification, agravitropic growth, and impaired lateral root organogenesis. Together, these data demonstrate a fundamental role for clathrin function in cell polarity, growth, patterning, and organogenesis in plants.},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Kitakura, Saeko and Vanneste, Steffen and Robert, Stéphanie and Löfke, Christian and Teichmann, Thomas and Tanaka, Hirokazu and Friml, Jiří},
	month = may,
	year = {2011},
	pages = {1920--1931},
}

Abstract Endocytosis is a crucial mechanism by which eukaryotic cells internalize extracellular and plasma membrane material, and it is required for a multitude of cellular and developmental processes in unicellular and multicellular organisms. In animals and yeast, the best characterized pathway for endocytosis depends on the function of the vesicle coat protein clathrin. Clathrin-mediated endocytosis has recently been demonstrated also in plant cells, but its physiological and developmental roles remain unclear. Here, we assessed the roles of the clathrin-mediated mechanism of endocytosis in plants by genetic means. We interfered with clathrin heavy chain (CHC) function through mutants and dominant-negative approaches in Arabidopsis thaliana and established tools to manipulate clathrin function in a cell type–specific manner. The chc2 single mutants and dominant-negative CHC1 (HUB) transgenic lines were defective in bulk endocytosis as well as in internalization of prominent plasma membrane proteins. Interference with clathrin-mediated endocytosis led to defects in constitutive endocytic recycling of PIN auxin transporters and their polar distribution in embryos and roots. Consistent with this, these lines had altered auxin distribution patterns and associated auxin transport-related phenotypes, such as aberrant embryo patterning, imperfect cotyledon specification, agravitropic growth, and impaired lateral root organogenesis. Together, these data demonstrate a fundamental role for clathrin function in cell polarity, growth, patterning, and organogenesis in plants.

@article{shimono_spatial_2011,
	title = {Spatial variation in local pollen flow and mating success in a {Picea} abies clone archive and their implications for a novel “breeding without breeding” strategy},
	volume = {7},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-010-0351-5},
	doi = {10/bvmxzx},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Shimono, Ayako and Wang, Xiao-Ru and Torimaru, Takeshi and Lindgren, Dag and Karlsson, Bo},
	month = jun,
	year = {2011},
	pages = {499--509},
}

@article{palm_cisplatin_2011,
	title = {Cisplatin binds human copper chaperone {Atox1} and promotes unfolding in vitro},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1012899108},
	doi = {10/cwg7dm},
	language = {en},
	number = {17},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Palm, M. E. and Weise, C. F. and Lundin, C. and Wingsle, G. and Nygren, Y. and Bjorn, E. and Naredi, P. and Wolf-Watz, M. and Wittung-Stafshede, P.},
	month = apr,
	year = {2011},
	pages = {6951--6956},
}

@article{hedwall_decreased_2011,
	title = {Decreased variation of forest understory vegetation is an effect of fertilisation in young stands of {Picea} abies},
	volume = {26},
	issn = {0282-7581},
	url = {https://doi.org/10.1080/02827581.2011.564397},
	doi = {10.1080/02827581.2011.564397},
	abstract = {The substitution of fossil fuels with biofuels to mitigate climate change has caused increased interest in enhancing forest biomass production through fertilisation. We investigated the effects of different fertilisation frequencies on the diversity of understory vegetation in young stands of Picea abies on five sites distributed in regions in the middle and south of Sweden. The treatments included fertilisation conducted annually, every second year or every third year, as well as an unfertilised control. A lower number of vascular plant species was observed on fertilised plots than on control plots, whereas the number of bryophyte species remained unchanged. Fertilised plots also showed a lower variance in species composition and a lower Shannon's diversity index than unfertilised plots. Fertilised plots were more similar to each other than unfertilised plots were to each other over the geographical range. The two most intensive fertilisation treatments had similar effects on the vegetation, whereas the effects of fertilisation conducted every third year were not as substantial. However, the treatment in which fertilisation occurred every third year implies a lower stem-wood production, and there is little knowledge of the long-term differences between the treatments. We conclude that fertilisation of young stands will lead to long-term changes in understory vegetation at the stand scale, whereas the effects at the landscape level are still largely unknown.},
	number = {S11},
	urldate = {2021-06-08},
	journal = {Scandinavian Journal of Forest Research},
	author = {Hedwall, Per-Ola and Brunet, Jörg and Nordin, Annika and Bergh, Johan},
	month = jun,
	year = {2011},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/02827581.2011.564397},
	keywords = {Norway spruce, Plant diversity, bryophytes, lichens, nitrogen},
	pages = {46--55},
}

The substitution of fossil fuels with biofuels to mitigate climate change has caused increased interest in enhancing forest biomass production through fertilisation. We investigated the effects of different fertilisation frequencies on the diversity of understory vegetation in young stands of Picea abies on five sites distributed in regions in the middle and south of Sweden. The treatments included fertilisation conducted annually, every second year or every third year, as well as an unfertilised control. A lower number of vascular plant species was observed on fertilised plots than on control plots, whereas the number of bryophyte species remained unchanged. Fertilised plots also showed a lower variance in species composition and a lower Shannon's diversity index than unfertilised plots. Fertilised plots were more similar to each other than unfertilised plots were to each other over the geographical range. The two most intensive fertilisation treatments had similar effects on the vegetation, whereas the effects of fertilisation conducted every third year were not as substantial. However, the treatment in which fertilisation occurred every third year implies a lower stem-wood production, and there is little knowledge of the long-term differences between the treatments. We conclude that fertilisation of young stands will lead to long-term changes in understory vegetation at the stand scale, whereas the effects at the landscape level are still largely unknown.

@article{elfving_arabidopsis_2011,
	title = {The {Arabidopsis} thaliana {Med25} mediator subunit integrates environmental cues to control plant development},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/108/20/8245},
	doi = {10.1073/pnas.1002981108},
	abstract = {Development in plants is controlled by abiotic environmental cues such as day length, light quality, temperature, drought, and salinity. These signals are sensed by a variety of systems and transmitted by different signal transduction pathways. Ultimately, these pathways are integrated to control expression of specific target genes, which encode proteins that regulate development and differentiation. The molecular mechanisms for such integration have remained elusive. We here show that a linear 130-amino-acids-long sequence in the Med25 subunit of the Arabidopsis thaliana Mediator is a common target for the drought response element binding protein 2A, zinc finger homeodomain 1, and Myb-like transcription factors which are involved in different stress response pathways. In addition, our results show that Med25 together with drought response element binding protein 2A also function in repression of PhyB-mediated light signaling and thus integrate signals from different regulatory pathways.},
	language = {en},
	number = {20},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Elfving, Nils and Davoine, Céline and Benlloch, Reyes and Blomberg, Jeanette and Brännström, Kristoffer and Müller, Dörte and Nilsson, Anders and Ulfstedt, Mikael and Ronne, Hans and Wingsle, Gunnar and Nilsson, Ove and Björklund, Stefan},
	month = may,
	year = {2011},
	pmid = {21536906},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {RNA polymerase II, phytochrome flowering time 1, transcriptional regulation},
	pages = {8245--8250},
}

Development in plants is controlled by abiotic environmental cues such as day length, light quality, temperature, drought, and salinity. These signals are sensed by a variety of systems and transmitted by different signal transduction pathways. Ultimately, these pathways are integrated to control expression of specific target genes, which encode proteins that regulate development and differentiation. The molecular mechanisms for such integration have remained elusive. We here show that a linear 130-amino-acids-long sequence in the Med25 subunit of the Arabidopsis thaliana Mediator is a common target for the drought response element binding protein 2A, zinc finger homeodomain 1, and Myb-like transcription factors which are involved in different stress response pathways. In addition, our results show that Med25 together with drought response element binding protein 2A also function in repression of PhyB-mediated light signaling and thus integrate signals from different regulatory pathways.

@article{hernandez-prieto_small_2011,
	title = {The small {CAB}-like proteins of the cyanobacterium {Synechocystis} sp. {PCC} 6803: {Their} involvement in chlorophyll biogenesis for {Photosystem} {II}},
	volume = {1807},
	issn = {00052728},
	shorttitle = {The small {CAB}-like proteins of the cyanobacterium {Synechocystis} sp. {PCC} 6803},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272811001083},
	doi = {10.1016/j.bbabio.2011.05.002},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Hernandez-Prieto, Miguel A. and Tibiletti, Tania and Abasova, Leyla and Kirilovsky, Diana and Vass, Imre and Funk, Christiane},
	month = sep,
	year = {2011},
	pages = {1143--1151},
}

@article{cambui_patterns_2011,
	title = {Patterns of {Plant} {Biomass} {Partitioning} {Depend} on {Nitrogen} {Source}},
	volume = {6},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0019211},
	doi = {10/d3w26r},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Cambui, Camila Aguetoni and Svennerstam, Henrik and Gruffman, Linda and Nordin, Annika and Ganeteg, Ulrika and Näsholm, Torgny},
	editor = {Weigelt, Alexandra},
	month = apr,
	year = {2011},
	pages = {e19211},
}

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

@article{kleczkowski_udp-sugar_2011,
	title = {{UDP}-{Sugar} {Pyrophosphorylase}: {A} {New} {Old} {Mechanism} for {Sugar} {Activation}},
	volume = {156},
	issn = {1532-2548},
	shorttitle = {{UDP}-{Sugar} {Pyrophosphorylase}},
	url = {https://academic.oup.com/plphys/article/156/1/3/6111433},
	doi = {10/dd7jxj},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Kleczkowski, Leszek A. and Decker, Daniel and Wilczynska, Malgorzata},
	month = may,
	year = {2011},
	pages = {3--10},
}

@article{lindahl_disulfide_2011,
	title = {The {Disulfide} {Proteome} and {Other} {Reactive} {Cysteine} {Proteomes}: {Analysis} and {Functional} {Significance}},
	volume = {14},
	issn = {1523-0864, 1557-7716},
	shorttitle = {The {Disulfide} {Proteome} and {Other} {Reactive} {Cysteine} {Proteomes}},
	url = {http://www.liebertpub.com/doi/10.1089/ars.2010.3551},
	doi = {10/cqjjqd},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {Antioxidants \& Redox Signaling},
	author = {Lindahl, Marika and Mata-Cabana, Alejandro and Kieselbach, Thomas},
	month = jun,
	year = {2011},
	pages = {2581--2642},
}

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

@article{selstam_relationship_2011,
	title = {The relationship between different spectral forms of the protochlorophyllide oxidoreductase complex and the structural organisation of prolamellar bodies isolated from {Zea} mays},
	volume = {108},
	issn = {0166-8595, 1573-5079},
	url = {http://link.springer.com/10.1007/s11120-011-9653-1},
	doi = {10/dbw6m6},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Photosynthesis Research},
	author = {Selstam, Eva and Brain, Anthony P. R. and Williams, W. Patrick},
	month = may,
	year = {2011},
	pages = {47--59},
}

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

Beyond their metabolic roles, sugars can also act as messengers in signal transduction. Trehalose, a sugar found in many species of plants and animals, is a non-reducing disaccharide composed of two glucose moieties. Its synthesis in plants is a two-step process, involving the production of trehalose-6-phosphate (T6P) catalyzed by trehalose-6-phosphate synthase (TPS) and its consecutive dephosphorylation to trehalose, catalyzed by trehalose-6-phosphate phosphatase (TPP). T6P has recently emerged as an important signaling metabolite, regulating carbon assimilation and sugar status in plants. In addition, T6P has also been demonstrated to play an essential role in plant development. This review recapitulates the recent advances we have made in understanding the role of T6P in coordinating diverse metabolic and developmental processes.

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

Plants undergo a major physiological change as they transition from vegetative growth to reproductive development. This transition is a result of responses to various endogenous and exogenous signals that later integrate to result in flowering. Five genetically defined pathways have been identified that control flowering. The vernalization pathway refers to the acceleration of flowering on exposure to a long period of cold. The photoperiod pathway refers to regulation of flowering in response to day length and quality of light perceived. The gibberellin pathway refers to the requirement of gibberellic acid for normal flowering patterns. The autonomous pathway refers to endogenous regulators that are independent of the photoperiod and gibberellin pathways. Most recently, an endogenous pathway that adds plant age to the control of flowering time has been described. The molecular mechanisms of these pathways have been studied extensively in Arabidopsis thaliana and several other flowering plants.

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

Plant development progresses through distinct phases: vegetative growth, followed by a reproductive phase and eventually seed set and senescence. The transitions between these phases are controlled by distinct genetic circuits that integrate endogenous and environmental cues. In recent years, however, it has become evident that the genetic networks that underlie these phase transitions share some common factors. Here, we review recent advances in the field of plant phase transitions, highlighting the role of two microRNAs - miR156 and miR172 - and their respective targets during these transitions. In addition, we discuss the evolutionary conservation of the functions of these miRNAs in regulating the control of plant developmental phase transitions.

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

Despite great advances in sequencing technologies, generating functional information for nonmodel organisms remains a challenge. One solution lies in an improved ability to predict genetic circuits based on primary DNA sequence in combination with detailed knowledge of regulatory proteins that have been characterized in model species. Here, we focus on the LEAFY (LFY) transcription factor, a conserved master regulator of floral development. Starting with biochemical and structural information, we built a biophysical model describing LFY DNA binding specificity in vitro that accurately predicts in vivo LFY binding sites in the Arabidopsis thaliana genome. Applying the model to other plant species, we could follow the evolution of the regulatory relationship between LFY and the AGAMOUS (AG) subfamily of MADS box genes and show that this link predates the divergence between monocots and eudicots. Remarkably, our model succeeds in detecting the connection between LFY and AG homologs despite extensive variation in binding sites. This demonstrates that the cis-element fluidity recently observed in animals also exists in plants, but the challenges it poses can be overcome with predictions grounded in a biophysical model. Therefore, our work opens new avenues to deduce the structure of regulatory networks from mere inspection of genomic sequences.

@article{greenham_retracted_2011,
	title = {{RETRACTED}: {The} {AFB4} {Auxin} {Receptor} {Is} a {Negative} {Regulator} of {Auxin} {Signaling} in {Seedlings}},
	volume = {21},
	issn = {09609822},
	shorttitle = {{RETRACTED}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S096098221100220X},
	doi = {10/fd497k},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Greenham, Katie and Santner, Aaron and Castillejo, Cristina and Mooney, Sutton and Sairanen, Ilkka and Ljung, Karin and Estelle, Mark},
	month = mar,
	year = {2011},
	pages = {520--525},
}

@article{johansson_partners_2011,
	title = {Partners in {Time}: {EARLY} {BIRD} {Associates} with {ZEITLUPE} and {Regulates} the {Speed} of the {Arabidopsis} {Clock}},
	volume = {155},
	issn = {1532-2548},
	shorttitle = {Partners in {Time}},
	url = {https://academic.oup.com/plphys/article/155/4/2108/6108867},
	doi = {10/bgh2rc},
	abstract = {Abstract
            The circadian clock of the model plant Arabidopsis (Arabidopsis thaliana) is made up of a complex series of interacting feedback loops whereby proteins regulate their own expression across day and night. early bird (ebi) is a circadian mutation that causes the clock to speed up: ebi plants have short circadian periods, early phase of clock gene expression, and are early flowering. We show that EBI associates with ZEITLUPE (ZTL), known to act in the plant clock as a posttranslational mediator of protein degradation. However, EBI is not degraded by its interaction with ZTL. Instead, ZTL counteracts the effect of EBI during the day and increases it at night, modulating the expression of key circadian components. The partnership of EBI with ZTL reveals a novel mechanism involved in controlling the complex transcription-translation feedback loops of the clock. This work highlights the importance of cross talk between the ubiquitination pathway and transcriptional control for regulation of the plant clock.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Johansson, Mikael and McWatters, Harriet G. and Bakó, László and Takata, Naoki and Gyula, Péter and Hall, Anthony and Somers, David E. and Millar, Andrew J. and Eriksson, Maria E.},
	month = mar,
	year = {2011},
	pages = {2108--2122},
}

Abstract The circadian clock of the model plant Arabidopsis (Arabidopsis thaliana) is made up of a complex series of interacting feedback loops whereby proteins regulate their own expression across day and night. early bird (ebi) is a circadian mutation that causes the clock to speed up: ebi plants have short circadian periods, early phase of clock gene expression, and are early flowering. We show that EBI associates with ZEITLUPE (ZTL), known to act in the plant clock as a posttranslational mediator of protein degradation. However, EBI is not degraded by its interaction with ZTL. Instead, ZTL counteracts the effect of EBI during the day and increases it at night, modulating the expression of key circadian components. The partnership of EBI with ZTL reveals a novel mechanism involved in controlling the complex transcription-translation feedback loops of the clock. This work highlights the importance of cross talk between the ubiquitination pathway and transcriptional control for regulation of the plant clock.

@article{svennerstam_transporters_2011,
	title = {Transporters in {Arabidopsis} roots mediating uptake of amino acids at naturally occurring concentrations},
	volume = {191},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2011.03699.x},
	doi = {10/d5k6tz},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Svennerstam, Henrik and Jämtgård, Sandra and Ahmad, Iftikhar and Huss‐Danell, Kerstin and Näsholm, Torgny and Ganeteg, Ulrika},
	month = jul,
	year = {2011},
	pages = {459--467},
}

@article{grebe_out_2011,
	title = {Out of the shade and into the light},
	volume = {13},
	issn = {1465-7392, 1476-4679},
	url = {http://www.nature.com/articles/ncb0411-347},
	doi = {10/cpvftj},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Nature Cell Biology},
	author = {Grebe, Markus},
	month = apr,
	year = {2011},
	pages = {347--349},
}

@article{rizzardi_tfl2lhp1_2011,
	title = {{TFL2}/{LHP1} is involved in auxin biosynthesis through positive regulation of {YUCCA} genes: {Positive} regulation of {YUCCA} genes by {TFL2}},
	volume = {65},
	issn = {09607412},
	shorttitle = {{TFL2}/{LHP1} is involved in auxin biosynthesis through positive regulation of {YUCCA} genes},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2010.04470.x},
	doi = {10/dr4w6d},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Rizzardi, Kristina and Landberg, Katarina and Nilsson, Lars and Ljung, Karin and Sundås-Larsson, Annika},
	month = mar,
	year = {2011},
	pages = {897--906},
}

@article{wagner_fitness_2011,
	title = {Fitness analyses of \textit{{Arabidopsis} thaliana} mutants depleted of {FtsH} metalloproteases and characterization of three {FtsH6} deletion mutants exposed to high light stress, senescence and chilling},
	volume = {191},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2011.03684.x},
	doi = {10/d4frq4},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Wagner, Raik and Aigner, Harald and Pružinská, Adriana and Jänkänpää, Hanna Johansson and Jansson, Stefan and Funk, Christiane},
	month = jul,
	year = {2011},
	pages = {449--458},
}

@article{lind_gene_2011,
	title = {{GENE} {FLOW} {AND} {SELECTION} {ON} {PHENOTYPIC} {PLASTICITY} {IN} {AN} {ISLAND} {SYSTEM} {OF} {RANA} {TEMPORARIA}: {GENE} {FLOW} {AND} {SELECTION} {ON} {PHENOTYPIC} {PLASTICITY}},
	volume = {65},
	issn = {00143820},
	shorttitle = {{GENE} {FLOW} {AND} {SELECTION} {ON} {PHENOTYPIC} {PLASTICITY} {IN} {AN} {ISLAND} {SYSTEM} {OF} {RANA} {TEMPORARIA}},
	url = {http://doi.wiley.com/10.1111/j.1558-5646.2010.01122.x},
	doi = {10/btddk8},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Evolution},
	author = {Lind, Martin I. and Ingvarsson, Pär K. and Johansson, Helena and Hall, David and Johansson, Frank},
	month = mar,
	year = {2011},
	pages = {684--697},
}

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

@article{cavel_plant-specific_2011,
	title = {A {Plant}-{Specific} {Transcription} {Factor} {IIB}-{Related} {Protein}, {pBRP2}, {Is} {Involved} in {Endosperm} {Growth} {Control}},
	volume = {6},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0017216},
	doi = {10/fpp395},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Cavel, Emilie and Pillot, Marion and Pontier, Dominique and Lahmy, Sylvie and Bies-Etheve, Natacha and Vega, Danielle and Grimanelli, Daniel and Lagrange, Thierry},
	editor = {Bendahmane, Mohammed},
	month = feb,
	year = {2011},
	pages = {e17216},
}

@article{raiola_pectin_2011,
	title = {Pectin {Methylesterase} {Is} {Induced} in \textit{{Arabidopsis}} upon {Infection} and {Is} {Necessary} for a {Successful} {Colonization} by {Necrotrophic} {Pathogens}},
	volume = {24},
	issn = {0894-0282, 1943-7706},
	url = {https://apsjournals.apsnet.org/doi/10.1094/MPMI-07-10-0157},
	doi = {10/fwswvk},
	abstract = {The ability of bacterial or fungal necrotrophs to produce enzymes capable of degrading pectin is often related to a successful initiation of the infective process. Pectin is synthesized in a highly methylesterified form and is subsequently de-esterified in muro by pectin methylesterase. De-esterification makes pectin more susceptible to the degradation by pectic enzymes such as endopolygalacturonases (endoPG) and pectate lyases secreted by necrotrophic pathogens during the first stages of infection. We show that, upon infection, Pectobacterium carotovorum and Botrytis cinerea induce in Arabidopsis a rapid expression of AtPME3 that acts as a susceptibility factor and is required for the initial colonization of the host tissue.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Molecular Plant-Microbe Interactions®},
	author = {Raiola, Alessandro and Lionetti, Vincenzo and Elmaghraby, Ibrahim and Immerzeel, Peter and Mellerowicz, Ewa J. and Salvi, Giovanni and Cervone, Felice and Bellincampi, Daniela},
	month = apr,
	year = {2011},
	pages = {432--440},
}

The ability of bacterial or fungal necrotrophs to produce enzymes capable of degrading pectin is often related to a successful initiation of the infective process. Pectin is synthesized in a highly methylesterified form and is subsequently de-esterified in muro by pectin methylesterase. De-esterification makes pectin more susceptible to the degradation by pectic enzymes such as endopolygalacturonases (endoPG) and pectate lyases secreted by necrotrophic pathogens during the first stages of infection. We show that, upon infection, Pectobacterium carotovorum and Botrytis cinerea induce in Arabidopsis a rapid expression of AtPME3 that acts as a susceptibility factor and is required for the initial colonization of the host tissue.

@article{boutte_fluorescent_2011,
	title = {Fluorescent in situ visualization of sterols in {Arabidopsis} roots},
	volume = {6},
	issn = {1754-2189, 1750-2799},
	url = {http://www.nature.com/articles/nprot.2011.323},
	doi = {10/d8nmps},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Nature Protocols},
	author = {Boutté, Yohann and Men, Shuzhen and Grebe, Markus},
	month = apr,
	year = {2011},
	pages = {446--456},
}

@article{li_fructose_2011,
	title = {Fructose sensitivity is suppressed in {Arabidopsis} by the transcription factor {ANAC089} lacking the membrane-bound domain},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/108/8/3436},
	doi = {10/bpszjb},
	abstract = {In living organisms sugars not only provide energy and carbon skeletons but also act as evolutionarily conserved signaling molecules. The three major soluble sugars in plants are sucrose, glucose, and fructose. Information on plant glucose and sucrose signaling is available, but to date no fructose-specific signaling pathway has been reported. In this study, sugar repression of seedling development was used to study fructose sensitivity in the Landsberg erecta (Ler)/Cape Verde Islands (Cvi) recombinant inbred line population, and eight fructose-sensing quantitative trait loci (QTLs) (FSQ1–8) were mapped. Among them, FSQ6 was confirmed to be a fructose-specific QTL by analyzing near-isogenic lines in which Cvi genomic fragments were introgressed in the Ler background. These results indicate the existence of a fructose-specific signaling pathway in Arabidopsis. Further analysis demonstrated that the FSQ6-associated fructose-signaling pathway functions independently of the hexokinase1 (HXK1) glucose sensor. Remarkably, fructose-specific FSQ6 downstream signaling interacts with abscisic acid (ABA)- and ethylene-signaling pathways, similar to HXK1-dependent glucose signaling. The Cvi allele of FSQ6 acts as a suppressor of fructose signaling. The FSQ6 gene was identified using map-based cloning approach, and FSQ6 was shown to encode the transcription factor gene Arabidopsis NAC (petunia No apical meristem and Arabidopsis transcription activation factor 1, 2 and Cup-shaped cotyledon 2) domain containing protein 89 (ANAC089). The Cvi allele of FSQ6/ANAC089 is a gain-of-function allele caused by a premature stop in the third exon of the gene. The truncated Cvi FSQ6/ANAC089 protein lacks a membrane association domain that is present in ANAC089 proteins from other Arabidopsis accessions. As a result, Cvi FSQ6/ANAC089 is constitutively active as a transcription factor in the nucleus.},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Li, Ping and Wind, Julia J. and Shi, Xiaoliang and Zhang, Honglei and Hanson, Johannes and Smeekens, Sjef C. and Teng, Sheng},
	month = feb,
	year = {2011},
	pmid = {21300879},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {fructose quantitative trait locus, map based cloning, natural variation, sugar signaling},
	pages = {3436--3441},
}

In living organisms sugars not only provide energy and carbon skeletons but also act as evolutionarily conserved signaling molecules. The three major soluble sugars in plants are sucrose, glucose, and fructose. Information on plant glucose and sucrose signaling is available, but to date no fructose-specific signaling pathway has been reported. In this study, sugar repression of seedling development was used to study fructose sensitivity in the Landsberg erecta (Ler)/Cape Verde Islands (Cvi) recombinant inbred line population, and eight fructose-sensing quantitative trait loci (QTLs) (FSQ1–8) were mapped. Among them, FSQ6 was confirmed to be a fructose-specific QTL by analyzing near-isogenic lines in which Cvi genomic fragments were introgressed in the Ler background. These results indicate the existence of a fructose-specific signaling pathway in Arabidopsis. Further analysis demonstrated that the FSQ6-associated fructose-signaling pathway functions independently of the hexokinase1 (HXK1) glucose sensor. Remarkably, fructose-specific FSQ6 downstream signaling interacts with abscisic acid (ABA)- and ethylene-signaling pathways, similar to HXK1-dependent glucose signaling. The Cvi allele of FSQ6 acts as a suppressor of fructose signaling. The FSQ6 gene was identified using map-based cloning approach, and FSQ6 was shown to encode the transcription factor gene Arabidopsis NAC (petunia No apical meristem and Arabidopsis transcription activation factor 1, 2 and Cup-shaped cotyledon 2) domain containing protein 89 (ANAC089). The Cvi allele of FSQ6/ANAC089 is a gain-of-function allele caused by a premature stop in the third exon of the gene. The truncated Cvi FSQ6/ANAC089 protein lacks a membrane association domain that is present in ANAC089 proteins from other Arabidopsis accessions. As a result, Cvi FSQ6/ANAC089 is constitutively active as a transcription factor in the nucleus.

@article{shevela_membrane-inlet_2011,
	title = {Membrane-inlet mass spectrometry reveals a high driving force for oxygen production by photosystem {II}},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1014249108},
	doi = {10/dtfj9n},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Shevela, Dmitriy and Beckmann, Katrin and Clausen, Jürgen and Junge, Wolfgang and Messinger, Johannes},
	month = mar,
	year = {2011},
	pages = {3602--3607},
}

@article{hall_adaptive_2011,
	title = {Adaptive evolution of the {Populus} tremula photoperiod pathway: {EVOLUTION} {OF} {THE} {PHOTOPERIOD} {PATHWAY} {IN} {POPULUS}},
	volume = {20},
	issn = {09621083},
	shorttitle = {Adaptive evolution of the {Populus} tremula photoperiod pathway},
	url = {http://doi.wiley.com/10.1111/j.1365-294X.2011.05014.x},
	doi = {10/cn8sq4},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Molecular Ecology},
	author = {Hall, David and Ma, Xiao-Fei and Ingvarsson, Pär K.},
	month = apr,
	year = {2011},
	pages = {1463--1474},
}

@article{granado-yela_temporal_2011,
	title = {Temporal matching among diurnal photosynthetic patterns within the crown of the evergreen sclerophyll {Olea} europaea {L}.: {Within}-crown photosynthetic patterns in {O}. europaea},
	volume = {34},
	issn = {01407791},
	shorttitle = {Temporal matching among diurnal photosynthetic patterns within the crown of the evergreen sclerophyll {Olea} europaea {L}.},
	url = {http://doi.wiley.com/10.1111/j.1365-3040.2011.02283.x},
	doi = {10/c233sd},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Plant, Cell \& Environment},
	author = {Granado-Yela, C. and García-Verdugo, C. and Carrillo, K. and Rubio De Casas, R. and Kleczkowski, L. A. and Balaguer, L.},
	month = may,
	year = {2011},
	pages = {800--810},
}

@article{lucas_short-root_2011,
	title = {{SHORT}-{ROOT} {Regulates} {Primary}, {Lateral}, and {Adventitious} {Root} {Development} in {Arabidopsis}},
	volume = {155},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/155/1/384/6111549},
	doi = {10/c9mbrr},
	abstract = {Abstract
            SHORT-ROOT (SHR) is a well-characterized regulator of radial patterning and indeterminacy of the Arabidopsis (Arabidopsis thaliana) primary root. However, its role during the elaboration of root system architecture remains unclear. We report that the indeterminate wild-type Arabidopsis root system was transformed into a determinate root system in the shr mutant when growing in soil or agar. The root growth behavior of the shr mutant results from its primary root apical meristem failing to initiate cell division following germination. The inability of shr to reactivate mitotic activity in the root apical meristem is associated with the progressive reduction in the abundance of auxin efflux carriers, PIN-FORMED1 (PIN1), PIN2, PIN3, PIN4, and PIN7. The loss of primary root growth in shr is compensated by the activation of anchor root primordia, whose tissues are radially patterned like the wild type. However, SHR function is not restricted to the primary root but is also required for the initiation and patterning of lateral root primordia. In addition, SHR is necessary to maintain the indeterminate growth of lateral and anchor roots. We conclude that SHR regulates a wide array of Arabidopsis root-related developmental processes.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Lucas, Mikaël and Swarup, Ranjan and Paponov, Ivan A. and Swarup, Kamal and Casimiro, Ilda and Lake, David and Peret, Benjamin and Zappala, Susan and Mairhofer, Stefan and Whitworth, Morag and Wang, Jiehua and Ljung, Karin and Marchant, Alan and Sandberg, Goran and Holdsworth, Michael J. and Palme, Klaus and Pridmore, Tony and Mooney, Sacha and Bennett, Malcolm J.},
	month = jan,
	year = {2011},
	pages = {384--398},
}

Abstract SHORT-ROOT (SHR) is a well-characterized regulator of radial patterning and indeterminacy of the Arabidopsis (Arabidopsis thaliana) primary root. However, its role during the elaboration of root system architecture remains unclear. We report that the indeterminate wild-type Arabidopsis root system was transformed into a determinate root system in the shr mutant when growing in soil or agar. The root growth behavior of the shr mutant results from its primary root apical meristem failing to initiate cell division following germination. The inability of shr to reactivate mitotic activity in the root apical meristem is associated with the progressive reduction in the abundance of auxin efflux carriers, PIN-FORMED1 (PIN1), PIN2, PIN3, PIN4, and PIN7. The loss of primary root growth in shr is compensated by the activation of anchor root primordia, whose tissues are radially patterned like the wild type. However, SHR function is not restricted to the primary root but is also required for the initiation and patterning of lateral root primordia. In addition, SHR is necessary to maintain the indeterminate growth of lateral and anchor roots. We conclude that SHR regulates a wide array of Arabidopsis root-related developmental processes.

@article{keerberg_quantitative_2011,
	title = {Quantitative analysis of photosynthetic carbon metabolism in protoplasts and intact leaves of barley. {Determination} of carbon fluxes and pool sizes of metabolites in different cellular compartments},
	volume = {103},
	issn = {03032647},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0303264710001978},
	doi = {10/dqjqsx},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Biosystems},
	author = {Keerberg, Olav and Ivanova, Hiie and Keerberg, Hille and Pärnik, Tiit and Talts, Peeter and Gardeström, Per},
	month = feb,
	year = {2011},
	pages = {291--301},
}

@incollection{liu_microtubules_2011,
	address = {New York, NY},
	title = {Microtubules, {MAPs} and {Xylem} {Formation}},
	volume = {2},
	isbn = {978-1-4419-0986-2 978-1-4419-0987-9},
	url = {http://link.springer.com/10.1007/978-1-4419-0987-9_13},
	language = {en},
	urldate = {2021-06-08},
	booktitle = {The {Plant} {Cytoskeleton}},
	publisher = {Springer New York},
	author = {Pesquet, Edouard and Lloyd, Clive},
	editor = {Liu, Bo},
	year = {2011},
	doi = {10.1007/978-1-4419-0987-9_13},
	note = {Series Title: Advances in Plant Biology},
	pages = {277--306},
}

@article{street_systems_2011,
	title = {A systems biology model of the regulatory network in {Populusleaves} reveals interacting regulators and conserved regulation},
	volume = {11},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/1471-2229-11-13},
	doi = {10/dkhmhb},
	abstract = {Green plant leaves have always fascinated biologists as hosts for photosynthesis and providers of basic energy to many food webs. Today, comprehensive databases of gene expression data enable us to apply increasingly more advanced computational methods for reverse-engineering the regulatory network of leaves, and to begin to understand the gene interactions underlying complex emergent properties related to stress-response and development. These new systems biology methods are now also being applied to organisms such as Populus, a woody perennial tree, in order to understand the specific characteristics of these species.},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Street, Nathaniel Robert and Jansson, Stefan and Hvidsten, Torgeir R.},
	month = jan,
	year = {2011},
	keywords = {Biotic Infection, Drought Stress, Nucleosome Assembly, System Biology Model, Transcriptional Module},
	pages = {13},
}

Green plant leaves have always fascinated biologists as hosts for photosynthesis and providers of basic energy to many food webs. Today, comprehensive databases of gene expression data enable us to apply increasingly more advanced computational methods for reverse-engineering the regulatory network of leaves, and to begin to understand the gene interactions underlying complex emergent properties related to stress-response and development. These new systems biology methods are now also being applied to organisms such as Populus, a woody perennial tree, in order to understand the specific characteristics of these species.

@article{nishikubo_xyloglucan_2011,
	title = {Xyloglucan endo-{Transglycosylase}-{Mediated} {Xyloglucan} {Rearrangements} in {Developing} {Wood} of {Hybrid} {Aspen}},
	volume = {155},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.110.166934},
	doi = {10/fswhm6},
	abstract = {Xyloglucan endo-transglycosylases (XETs) encoded by xyloglucan endo-transglycosylases/hydrolase (XTH) genes modify the xyloglucan-cellulose framework of plant cell walls, thereby regulating their expansion and strength. To evaluate the importance of XET in wood development, we studied xyloglucan dynamics and XTH gene expression in developing wood and modified XET activity in hybrid aspen (Populus tremula × tremuloides) by overexpressing PtxtXET16-34. We show that developmental modifications during xylem differentiation include changes from loosely to tightly bound forms of xyloglucan and increases in the abundance of fucosylated xyloglucan epitope recognized by the CCRC-M1 antibody. We found that at least 16 Populus  XTH genes, all likely encoding XETs, are expressed in developing wood. Five genes were highly and ubiquitously expressed, whereas PtxtXET16-34 was expressed more weakly but specifically in developing wood. Transgenic up-regulation of XET activity induced changes in cell wall xyloglucan, but its effects were dependent on developmental stage. For instance, XET overexpression increased abundance of the CCRC-M1 epitope in cambial cells and xylem cells in early stages of differentiation but not in mature xylem. Correspondingly, an increase in tightly bound xyloglucan content was observed in primary-walled xylem but a decrease was seen in secondary-walled xylem. Thus, in young xylem cells, XET activity limits xyloglucan incorporation into the tightly bound wall network but removes it from cell walls in older cells. XET overexpression promoted vessel element growth but not fiber expansion. We suggest that the amount of nascent xyloglucan relative to XET is an important determinant of whether XET strengthens or loosens the cell wall.},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Nishikubo, Nobuyuki and Takahashi, Junko and Roos, Alexandra A. and Derba-Maceluch, Marta and Piens, Kathleen and Brumer, Harry and Teeri, Tuula T. and Stålbrand, Henrik and Mellerowicz, Ewa J.},
	month = jan,
	year = {2011},
	pages = {399--413},
}

Xyloglucan endo-transglycosylases (XETs) encoded by xyloglucan endo-transglycosylases/hydrolase (XTH) genes modify the xyloglucan-cellulose framework of plant cell walls, thereby regulating their expansion and strength. To evaluate the importance of XET in wood development, we studied xyloglucan dynamics and XTH gene expression in developing wood and modified XET activity in hybrid aspen (Populus tremula × tremuloides) by overexpressing PtxtXET16-34. We show that developmental modifications during xylem differentiation include changes from loosely to tightly bound forms of xyloglucan and increases in the abundance of fucosylated xyloglucan epitope recognized by the CCRC-M1 antibody. We found that at least 16 Populus  XTH genes, all likely encoding XETs, are expressed in developing wood. Five genes were highly and ubiquitously expressed, whereas PtxtXET16-34 was expressed more weakly but specifically in developing wood. Transgenic up-regulation of XET activity induced changes in cell wall xyloglucan, but its effects were dependent on developmental stage. For instance, XET overexpression increased abundance of the CCRC-M1 epitope in cambial cells and xylem cells in early stages of differentiation but not in mature xylem. Correspondingly, an increase in tightly bound xyloglucan content was observed in primary-walled xylem but a decrease was seen in secondary-walled xylem. Thus, in young xylem cells, XET activity limits xyloglucan incorporation into the tightly bound wall network but removes it from cell walls in older cells. XET overexpression promoted vessel element growth but not fiber expansion. We suggest that the amount of nascent xyloglucan relative to XET is an important determinant of whether XET strengthens or loosens the cell wall.

@article{huesgen_recombinant_2011,
	title = {Recombinant {Deg}/{HtrA} proteases from {Synechocystis} sp. {PCC} 6803 differ in substrate specificity, biochemical characteristics and mechanism},
	volume = {435},
	issn = {0264-6021, 1470-8728},
	url = {https://portlandpress.com/biochemj/article/435/3/733/45597/Recombinant-DegHtrA-proteases-from-Synechocystis},
	doi = {10/cjq4hx},
	abstract = {Cyanobacteria require efficient protein-quality-control mechanisms to survive under dynamic, often stressful, environmental conditions. It was reported that three serine proteases, HtrA (high temperature requirement A), HhoA (HtrA homologue A) and HhoB (HtrA homologue B), are important for survival of Synechocystis sp. PCC 6803 under high light and temperature stresses and might have redundant physiological functions. In the present paper, we show that all three proteases can degrade unfolded model substrates, but differ with respect to cleavage sites, temperature and pH optima. For recombinant HhoA, and to a lesser extent for HtrA, we observed an interesting shift in the pH optimum from slightly acidic to alkaline in the presence of Mg2+ and Ca2+ ions. All three proteases formed different homo-oligomeric complexes with and without substrate, implying mechanistic differences in comparison with each other and with the well-studied Escherichia coli orthologues DegP (degradation of periplasmic proteins P) and DegS. Deletion of the PDZ domain decreased, but did not abolish, the proteolytic activity of all three proteases, and prevented substrate-induced formation of complexes higher than trimers by HtrA and HhoA. In summary, biochemical characterization of HtrA, HhoA and HhoB lays the foundation for a better understanding of their overlapping, but not completely redundant, stress-resistance functions in Synechocystis sp. PCC 6803.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Biochemical Journal},
	author = {Huesgen, Pitter F. and Miranda, Helder and Lam, XuanTam and Perthold, Manuela and Schuhmann, Holger and Adamska, Iwona and Funk, Christiane},
	month = may,
	year = {2011},
	pages = {733--742},
}

Cyanobacteria require efficient protein-quality-control mechanisms to survive under dynamic, often stressful, environmental conditions. It was reported that three serine proteases, HtrA (high temperature requirement A), HhoA (HtrA homologue A) and HhoB (HtrA homologue B), are important for survival of Synechocystis sp. PCC 6803 under high light and temperature stresses and might have redundant physiological functions. In the present paper, we show that all three proteases can degrade unfolded model substrates, but differ with respect to cleavage sites, temperature and pH optima. For recombinant HhoA, and to a lesser extent for HtrA, we observed an interesting shift in the pH optimum from slightly acidic to alkaline in the presence of Mg2+ and Ca2+ ions. All three proteases formed different homo-oligomeric complexes with and without substrate, implying mechanistic differences in comparison with each other and with the well-studied Escherichia coli orthologues DegP (degradation of periplasmic proteins P) and DegS. Deletion of the PDZ domain decreased, but did not abolish, the proteolytic activity of all three proteases, and prevented substrate-induced formation of complexes higher than trimers by HtrA and HhoA. In summary, biochemical characterization of HtrA, HhoA and HhoB lays the foundation for a better understanding of their overlapping, but not completely redundant, stress-resistance functions in Synechocystis sp. PCC 6803.

@article{pesquet_ethylene_2011,
	title = {Ethylene stimulates tracheary element differentiation in \textit{{Zinnia} elegans} cell cultures},
	volume = {190},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2010.03600.x},
	doi = {10/cpkfn3},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Pesquet, Edouard and Tuominen, Hannele},
	month = apr,
	year = {2011},
	pages = {138--149},
}

@article{ingvarsson_association_2011,
	title = {Association genetics of complex traits in plants},
	volume = {189},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2010.03593.x},
	doi = {10/c2w6s3},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Ingvarsson, Pär K. and Street, Nathaniel R.},
	month = mar,
	year = {2011},
	pages = {909--922},
}

@article{searle_leaf_2011,
	title = {Leaf respiration and alternative oxidase in field‐grown alpine grasses respond to natural changes in temperature and light},
	volume = {189},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2010.03557.x},
	doi = {10/bjq25k},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Searle, Stephanie Y. and Thomas, Samuel and Griffin, Kevin L. and Horton, Travis and Kornfeld, Ari and Yakir, Dan and Hurry, Vaughan and Turnbull, Matthew H.},
	month = mar,
	year = {2011},
	pages = {1027--1039},
}

@article{sun_possible_2011,
	title = {Possible {Effect} {From} {Shear} {Stress} on {Maturation} of {Somatic} {Embryos} of {Norway} {Spruce} ({Picea} abies)},
	volume = {108},
	issn = {00063592},
	url = {http://doi.wiley.com/10.1002/bit.23040},
	doi = {10/cpn47k},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Biotechnology and Bioengineering},
	author = {Sun, Hong and Aidun, Cyrus K. and Egertsdotter, Ulrika},
	month = may,
	year = {2011},
	pages = {1089--1099},
}

@article{garcia-cerdan_psbw_2011,
	title = {The {PsbW} protein stabilizes the supramolecular organization of photosystem {II} in higher plants: {PsbW} needed for {PSII} supercomplexes},
	volume = {65},
	issn = {09607412},
	shorttitle = {The {PsbW} protein stabilizes the supramolecular organization of photosystem {II} in higher plants},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2010.04429.x},
	doi = {10/fs5qqw},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {García-Cerdán, José G. and Kovács, Laszlo and Tóth, Tünde and Kereïche, Sami and Aseeva, Elena and Boekema, Egbert J. and Mamedov, Fikret and Funk, Christiane and Schröder, Wolfgang P.},
	month = feb,
	year = {2011},
	pages = {368--381},
}

@article{igamberdiev_optimization_2011,
	title = {Optimization of {CO2} fixation in photosynthetic cells via thermodynamic buffering},
	volume = {103},
	issn = {03032647},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0303264710001747},
	doi = {10/d9xqmp},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Biosystems},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = feb,
	year = {2011},
	pages = {224--229},
}