Publications 2014

@article{tran_mn4ca_2014,
	title = {The {Mn4Ca} photosynthetic water-oxidation catalyst studied by simultaneous {X}-ray spectroscopy and crystallography using an {X}-ray free-electron laser},
	volume = {369},
	url = {https://royalsocietypublishing.org/doi/10.1098/rstb.2013.0324},
	doi = {10.1098/rstb.2013.0324},
	abstract = {The structure of photosystem II and the catalytic intermediate states of the Mn4CaO5 cluster involved in water oxidation have been studied intensively over the past several years. An understanding of the sequential chemistry of light absorption and the mechanism of water oxidation, however, requires a new approach beyond the conventional steady-state crystallography and X-ray spectroscopy at cryogenic temperatures. In this report, we present the preliminary progress using an X-ray free-electron laser to determine simultaneously the light-induced protein dynamics via crystallography and the local chemistry that occurs at the catalytic centre using X-ray spectroscopy under functional conditions at room temperature.},
	number = {1647},
	urldate = {2024-12-10},
	journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
	author = {Tran, Rosalie and Kern, Jan and Hattne, Johan and Koroidov, Sergey and Hellmich, Julia and Alonso-Mori, Roberto and Sauter, Nicholas K. and Bergmann, Uwe and Messinger, Johannes and Zouni, Athina and Yano, Junko and Yachandra, Vittal K.},
	month = jul,
	year = {2014},
	note = {Publisher: Royal Society},
	keywords = {X-ray crystallography, X-ray emission spectroscopy, X-ray free-electron laser, manganese, oxygen-evolving complex, photosystem II},
	pages = {20130324},
}

The structure of photosystem II and the catalytic intermediate states of the Mn4CaO5 cluster involved in water oxidation have been studied intensively over the past several years. An understanding of the sequential chemistry of light absorption and the mechanism of water oxidation, however, requires a new approach beyond the conventional steady-state crystallography and X-ray spectroscopy at cryogenic temperatures. In this report, we present the preliminary progress using an X-ray free-electron laser to determine simultaneously the light-induced protein dynamics via crystallography and the local chemistry that occurs at the catalytic centre using X-ray spectroscopy under functional conditions at room temperature.

@article{pham_electrochemically_2014,
	series = {Photosynthesis {Research} for {Sustainability}: {Keys} to {Produce} {Clean} {Energy}},
	title = {Electrochemically produced hydrogen peroxide affects {Joliot}-type oxygen-evolution measurements of photosystem {II}},
	volume = {1837},
	issn = {0005-2728},
	url = {https://www.sciencedirect.com/science/article/pii/S0005272814000152},
	doi = {10.1016/j.bbabio.2014.01.013},
	abstract = {The main technique employed to characterize the efficiency of water-splitting in photosynthetic preparations in terms of miss and double hit parameters and for the determination of Si (i=2,3,0) state lifetimes is the measurement of flash-induced oxygen oscillation pattern on bare platinum (Joliot-type) electrodes. We demonstrate here that this technique is not innocent. Polarization of the electrode against an Ag/AgCl electrode leads to a time-dependent formation of hydrogen peroxide by two-electron reduction of dissolved oxygen continuously supplied by the flow buffer. While the miss and double hit parameters are almost unaffected by H2O2, a time dependent reduction of S1 to S−1 occurs over a time period of 20min. The S1 reduction can be largely prevented by adding catalase or by removing O2 from the flow buffer with N2. Importantly, we demonstrate that even at the shortest possible polarization times (40s in our set up) the S2 and S0 decays are significantly accelerated by the side reaction with H2O2. The removal of hydrogen peroxide leads to unperturbed S2 state data that reveal three instead of the traditionally reported two phases of decay. In addition, even under the best conditions (catalase+N2; 40s polarization) about 4\% of S−1 state is observed in well dark-adapted samples, likely indicating limitations of the equal fit approach. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: Keys to Produce Clean Energy.},
	number = {9},
	urldate = {2024-12-10},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Pham, Long Vo and Messinger, Johannes},
	month = sep,
	year = {2014},
	keywords = {Hydrogen peroxide (HO), Manganese, Oxygen evolving complex (OEC), Photosystem II (PSII), Water oxidation},
	pages = {1411--1416},
}

The main technique employed to characterize the efficiency of water-splitting in photosynthetic preparations in terms of miss and double hit parameters and for the determination of Si (i=2,3,0) state lifetimes is the measurement of flash-induced oxygen oscillation pattern on bare platinum (Joliot-type) electrodes. We demonstrate here that this technique is not innocent. Polarization of the electrode against an Ag/AgCl electrode leads to a time-dependent formation of hydrogen peroxide by two-electron reduction of dissolved oxygen continuously supplied by the flow buffer. While the miss and double hit parameters are almost unaffected by H2O2, a time dependent reduction of S1 to S−1 occurs over a time period of 20min. The S1 reduction can be largely prevented by adding catalase or by removing O2 from the flow buffer with N2. Importantly, we demonstrate that even at the shortest possible polarization times (40s in our set up) the S2 and S0 decays are significantly accelerated by the side reaction with H2O2. The removal of hydrogen peroxide leads to unperturbed S2 state data that reveal three instead of the traditionally reported two phases of decay. In addition, even under the best conditions (catalase+N2; 40s polarization) about 4% of S−1 state is observed in well dark-adapted samples, likely indicating limitations of the equal fit approach. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: Keys to Produce Clean Energy.

@article{nilsson_substratewater_2014,
	title = {Substrate–water exchange in photosystem {II} is arrested before dioxygen formation},
	volume = {5},
	copyright = {2014 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/ncomms5305},
	doi = {10.1038/ncomms5305},
	abstract = {Light-driven oxidation of water into dioxygen, catalysed by the oxygen-evolving complex (OEC) in photosystem II, is essential for life on Earth and provides the blueprint for devices for producing fuel from sunlight. Although the structure of the OEC is known at atomic level for its dark-stable state, the mechanism by which water is oxidized remains unsettled. Important mechanistic information was gained in the past two decades by mass spectrometric studies of the H218O/H216O substrate–water exchange in the four (semi) stable redox states of the OEC. However, until now such data were not attainable in the transient states formed immediately before the O–O bond formation. Using modified photosystem II complexes displaying up to 40-fold slower O2 production rates, we show here that in the transient state the substrate–water exchange is dramatically slowed as compared with the earlier S states. This further constrains the possible sites for substrate–water binding in photosystem II.},
	language = {en},
	number = {1},
	urldate = {2024-12-10},
	journal = {Nature Communications},
	author = {Nilsson, Håkan and Rappaport, Fabrice and Boussac, Alain and Messinger, Johannes},
	month = jul,
	year = {2014},
	note = {Publisher: Nature Publishing Group},
	keywords = {Bioenergetics, Photosystem II},
	pages = {4305},
}

Light-driven oxidation of water into dioxygen, catalysed by the oxygen-evolving complex (OEC) in photosystem II, is essential for life on Earth and provides the blueprint for devices for producing fuel from sunlight. Although the structure of the OEC is known at atomic level for its dark-stable state, the mechanism by which water is oxidized remains unsettled. Important mechanistic information was gained in the past two decades by mass spectrometric studies of the H218O/H216O substrate–water exchange in the four (semi) stable redox states of the OEC. However, until now such data were not attainable in the transient states formed immediately before the O–O bond formation. Using modified photosystem II complexes displaying up to 40-fold slower O2 production rates, we show here that in the transient state the substrate–water exchange is dramatically slowed as compared with the earlier S states. This further constrains the possible sites for substrate–water binding in photosystem II.

@article{nilsson_substrate_2014,
	title = {Substrate water exchange in photosystem {II} core complexes of the extremophilic red alga \textit{{Cyanidioschyzon} merolae}},
	volume = {1837},
	issn = {0005-2728},
	url = {https://www.sciencedirect.com/science/article/pii/S0005272814001078},
	doi = {10.1016/j.bbabio.2014.04.001},
	abstract = {The binding affinity of the two substrate–water molecules to the water-oxidizing Mn4CaO5 catalyst in photosystem II core complexes of the extremophilic red alga Cyanidioschyzon merolae was studied in the S2 and S3 states by the exchange of bound 16O-substrate against 18O-labeled water. The rate of this exchange was detected via the membrane-inlet mass spectrometric analysis of flash-induced oxygen evolution. For both redox states a fast and slow phase of water-exchange was resolved at the mixed labeled m/z 34 mass peak: kf=52±8s−1 and ks=1.9±0.3s−1 in the S2 state, and kf=42±2s−1 and kslow=1.2±0.3s−1 in S3, respectively. Overall these exchange rates are similar to those observed previously with preparations of other organisms. The most remarkable finding is a significantly slower exchange at the fast substrate–water site in the S2 state, which confirms beyond doubt that both substrate–water molecules are already bound in the S2 state. This leads to a very small change of the affinity for both the fast and the slowly exchanging substrates during the S2→S3 transition. Implications for recent models for water-oxidation are briefly discussed.},
	number = {8},
	urldate = {2024-12-10},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Nilsson, Håkan and Krupnik, Tomasz and Kargul, Joanna and Messinger, Johannes},
	month = aug,
	year = {2014},
	keywords = {Membrane-inlet mass spectrometry, Oxygen evolution, Photosystem II, Substrate–water exchange, Water oxidation},
	pages = {1257--1262},
}

The binding affinity of the two substrate–water molecules to the water-oxidizing Mn4CaO5 catalyst in photosystem II core complexes of the extremophilic red alga Cyanidioschyzon merolae was studied in the S2 and S3 states by the exchange of bound 16O-substrate against 18O-labeled water. The rate of this exchange was detected via the membrane-inlet mass spectrometric analysis of flash-induced oxygen evolution. For both redox states a fast and slow phase of water-exchange was resolved at the mixed labeled m/z 34 mass peak: kf=52±8s−1 and ks=1.9±0.3s−1 in the S2 state, and kf=42±2s−1 and kslow=1.2±0.3s−1 in S3, respectively. Overall these exchange rates are similar to those observed previously with preparations of other organisms. The most remarkable finding is a significantly slower exchange at the fast substrate–water site in the S2 state, which confirms beyond doubt that both substrate–water molecules are already bound in the S2 state. This leads to a very small change of the affinity for both the fast and the slowly exchanging substrates during the S2→S3 transition. Implications for recent models for water-oxidation are briefly discussed.

@article{messinger_photosynthesis_2014,
	title = {Photosynthesis: from natural to artificial},
	volume = {16},
	issn = {1463-9084},
	shorttitle = {Photosynthesis},
	url = {https://pubs.rsc.org/en/content/articlelanding/2014/cp/c4cp90053g},
	doi = {10.1039/C4CP90053G},
	abstract = {A graphical abstract is available for this content},
	language = {en},
	number = {24},
	urldate = {2024-12-10},
	journal = {Physical Chemistry Chemical Physics},
	author = {Messinger, Johannes and Lubitz, Wolfgang and Shen, Jian-Ren},
	month = may,
	year = {2014},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {11810--11811},
}

A graphical abstract is available for this content

@article{messinger_warwick_2014,
	title = {Warwick {Hillier}: a tribute},
	volume = {122},
	issn = {1573-5079},
	shorttitle = {Warwick {Hillier}},
	url = {https://doi.org/10.1007/s11120-014-0025-5},
	doi = {10.1007/s11120-014-0025-5},
	abstract = {Warwick Hillier (October 18, 1967–January 10, 2014) made seminal contributions to our understanding of photosynthetic water oxidation employing membrane inlet mass spectrometry and FTIR spectroscopy. This article offers a collection of historical perspectives on the scientific impact of Warwick Hillier’s work and tributes to the personal impact his life and ideas had on his collaborators and colleagues.},
	language = {en},
	number = {1},
	urldate = {2024-12-10},
	journal = {Photosynthesis Research},
	author = {Messinger, Johannes and Debus, Richard and Dismukes, G. Charles},
	month = oct,
	year = {2014},
	keywords = {Bicarbonate, FTIR, Isotopes, Mass spectrometry, Oxygenic photosynthesis, Photosystem II},
	pages = {1--11},
}

Warwick Hillier (October 18, 1967–January 10, 2014) made seminal contributions to our understanding of photosynthetic water oxidation employing membrane inlet mass spectrometry and FTIR spectroscopy. This article offers a collection of historical perspectives on the scientific impact of Warwick Hillier’s work and tributes to the personal impact his life and ideas had on his collaborators and colleagues.

@article{liang_improving_2014,
	title = {Improving {BiVO4} photoanodes for solar water splitting through surface passivation},
	volume = {16},
	issn = {1463-9084},
	url = {https://pubs.rsc.org/en/content/articlelanding/2014/cp/c4cp00674g},
	doi = {10.1039/C4CP00674G},
	abstract = {BiVO4 has shown great potential as a semiconductor photoanode for solar water splitting. Significant improvements made during recent years allowed researchers to obtain a photocurrent density of up to 4.0 mA cm−2 (AM1.5 sunlight illumination, 1.23 VRHE bias). For further improvements of the BiVO4 photoelectrodes, a deep understanding of the processes occurring at the BiVO4–H2O interface is crucial. Employing an electrochemical loading and removal process of NiOx, we show here that carrier recombination at this interface strongly affects the photocurrents. The removal of NiOx species by electrochemical treatment in a phosphate electrolyte leads to significantly increased photocurrents for BiVO4 photoelectrodes. At a bias of 1.23 VRHE, the Incident Photon-to-Current Efficiency (IPCE) at 450 nm reaches 43\% for the passivated BiVO4 electrode under back side illumination. A model incorporating heterogeneity of NiOx centers on the BiVO4 surface (OER catalytic centers, recombination centers, and passivation centers) is proposed to explain this improved performance.},
	language = {en},
	number = {24},
	urldate = {2024-12-10},
	journal = {Physical Chemistry Chemical Physics},
	author = {Liang, Yongqi and Messinger, Johannes},
	month = may,
	year = {2014},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {12014--12020},
}

BiVO4 has shown great potential as a semiconductor photoanode for solar water splitting. Significant improvements made during recent years allowed researchers to obtain a photocurrent density of up to 4.0 mA cm−2 (AM1.5 sunlight illumination, 1.23 VRHE bias). For further improvements of the BiVO4 photoelectrodes, a deep understanding of the processes occurring at the BiVO4–H2O interface is crucial. Employing an electrochemical loading and removal process of NiOx, we show here that carrier recombination at this interface strongly affects the photocurrents. The removal of NiOx species by electrochemical treatment in a phosphate electrolyte leads to significantly increased photocurrents for BiVO4 photoelectrodes. At a bias of 1.23 VRHE, the Incident Photon-to-Current Efficiency (IPCE) at 450 nm reaches 43% for the passivated BiVO4 electrode under back side illumination. A model incorporating heterogeneity of NiOx centers on the BiVO4 surface (OER catalytic centers, recombination centers, and passivation centers) is proposed to explain this improved performance.

@article{kern_taking_2014,
	title = {Taking snapshots of photosynthetic water oxidation using femtosecond {X}-ray diffraction and spectroscopy},
	volume = {5},
	copyright = {2014 Springer Nature Limited},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/ncomms5371},
	doi = {10.1038/ncomms5371},
	abstract = {The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F’ state (250 μs after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O–O bond formation, coupled to Mn reduction, does not yet occur within 250 μs after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 Å. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.},
	language = {en},
	number = {1},
	urldate = {2024-12-10},
	journal = {Nature Communications},
	author = {Kern, Jan and Tran, Rosalie and Alonso-Mori, Roberto and Koroidov, Sergey and Echols, Nathaniel and Hattne, Johan and Ibrahim, Mohamed and Gul, Sheraz and Laksmono, Hartawan and Sierra, Raymond G. and Gildea, Richard J. and Han, Guangye and Hellmich, Julia and Lassalle-Kaiser, Benedikt and Chatterjee, Ruchira and Brewster, Aaron S. and Stan, Claudiu A. and Glöckner, Carina and Lampe, Alyssa and DiFiore, Dörte and Milathianaki, Despina and Fry, Alan R. and Seibert, M. Marvin and Koglin, Jason E. and Gallo, Erik and Uhlig, Jens and Sokaras, Dimosthenis and Weng, Tsu-Chien and Zwart, Petrus H. and Skinner, David E. and Bogan, Michael J. and Messerschmidt, Marc and Glatzel, Pieter and Williams, Garth J. and Boutet, Sébastien and Adams, Paul D. and Zouni, Athina and Messinger, Johannes and Sauter, Nicholas K. and Bergmann, Uwe and Yano, Junko and Yachandra, Vittal K.},
	month = jul,
	year = {2014},
	note = {Publisher: Nature Publishing Group},
	keywords = {Biophysics, Optical spectroscopy, Photosynthesis, X-ray diffraction},
	pages = {4371},
}

The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F’ state (250 μs after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O–O bond formation, coupled to Mn reduction, does not yet occur within 250 μs after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 Å. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.

@article{hattne_accurate_2014,
	title = {Accurate macromolecular structures using minimal measurements from {X}-ray free-electron lasers},
	volume = {11},
	copyright = {2014 Springer Nature America, Inc.},
	issn = {1548-7105},
	url = {https://www.nature.com/articles/nmeth.2887},
	doi = {10.1038/nmeth.2887},
	abstract = {A computational approach and software tool, cctbx.xfel, enables the determination of accurate macromolecular structure factors using a relatively small number of serial femtosecond crystallography diffraction snapshots.},
	language = {en},
	number = {5},
	urldate = {2024-12-10},
	journal = {Nature Methods},
	author = {Hattne, Johan and Echols, Nathaniel and Tran, Rosalie and Kern, Jan and Gildea, Richard J. and Brewster, Aaron S. and Alonso-Mori, Roberto and Glöckner, Carina and Hellmich, Julia and Laksmono, Hartawan and Sierra, Raymond G. and Lassalle-Kaiser, Benedikt and Lampe, Alyssa and Han, Guangye and Gul, Sheraz and DiFiore, Dörte and Milathianaki, Despina and Fry, Alan R. and Miahnahri, Alan and White, William E. and Schafer, Donald W. and Seibert, M. Marvin and Koglin, Jason E. and Sokaras, Dimosthenis and Weng, Tsu-Chien and Sellberg, Jonas and Latimer, Matthew J. and Glatzel, Pieter and Zwart, Petrus H. and Grosse-Kunstleve, Ralf W. and Bogan, Michael J. and Messerschmidt, Marc and Williams, Garth J. and Boutet, Sébastien and Messinger, Johannes and Zouni, Athina and Yano, Junko and Bergmann, Uwe and Yachandra, Vittal K. and Adams, Paul D. and Sauter, Nicholas K.},
	month = may,
	year = {2014},
	note = {Publisher: Nature Publishing Group},
	keywords = {Nanocrystallography, Protein analysis, Proteins, Software},
	pages = {545--548},
}

A computational approach and software tool, cctbx.xfel, enables the determination of accurate macromolecular structure factors using a relatively small number of serial femtosecond crystallography diffraction snapshots.

@article{han_hydration_2014,
	title = {Hydration of the oxygen-evolving complex of photosystem {II} probed in the dark-stable {S1} state using proton {NMR} dispersion profiles},
	volume = {16},
	issn = {1463-9084},
	url = {https://pubs.rsc.org/en/content/articlelanding/2014/cp/c3cp55232b},
	doi = {10.1039/C3CP55232B},
	abstract = {The hydration of the oxygen-evolving complex (OEC) was characterized in the dark stable S1 state of photosystem II using water R1(ω) NMR dispersion (NMRD) profiles. The R1(ω) NMRD profiles were recorded over a frequency range from 0.01 MHz to 40 MHz for both intact and Mn-depleted photosystem II core complexes from Thermosynechococcus vulcanus (T. vulcanus). The intact-minus-(Mn)-depleted difference NMRD profiles show a characteristic dispersion from approximately 0.03 MHz to 1 MHz, which is interpreted on the basis of the Solomon–Bloembergen–Morgan (SBM) and the slow motion theories as being due to a paramagnetic enhanced relaxation (PRE) of water protons. Both theories are qualitatively consistent with the ST = 1, g = 4.9 paramagnetic state previously described for the S1 state of the OEC; however, an alternative explanation involving the loss of a separate class of long-lived internal waters due to the Mn-depletion procedure can presently not be ruled out. Using a point-dipole approximation the PRE-NMRD effect can be described as being caused by 1–2 water molecules that are located about 10 Å away from the spin center of the Mn4CaO5 cluster in the OEC. The application of the SBM theory to the dispersion observed for PSII in the S1 state is questionable, because the parameters extracted do not fulfil the presupposed perturbation criterion. In contrast, the slow motion theory gives a consistent picture indicating that the water molecules are in fast chemical exchange with the bulk (τw {\textless} 1 μs). The modulation of the zero-field splitting (ZFS) interaction suggests a (restricted) reorientation/structural equilibrium of the Mn4CaO5 cluster with a characteristic time constant of τZFS = 0.6–0.9 μs.},
	language = {en},
	number = {24},
	urldate = {2024-12-10},
	journal = {Physical Chemistry Chemical Physics},
	author = {Han, Guangye and Huang, Yang and Koua, Faisal Hammad Mekky and Shen, Jian-Ren and Westlund, Per-Olof and Messinger, Johannes},
	month = may,
	year = {2014},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {11924--11935},
}

The hydration of the oxygen-evolving complex (OEC) was characterized in the dark stable S1 state of photosystem II using water R1(ω) NMR dispersion (NMRD) profiles. The R1(ω) NMRD profiles were recorded over a frequency range from 0.01 MHz to 40 MHz for both intact and Mn-depleted photosystem II core complexes from Thermosynechococcus vulcanus (T. vulcanus). The intact-minus-(Mn)-depleted difference NMRD profiles show a characteristic dispersion from approximately 0.03 MHz to 1 MHz, which is interpreted on the basis of the Solomon–Bloembergen–Morgan (SBM) and the slow motion theories as being due to a paramagnetic enhanced relaxation (PRE) of water protons. Both theories are qualitatively consistent with the ST = 1, g = 4.9 paramagnetic state previously described for the S1 state of the OEC; however, an alternative explanation involving the loss of a separate class of long-lived internal waters due to the Mn-depletion procedure can presently not be ruled out. Using a point-dipole approximation the PRE-NMRD effect can be described as being caused by 1–2 water molecules that are located about 10 Å away from the spin center of the Mn4CaO5 cluster in the OEC. The application of the SBM theory to the dispersion observed for PSII in the S1 state is questionable, because the parameters extracted do not fulfil the presupposed perturbation criterion. In contrast, the slow motion theory gives a consistent picture indicating that the water molecules are in fast chemical exchange with the bulk (τw \textless 1 μs). The modulation of the zero-field splitting (ZFS) interaction suggests a (restricted) reorientation/structural equilibrium of the Mn4CaO5 cluster with a characteristic time constant of τZFS = 0.6–0.9 μs.

@article{arafa_dinuclear_2014,
	title = {Dinuclear manganese complexes for water oxidation: evaluation of electronic effects and catalytic activity},
	volume = {16},
	issn = {1463-9084},
	shorttitle = {Dinuclear manganese complexes for water oxidation},
	url = {https://pubs.rsc.org/en/content/articlelanding/2014/cp/c3cp54800g},
	doi = {10.1039/C3CP54800G},
	abstract = {During recent years significant progress has been made towards the realization of a sustainable and carbon-neutral energy economy. One promising approach is photochemical splitting of H2O into O2 and solar fuels, such as H2. However, the bottleneck in such artificial photosynthetic schemes is the H2O oxidation half reaction where more efficient catalysts are required that lower the kinetic barrier for this process. In particular catalysts based on earth-abundant metals are highly attractive compared to catalysts comprised of noble metals. We have now synthesized a library of dinuclear Mn2II,III catalysts for H2O oxidation and studied how the incorporation of different substituents affected the electronics and catalytic efficiency. It was found that the incorporation of a distal carboxyl group into the ligand scaffold resulted in a catalyst with increased catalytic activity, most likely because of the fact that the distal group is able to promote proton-coupled electron transfer (PCET) from the high-valent Mn species, thus facilitating O–O bond formation.},
	language = {en},
	number = {24},
	urldate = {2024-12-10},
	journal = {Physical Chemistry Chemical Physics},
	author = {Arafa, Wael A. A. and Kärkäs, Markus D. and Lee, Bao-Lin and Åkermark, Torbjörn and Liao, Rong-Zhen and Berends, Hans-Martin and Messinger, Johannes and Siegbahn, Per E. M. and Åkermark, Björn},
	month = may,
	year = {2014},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {11950--11964},
}

During recent years significant progress has been made towards the realization of a sustainable and carbon-neutral energy economy. One promising approach is photochemical splitting of H2O into O2 and solar fuels, such as H2. However, the bottleneck in such artificial photosynthetic schemes is the H2O oxidation half reaction where more efficient catalysts are required that lower the kinetic barrier for this process. In particular catalysts based on earth-abundant metals are highly attractive compared to catalysts comprised of noble metals. We have now synthesized a library of dinuclear Mn2II,III catalysts for H2O oxidation and studied how the incorporation of different substituents affected the electronics and catalytic efficiency. It was found that the incorporation of a distal carboxyl group into the ligand scaffold resulted in a catalyst with increased catalytic activity, most likely because of the fact that the distal group is able to promote proton-coupled electron transfer (PCET) from the high-valent Mn species, thus facilitating O–O bond formation.

@incollection{bellini_adventitious_2014,
	title = {Adventitious {Roots}},
	copyright = {Copyright © 2014 John Wiley \& Sons, Ltd. All rights reserved.},
	isbn = {978-0-470-01590-2},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470015902.a0002061.pub2},
	abstract = {The root system of a plant is composed of the primary, lateral and adventitious roots (ARs). Lateral roots always develop from roots, whereas ARs form from stem or leaf-derived cells. AR formation is part of the normal development of the plant and occurs naturally, like in most monocotyledonous for which they constitute the main root system or in many dicotyledonous species that propagate vegetatively. Adventitious rooting is an essential step for vegetative propagation of economically important horticultural and woody species as it allows clonal propagation and rapid fixation of superior genotypes prior to their introduction into production or breeding programmes. Development of ARs is a complex process that is affected by multiple endogenous and environmental factors, including phytohormones; light; nutritional status; associated stress responses, such as wounding; and genetic characteristics. Key Concepts: ARs are the main root system for monocots. ARs are an adaptative response to environmental changes. ARs are required for vegetative propagation of plants. ARs arise from any organ of the plant but the root. ARs originate from different cell types depending on the organ or the species. ARs can be induced by ECMs or Agrobacterium rhizogenes. ARdevelopment is controlled by environmental factors. Adventitious rooting is an age-dependant process. Auxin cross talks with other hormones to control adventitious rooting. Adventitious rooting is a complex quantitative genetic trait.},
	language = {en},
	urldate = {2024-10-07},
	booktitle = {{eLS}},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Bellini, Catherine},
	year = {2014},
	doi = {10.1002/9780470015902.a0002061.pub2},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9780470015902.a0002061.pub2},
	keywords = {abiotic factors, adventitious roots, biotic factors, plant hormones, vegetative propagation},
}

The root system of a plant is composed of the primary, lateral and adventitious roots (ARs). Lateral roots always develop from roots, whereas ARs form from stem or leaf-derived cells. AR formation is part of the normal development of the plant and occurs naturally, like in most monocotyledonous for which they constitute the main root system or in many dicotyledonous species that propagate vegetatively. Adventitious rooting is an essential step for vegetative propagation of economically important horticultural and woody species as it allows clonal propagation and rapid fixation of superior genotypes prior to their introduction into production or breeding programmes. Development of ARs is a complex process that is affected by multiple endogenous and environmental factors, including phytohormones; light; nutritional status; associated stress responses, such as wounding; and genetic characteristics. Key Concepts: ARs are the main root system for monocots. ARs are an adaptative response to environmental changes. ARs are required for vegetative propagation of plants. ARs arise from any organ of the plant but the root. ARs originate from different cell types depending on the organ or the species. ARs can be induced by ECMs or Agrobacterium rhizogenes. ARdevelopment is controlled by environmental factors. Adventitious rooting is an age-dependant process. Auxin cross talks with other hormones to control adventitious rooting. Adventitious rooting is a complex quantitative genetic trait.

@article{novakova_sac_2014,
	title = {{SAC} phosphoinositide phosphatases at the tonoplast mediate vacuolar function in {Arabidopsis}},
	volume = {111},
	url = {https://www.pnas.org/doi/10.1073/pnas.1324264111},
	doi = {10.1073/pnas.1324264111},
	abstract = {Phosphatidylinositol (PtdIns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, PtdIns3P and PtdIns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vacuolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2–SAC5 localize to the tonoplast along with PtdIns3P, the presumable product of their activity. In SAC gain- and loss-of-function mutants, the levels of PtdIns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with PtdIns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2–SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants.},
	number = {7},
	urldate = {2024-10-02},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Nováková, Petra and Hirsch, Sibylle and Feraru, Elena and Tejos, Ricardo and van Wijk, Ringo and Viaene, Tom and Heilmann, Mareike and Lerche, Jennifer and De Rycke, Riet and Feraru, Mugurel I. and Grones, Peter and Van Montagu, Marc and Heilmann, Ingo and Munnik, Teun and Friml, Jiří},
	month = feb,
	year = {2014},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	pages = {2818--2823},
}

Phosphatidylinositol (PtdIns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, PtdIns3P and PtdIns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vacuolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2–SAC5 localize to the tonoplast along with PtdIns3P, the presumable product of their activity. In SAC gain- and loss-of-function mutants, the levels of PtdIns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with PtdIns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2–SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants.

@article{kremnev_plastid_2014,
	title = {Plastid encoded {RNA} polymerase activity and expression of photosynthesis genes required for embryo and seed development in {Arabidopsis}},
	volume = {5},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/article/10.3389/fpls.2014.00385/abstract},
	doi = {10/f24spf},
	urldate = {2021-06-08},
	journal = {Frontiers in Plant Science},
	author = {Kremnev, Dmitry and Strand, Åsa},
	month = aug,
	year = {2014},
}

@article{swarts_novel_2014,
	title = {Novel {Methods} to {Optimize} {Genotypic} {Imputation} for {Low}-{Coverage}, {Next}-{Generation} {Sequence} {Data} in {Crop} {Plants}},
	volume = {7},
	copyright = {© 2014 The Authors.},
	issn = {1940-3372},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.3835/plantgenome2014.05.0023},
	doi = {10.3835/plantgenome2014.05.0023},
	abstract = {Next-generation sequencing technology such as genotyping-by-sequencing (GBS) made low-cost, but often low-coverage, whole-genome sequencing widely available. Extensive inbreeding in crop plants provides an untapped, high quality source of phased haplotypes for imputing missing genotypes. We introduce Full-Sib Family Haplotype Imputation (FSFHap), optimized for full-sib populations, and a generalized method, Fast Inbred Line Library ImputatioN (FILLIN), to rapidly and accurately impute missing genotypes in GBS-type data with ordered markers. FSFHap and FILLIN impute missing genotypes with high accuracy in GBS-genotyped maize (Zea mays L.) inbred lines and breeding populations, while Beagle v. 4 is still preferable for diverse heterozygous populations. FILLIN and FSFHap are implemented in TASSEL 5.0.},
	language = {en},
	number = {3},
	urldate = {2024-03-22},
	journal = {The Plant Genome},
	author = {Swarts, Kelly and Li, Huihui and Romero Navarro, J. Alberto and An, Dong and Romay, Maria Cinta and Hearne, Sarah and Acharya, Charlotte and Glaubitz, Jeffrey C. and Mitchell, Sharon and Elshire, Robert J. and Buckler, Edward S. and Bradbury, Peter J.},
	year = {2014},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.3835/plantgenome2014.05.0023},
	pages = {plantgenome2014.05.0023},
}

Next-generation sequencing technology such as genotyping-by-sequencing (GBS) made low-cost, but often low-coverage, whole-genome sequencing widely available. Extensive inbreeding in crop plants provides an untapped, high quality source of phased haplotypes for imputing missing genotypes. We introduce Full-Sib Family Haplotype Imputation (FSFHap), optimized for full-sib populations, and a generalized method, Fast Inbred Line Library ImputatioN (FILLIN), to rapidly and accurately impute missing genotypes in GBS-type data with ordered markers. FSFHap and FILLIN impute missing genotypes with high accuracy in GBS-genotyped maize (Zea mays L.) inbred lines and breeding populations, while Beagle v. 4 is still preferable for diverse heterozygous populations. FILLIN and FSFHap are implemented in TASSEL 5.0.

@article{nookaraju_enhanced_2014,
	title = {Enhanced accumulation of fatty acids and triacylglycerols in transgenic tobacco stems for enhanced bioenergy production},
	volume = {33},
	issn = {1432-203X},
	url = {https://doi.org/10.1007/s00299-014-1582-y},
	doi = {10.1007/s00299-014-1582-y},
	abstract = {We report a novel approach for enhanced accumulation of fatty acids and triacylglycerols for utilization as biodiesel in transgenic tobacco stems through xylem-specific expression ofArabidopsis DGAT1andLEC2genes.},
	language = {en},
	number = {7},
	urldate = {2023-11-14},
	journal = {Plant Cell Reports},
	author = {Nookaraju, Akula and Pandey, Shashank K. and Fujino, Takeshi and Kim, Ju Young and Suh, Mi Chung and Joshi, Chandrashekhar P.},
	month = jul,
	year = {2014},
	keywords = {Biodiesel, Renewable energy, Tobacco, Triacylglycerols, Xylem},
	pages = {1041--1052},
}

We report a novel approach for enhanced accumulation of fatty acids and triacylglycerols for utilization as biodiesel in transgenic tobacco stems through xylem-specific expression ofArabidopsis DGAT1andLEC2genes.

@article{zhao_weak_2014,
	title = {Weak crossability barrier but strong juvenile selection supports ecological speciation of the hybrid pine {Pinus} {Densata} on the tibetan plateau},
	volume = {68},
	issn = {0014-3820},
	url = {https://doi.org/10.1111/evo.12496},
	doi = {10.1111/evo.12496},
	abstract = {Determining how a new hybrid lineage can achieve reproductive isolation is a key to understanding the process and mechanisms of homoploid hybrid speciation. Here, we evaluated the degree and nature of reproductive isolation between the ecologically successful hybrid species Pinus densata and its parental species P. tabuliformis and P. yunnanensis. We performed interspecific crosses among the three species to assess their crossability. We then conducted reciprocal transplantation experiments to evaluate their fitness differentiation, and to examine how natural populations representing different directions of introgression differ in adaptation. The crossing experiments revealed weak genetic barriers among the species. The transplantation trials showed manifest evidence of local adaptation as the three species all performed best in their native habitats. Pinus densata populations from the western edge of its distribution have evolved a strong local adaptation to the specific habitat in that range; populations representing different directions of introgressants with the two parental species all showed fitness disadvantages in this P. densata habitat. These observations illustrate that premating isolation through selection against immigrants from other habitat types or postzygotic isolation through selection against backcrosses between the three species is strong. Thus, ecological selection in combination with endogenous components and geographic isolation has likely played a significant role in the speciation of P. densata.},
	number = {11},
	urldate = {2023-04-27},
	journal = {Evolution},
	author = {Zhao, Wei and Meng, Jingxiang and Wang, Baosheng and Zhang, Lisha and Xu, Yulan and Zeng, Qing-Yin and Li, Yue and Mao, Jian-Feng and Wang, Xiao-Ru},
	month = nov,
	year = {2014},
	pages = {3120--3133},
}

Determining how a new hybrid lineage can achieve reproductive isolation is a key to understanding the process and mechanisms of homoploid hybrid speciation. Here, we evaluated the degree and nature of reproductive isolation between the ecologically successful hybrid species Pinus densata and its parental species P. tabuliformis and P. yunnanensis. We performed interspecific crosses among the three species to assess their crossability. We then conducted reciprocal transplantation experiments to evaluate their fitness differentiation, and to examine how natural populations representing different directions of introgression differ in adaptation. The crossing experiments revealed weak genetic barriers among the species. The transplantation trials showed manifest evidence of local adaptation as the three species all performed best in their native habitats. Pinus densata populations from the western edge of its distribution have evolved a strong local adaptation to the specific habitat in that range; populations representing different directions of introgressants with the two parental species all showed fitness disadvantages in this P. densata habitat. These observations illustrate that premating isolation through selection against immigrants from other habitat types or postzygotic isolation through selection against backcrosses between the three species is strong. Thus, ecological selection in combination with endogenous components and geographic isolation has likely played a significant role in the speciation of P. densata.

@article{xing_needle_2014,
	title = {Needle morphological evidence of the homoploid hybrid origin of {Pinus} densata based on analysis of artificial hybrids and the putative parents, {Pinus} tabuliformis and {Pinus} yunnanensis},
	volume = {4},
	issn = {2045-7758},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.1062},
	doi = {10.1002/ece3.1062},
	abstract = {Genetic analyses indicate that Pinus densata is a natural homoploid hybrid originating from Pinus tabuliformis and Pinus yunnanensis. Needle morphological and anatomical features show relative species stability and can be used to identify coniferous species. Comparative analyses of these needle characteristics and phenotypic differences between the artificial hybrids, P. densata, and parental species can be used to determine the genetic and phenotypic evolutionary consequences of natural hybridization. Twelve artificial hybrid families, the two parental species, and P. densata were seeded in a high-altitude habitat in Linzhi, Tibet. The needles of artificial hybrids and the three pine species were collected, and 24 needle morphological and anatomical traits were analyzed. Based on these results, variations in 10 needle traits among artificial hybrid families and 22 traits among species and artificial hybrids were predicted and found to be under moderate genetic control. Nineteen needle traits in artificial hybrids were similar to those in P. densata and between the two parental species, P. tabuliformis and P. yunnanensis. The ratio of plants with three needle clusters in artificial hybrids was 22.92\%, which was very similar to P. densata. The eight needle traits (needle length, the mean number of stomata in sections 2 mm in length of the convex and flat sides of the needle, mean stomatal density, mesophyll/vascular bundle area ratio, mesophyll/resin canal area ratio, mesophyll/(resin canals and vascular bundles) area ratio, vascular bundle/resin canal area ratio) relative to physiological adaptability were similar to the artificial hybrids and P. densata. The similar needle features between the artificial hybrids and P. densata could be used to verify the homoploid hybrid origin of P. densata and helps to better understand of the hybridization roles in adaptation and speciation in plants.},
	language = {en},
	number = {10},
	urldate = {2023-04-27},
	journal = {Ecology and Evolution},
	author = {Xing, Fangqian and Mao, Jian-Feng and Meng, Jingxiang and Dai, Jianfeng and Zhao, Wei and Liu, Hao and Xing, Zhen and Zhang, Hua and Wang, Xiao-Ru and Li, Yue},
	year = {2014},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.1062},
	keywords = {Anatomy, Pinus densata, Pinus tabuliformis, Pinus yunnanensis, artificial hybrid, morphology},
	pages = {1890--1902},
}

Genetic analyses indicate that Pinus densata is a natural homoploid hybrid originating from Pinus tabuliformis and Pinus yunnanensis. Needle morphological and anatomical features show relative species stability and can be used to identify coniferous species. Comparative analyses of these needle characteristics and phenotypic differences between the artificial hybrids, P. densata, and parental species can be used to determine the genetic and phenotypic evolutionary consequences of natural hybridization. Twelve artificial hybrid families, the two parental species, and P. densata were seeded in a high-altitude habitat in Linzhi, Tibet. The needles of artificial hybrids and the three pine species were collected, and 24 needle morphological and anatomical traits were analyzed. Based on these results, variations in 10 needle traits among artificial hybrid families and 22 traits among species and artificial hybrids were predicted and found to be under moderate genetic control. Nineteen needle traits in artificial hybrids were similar to those in P. densata and between the two parental species, P. tabuliformis and P. yunnanensis. The ratio of plants with three needle clusters in artificial hybrids was 22.92%, which was very similar to P. densata. The eight needle traits (needle length, the mean number of stomata in sections 2 mm in length of the convex and flat sides of the needle, mean stomatal density, mesophyll/vascular bundle area ratio, mesophyll/resin canal area ratio, mesophyll/(resin canals and vascular bundles) area ratio, vascular bundle/resin canal area ratio) relative to physiological adaptability were similar to the artificial hybrids and P. densata. The similar needle features between the artificial hybrids and P. densata could be used to verify the homoploid hybrid origin of P. densata and helps to better understand of the hybridization roles in adaptation and speciation in plants.

@article{dong_strategy_2014,
	title = {A strategy for characterization of persistent heteroduplex {DNA} in higher plants},
	volume = {80},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.12631},
	doi = {10.1111/tpj.12631},
	abstract = {Heteroduplex DNA (hDNA) generated during homologous recombination (HR) is an important component that shapes genetic diversity in sexually reproducing organisms. However, studies of this process in higher plants are limited. This is because hDNAs are difficult to capture in higher plants as their reproductive developmental model only produces normal gametes and does not preserve the mitotic products of the post-meiotic segregation (PMS) process which is crucial for studying hDNAs. In this study, using the model system for tree and woody perennial plant biology (Populus), we propose a strategy for characterizing hDNAs in higher plants. We captured hDNAs by constructing triploid hybrids originating from a cross between unreduced 2n eggs (containing hDNA information as a result of inhibition chromosome segregation at the PMS stage) with normal male gametes. These triploid hybrids allowed us to detect the frequency and location of persistent hDNAs resulting from HR at the molecular level. We found that the frequency of persistent hDNAs, which ranged from 5.3 to 76.6\%, was related to locations of the simple sequence repeat markers at the chromosomes, such as the locus–centromere distance, the surrounding DNA sequence and epigenetic information, and the richness of protein-coding transcripts at these loci. In summary, this study provides a method for characterizing persistent hDNAs in higher plants. When high-throughput sequencing techniques can be incorporated, genome-wide persistent hDNA assays for higher plants can be easily carried out using the strategy presented in this study.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {The Plant Journal},
	author = {Dong, Chun-Bo and Mao, Jian-Feng and Suo, Yu-Jing and Shi, Le and Wang, Jun and Zhang, Ping-Dong and Kang, Xiang-Yang},
	year = {2014},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.12631},
	keywords = {Populus pseudo-simonii × Populus nigra ‘Zheyin3\#’, Populus × beijingensis, heteroduplex DNA, post-meiotic segregation, triploid},
	pages = {282--291},
}

Heteroduplex DNA (hDNA) generated during homologous recombination (HR) is an important component that shapes genetic diversity in sexually reproducing organisms. However, studies of this process in higher plants are limited. This is because hDNAs are difficult to capture in higher plants as their reproductive developmental model only produces normal gametes and does not preserve the mitotic products of the post-meiotic segregation (PMS) process which is crucial for studying hDNAs. In this study, using the model system for tree and woody perennial plant biology (Populus), we propose a strategy for characterizing hDNAs in higher plants. We captured hDNAs by constructing triploid hybrids originating from a cross between unreduced 2n eggs (containing hDNA information as a result of inhibition chromosome segregation at the PMS stage) with normal male gametes. These triploid hybrids allowed us to detect the frequency and location of persistent hDNAs resulting from HR at the molecular level. We found that the frequency of persistent hDNAs, which ranged from 5.3 to 76.6%, was related to locations of the simple sequence repeat markers at the chromosomes, such as the locus–centromere distance, the surrounding DNA sequence and epigenetic information, and the richness of protein-coding transcripts at these loci. In summary, this study provides a method for characterizing persistent hDNAs in higher plants. When high-throughput sequencing techniques can be incorporated, genome-wide persistent hDNA assays for higher plants can be easily carried out using the strategy presented in this study.

@article{brandt_homeodomain_2014,
	title = {Homeodomain leucine-zipper proteins and their role in synchronizing growth and development with the environment},
	volume = {56},
	issn = {1744-7909},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jipb.12185},
	doi = {10.1111/jipb.12185},
	abstract = {The Arabidopsis (Arabidopsis thaliana L.) genome encodes for four distinct classes of homeodomain leucine-zipper (HD-ZIP) transcription factors (HD-ZIPI to HD-ZIPIV), which are all organized in multi-gene families. HD-ZIP transcription factors act as sequence-specific DNA-binding proteins that are able to control the expression level of target genes. While HD-ZIPI and HD-ZIPII proteins are mainly associated with environmental responses, HD-ZIPIII and HD-ZIPIV are primarily known to act as patterning factors. Recent studies have challenged this view. It appears that several of the different HD-ZIP families interact genetically to align both morphogenesis and environmental responses, most likely by modulating phytohormone-signaling networks.},
	language = {en},
	number = {6},
	urldate = {2022-11-30},
	journal = {Journal of Integrative Plant Biology},
	author = {Brandt, Ronny and Cabedo, Marc and Xie, Yakun and Wenkel, Stephan},
	year = {2014},
	keywords = {KANADI, REVOLUTA, Transcription factors, abscisic acid, auxin, homeodomain, leaf development, leucine zipper, light signaling, microRNA, water stress},
	pages = {518--526},
}

The Arabidopsis (Arabidopsis thaliana L.) genome encodes for four distinct classes of homeodomain leucine-zipper (HD-ZIP) transcription factors (HD-ZIPI to HD-ZIPIV), which are all organized in multi-gene families. HD-ZIP transcription factors act as sequence-specific DNA-binding proteins that are able to control the expression level of target genes. While HD-ZIPI and HD-ZIPII proteins are mainly associated with environmental responses, HD-ZIPIII and HD-ZIPIV are primarily known to act as patterning factors. Recent studies have challenged this view. It appears that several of the different HD-ZIP families interact genetically to align both morphogenesis and environmental responses, most likely by modulating phytohormone-signaling networks.

@article{xie_revoluta_2014,
	title = {{REVOLUTA} and {WRKY53} connect early and late leaf development in {Arabidopsis}},
	volume = {141},
	issn = {0950-1991},
	url = {https://doi.org/10.1242/dev.117689},
	doi = {10.1242/dev.117689},
	abstract = {As sessile organisms, plants have to continuously adjust growth and development to ever-changing environmental conditions. At the end of the growing season, annual plants induce leaf senescence to reallocate nutrients and energy-rich substances from the leaves to the maturing seeds. Thus, leaf senescence is a means with which to increase reproductive success and is therefore tightly coupled to the developmental age of the plant. However, senescence can also be induced in response to sub-optimal growth conditions as an exit strategy, which is accompanied by severely reduced yield. Here, we show that class III homeodomain leucine zipper (HD-ZIPIII) transcription factors, which are known to be involved in basic pattern formation, have an additional role in controlling the onset of leaf senescence in Arabidopsis. Several potential direct downstream genes of the HD-ZIPIII protein REVOLUTA (REV) have known roles in environment-controlled physiological processes. We report that REV acts as a redox-sensitive transcription factor, and directly and positively regulates the expression of WRKY53, a master regulator of age-induced leaf senescence. HD-ZIPIII proteins are required for the full induction of WRKY53 in response to oxidative stress, and mutations in HD-ZIPIII genes strongly delay the onset of senescence. Thus, a crosstalk between early and late stages of leaf development appears to contribute to reproductive success.},
	number = {24},
	urldate = {2022-11-30},
	journal = {Development},
	author = {Xie, Yakun and Huhn, Kerstin and Brandt, Ronny and Potschin, Maren and Bieker, Stefan and Straub, Daniel and Doll, Jasmin and Drechsler, Thomas and Zentgraf, Ulrike and Wenkel, Stephan},
	month = dec,
	year = {2014},
	pages = {4772--4783},
}

As sessile organisms, plants have to continuously adjust growth and development to ever-changing environmental conditions. At the end of the growing season, annual plants induce leaf senescence to reallocate nutrients and energy-rich substances from the leaves to the maturing seeds. Thus, leaf senescence is a means with which to increase reproductive success and is therefore tightly coupled to the developmental age of the plant. However, senescence can also be induced in response to sub-optimal growth conditions as an exit strategy, which is accompanied by severely reduced yield. Here, we show that class III homeodomain leucine zipper (HD-ZIPIII) transcription factors, which are known to be involved in basic pattern formation, have an additional role in controlling the onset of leaf senescence in Arabidopsis. Several potential direct downstream genes of the HD-ZIPIII protein REVOLUTA (REV) have known roles in environment-controlled physiological processes. We report that REV acts as a redox-sensitive transcription factor, and directly and positively regulates the expression of WRKY53, a master regulator of age-induced leaf senescence. HD-ZIPIII proteins are required for the full induction of WRKY53 in response to oxidative stress, and mutations in HD-ZIPIII genes strongly delay the onset of senescence. Thus, a crosstalk between early and late stages of leaf development appears to contribute to reproductive success.

@article{sylak-glassman_distinct_2014,
	title = {Distinct roles of the photosystem {II} protein {PsbS} and zeaxanthin in the regulation of light harvesting in plants revealed by fluorescence lifetime snapshots},
	volume = {111},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1418317111},
	doi = {10/f6sjhj},
	abstract = {The photosystem II (PSII) protein PsbS and the enzyme violaxanthin deepoxidase (VDE) are known to influence the dynamics of energy-dependent quenching (qE), the component of nonphotochemical quenching (NPQ) that allows plants to respond to fast fluctuations in light intensity. Although the absence of PsbS and VDE has been shown to change the amount of quenching, there have not been any measurements that can detect whether the presence of these proteins alters the type of quenching that occurs. The chlorophyll fluorescence lifetime probes the excited-state chlorophyll relaxation dynamics and can be used to determine the amount of quenching as well as whether two different genotypes with the same amount of NPQ have similar dynamics of excited-state chlorophyll relaxation. We measured the fluorescence lifetimes on whole leaves of Arabidopsis thaliana throughout the induction and relaxation of NPQ for wild type and the qE mutants, npq4, which lacks PsbS; npq1, which lacks VDE and cannot convert violaxanthin to zeaxanthin; and npq1 npq4, which lacks both VDE and PsbS. These measurements show that although PsbS changes the amount of quenching and the rate at which quenching turns on, it does not affect the relaxation dynamics of excited chlorophyll during quenching. In addition, the data suggest that PsbS responds not only to ΔpH but also to the Δψ across the thylakoid membrane. In contrast, the presence of VDE, which is necessary for the accumulation of zeaxanthin, affects the excited-state chlorophyll relaxation dynamics.},
	language = {en},
	number = {49},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Sylak-Glassman, Emily J. and Malnoë, Alizée and De Re, Eleonora and Brooks, Matthew D. and Fischer, Alexandra Lee and Niyogi, Krishna K. and Fleming, Graham R.},
	month = dec,
	year = {2014},
	pages = {17498--17503},
}

The photosystem II (PSII) protein PsbS and the enzyme violaxanthin deepoxidase (VDE) are known to influence the dynamics of energy-dependent quenching (qE), the component of nonphotochemical quenching (NPQ) that allows plants to respond to fast fluctuations in light intensity. Although the absence of PsbS and VDE has been shown to change the amount of quenching, there have not been any measurements that can detect whether the presence of these proteins alters the type of quenching that occurs. The chlorophyll fluorescence lifetime probes the excited-state chlorophyll relaxation dynamics and can be used to determine the amount of quenching as well as whether two different genotypes with the same amount of NPQ have similar dynamics of excited-state chlorophyll relaxation. We measured the fluorescence lifetimes on whole leaves of Arabidopsis thaliana throughout the induction and relaxation of NPQ for wild type and the qE mutants, npq4, which lacks PsbS; npq1, which lacks VDE and cannot convert violaxanthin to zeaxanthin; and npq1 npq4, which lacks both VDE and PsbS. These measurements show that although PsbS changes the amount of quenching and the rate at which quenching turns on, it does not affect the relaxation dynamics of excited chlorophyll during quenching. In addition, the data suggest that PsbS responds not only to ΔpH but also to the Δψ across the thylakoid membrane. In contrast, the presence of VDE, which is necessary for the accumulation of zeaxanthin, affects the excited-state chlorophyll relaxation dynamics.

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

The transition from vegetative to reproductive development, or floral transition, is a crucial event in the life cycle of plants. Work carried out over the last decades has shown how environmental signals, such as seasonal changes in the day length and temperature, are perceived and accurately integrated into genetically defined pathways to properly time the induction of flowering. In addition to seasonal fluctuations, plants must cope with a vast array of often stressful conditions that greatly affect metabolism and physiology. In this context, plant hormones and sugars have emerged as important endogenous signalling molecules mediating the transition to the reproductive phase. In this chapter we report the recent advances in understanding the molecular basis underlying the transition to flowering in response to these endogenous signals.

@article{boussardon_cytidine_2014,
	title = {The cytidine deaminase signature {HxE}(x){nCxxC} of {DYW1} binds zinc and is necessary for {RNA} editing of {ndhD}-1},
	volume = {203},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.12928},
	doi = {10/f6cv49},
	abstract = {In flowering plants, RNA editing involves deamination of specific cytidines to uridines in both mitochondrial and chloroplast transcripts. Pentatricopeptide repeat (PPR) proteins and multiple organellar RNA editing factor (MORF) proteins have been shown to be involved in RNA editing but none have been shown to possess cytidine deaminase activity. The DYW domain of some PPR proteins contains a highly conserved signature resembling the zinc-binding active site motif of known nucleotide deaminases. We modified these highly conserved amino acids in the DYW motif of DYW1, an editing factor required for editing of the ndhD-1 site in Arabidopsis chloroplasts. We demonstrate that several amino acids of this signature motif are required for RNA editing in vivo and for zinc binding in vitro. We conclude that the DYW domain of DYW1 has features in common with cytidine deaminases, reinforcing the hypothesis that this domain forms part of the active enzyme that carries out RNA editing in plants.},
	language = {en},
	number = {4},
	urldate = {2021-09-02},
	journal = {New Phytologist},
	author = {Boussardon, Clément and Avon, Alexandra and Kindgren, Peter and Bond, Charles S. and Challenor, Michael and Lurin, Claire and Small, Ian},
	year = {2014},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.12928},
	keywords = {DYW domain, RNA editing, cytidine deaminase, pentatricopeptide repeat (PPR) proteins, zinc-binding motif},
	pages = {1090--1095},
}

In flowering plants, RNA editing involves deamination of specific cytidines to uridines in both mitochondrial and chloroplast transcripts. Pentatricopeptide repeat (PPR) proteins and multiple organellar RNA editing factor (MORF) proteins have been shown to be involved in RNA editing but none have been shown to possess cytidine deaminase activity. The DYW domain of some PPR proteins contains a highly conserved signature resembling the zinc-binding active site motif of known nucleotide deaminases. We modified these highly conserved amino acids in the DYW motif of DYW1, an editing factor required for editing of the ndhD-1 site in Arabidopsis chloroplasts. We demonstrate that several amino acids of this signature motif are required for RNA editing in vivo and for zinc binding in vitro. We conclude that the DYW domain of DYW1 has features in common with cytidine deaminases, reinforcing the hypothesis that this domain forms part of the active enzyme that carries out RNA editing in plants.

@article{la_rosa_large-scale_2014,
	title = {Large-{Scale} {Identification} of {Gibberellin}-{Related} {Transcription} {Factors} {Defines} {Group} {VII} {ETHYLENE} {RESPONSE} {FACTORS} as {Functional} {DELLA} {Partners}},
	volume = {166},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/166/2/1022-1032/6113228},
	doi = {10/f3p5k4},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {PLANT PHYSIOLOGY},
	author = {la Rosa, N. M.-d. and Sotillo, B. and Miskolczi, P. and Gibbs, D. J. and Vicente, J. and Carbonero, P. and Onate-Sanchez, L. and Holdsworth, M. J. and Bhalerao, Rishikesh P. and Alabadi, D. and Blazquez, M. A.},
	month = oct,
	year = {2014},
	pages = {1022--1032},
}

@article{lallement_still_2014,
	title = {The still mysterious roles of cysteine-containing glutathione transferases in plants},
	volume = {5},
	issn = {1663-9812},
	url = {http://journal.frontiersin.org/article/10.3389/fphar.2014.00192/abstract},
	doi = {10/f3n4qc},
	urldate = {2021-06-08},
	journal = {Frontiers in Pharmacology},
	author = {Lallement, Pierre-Alexandre and Brouwer, Bastiaan and Keech, Olivier and Hecker, Arnaud and Rouhier, Nicolas},
	month = aug,
	year = {2014},
}

@article{zhang_pirin2_2014,
	title = {{PIRIN2} stabilizes cysteine protease {XCP2} and increases susceptibility to the vascular pathogen {Ralstonia} solanacearum in {Arabidopsis}},
	volume = {79},
	copyright = {© 2014 The Authors The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.12602},
	doi = {10/f24qpz},
	abstract = {PIRIN (PRN) is a member of the functionally diverse cupin protein superfamily. There are four members of the Arabidopsis thaliana PRN family, but the roles of these proteins are largely unknown. Here we describe a function of the Arabidopsis PIRIN2 (PRN2) that is related to susceptibility to the bacterial plant pathogen Ralstonia solanacearum. Two prn2 mutant alleles displayed decreased disease development and bacterial growth in response to R. solanacearum infection. We elucidated the underlying molecular mechanism by analyzing PRN2 interactions with the papain-like cysteine proteases (PLCPs) XCP2, RD21A, and RD21B, all of which bound to PRN2 in yeast two-hybrid assays and in Arabidopsis protoplast co-immunoprecipitation assays. We show that XCP2 is stabilized by PRN2 through inhibition of its autolysis on the basis of PLCP activity profiling assays and enzymatic assays with recombinant protein. The stabilization of XCP2 by PRN2 was also confirmed in planta. Like prn2 mutants, an xcp2 single knockout mutant and xcp2 prn2 double knockout mutant displayed decreased susceptibility to R. solanacearum, suggesting that stabilization of XCP2 by PRN2 underlies susceptibility to R. solanacearum in Arabidopsis.},
	language = {en},
	number = {6},
	urldate = {2021-06-21},
	journal = {The Plant Journal},
	author = {Zhang, Bo and Tremousaygue, Dominique and Denancé, Nicolas and Esse, H. Peter van and Hörger, Anja C. and Dabos, Patrick and Goffner, Deborah and Thomma, Bart P. H. J. and Hoorn, Renier A. L. van der and Tuominen, Hannele},
	year = {2014},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.12602},
	keywords = {Arabidopsis thaliana, PIRIN2, Ralstonia solanacearum, XCP2, papain-like cysteine protease, vascular pathogen},
	pages = {1009--1019},
}

PIRIN (PRN) is a member of the functionally diverse cupin protein superfamily. There are four members of the Arabidopsis thaliana PRN family, but the roles of these proteins are largely unknown. Here we describe a function of the Arabidopsis PIRIN2 (PRN2) that is related to susceptibility to the bacterial plant pathogen Ralstonia solanacearum. Two prn2 mutant alleles displayed decreased disease development and bacterial growth in response to R. solanacearum infection. We elucidated the underlying molecular mechanism by analyzing PRN2 interactions with the papain-like cysteine proteases (PLCPs) XCP2, RD21A, and RD21B, all of which bound to PRN2 in yeast two-hybrid assays and in Arabidopsis protoplast co-immunoprecipitation assays. We show that XCP2 is stabilized by PRN2 through inhibition of its autolysis on the basis of PLCP activity profiling assays and enzymatic assays with recombinant protein. The stabilization of XCP2 by PRN2 was also confirmed in planta. Like prn2 mutants, an xcp2 single knockout mutant and xcp2 prn2 double knockout mutant displayed decreased susceptibility to R. solanacearum, suggesting that stabilization of XCP2 by PRN2 underlies susceptibility to R. solanacearum in Arabidopsis.

@article{bhalerao_auxin_2014,
	title = {Auxin gradients across wood - instructive or incidental?},
	volume = {151},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12134},
	doi = {10/f3p7dx},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Bhalerao, Rishikesh P. and Fischer, Urs},
	month = may,
	year = {2014},
	pages = {43--51},
}

@article{suorsa_dark-adapted_2014,
	title = {Dark-adapted spinach thylakoid protein heterogeneity offers insights into the photosystem {II} repair cycle},
	volume = {1837},
	issn = {00052728},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272813002089},
	doi = {10/f22f4c},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Suorsa, Marjaana and Rantala, Marjaana and Danielsson, Ravi and Järvi, Sari and Paakkarinen, Virpi and Schröder, Wolfgang P. and Styring, Stenbjörn and Mamedov, Fikret and Aro, Eva-Mari},
	month = sep,
	year = {2014},
	pages = {1463--1471},
}

@article{ma_auxin_2014,
	title = {Auxin biology revealed by small molecules},
	volume = {151},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12128},
	doi = {10/f3p65j},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Ma, Qian and Robert, Stéphanie},
	month = may,
	year = {2014},
	pages = {25--42},
}

@article{decker_luminescence-based_2014,
	title = {A luminescence-based assay of {UDP}-sugar producing pyrophosphorylases},
	volume = {6},
	issn = {1759-9660, 1759-9679},
	url = {http://xlink.rsc.org/?DOI=C3AY41811A},
	doi = {10/f2z926},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Anal. Methods},
	author = {Decker, Daniel and Lindberg, Stina and Eriksson, Jonas and Kleczkowski, Leszek A.},
	year = {2014},
	pages = {57--61},
}

@article{marino_family-wide_2014,
	title = {Family-wide characterization of matrix metalloproteinases from {Arabidopsis} thaliana reveals their distinct proteolytic activity and cleavage site specificity},
	volume = {457},
	issn = {0264-6021, 1470-8728},
	url = {https://portlandpress.com/biochemj/article/457/2/335/46342/Familywide-characterization-of-matrix},
	doi = {10/f23tpd},
	abstract = {The five recombinant MMP-like proteins of Arabidopsis thaliana have specific biochemical properties. Detailed analysis of their sequence specificity using proteomic identification of protease cleavage sites revealed cleavage profiles similar to human MMPs.},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Biochemical Journal},
	author = {Marino, Giada and Huesgen, Pitter F. and Eckhard, Ulrich and Overall, Christopher M. and Schröder, Wolfgang P. and Funk, Christiane},
	month = jan,
	year = {2014},
	pages = {335--346},
}

The five recombinant MMP-like proteins of Arabidopsis thaliana have specific biochemical properties. Detailed analysis of their sequence specificity using proteomic identification of protease cleavage sites revealed cleavage profiles similar to human MMPs.

@article{gundale_anthropogenic_2014,
	title = {Anthropogenic nitrogen deposition in boreal forests has a minor impact on the global carbon cycle},
	volume = {20},
	issn = {13541013},
	url = {http://doi.wiley.com/10.1111/gcb.12422},
	doi = {10/f2zqdf},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Global Change Biology},
	author = {Gundale, Michael J. and From, Fredrik and Bach, Lisbet H. and Nordin, Annika},
	month = jan,
	year = {2014},
	pages = {276--286},
}

@article{disante_alleviation_2014,
	title = {Alleviation of {Zn} toxicity by low water availability},
	volume = {150},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12095},
	doi = {10/f25dnq},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Disante, Karen B. and Cortina, Jordi and Vilagrosa, Alberto and Fuentes, David and Hernández, Encarni I. and Ljung, Karin},
	month = mar,
	year = {2014},
	pages = {412--424},
}

@article{mounier_auxin-mediated_2014,
	title = {Auxin-mediated nitrate signalling by {NRT1}.1 participates in the adaptive response of \textit{{Arabidopsis}} root architecture to the spatial heterogeneity of nitrate availability: {Nitrate} signalling by {NRT1}.1},
	volume = {37},
	issn = {01407791},
	shorttitle = {Auxin-mediated nitrate signalling by {NRT1}.1 participates in the adaptive response of \textit{{Arabidopsis}} root architecture to the spatial heterogeneity of nitrate availability},
	url = {http://doi.wiley.com/10.1111/pce.12143},
	doi = {10/f24x7s},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant, Cell \& Environment},
	author = {Mounier, Emmanuelle and Pervent, Marjorie and Ljung, Karin and Gojon, Alain and Nacry, Philippe},
	month = jan,
	year = {2014},
	pages = {162--174},
}

@article{maharjan_arabidopsis_2014,
	title = {Arabidopsis \textit{gulliver1/superroot2‐7} identifies a metabolic basis for auxin and brassinosteroid synergy},
	volume = {80},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.12678},
	doi = {10/f3m3r2},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Maharjan, Puna M. and Dilkes, Brian P. and Fujioka, Shozo and Pěnčík, Aleš and Ljung, Karin and Burow, Meike and Halkier, Barbara A. and Choe, Sunghwa},
	month = dec,
	year = {2014},
	pages = {797--808},
}

@article{nasholm_genetics_2014,
	title = {Genetics of superior growth traits in trees are being mapped but will the faster-growing risk-takers make it in the wild?},
	volume = {34},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpu112},
	doi = {10/f3p5bh},
	language = {en},
	number = {11},
	urldate = {2021-06-08},
	journal = {Tree Physiology},
	author = {Nasholm, T. and Palmroth, S. and Ganeteg, U. and Moshelion, M. and Hurry, V. and Franklin, O.},
	month = nov,
	year = {2014},
	pages = {1141--1148},
}

@article{gerber_using_2014,
	title = {Using imaging {ToF}‐{SIMS} data to determine the cell wall thickness of fibers in wood},
	volume = {46},
	issn = {0142-2421, 1096-9918},
	url = {https://onlinelibrary.wiley.com/doi/10.1002/sia.5661},
	doi = {10/f25k78},
	language = {en},
	number = {S1},
	urldate = {2021-06-08},
	journal = {Surface and Interface Analysis},
	author = {Gerber, Lorenz and Hoang, Viet Mai and Tran, Linh and Kiet, Hoang Anh Tuan and Malmberg, Per and Hanrieder, Jörg and Ewing, Andrew},
	month = nov,
	year = {2014},
	pages = {225--228},
}

@article{franklin_how_2014,
	title = {How eco-evolutionary principles can guide tree breeding and tree biotechnology for enhanced productivity},
	volume = {34},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpu111},
	doi = {10/f3m28v},
	language = {en},
	number = {11},
	urldate = {2021-06-08},
	journal = {Tree Physiology},
	author = {Franklin, O. and Palmroth, S. and Nasholm, T.},
	month = nov,
	year = {2014},
	pages = {1149--1166},
}

@article{lin_effect_2014,
	title = {Effect of genotype-by-spacing interaction on radiata pine wood density},
	volume = {77},
	issn = {0004-9158},
	url = {http://www.tandfonline.com/doi/abs/10.1080/00049158.2014.980878},
	doi = {10/f3p3hg},
	language = {en},
	number = {3-4},
	urldate = {2021-06-08},
	journal = {Australian Forestry},
	author = {Lin, Yuanzhen and Yang, Huixiao and Ivković, Miloš and Gapare, Washington J. and Matheson, A. Colin and Wu, Harry X.},
	month = oct,
	year = {2014},
	pages = {203--211},
}

@article{keefover-ring_phenylpropanoid_2014,
	title = {Phenylpropanoid glycosides of {Mimulus} guttatus (yellow monkeyflower)},
	volume = {10},
	issn = {18743900},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1874390014001529},
	doi = {10/f3nswx},
	language = {en},
	urldate = {2021-06-08},
	journal = {Phytochemistry Letters},
	author = {Keefover-Ring, Ken and Holeski, Liza M. and Bowers, M. Deane and Clauss, Allen D. and Lindroth, Richard L.},
	month = dec,
	year = {2014},
	pages = {132--139},
}

@article{viaene_directional_2014,
	title = {Directional {Auxin} {Transport} {Mechanisms} in {Early} {Diverging} {Land} {Plants}},
	volume = {24},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982214012196},
	doi = {10/f3pxg8},
	language = {en},
	number = {23},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Viaene, Tom and Landberg, Katarina and Thelander, Mattias and Medvecka, Eva and Pederson, Eric and Feraru, Elena and Cooper, Endymion D. and Karimi, Mansour and Delwiche, Charles F. and Ljung, Karin and Geisler, Markus and Sundberg, Eva and Friml, Jiří},
	month = dec,
	year = {2014},
	pages = {2786--2791},
}

@article{gamm_increased_2014,
	title = {Increased sucrose levels mediate selective {mRNA} translation in {Arabidopsis}},
	volume = {14},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0306-3},
	doi = {10/f3nrb4},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Gamm, Magdalena and Peviani, Alessia and Honsel, Anne and Snel, Berend and Smeekens, Sjef and Hanson, Johannes},
	month = dec,
	year = {2014},
	pages = {306},
}

@article{fries_stem_2014,
	title = {Stem damage of lodgepole pine clonal cuttings in relation to wood and fiber traits, acoustic velocity, and spiral grain},
	volume = {29},
	issn = {0282-7581, 1651-1891},
	url = {http://www.tandfonline.com/doi/abs/10.1080/02827581.2014.978886},
	doi = {10/f3pxdm},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Scandinavian Journal of Forest Research},
	author = {Fries, Anders and Ulvcrona, Thomas and Wu, Harry X. and Kroon, Johan},
	month = nov,
	year = {2014},
	pages = {764--776},
}

@article{li_characterizing_2014,
	title = {Characterizing compression wood formed in radiata pine branches},
	volume = {35},
	issn = {0928-1541, 2294-1932},
	url = {https://brill.com/view/journals/iawa/35/4/article-p385_4.xml},
	doi = {10/f3p3vv},
	abstract = {The formation of reaction wood is an adaptive feature of trees in response to various mechanical forces. In gymnosperms, reaction wood consists of compression wood (CW) and opposite wood (OW) that are formed on the underside and upperside of bent trunks and branches. Although reaction wood formed in bent trunks has been extensively investigated, relatively little has been reported from conifer branches. In this study SilviScan® technology was used to characterize radiata pine branches at high resolution. Compared to OW formed in the branches, CW showed greater growth, darker colour, thicker tracheid walls, higher coarseness, larger microfibril angle (MFA), higher wood density, lower extensional stiffness and smaller internal specific surface area. However, tracheids of CW were similar to those of OW in their radial and tangential diameters. These results indicated that gravity influenced tracheid cell division and secondary wall formation but had limited impact on primary wall expansion. Furthermore, seasonal patterns of CW formation were not observed in the branches from cambial age 4 while earlywood and latewood were clearly separated in all rings of OW. The marked change of MFA during reaction wood formation suggested that branches could be ideal materials for further study of cellulose microfibril orientation.},
	number = {4},
	urldate = {2021-06-08},
	journal = {IAWA Journal},
	author = {Li, Xinguo and Evans, Robert and Gapare, Washington and Yang, Xiaohui and Wu, Harry X.},
	month = dec,
	year = {2014},
	pages = {385--394},
}

The formation of reaction wood is an adaptive feature of trees in response to various mechanical forces. In gymnosperms, reaction wood consists of compression wood (CW) and opposite wood (OW) that are formed on the underside and upperside of bent trunks and branches. Although reaction wood formed in bent trunks has been extensively investigated, relatively little has been reported from conifer branches. In this study SilviScan® technology was used to characterize radiata pine branches at high resolution. Compared to OW formed in the branches, CW showed greater growth, darker colour, thicker tracheid walls, higher coarseness, larger microfibril angle (MFA), higher wood density, lower extensional stiffness and smaller internal specific surface area. However, tracheids of CW were similar to those of OW in their radial and tangential diameters. These results indicated that gravity influenced tracheid cell division and secondary wall formation but had limited impact on primary wall expansion. Furthermore, seasonal patterns of CW formation were not observed in the branches from cambial age 4 while earlywood and latewood were clearly separated in all rings of OW. The marked change of MFA during reaction wood formation suggested that branches could be ideal materials for further study of cellulose microfibril orientation.

@article{mahler_synergy_2014,
	title = {Synergy: {A} {Web} {Resource} for {Exploring} {Gene} {Regulation} in {Synechocystis} sp. {PCC6803}},
	volume = {9},
	issn = {1932-6203},
	shorttitle = {Synergy},
	url = {https://dx.plos.org/10.1371/journal.pone.0113496},
	doi = {10/f3nwpw},
	language = {en},
	number = {11},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Mähler, Niklas and Cheregi, Otilia and Funk, Christiane and Netotea, Sergiu and Hvidsten, Torgeir R.},
	editor = {Mariño-Ramírez, Leonardo},
	month = nov,
	year = {2014},
	pages = {e113496},
}

@incollection{sanchez-serrano_immunocytochemical_2014,
	address = {Totowa, NJ},
	title = {Immunocytochemical {Fluorescent} {In} {Situ} {Visualization} of {Proteins} {In} {Arabidopsis}},
	volume = {1062},
	isbn = {978-1-62703-579-8 978-1-62703-580-4},
	url = {http://link.springer.com/10.1007/978-1-62703-580-4_24},
	urldate = {2021-06-08},
	booktitle = {Arabidopsis {Protocols}},
	publisher = {Humana Press},
	author = {Boutté, Yohann and Grebe, Markus},
	editor = {Sanchez-Serrano, Jose J. and Salinas, Julio},
	year = {2014},
	doi = {10.1007/978-1-62703-580-4_24},
	note = {Series Title: Methods in Molecular Biology},
	pages = {453--472},
}

@article{zhang_comparison_2014,
	title = {Comparison of allelic diversity between native gene resource plantings and selections in open-pollinated progeny test of {Pinus} radiata {D}. {Don}.},
	volume = {63},
	issn = {2509-8934},
	url = {https://www.sciendo.com/article/10.1515/sg-2014-0027},
	doi = {10/gjcm3w},
	abstract = {Genetic diversity within radiata pine first generation of open-pollinated selections (OPS) from the native resource stands was compared with that observed in native populations to monitor potential changes in genetic diversity during domestication. Genetic diversity was estimated using 58 single nucleotide polymorphisms (SNPs) from 8 expressed genes. Nucleotide diversity maintained in first generation of selections (OPS) (mean ␲ = 0.0036; mean ␪w = 0.0058) was similar to that found within the native population material (mean ␲ = 0.0043; mean for ␪w = 0.0065). Likewise, mean values for expected heterozygosity (H ) within E and between native population material and OPS were similar (mean = 0.27 ± 0.04) and not significantly different (P = 0.068). Also, the overall distribution of allele frequency classes was not significantly different between native population material and OPS. These results point to no evidence of loss of diversity in OPS due to artificial selection. One possible reason is that the domestication of the OPS is at a very early stage. Another may be that artificial selection in the OPS was based on tree growth and form, not wood properties. The genes selected in this study are mostly involved in cell wall formation, thus genetic diversity of these genes should remain stable between natural population and OPS, unless there was a significant sampling bias in the OPS. Although the SNP information suggests similarities among mainland populations, results from quantitative genetic studies found large provenance differences for growth-, morphological-, stem-form traits, and disease resistance. Determining the threshold at which genetic diversity levels will be significantly reduced during selection should help breeders to make informed decisions regarding the intensity of selection in managed breeding populations as well as gene resource populations.},
	language = {en},
	number = {1-6},
	urldate = {2021-06-08},
	journal = {Silvae Genetica},
	author = {Zhang, L. and Huanqiong, N. and Gapare, Washington J. and Dillon, S. K. and Li, X. and Wu, H. X.},
	month = dec,
	year = {2014},
	pages = {213--221},
}

Genetic diversity within radiata pine first generation of open-pollinated selections (OPS) from the native resource stands was compared with that observed in native populations to monitor potential changes in genetic diversity during domestication. Genetic diversity was estimated using 58 single nucleotide polymorphisms (SNPs) from 8 expressed genes. Nucleotide diversity maintained in first generation of selections (OPS) (mean ␲ = 0.0036; mean ␪w = 0.0058) was similar to that found within the native population material (mean ␲ = 0.0043; mean for ␪w = 0.0065). Likewise, mean values for expected heterozygosity (H ) within E and between native population material and OPS were similar (mean = 0.27 ± 0.04) and not significantly different (P = 0.068). Also, the overall distribution of allele frequency classes was not significantly different between native population material and OPS. These results point to no evidence of loss of diversity in OPS due to artificial selection. One possible reason is that the domestication of the OPS is at a very early stage. Another may be that artificial selection in the OPS was based on tree growth and form, not wood properties. The genes selected in this study are mostly involved in cell wall formation, thus genetic diversity of these genes should remain stable between natural population and OPS, unless there was a significant sampling bias in the OPS. Although the SNP information suggests similarities among mainland populations, results from quantitative genetic studies found large provenance differences for growth-, morphological-, stem-form traits, and disease resistance. Determining the threshold at which genetic diversity levels will be significantly reduced during selection should help breeders to make informed decisions regarding the intensity of selection in managed breeding populations as well as gene resource populations.

@article{de_la_torre_insights_2014,
	title = {Insights into {Conifer} {Giga}-{Genomes}},
	volume = {166},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/166/4/1724-1732/6113514},
	doi = {10/f25hfn},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {De La Torre, Amanda R. and Birol, Inanc and Bousquet, Jean and Ingvarsson, Pär K. and Jansson, Stefan and Jones, Steven J.M. and Keeling, Christopher I. and MacKay, John and Nilsson, Ove and Ritland, Kermit and Street, Nathaniel and Yanchuk, Alvin and Zerbe, Philipp and Bohlmann, Jörg},
	month = dec,
	year = {2014},
	pages = {1724--1732},
}

@article{axelsson_belowground_2014,
	title = {Belowground {Competition} {Directs} {Spatial} {Patterns} of {Seedling} {Growth} in {Boreal} {Pine} {Forests} in {Fennoscandia}},
	volume = {5},
	issn = {1999-4907},
	url = {http://www.mdpi.com/1999-4907/5/9/2106},
	doi = {10/f25mnq},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {Forests},
	author = {Axelsson, E. and Lundmark, Tomas and Högberg, Peter and Nordin, Annika},
	month = sep,
	year = {2014},
	pages = {2106--2121},
}

@article{liebsch_class_2014,
	title = {Class {I} {KNOX} transcription factors promote differentiation of cambial derivatives into xylem fibers in the \textit{{Arabidopsis}} hypocotyl},
	volume = {141},
	issn = {1477-9129, 0950-1991},
	url = {https://journals.biologists.com/dev/article/141/22/4311/46487/Class-I-KNOX-transcription-factors-promote},
	doi = {10/f3p5d6},
	abstract = {The class I KNOX transcription factors SHOOT MERISTEMLESS (STM) and KNAT1 are important regulators of meristem maintenance in shoot apices, with a dual role of promoting cell proliferation and inhibiting differentiation. We examined whether they control stem cell maintenance in the cambium of Arabidopsis hypocotyls, a wood-forming lateral meristem, in a similar fashion as in the shoot apical meristem. Weak loss-of-function alleles of KNAT1 and STM led to reduced formation of xylem fibers – highly differentiated cambial derivatives – whereas cell proliferation in the cambium was only mildly affected. In a knat1;stm double mutant, xylem fiber differentiation was completely abolished, but residual cambial activity was maintained. Expression of early and late markers of xylary cell differentiation was globally reduced in the knat1;stm double mutant. KNAT1 and STM were found to act through transcriptional repression of the meristem boundary genes BLADE-ON-PETIOLE 1 (BOP1) and BOP2 on xylem fiber differentiation. Together, these data indicate that, in the cambium, KNAT1 and STM, contrary to their function in the shoot apical meristem, promote cell differentiation through repression of BOP genes.},
	language = {en},
	number = {22},
	urldate = {2021-06-08},
	journal = {Development},
	author = {Liebsch, Daniela and Sunaryo, Widi and Holmlund, Mattias and Norberg, Mikael and Zhang, Jing and Hall, Hardy C. and Helizon, Hanna and Jin, Xu and Helariutta, Ykä and Nilsson, Ove and Polle, Andrea and Fischer, Urs},
	month = nov,
	year = {2014},
	pages = {4311--4319},
}

The class I KNOX transcription factors SHOOT MERISTEMLESS (STM) and KNAT1 are important regulators of meristem maintenance in shoot apices, with a dual role of promoting cell proliferation and inhibiting differentiation. We examined whether they control stem cell maintenance in the cambium of Arabidopsis hypocotyls, a wood-forming lateral meristem, in a similar fashion as in the shoot apical meristem. Weak loss-of-function alleles of KNAT1 and STM led to reduced formation of xylem fibers – highly differentiated cambial derivatives – whereas cell proliferation in the cambium was only mildly affected. In a knat1;stm double mutant, xylem fiber differentiation was completely abolished, but residual cambial activity was maintained. Expression of early and late markers of xylary cell differentiation was globally reduced in the knat1;stm double mutant. KNAT1 and STM were found to act through transcriptional repression of the meristem boundary genes BLADE-ON-PETIOLE 1 (BOP1) and BOP2 on xylem fiber differentiation. Together, these data indicate that, in the cambium, KNAT1 and STM, contrary to their function in the shoot apical meristem, promote cell differentiation through repression of BOP genes.

@article{hoenicka_successful_2014,
	title = {Successful crossings with early flowering transgenic poplar: interspecific crossings, but not transgenesis, promoted aberrant phenotypes in offspring},
	volume = {12},
	issn = {14677644},
	shorttitle = {Successful crossings with early flowering transgenic poplar},
	url = {http://doi.wiley.com/10.1111/pbi.12213},
	doi = {10/f3p652},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Plant Biotechnology Journal},
	author = {Hoenicka, Hans and Lehnhardt, Denise and Nilsson, Ove and Hanelt, Dieter and Fladung, Matthias},
	month = oct,
	year = {2014},
	pages = {1066--1074},
}

@article{zamioudis_-glucosidase_2014,
	title = {β-{Glucosidase} {BGLU42} is a {MYB72}-dependent key regulator of rhizobacteria-induced systemic resistance and modulates iron deficiency responses in \textit{{Arabidopsis}} roots},
	volume = {204},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.12980},
	doi = {10/f3nsht},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Zamioudis, Christos and Hanson, Johannes and Pieterse, Corné M. J.},
	month = oct,
	year = {2014},
	pages = {368--379},
}

@article{robinson_populus_2014,
	title = {Populus tremula ({European} aspen) shows no evidence of sexual dimorphism},
	volume = {14},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0276-5},
	doi = {10/f25brv},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Robinson, Kathryn M and Delhomme, Nicolas and Mähler, Niklas and Schiffthaler, Bastian and Önskog, Jenny and Albrectsen, Benedicte R and Ingvarsson, Pär K and Hvidsten, Torgeir R and Jansson, Stefan and Street, Nathaniel R},
	month = dec,
	year = {2014},
	pages = {276},
}

@article{zulfugarov_production_2014,
	title = {Production of superoxide from {Photosystem} {II} in a rice ({Oryza} {sativaL}.) mutant lacking {PsbS}},
	volume = {14},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0242-2},
	doi = {10/f3m3zb},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Zulfugarov, Ismayil S and Tovuu, Altanzaya and Eu, Young-Jae and Dogsom, Bolormaa and Poudyal, Roshan Sharma and Nath, Krishna and Hall, Michael and Banerjee, Mainak and Yoon, Ung Chan and Moon, Yong-Hwan and An, Gynheung and Jansson, Stefan and Lee, Choon-Hwan},
	month = dec,
	year = {2014},
	pages = {242},
}

@article{hiltscher_radical_2014,
	title = {The radical induced cell death protein 1 ({RCD1}) supports transcriptional activation of genes for chloroplast antioxidant enzymes},
	volume = {5},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2014.00475/full},
	doi = {10/f3ptxk},
	abstract = {The rimb1 (redox imbalanced 1) mutation was mapped to the RCD1 locus (radical-induced cell death 1; At1g32230) demonstrating that a major factor involved in redox-regulation genes for chloroplast antioxidant enzymes and protection against photooxidative stress, RIMB1, is identical to the regulator of disease response reactions and cell death, RCD1. Discovering this link let to our investigation of its regulatory mechanism. We show in yeast that RCD1 can physically interact with the transcription factor Rap2.4a which provides redox-sensitivity to nuclear expression of genes for chloroplast antioxidant enzymes. In the rimb1 (rcd1-6) mutant a single nucleotide exchange results in a truncated RCD1 protein lacking the transcription factor binding site. Protein-protein interaction between full-length RCD1 and Rap2.4a is supported by H2O2, but not sensitive to the antioxidants dithiotreitol and ascorbate. In combination with transcript abundance analysis in Arabidopsis, it is concluded that RCD1 stabilizes the Rap2.4-dependent redox-regulation of the genes encoding chloroplast antioxidant enzymes in a widely redox-independent manner. Over the years, rcd1-mutant alleles have been described to develop symptoms like chlorosis, lesions along the leaf rims and in the mesophyll and (secondary) induction of extra- and intra-plastidic antioxidant defense mechanisms. All these rcd1 mutant characteristics were observed in rcd1-6 to succeed low activation of the chloroplast antioxidant system and glutathione biosynthesis. We conclude that RCD1 protects plant cells from running into ROS (reactive oxygen species)-triggered programs, such as cell death and activation of pathogen-responsive genes (PR genes) and extra-plastidic antioxidant enzymes, by supporting the induction of the chloroplast antioxidant system.},
	language = {English},
	urldate = {2021-06-08},
	journal = {Frontiers in Plant Science},
	author = {Hiltscher, Heiko and Rudnik, Radoslaw and Shaikhali, Jehad and Heiber, Isabelle and Mellenthin, Marina and Meirelles Duarte, Iuri and Schuster, Günter and Kahmann, Uwe and Baier, Margarete},
	year = {2014},
	note = {Publisher: Frontiers},
	keywords = {Arabidopsis, RCD1, ROS, antioxidant system, chloroplast},
}

The rimb1 (redox imbalanced 1) mutation was mapped to the RCD1 locus (radical-induced cell death 1; At1g32230) demonstrating that a major factor involved in redox-regulation genes for chloroplast antioxidant enzymes and protection against photooxidative stress, RIMB1, is identical to the regulator of disease response reactions and cell death, RCD1. Discovering this link let to our investigation of its regulatory mechanism. We show in yeast that RCD1 can physically interact with the transcription factor Rap2.4a which provides redox-sensitivity to nuclear expression of genes for chloroplast antioxidant enzymes. In the rimb1 (rcd1-6) mutant a single nucleotide exchange results in a truncated RCD1 protein lacking the transcription factor binding site. Protein-protein interaction between full-length RCD1 and Rap2.4a is supported by H2O2, but not sensitive to the antioxidants dithiotreitol and ascorbate. In combination with transcript abundance analysis in Arabidopsis, it is concluded that RCD1 stabilizes the Rap2.4-dependent redox-regulation of the genes encoding chloroplast antioxidant enzymes in a widely redox-independent manner. Over the years, rcd1-mutant alleles have been described to develop symptoms like chlorosis, lesions along the leaf rims and in the mesophyll and (secondary) induction of extra- and intra-plastidic antioxidant defense mechanisms. All these rcd1 mutant characteristics were observed in rcd1-6 to succeed low activation of the chloroplast antioxidant system and glutathione biosynthesis. We conclude that RCD1 protects plant cells from running into ROS (reactive oxygen species)-triggered programs, such as cell death and activation of pathogen-responsive genes (PR genes) and extra-plastidic antioxidant enzymes, by supporting the induction of the chloroplast antioxidant system.

@article{chen_inheritance_2014,
	title = {Inheritance of growth and solid wood quality traits in a large {Norway} spruce population tested at two locations in southern {Sweden}},
	volume = {10},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-014-0761-x},
	doi = {10/f3ndqx},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Chen, Zhi-Qiang and Gil, María Rosario García and Karlsson, Bo and Lundqvist, Sven-Olof and Olsson, Lars and Wu, Harry X.},
	month = oct,
	year = {2014},
	pages = {1291--1303},
}

@article{li_functional_2014,
	title = {Functional {Multi}-{Locus} {QTL} {Mapping} of {Temporal} {Trends} in {Scots} {Pine} {Wood} {Traits}},
	volume = {4},
	issn = {2160-1836},
	url = {https://academic.oup.com/g3journal/article/4/12/2365/6025852},
	doi = {10/f3p5gx},
	abstract = {Abstract
            Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g., increment cores), thus ignoring systematic within-tree trends. In this study, functional QTL mapping was performed for a set of important wood properties in increment cores from a 17-yr-old Scots pine (Pinus sylvestris L.) full-sib family with the aim of detecting wood trait QTL for general intercepts (means) and for linear slopes by increasing cambial age. Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 to 9 time points, 91 to 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP), and single nucleotide polymorphism (SNP) markers. The first method was a multilevel LASSO analysis whereby trend parameter estimation and QTL mapping were conducted consecutively; the second method was our Bayesian linear mixed model whereby trends and underlying genetic effects were estimated simultaneously. We also compared several different hypothesis testing methods under either the LASSO or the Bayesian framework to perform QTL inference. In total, five and four significant QTL were observed for the intercepts and slopes, respectively, across wood traits such as earlywood percentage, wood density, radial fiberwidth, and spiral grain angle. Four of these QTL were represented by candidate gene SNPs, thus providing promising targets for future research in QTL mapping and molecular function. Bayesian and LASSO methods both detected similar sets of QTL given datasets that comprised large numbers of individuals.},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Li, Zitong and Hallingbäck, Henrik R and Abrahamsson, Sara and Fries, Anders and Gull, Bengt Andersson and Sillanpää, Mikko J and García-Gil, M Rosario},
	month = dec,
	year = {2014},
	pages = {2365--2379},
}

Abstract Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g., increment cores), thus ignoring systematic within-tree trends. In this study, functional QTL mapping was performed for a set of important wood properties in increment cores from a 17-yr-old Scots pine (Pinus sylvestris L.) full-sib family with the aim of detecting wood trait QTL for general intercepts (means) and for linear slopes by increasing cambial age. Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 to 9 time points, 91 to 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP), and single nucleotide polymorphism (SNP) markers. The first method was a multilevel LASSO analysis whereby trend parameter estimation and QTL mapping were conducted consecutively; the second method was our Bayesian linear mixed model whereby trends and underlying genetic effects were estimated simultaneously. We also compared several different hypothesis testing methods under either the LASSO or the Bayesian framework to perform QTL inference. In total, five and four significant QTL were observed for the intercepts and slopes, respectively, across wood traits such as earlywood percentage, wood density, radial fiberwidth, and spiral grain angle. Four of these QTL were represented by candidate gene SNPs, thus providing promising targets for future research in QTL mapping and molecular function. Bayesian and LASSO methods both detected similar sets of QTL given datasets that comprised large numbers of individuals.

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

@article{pietrzykowska_light-harvesting_2014,
	title = {The {Light}-{Harvesting} {Chlorophyll} a/b {Binding} {Proteins} {Lhcb1} and {Lhcb2} {Play} {Complementary} {Roles} during {State} {Transitions} in {Arabidopsis}},
	volume = {26},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/26/9/3646-3660/6100356},
	doi = {10/f25cg8},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Pietrzykowska, M. and Suorsa, M. and Semchonok, D. A. and Tikkanen, M. and Boekema, E. J. and Aro, E.-M. and Jansson, S.},
	month = sep,
	year = {2014},
	pages = {3646--3660},
}

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

@article{pratt_genetically_2014,
	title = {Genetically based latitudinal variation in \textit{{Artemisia} californica} secondary chemistry},
	volume = {123},
	issn = {00301299},
	url = {http://doi.wiley.com/10.1111/oik.01156},
	doi = {10/f25bc5},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Oikos},
	author = {Pratt, Jessica D. and Keefover-Ring, Ken and Liu, Lawrence Y. and Mooney, Kailen A.},
	month = aug,
	year = {2014},
	pages = {953--963},
}

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

@article{ranade_comparative_2014,
	title = {Comparative in silicoanalysis of {EST}-{SSRs} in angiosperm and gymnosperm tree genera},
	volume = {14},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0220-8},
	doi = {10/f3p257},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Ranade, Sonali Sachin and Lin, Yao-Cheng and Zuccolo, Andrea and Van de Peer, Yves and García-Gil, María del Rosario},
	month = dec,
	year = {2014},
	pages = {220},
}

@article{de_rybel_integration_2014,
	title = {Integration of growth and patterning during vascular tissue formation in \textit{{Arabidopsis}}},
	volume = {345},
	issn = {0036-8075, 1095-9203},
	url = {https://www.sciencemag.org/lookup/doi/10.1126/science.1255215},
	doi = {10/f3p69f},
	abstract = {Coordination of cell division and pattern formation is central to tissue and organ development, particularly in plants where walls prevent cell migration. Auxin and cytokinin are both critical for division and patterning, but it is unknown how these hormones converge upon tissue development. We identify a genetic network that reinforces an early embryonic bias in auxin distribution to create a local, nonresponding cytokinin source within the root vascular tissue. Experimental and theoretical evidence shows that these cells act as a tissue organizer by positioning the domain of oriented cell divisions. We further demonstrate that the auxin-cytokinin interaction acts as a spatial incoherent feed-forward loop, which is essential to generate distinct hormonal response zones, thus establishing a stable pattern within a growing vascular tissue.},
	language = {en},
	number = {6197},
	urldate = {2021-06-08},
	journal = {Science},
	author = {De Rybel, Bert and Adibi, Milad and Breda, Alice S. and Wendrich, Jos R. and Smit, Margot E. and Novák, Ondřej and Yamaguchi, Nobutoshi and Yoshida, Saiko and Van Isterdael, Gert and Palovaara, Joakim and Nijsse, Bart and Boekschoten, Mark V. and Hooiveld, Guido and Beeckman, Tom and Wagner, Doris and Ljung, Karin and Fleck, Christian and Weijers, Dolf},
	month = aug,
	year = {2014},
	pages = {1255215},
}

Coordination of cell division and pattern formation is central to tissue and organ development, particularly in plants where walls prevent cell migration. Auxin and cytokinin are both critical for division and patterning, but it is unknown how these hormones converge upon tissue development. We identify a genetic network that reinforces an early embryonic bias in auxin distribution to create a local, nonresponding cytokinin source within the root vascular tissue. Experimental and theoretical evidence shows that these cells act as a tissue organizer by positioning the domain of oriented cell divisions. We further demonstrate that the auxin-cytokinin interaction acts as a spatial incoherent feed-forward loop, which is essential to generate distinct hormonal response zones, thus establishing a stable pattern within a growing vascular tissue.

@article{angelcheva_metabolomic_2014,
	title = {Metabolomic analysis of extreme freezing tolerance in {Siberian} spruce ( \textit{ {\textless}span style="font-variant:small-caps;"{\textgreater}{P}{\textless}/span{\textgreater} icea obovata } )},
	volume = {204},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Metabolomic analysis of extreme freezing tolerance in {Siberian} spruce ( {\textless}i{\textgreater} {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.12950},
	doi = {10/f242x5},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Angelcheva, Liudmila and Mishra, Yogesh and Antti, Henrik and Kjellsen, Trygve D. and Funk, Christiane and Strimbeck, Richard G. and Schröder, Wolfgang P.},
	month = nov,
	year = {2014},
	pages = {545--555},
}

@article{businge_possible_2014,
	title = {A possible biochemical basis for fructose-induced inhibition of embryo development in {Norway} spruce ({Picea} abies)},
	volume = {34},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpu053},
	doi = {10/f3m3sv},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Tree Physiology},
	author = {Businge, E. and Egertsdotter, U.},
	month = jun,
	year = {2014},
	pages = {657--669},
}

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

@incollection{otegui_sterol_2014,
	address = {New York, NY},
	title = {Sterol {Dynamics} {During} {Endocytic} {Trafficking} in {Arabidopsis}},
	volume = {1209},
	isbn = {978-1-4939-1419-7 978-1-4939-1420-3},
	url = {http://link.springer.com/10.1007/978-1-4939-1420-3_2},
	urldate = {2021-06-08},
	booktitle = {Plant {Endosomes}},
	publisher = {Springer New York},
	author = {Stanislas, Thomas and Grebe, Markus and Boutté, Yohann},
	editor = {Otegui, Marisa S.},
	year = {2014},
	doi = {10.1007/978-1-4939-1420-3_2},
	note = {Series Title: Methods in Molecular Biology},
	pages = {13--29},
}

@article{rigal_unraveling_2014,
	title = {Unraveling plant hormone signaling through the use of small molecules},
	volume = {5},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2014.00373/full},
	doi = {10/f3m3b6},
	abstract = {Plants have acquired the capacity to grow continuously and adjust their morphology in response to endogenous and external signals, leading to a high architectural plasticity. The dynamic and differential distribution of phytohormones is an essential factor in these developmental changes. Phytohormone perception is a fast but complex process modulating specific developmental reprogramming. In recent years, chemical genomics or the use of small molecules to modulate target protein function has emerged as a powerful strategy to study complex biological processes in plants such as hormone signaling. Small molecules can be applied in a conditional, dose-dependent and reversible manner, with the advantage of circumventing the limitations of lethality and functional redundancy inherent to traditional mutant screens. High-throughput screening of diverse chemical libraries has led to the identification of bioactive molecules able to induce plant hormone-related phenotypes. Characterization of the cognate targets and pathways of those molecules has allowed the identification of novel regulatory components, providing new insights into the molecular mechanisms of plant hormone signaling. An extensive structure-activity relationship (SAR) analysis of the natural phytohormones, their designed synthetic analogues and newly identified bioactive molecules has led to the determination of the structural requirements essential for their bioactivity. In this review, we will summarize the so far identified small molecules and their structural variants targeting specific phytohormone signaling pathways. We will highlight how the SAR analyses have enabled better interrogation of the molecular mechanisms of phytohormone responses. Finally, we will discuss how labeled/tagged hormone analogues can be exploited, as compelling tools to better understand hormone signaling and transport mechanisms.},
	language = {English},
	urldate = {2021-06-08},
	journal = {Frontiers in Plant Science},
	author = {Rigal, Adeline and Ma, Qian and Robert, Stéphanie},
	year = {2014},
	note = {Publisher: Frontiers},
	keywords = {agonists and antagonists, hormone signaling, labeled molecule, phytohormones, structure-activity relationship},
}

Plants have acquired the capacity to grow continuously and adjust their morphology in response to endogenous and external signals, leading to a high architectural plasticity. The dynamic and differential distribution of phytohormones is an essential factor in these developmental changes. Phytohormone perception is a fast but complex process modulating specific developmental reprogramming. In recent years, chemical genomics or the use of small molecules to modulate target protein function has emerged as a powerful strategy to study complex biological processes in plants such as hormone signaling. Small molecules can be applied in a conditional, dose-dependent and reversible manner, with the advantage of circumventing the limitations of lethality and functional redundancy inherent to traditional mutant screens. High-throughput screening of diverse chemical libraries has led to the identification of bioactive molecules able to induce plant hormone-related phenotypes. Characterization of the cognate targets and pathways of those molecules has allowed the identification of novel regulatory components, providing new insights into the molecular mechanisms of plant hormone signaling. An extensive structure-activity relationship (SAR) analysis of the natural phytohormones, their designed synthetic analogues and newly identified bioactive molecules has led to the determination of the structural requirements essential for their bioactivity. In this review, we will summarize the so far identified small molecules and their structural variants targeting specific phytohormone signaling pathways. We will highlight how the SAR analyses have enabled better interrogation of the molecular mechanisms of phytohormone responses. Finally, we will discuss how labeled/tagged hormone analogues can be exploited, as compelling tools to better understand hormone signaling and transport mechanisms.

@article{bian_genetic_2014,
	title = {Genetic parameters and genotype–environment interactions of {Chinese} fir ( \textit{{Cunninghamia} lanceolata} ) in {Fujian} {Province}},
	volume = {44},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2013-0427},
	doi = {10/f3pxpf},
	abstract = {Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is the most commercially important conifer in China, and the Nanjing Forestry University – Fujian Province Chinese fir Cooperation (NJFU – Fujian Cooperation) breeding program has advanced it into the third cycle of selection and breeding. In this paper, we estimated genetic parameters from four sites for 80 half-sib families and summarized previous estimates of genetic parameters in Chinese fir with an objective to propose optimal breeding strategy. Heritability averaged 0.20 and 0.14 for height and diameter at breast height (DBH), respectively, for the four sites. A significant genotype–environment interaction (G × E) for growth was also observed among the four sites, with the greatest interactions between a marginal site and the three central sites in the Fujian Province Chinese fir plantation region. The average estimated type-B genetic correlation between the marginal site and the three central sites was 0.08 for height and –0.09 for DBH. However, the highly productive families were among the most stable across the four sites. The results from this study in combination with summarized genetic parameters from literature were used to discuss and propose an optimal breeding strategy for the third generation of the breeding program for Chinese firs in Fujian Province.},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Canadian Journal of Forest Research},
	author = {Bian, Liming and Shi, Jisen and Zheng, Renhua and Chen, Jinhui and Wu, Harry X.},
	month = jun,
	year = {2014},
	pages = {582--592},
}

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is the most commercially important conifer in China, and the Nanjing Forestry University – Fujian Province Chinese fir Cooperation (NJFU – Fujian Cooperation) breeding program has advanced it into the third cycle of selection and breeding. In this paper, we estimated genetic parameters from four sites for 80 half-sib families and summarized previous estimates of genetic parameters in Chinese fir with an objective to propose optimal breeding strategy. Heritability averaged 0.20 and 0.14 for height and diameter at breast height (DBH), respectively, for the four sites. A significant genotype–environment interaction (G × E) for growth was also observed among the four sites, with the greatest interactions between a marginal site and the three central sites in the Fujian Province Chinese fir plantation region. The average estimated type-B genetic correlation between the marginal site and the three central sites was 0.08 for height and –0.09 for DBH. However, the highly productive families were among the most stable across the four sites. The results from this study in combination with summarized genetic parameters from literature were used to discuss and propose an optimal breeding strategy for the third generation of the breeding program for Chinese firs in Fujian Province.

@article{procko_cotyledon-generated_2014,
	title = {Cotyledon-{Generated} {Auxin} {Is} {Required} for {Shade}-{Induced} {Hypocotyl} {Growth} in \textit{{Brassica} rapa}},
	volume = {165},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/165/3/1285/6113202},
	doi = {10/f3p44r},
	abstract = {Abstract
            Plant architecture is optimized for the local light environment. In response to foliar shade or neighbor proximity (low red to far-red light), some plant species exhibit shade-avoiding phenotypes, including increased stem and hypocotyl growth, which increases the likelihood of outgrowing competitor plants. If shade persists, early flowering and the reallocation of growth resources to stem elongation ultimately affect the yield of harvestable tissues in crop species. Previous studies have shown that hypocotyl growth in low red to far-red shade is largely dependent on the photoreceptor phytochrome B and the phytohormone auxin. However, where shade is perceived in the plant and how auxin regulates growth spatially are less well understood. Using the oilseed and vegetable crop species Brassica rapa, we show that the perception of low red to far-red shade by the cotyledons triggers hypocotyl cell elongation and auxin target gene expression. Furthermore, we find that following shade perception, elevated auxin levels occur in a basipetal gradient away from the cotyledons and that this is coincident with a gradient of auxin target gene induction. These results show that cotyledon-generated auxin regulates hypocotyl elongation. In addition, we find in mature B. rapa plants that simulated shade does not affect seed oil composition but may affect seed yield. This suggests that in field settings where mutual shading between plants may occur, a balance between plant density and seed yield per plant needs to be achieved for maximum oil yield, while oil composition might remain constant.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Procko, Carl and Crenshaw, Charisse Michelle and Ljung, Karin and Noel, Joseph Patrick and Chory, Joanne},
	month = jun,
	year = {2014},
	pages = {1285--1301},
}

Abstract Plant architecture is optimized for the local light environment. In response to foliar shade or neighbor proximity (low red to far-red light), some plant species exhibit shade-avoiding phenotypes, including increased stem and hypocotyl growth, which increases the likelihood of outgrowing competitor plants. If shade persists, early flowering and the reallocation of growth resources to stem elongation ultimately affect the yield of harvestable tissues in crop species. Previous studies have shown that hypocotyl growth in low red to far-red shade is largely dependent on the photoreceptor phytochrome B and the phytohormone auxin. However, where shade is perceived in the plant and how auxin regulates growth spatially are less well understood. Using the oilseed and vegetable crop species Brassica rapa, we show that the perception of low red to far-red shade by the cotyledons triggers hypocotyl cell elongation and auxin target gene expression. Furthermore, we find that following shade perception, elevated auxin levels occur in a basipetal gradient away from the cotyledons and that this is coincident with a gradient of auxin target gene induction. These results show that cotyledon-generated auxin regulates hypocotyl elongation. In addition, we find in mature B. rapa plants that simulated shade does not affect seed oil composition but may affect seed yield. This suggests that in field settings where mutual shading between plants may occur, a balance between plant density and seed yield per plant needs to be achieved for maximum oil yield, while oil composition might remain constant.

@article{oyewole_direct_2014,
	title = {Direct estimation of mass flow and diffusion of nitrogen compounds in solution and soil},
	volume = {201},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.12553},
	doi = {10/f24qrp},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Oyewole, Olusegun Ayodeji and Inselsbacher, Erich and Näsholm, Torgny},
	month = feb,
	year = {2014},
	pages = {1056--1064},
}

@article{inselsbacher_early_2014,
	title = {Early season dynamics of soil nitrogen fluxes in fertilized and unfertilized boreal forests},
	volume = {74},
	issn = {00380717},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0038071714001011},
	doi = {10/f3p5b8},
	language = {en},
	urldate = {2021-06-08},
	journal = {Soil Biology and Biochemistry},
	author = {Inselsbacher, Erich and Oyewole, Olusegun Ayodeji and Näsholm, Torgny},
	month = jul,
	year = {2014},
	pages = {167--176},
}

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

@article{de_jong_auxin_2014,
	title = {Auxin and {Strigolactone} {Signaling} {Are} {Required} for {Modulation} of {Arabidopsis} {Shoot} {Branching} by {Nitrogen} {Supply}},
	volume = {166},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/166/1/384/6113280},
	doi = {10/f3p27f},
	abstract = {Abstract
            The degree of shoot branching is strongly affected by environmental conditions, such as nutrient availability. Here we demonstrate that nitrate limitation reduces shoot branching in Arabidopsis (Arabidopsis thaliana) both by delaying axillary bud activation and by attenuating the basipetal sequence of bud activation that is triggered following floral transition. Ammonium supply has similar effects, suggesting that they are caused by plant nitrogen (N) status, rather than direct nitrate signaling. We identify increased auxin export from active shoot apices, resulting in increased auxin in the polar auxin transport stream of the main stem, as a likely cause for the suppression of basal branches. Consistent with this idea, in the auxin response mutant axr1 and the strigolactone biosynthesis mutant more axillary growth1, increased retention of basal branches on low N is associated with a failure to increase auxin in the main stem. The complex interactions between the hormones that regulate branching make it difficult to rule out other mechanisms of N action, such as up-regulation of strigolactone synthesis. However, the proposed increase in auxin export from active buds can also explain how reduced shoot branching is achieved without compromising root growth, leading to the characteristic shift in relative biomass allocation to the root when N is limiting.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {de Jong, Maaike and George, Gilu and Ongaro, Veronica and Williamson, Lisa and Willetts, Barbara and Ljung, Karin and McCulloch, Hayley and Leyser, Ottoline},
	month = aug,
	year = {2014},
	pages = {384--395},
}

Abstract The degree of shoot branching is strongly affected by environmental conditions, such as nutrient availability. Here we demonstrate that nitrate limitation reduces shoot branching in Arabidopsis (Arabidopsis thaliana) both by delaying axillary bud activation and by attenuating the basipetal sequence of bud activation that is triggered following floral transition. Ammonium supply has similar effects, suggesting that they are caused by plant nitrogen (N) status, rather than direct nitrate signaling. We identify increased auxin export from active shoot apices, resulting in increased auxin in the polar auxin transport stream of the main stem, as a likely cause for the suppression of basal branches. Consistent with this idea, in the auxin response mutant axr1 and the strigolactone biosynthesis mutant more axillary growth1, increased retention of basal branches on low N is associated with a failure to increase auxin in the main stem. The complex interactions between the hormones that regulate branching make it difficult to rule out other mechanisms of N action, such as up-regulation of strigolactone synthesis. However, the proposed increase in auxin export from active buds can also explain how reduced shoot branching is achieved without compromising root growth, leading to the characteristic shift in relative biomass allocation to the root when N is limiting.

@article{vico_snowed_2014,
	title = {Snowed in for survival: {Quantifying} the risk of winter damage to overwintering field crops in northern temperate latitudes},
	volume = {197},
	issn = {01681923},
	shorttitle = {Snowed in for survival},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0168192314001452},
	doi = {10/f25c8w},
	language = {en},
	urldate = {2021-06-08},
	journal = {Agricultural and Forest Meteorology},
	author = {Vico, Giulia and Hurry, Vaughan and Weih, Martin},
	month = oct,
	year = {2014},
	pages = {65--75},
}

@article{lundmark_potential_2014,
	title = {Potential {Roles} of {Swedish} {Forestry} in the {Context} of {Climate} {Change} {Mitigation}},
	volume = {5},
	issn = {1999-4907},
	url = {http://www.mdpi.com/1999-4907/5/4/557},
	doi = {10/f23f7n},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Forests},
	author = {Lundmark, Tomas and Bergh, Johan and Hofer, Peter and Lundström, Anders and Nordin, Annika and Poudel, Bishnu and Sathre, Roger and Taverna, Ruedi and Werner, Frank},
	month = mar,
	year = {2014},
	pages = {557--578},
}

@article{legue_adventitious_2014,
	title = {Adventitious root formation in tree species: involvement of transcription factors},
	volume = {151},
	issn = {00319317},
	shorttitle = {Adventitious root formation in tree species},
	url = {http://doi.wiley.com/10.1111/ppl.12197},
	doi = {10/f3m23c},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Legué, Valérie and Rigal, Adeline and Bhalerao, Rishikesh P.},
	month = jun,
	year = {2014},
	pages = {192--198},
}

@article{pacurar_novel_2014,
	title = {A {Novel} {Viable} {Allele} of {Arabidopsis} {CULLIN1} {Identified} in a {Screen} for {Superroot2} {Suppressors} by {Next} {Generation} {Sequencing}-{Assisted} {Mapping}},
	volume = {9},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0100846},
	doi = {10/f22p63},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Pacurar, Daniel I. and Pacurar, Monica L. and Pacurar, Andrea M. and Gutierrez, Laurent and Bellini, Catherine},
	editor = {Zwick, Michael Edward.},
	month = jun,
	year = {2014},
	pages = {e100846},
}

@article{roe_fitness_2014,
	title = {Fitness dynamics within a poplar hybrid zone: {\textless}span style="font-variant:small-caps;"{\textgreater}{II}{\textless}/span{\textgreater} . {Impact} of exotic sex on native poplars in an urban jungle},
	volume = {4},
	issn = {2045-7758, 2045-7758},
	shorttitle = {Fitness dynamics within a poplar hybrid zone},
	url = {https://onlinelibrary.wiley.com/doi/10.1002/ece3.1028},
	doi = {10/f22wr4},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {Ecology and Evolution},
	author = {Roe, Amanda D. and MacQuarrie, Chris J.K. and Gros‐Louis, Marie‐Claude and Simpson, J. Dale and Lamarche, Josyanne and Beardmore, Tannis and Thompson, Stacey L. and Tanguay, Philippe and Isabel, Nathalie},
	month = may,
	year = {2014},
	pages = {1876--1889},
}

@article{kunz_functional_2014,
	title = {Functional {Dissection} of {Sugar} {Signals} {Affecting} {Gene} {Expression} in {Arabidopsis} thaliana},
	volume = {9},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0100312},
	doi = {10/f23qnk},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Kunz, Sabine and Pesquet, Edouard and Kleczkowski, Leszek A.},
	editor = {Wu, Keqiang},
	month = jun,
	year = {2014},
	pages = {e100312},
}

@article{hallingback_single_2014,
	title = {Single versus subdivided population strategies in breeding against an adverse genetic correlation},
	volume = {10},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-014-0707-3},
	doi = {10/f3p5jd},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Hallingbäck, Henrik R. and Sánchez, Leopoldo and Wu, Harry X.},
	month = jun,
	year = {2014},
	pages = {605--617},
}

@article{gerber_deficient_2014,
	title = {Deficient sucrose synthase activity in developing wood does not specifically affect cellulose biosynthesis, but causes an overall decrease in cell wall polymers},
	volume = {203},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.12888},
	doi = {10/f3p3rs},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Gerber, Lorenz and Zhang, Bo and Roach, Melissa and Rende, Umut and Gorzsás, András and Kumar, Manoj and Burgert, Ingo and Niittylä, Totte and Sundberg, Björn},
	month = sep,
	year = {2014},
	pages = {1220--1230},
}

@article{li_adp1_2014,
	title = {{ADP1} {Affects} {Plant} {Architecture} by {Regulating} {Local} {Auxin} {Biosynthesis}},
	volume = {10},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1003954},
	doi = {10/f3p7dr},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {PLoS Genetics},
	author = {Li, Ruixi and Li, Jieru and Li, Shibai and Qin, Genji and Novák, Ondřej and Pěnčík, Aleš and Ljung, Karin and Aoyama, Takashi and Liu, Jingjing and Murphy, Angus and Gu, Hongya and Tsuge, Tomohiko and Qu, Li-Jia},
	editor = {Copenhaver, Gregory P.},
	month = jan,
	year = {2014},
	pages = {e1003954},
}

@article{vain_cellulase_2014,
	title = {The {Cellulase} {KORRIGAN} {Is} {Part} of the {Cellulose} {Synthase} {Complex}},
	volume = {165},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/165/4/1521/6113133},
	doi = {10/gkgdgm},
	abstract = {Abstract
            Plant growth and organ formation depend on the oriented deposition of load-bearing cellulose microfibrils in the cell wall. Cellulose is synthesized by a large relative molecular weight cellulose synthase complex (CSC), which comprises at least three distinct cellulose synthases. Cellulose synthesis in plants or bacteria also requires the activity of an endo-1,4-β-d-glucanase, the exact function of which in the synthesis process is not known. Here, we show, to our knowledge for the first time, that a leaky mutation in the Arabidopsis (Arabidopsis thaliana) membrane-bound endo-1,4-β-d-glucanase KORRIGAN1 (KOR1) not only caused reduced CSC movement in the plasma membrane but also a reduced cellulose synthesis inhibitor-induced accumulation of CSCs in intracellular compartments. This suggests a role for KOR1 both in the synthesis of cellulose microfibrils and in the intracellular trafficking of CSCs. Next, we used a multidisciplinary approach, including live cell imaging, gel filtration chromatography analysis, split ubiquitin assays in yeast (Saccharomyces cerevisiae NMY51), and bimolecular fluorescence complementation, to show that, in contrast to previous observations, KOR1 is an integral part of the primary cell wall CSC in the plasma membrane.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Vain, Thomas and Crowell, Elizabeth Faris and Timpano, Hélène and Biot, Eric and Desprez, Thierry and Mansoori, Nasim and Trindade, Luisa M. and Pagant, Silvère and Robert, Stéphanie and Höfte, Herman and Gonneau, Martine and Vernhettes, Samantha},
	month = aug,
	year = {2014},
	pages = {1521--1532},
}

Abstract Plant growth and organ formation depend on the oriented deposition of load-bearing cellulose microfibrils in the cell wall. Cellulose is synthesized by a large relative molecular weight cellulose synthase complex (CSC), which comprises at least three distinct cellulose synthases. Cellulose synthesis in plants or bacteria also requires the activity of an endo-1,4-β-d-glucanase, the exact function of which in the synthesis process is not known. Here, we show, to our knowledge for the first time, that a leaky mutation in the Arabidopsis (Arabidopsis thaliana) membrane-bound endo-1,4-β-d-glucanase KORRIGAN1 (KOR1) not only caused reduced CSC movement in the plasma membrane but also a reduced cellulose synthesis inhibitor-induced accumulation of CSCs in intracellular compartments. This suggests a role for KOR1 both in the synthesis of cellulose microfibrils and in the intracellular trafficking of CSCs. Next, we used a multidisciplinary approach, including live cell imaging, gel filtration chromatography analysis, split ubiquitin assays in yeast (Saccharomyces cerevisiae NMY51), and bimolecular fluorescence complementation, to show that, in contrast to previous observations, KOR1 is an integral part of the primary cell wall CSC in the plasma membrane.

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

@article{hong_high_2014,
	title = {High negative genetic correlations between growth traits and wood properties suggest incorporating multiple traits selection including economic weights for the future {Scots} pine breeding programs},
	volume = {71},
	issn = {1286-4560, 1297-966X},
	url = {http://link.springer.com/10.1007/s13595-014-0359-3},
	doi = {10/f3p4zt},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Annals of Forest Science},
	author = {Hong, Zhou and Fries, Anders and Wu, Harry X.},
	month = jun,
	year = {2014},
	pages = {463--472},
}

@article{chong_o-acetylation_2014,
	title = {O-{Acetylation} of glucuronoxylan in {Arabidopsis} thaliana wild type and its change in xylan biosynthesis mutants},
	volume = {24},
	issn = {0959-6658, 1460-2423},
	url = {https://academic.oup.com/glycob/article-lookup/doi/10.1093/glycob/cwu017},
	doi = {10/f3p478},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Glycobiology},
	author = {Chong, Sun-Li and Virkki, Liisa and Maaheimo, Hannu and Juvonen, Minna and Derba-Maceluch, Marta and Koutaniemi, Sanna and Roach, Melissa and Sundberg, Björn and Tuomainen, Päivi and Mellerowicz, Ewa J and Tenkanen, Maija},
	month = jun,
	year = {2014},
	pages = {494--506},
}

@article{roe_fitness_2014,
	title = {Fitness dynamics within a poplar hybrid zone: {I}. {\textless}span style="font-variant:small-caps;"{\textgreater}{P}{\textless}/span{\textgreater} rezygotic and postzygotic barriers impacting a native poplar hybrid stand},
	volume = {4},
	issn = {2045-7758, 2045-7758},
	shorttitle = {Fitness dynamics within a poplar hybrid zone},
	url = {https://onlinelibrary.wiley.com/doi/10.1002/ece3.1029},
	doi = {10/f24bmn},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {Ecology and Evolution},
	author = {Roe, Amanda D. and MacQuarrie, Chris J. K. and Gros‐Louis, Marie‐Claude and Simpson, J. Dale and Lamarche, Josyanne and Beardmore, Tannis and Thompson, Stacey L. and Tanguay, Philippe and Isabel, Nathalie},
	month = may,
	year = {2014},
	pages = {1629--1647},
}

@article{hogberg_potential_2014,
	title = {The potential for the genetic improvement of sawn timber traits in \textit{{Picea} abies}},
	volume = {44},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2013-0382},
	doi = {10/f2z4gw},
	abstract = {This study evaluated the potential for the selective genetic improvement of the structural quality traits important in sawn Norway spruce (Picea abies (L.) Karst.) timber based on early and nondestructively assessed field traits. From a 34-year-old Norway spruce trial situated in southern Sweden, 401 butt logs were sampled and sawn to produce two 50 × 100 mm boards that were dried to an 18\% moisture content. Structural quality traits were assessed, and genetic parameters were estimated, including additive genetic variance, heritability, and their genetic correlations with field traits. Board twisting, density, and modulus of elasticity (MOE, stiffness) were found to have appreciable heritabilities (0.23–0.44). Board twist was found to have a strong genetic correlation with grain angle measured under bark in the field (0.93), and both board MOE and density exhibited strong genetic correlations with field-assessed pilodyn penetration (–0.75 and –0.91, respectively). Although these observations were made on a thinning material comprising mainly juvenile wood, they nonetheless suggest grain angle and pilodyn penetration to be promising candidates as selection criteria for Norway spruce breeding. Heritabilities of other sawn timber traits were lower and the genetic correlations between these traits and field traits were also lower, variable, and had large estimation errors.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Canadian Journal of Forest Research},
	author = {Högberg, Karl-Anders and Hallingbäck, Henrik R. and Säll, Harald and Johansson, Marie and Jansson, Gunnar},
	month = apr,
	year = {2014},
	pages = {273--280},
}

This study evaluated the potential for the selective genetic improvement of the structural quality traits important in sawn Norway spruce (Picea abies (L.) Karst.) timber based on early and nondestructively assessed field traits. From a 34-year-old Norway spruce trial situated in southern Sweden, 401 butt logs were sampled and sawn to produce two 50 × 100 mm boards that were dried to an 18% moisture content. Structural quality traits were assessed, and genetic parameters were estimated, including additive genetic variance, heritability, and their genetic correlations with field traits. Board twisting, density, and modulus of elasticity (MOE, stiffness) were found to have appreciable heritabilities (0.23–0.44). Board twist was found to have a strong genetic correlation with grain angle measured under bark in the field (0.93), and both board MOE and density exhibited strong genetic correlations with field-assessed pilodyn penetration (–0.75 and –0.91, respectively). Although these observations were made on a thinning material comprising mainly juvenile wood, they nonetheless suggest grain angle and pilodyn penetration to be promising candidates as selection criteria for Norway spruce breeding. Heritabilities of other sawn timber traits were lower and the genetic correlations between these traits and field traits were also lower, variable, and had large estimation errors.

@article{marhavy_cytokinin_2014,
	title = {Cytokinin {Controls} {Polarity} of {PIN1}-{Dependent} {Auxin} {Transport} during {Lateral} {Root} {Organogenesis}},
	volume = {24},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982214004023},
	doi = {10/f52zbg},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Marhavý, Peter and Duclercq, Jérôme and Weller, Benjamin and Feraru, Elena and Bielach, Agnieszka and Offringa, Remko and Friml, Jiří and Schwechheimer, Claus and Murphy, Angus and Benková, Eva},
	month = may,
	year = {2014},
	pages = {1031--1037},
}

@article{hersch_light_2014,
	title = {Light intensity modulates the regulatory network of the shade avoidance response in {Arabidopsis}},
	volume = {111},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1320355111},
	doi = {10/f3p63k},
	language = {en},
	number = {17},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Hersch, M. and Lorrain, S. and de Wit, M. and Trevisan, M. and Ljung, K. and Bergmann, S. and Fankhauser, C.},
	month = apr,
	year = {2014},
	pages = {6515--6520},
}

@article{torabi_psbn_2014,
	title = {{PsbN} {Is} {Required} for {Assembly} of the {Photosystem} {II} {Reaction} {Center} in \textit{{Nicotiana} tabacum}},
	volume = {26},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/26/3/1183-1199/6099818},
	doi = {10/f22n5k},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Torabi, Salar and Umate, Pavan and Manavski, Nikolay and Plöchinger, Magdalena and Kleinknecht, Laura and Bogireddi, Hanumakumar and Herrmann, Reinhold G. and Wanner, Gerhard and Schröder, Wolfgang P. and Meurer, Jörg},
	month = mar,
	year = {2014},
	pages = {1183--1199},
}

@article{wang_increased_2014,
	title = {Increased genetic divergence between two closely related fir species in areas of range overlap},
	volume = {4},
	issn = {2045-7758, 2045-7758},
	url = {https://onlinelibrary.wiley.com/doi/10.1002/ece3.1007},
	doi = {10/f23ttd},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Ecology and Evolution},
	author = {Wang, Jing and Abbott, Richard J. and Ingvarsson, Pär K. and Liu, Jianquan},
	month = apr,
	year = {2014},
	pages = {1019--1029},
}

@article{plett_ethylene_2014,
	title = {Ethylene and jasmonic acid act as negative modulators during mutualistic symbiosis between \textit{ {\textless}span style="font-variant:small-caps;"{\textgreater}{L}{\textless}/span{\textgreater} accaria bicolor } and \textit{ {\textless}span style="font-variant:small-caps;"{\textgreater}{P}{\textless}/span{\textgreater} opulus } roots},
	volume = {202},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Ethylene and jasmonic acid act as negative modulators during mutualistic symbiosis between {\textless}i{\textgreater} {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.12655},
	doi = {10/f3m26h},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Plett, Jonathan M. and Khachane, Amit and Ouassou, Malika and Sundberg, Björn and Kohler, Annegret and Martin, Francis},
	month = apr,
	year = {2014},
	pages = {270--286},
}

@article{igamberdiev_activity_2014,
	title = {Activity of the mitochondrial pyruvate dehydrogenase complex in plants is stimulated in the presence of malate},
	volume = {19},
	issn = {15677249},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1567724914000440},
	doi = {10/f3n5m7},
	language = {en},
	urldate = {2021-06-08},
	journal = {Mitochondrion},
	author = {Igamberdiev, Abir U. and Lernmark, Ulrikа and Gardeström, Per},
	month = nov,
	year = {2014},
	pages = {184--190},
}

@article{pacurar_identification_2014,
	title = {Identification of new adventitious rooting mutants amongst suppressors of the {Arabidopsis} thaliana superroot2 mutation},
	volume = {65},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/eru026},
	doi = {10/f23rss},
	abstract = {The plant hormone auxin plays a central role in adventitious rooting and is routinely used with many economically important, vegetatively propagated plant species to promote adventitious root initiation and development on cuttings. Nevertheless the molecular mechanisms through which it acts are only starting to emerge. The Arabidopsis superroot2-1 (sur2-1) mutant overproduces auxin and, as a consequence, develops excessive adventitious roots in the hypocotyl. In order to increase the knowledge of adventitious rooting and of auxin signalling pathways and crosstalk, this study performed a screen for suppressors of superroot2-1 phenotype. These suppressors provide a new resource for discovery of genetic players involved in auxin signalling pathways or at the crosstalk of auxin and other hormones or environmental signals. This study reports the identification and characterization of 26 sur2-1 suppressor mutants, several of which were identified as mutations in candidate genes involved in either auxin biosynthesis or signalling. In addition to confirming the role of auxin as a central regulator of adventitious rooting, superroot2 suppressors indicated possible crosstalk with ethylene signalling in this process.},
	number = {6},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Pacurar, Daniel Ioan and Pacurar, Monica Lacramioara and Bussell, John Desmond and Schwambach, Joseli and Pop, Tiberia Ioana and Kowalczyk, Mariusz and Gutierrez, Laurent and Cavel, Emilie and Chaabouni, Salma and Ljung, Karin and Fett-Neto, Arthur Germano and Pamfil, Doru and Bellini, Catherine},
	month = apr,
	year = {2014},
	pages = {1605--1618},
}

The plant hormone auxin plays a central role in adventitious rooting and is routinely used with many economically important, vegetatively propagated plant species to promote adventitious root initiation and development on cuttings. Nevertheless the molecular mechanisms through which it acts are only starting to emerge. The Arabidopsis superroot2-1 (sur2-1) mutant overproduces auxin and, as a consequence, develops excessive adventitious roots in the hypocotyl. In order to increase the knowledge of adventitious rooting and of auxin signalling pathways and crosstalk, this study performed a screen for suppressors of superroot2-1 phenotype. These suppressors provide a new resource for discovery of genetic players involved in auxin signalling pathways or at the crosstalk of auxin and other hormones or environmental signals. This study reports the identification and characterization of 26 sur2-1 suppressor mutants, several of which were identified as mutations in candidate genes involved in either auxin biosynthesis or signalling. In addition to confirming the role of auxin as a central regulator of adventitious rooting, superroot2 suppressors indicated possible crosstalk with ethylene signalling in this process.

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

In multicellular organisms, cellular differences in gene activity are a prerequisite for differentiation and establishment of cell types. In order to study transcriptome profiles, specific cell types have to be isolated from a given tissue or even the whole organism. However, whole-transcriptome analysis of early embryos in flowering plants has been hampered by their size and inaccessibility. Here, we describe the purification of nuclear RNA from early stage Arabidopsis thaliana embryos using fluorescence-activated nuclear sorting (FANS) to generate expression profiles of early stages of the whole embryo, the proembryo and the suspensor. We validated our datasets of differentially expressed candidate genes by promoter-reporter gene fusions and in situ hybridization. Our study revealed that different classes of genes with respect to biological processes and molecular functions are preferentially expressed either in the proembryo or in the suspensor. This method can be used especially for tissues with a limited cell population and inaccessible tissue types. Furthermore, we provide a valuable resource for research on Arabidopsis early embryogenesis.

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

Most molecular-genetic studies of plant defense responses to arthropod herbivores have focused on insects. However, plant-feeding mites are also pests of diverse plants, and mites induce different patterns of damage to plant tissues than do well-studied insects (e.g. lepidopteran larvae or aphids). The two-spotted spider mite (Tetranychus urticae) is among the most significant mite pests in agriculture, feeding on a staggering number of plant hosts. To understand the interactions between spider mite and a plant at the molecular level, we examined reciprocal genome-wide responses of mites and its host Arabidopsis (Arabidopsis thaliana). Despite differences in feeding guilds, we found that transcriptional responses of Arabidopsis to mite herbivory resembled those observed for lepidopteran herbivores. Mutant analysis of induced plant defense pathways showed functionally that only a subset of induced programs, including jasmonic acid signaling and biosynthesis of indole glucosinolates, are central to Arabidopsis's defense to mite herbivory. On the herbivore side, indole glucosinolates dramatically increased mite mortality and development times. We identified an indole glucosinolate dose-dependent increase in the number of differentially expressed mite genes belonging to pathways associated with detoxification of xenobiotics. This demonstrates that spider mite is sensitive to Arabidopsis defenses that have also been associated with the deterrence of insect herbivores that are very distantly related to chelicerates. Our findings provide molecular insights into the nature of, and response to, herbivory for a representative of a major class of arthropod herbivores.

@article{koroidov_mobile_2014,
	title = {Mobile hydrogen carbonate acts as proton acceptor in photosynthetic water oxidation},
	volume = {111},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1323277111},
	doi = {10/f2z4cv},
	language = {en},
	number = {17},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Koroidov, S. and Shevela, D. and Shutova, T. and Samuelsson, G. and Messinger, J.},
	month = apr,
	year = {2014},
	pages = {6299--6304},
}

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

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

@article{fan_echidna_2014,
	title = {{ECHIDNA} {Protein} {Impacts} on {Male} {Fertility} in {Arabidopsis} by {Mediating} trans-{Golgi} {Network} {Secretory} {Trafficking} during {Anther} and {Pollen} {Development}},
	volume = {164},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/164/3/1338/6113057},
	doi = {10/f3pts4},
	abstract = {Abstract
            The trans-Golgi network (TGN) plays a central role in cellular secretion and has been implicated in sorting cargo destined for the plasma membrane. Previously, the Arabidopsis (Arabidopsis thaliana) echidna (ech) mutant was shown to exhibit a dwarf phenotype due to impaired cell expansion. However, ech also has a previously uncharacterized phenotype of reduced male fertility. This semisterility is due to decreased anther size and reduced amounts of pollen but also to decreased pollen viability, impaired anther opening, and pollen tube growth. An ECH translational fusion (ECHPro:ECH-YELLOW FLUORESCENT PROTEIN) revealed developmentally regulated tissue-specific expression, with expression in the tapetum during early anther development and microspore release and subsequent expression in the pollen, pollen tube, and stylar tissues. Pollen viability and production, along with germination and pollen tube growth, were all impaired. The ech anther endothecium secondary wall thickening also appeared reduced and disorganized, resulting in incomplete anther opening. This did not appear to be due to anther secondary thickening regulatory genes but perhaps to altered secretion of wall materials through the TGN as a consequence of the absence of the ECH protein. ECH expression is critical for a variety of aspects of male reproduction, including the production of functional pollen grains, their effective release, germination, and tube formation. These stages of pollen development are fundamentally influenced by TGN trafficking of hormones and wall components. Overall, this suggests that the fertility defect is multifaceted, with the TGN trafficking playing a significant role in the process of both pollen formation and subsequent fertilization.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Fan, Xinping and Yang, Caiyun and Klisch, Doris and Ferguson, Alison and Bhaellero, Rishi P. and Niu, Xiwu and Wilson, Zoe A.},
	month = mar,
	year = {2014},
	pages = {1338--1349},
}

Abstract The trans-Golgi network (TGN) plays a central role in cellular secretion and has been implicated in sorting cargo destined for the plasma membrane. Previously, the Arabidopsis (Arabidopsis thaliana) echidna (ech) mutant was shown to exhibit a dwarf phenotype due to impaired cell expansion. However, ech also has a previously uncharacterized phenotype of reduced male fertility. This semisterility is due to decreased anther size and reduced amounts of pollen but also to decreased pollen viability, impaired anther opening, and pollen tube growth. An ECH translational fusion (ECHPro:ECH-YELLOW FLUORESCENT PROTEIN) revealed developmentally regulated tissue-specific expression, with expression in the tapetum during early anther development and microspore release and subsequent expression in the pollen, pollen tube, and stylar tissues. Pollen viability and production, along with germination and pollen tube growth, were all impaired. The ech anther endothecium secondary wall thickening also appeared reduced and disorganized, resulting in incomplete anther opening. This did not appear to be due to anther secondary thickening regulatory genes but perhaps to altered secretion of wall materials through the TGN as a consequence of the absence of the ECH protein. ECH expression is critical for a variety of aspects of male reproduction, including the production of functional pollen grains, their effective release, germination, and tube formation. These stages of pollen development are fundamentally influenced by TGN trafficking of hormones and wall components. Overall, this suggests that the fertility defect is multifaceted, with the TGN trafficking playing a significant role in the process of both pollen formation and subsequent fertilization.

@article{gruffman_plant_2014,
	title = {Plant nitrogen status and co-occurrence of organic and inorganic nitrogen sources influence root uptake by {Scots} pine seedlings},
	volume = {34},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpt121},
	doi = {10/f25fj6},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Tree Physiology},
	author = {Gruffman, L. and Jamtgard, S. and Nasholm, T.},
	month = feb,
	year = {2014},
	pages = {205--213},
}

@article{stirk_effect_2014,
	title = {Effect of light on growth and endogenous hormones in {Chlorella} minutissima ({Trebouxiophyceae})},
	volume = {79},
	issn = {09819428},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0981942814000837},
	doi = {10/f3p3qd},
	language = {en},
	urldate = {2021-06-08},
	journal = {Plant Physiology and Biochemistry},
	author = {Stirk, W.A. and Bálint, P. and Tarkowská, D. and Novák, O. and Maróti, G. and Ljung, K. and Turečková, V. and Strnad, M. and Ördög, V. and van Staden, J.},
	month = jun,
	year = {2014},
	pages = {66--76},
}

@article{azeez_tree_2014,
	title = {A {Tree} {Ortholog} of {APETALA1} {Mediates} {Photoperiodic} {Control} of {Seasonal} {Growth}},
	volume = {24},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S096098221400205X},
	doi = {10/f3ndt6},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Azeez, Abdul and Miskolczi, Pál and Tylewicz, Szymon and Bhalerao, Rishikesh P.},
	month = mar,
	year = {2014},
	pages = {717--724},
}

@article{brouwer_response_2014,
	title = {In response to partial plant shading, the lack of phytochrome {A} does not directly induce leaf senescence but alters the fine-tuning of chlorophyll biosynthesis},
	volume = {65},
	issn = {1460-2431, 0022-0957},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/eru060},
	doi = {10/f22wjn},
	language = {en},
	number = {14},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Brouwer, Bastiaan and Gardeström, Per and Keech, Olivier},
	month = jul,
	year = {2014},
	pages = {4037--4049},
}

@article{paudyal_trafficking_2014,
	title = {Trafficking modulator {TENin1} inhibits endocytosis, causes endomembrane protein accumulation at the pre-vacuolar compartment and impairs gravitropic response in {Arabidopsis} thaliana},
	volume = {460},
	issn = {0264-6021, 1470-8728},
	url = {https://portlandpress.com/biochemj/article/460/2/177/46675/Trafficking-modulator-TENin1-inhibits-endocytosis},
	doi = {10/f3m25k},
	abstract = {In the present study a detailed characterization of a small molecule inhibitor of protein trafficking and gravitropic response is described. We also identified two Arabidopsis thaliana ecotypes that display resistance to this compound. The ecotypes and chemical provide useful tool to investigate protein trafficking.},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Biochemical Journal},
	author = {Paudyal, Rupesh and Jamaluddin, Adam and Warren, James P. and Doyle, Siamsa M. and Robert, Stéphanie and Warriner, Stuart L. and Baker, Alison},
	month = jun,
	year = {2014},
	pages = {177--185},
}

In the present study a detailed characterization of a small molecule inhibitor of protein trafficking and gravitropic response is described. We also identified two Arabidopsis thaliana ecotypes that display resistance to this compound. The ecotypes and chemical provide useful tool to investigate protein trafficking.

@article{escamez_programmes_2014,
	title = {Programmes of cell death and autolysis in tracheary elements: when a suicidal cell arranges its own corpse removal},
	volume = {65},
	issn = {1460-2431, 0022-0957},
	shorttitle = {Programmes of cell death and autolysis in tracheary elements},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/eru057},
	doi = {10/f234sm},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Escamez, Sacha and Tuominen, Hannele},
	month = mar,
	year = {2014},
	pages = {1313--1321},
}

@article{blanco_interaction_2014,
	title = {Interaction between plastid and mitochondrial retrograde signalling pathways during changes to plastid redox status},
	volume = {369},
	issn = {0962-8436, 1471-2970},
	url = {https://royalsocietypublishing.org/doi/10.1098/rstb.2013.0231},
	doi = {10/f226pk},
	abstract = {Mitochondria and chloroplasts depend upon each other; photosynthesis provides substrates for mitochondrial respiration and mitochondrial metabolism is essential for sustaining photosynthetic carbon assimilation. In addition, mitochondrial respiration protects photosynthesis against photoinhibition by dissipating excess redox equivalents from the chloroplasts. Genetic defects in mitochondrial function result in an excessive reduction and energization of the chloroplast. Thus, it is clear that the activities of mitochondria and plastids need to be coordinated, but the manner by which the organelles communicate to coordinate their activities is unknown. The
              regulator of alternative oxidase
              (
              rao1)
              mutant was isolated as a mutant unable to induce
              AOX1a
              expression in response to the inhibitor of the mitochondrial cytochrome
              c
              reductase (complex III), antimycin A.
              RAO1
              encodes the nuclear localized cyclin-dependent kinase E1 (CDKE1). Interestingly, the
              rao1
              mutant demonstrates a genome uncoupled phenotype also in response to redox changes in the photosynthetic electron transport chain. Thus, CDKE1 was shown to regulate both
              LIGHT HARVESTING COMPLEX B
              (
              LHCB
              ) and
              ALTERNATIVE OXIDASE 1
              (
              AOX1a
              ) expression in response to retrograde signals. Our results suggest that CDKE1 is a central nuclear component integrating mitochondrial and plastid retrograde signals and plays a role in regulating energy metabolism during the response to stress.},
	language = {en},
	number = {1640},
	urldate = {2021-06-08},
	journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
	author = {Blanco, Nicolás E. and Guinea-Díaz, Manuel and Whelan, James and Strand, Åsa},
	month = apr,
	year = {2014},
	pages = {20130231},
}

Mitochondria and chloroplasts depend upon each other; photosynthesis provides substrates for mitochondrial respiration and mitochondrial metabolism is essential for sustaining photosynthetic carbon assimilation. In addition, mitochondrial respiration protects photosynthesis against photoinhibition by dissipating excess redox equivalents from the chloroplasts. Genetic defects in mitochondrial function result in an excessive reduction and energization of the chloroplast. Thus, it is clear that the activities of mitochondria and plastids need to be coordinated, but the manner by which the organelles communicate to coordinate their activities is unknown. The regulator of alternative oxidase ( rao1) mutant was isolated as a mutant unable to induce AOX1a expression in response to the inhibitor of the mitochondrial cytochrome c reductase (complex III), antimycin A. RAO1 encodes the nuclear localized cyclin-dependent kinase E1 (CDKE1). Interestingly, the rao1 mutant demonstrates a genome uncoupled phenotype also in response to redox changes in the photosynthetic electron transport chain. Thus, CDKE1 was shown to regulate both LIGHT HARVESTING COMPLEX B ( LHCB ) and ALTERNATIVE OXIDASE 1 ( AOX1a ) expression in response to retrograde signals. Our results suggest that CDKE1 is a central nuclear component integrating mitochondrial and plastid retrograde signals and plays a role in regulating energy metabolism during the response to stress.

@article{bellini_adventitious_2014,
	title = {Adventitious {Roots} and {Lateral} {Roots}: {Similarities} and {Differences}},
	volume = {65},
	issn = {1543-5008, 1545-2123},
	shorttitle = {Adventitious {Roots} and {Lateral} {Roots}},
	url = {http://www.annualreviews.org/doi/10.1146/annurev-arplant-050213-035645},
	doi = {10/f2z6rb},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Annual Review of Plant Biology},
	author = {Bellini, Catherine and Pacurar, Daniel I. and Perrone, Irene},
	month = apr,
	year = {2014},
	pages = {639--666},
}

@article{pacurar_auxin_2014,
	title = {Auxin is a central player in the hormone cross-talks that control adventitious rooting},
	volume = {151},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12171},
	doi = {10/f2264z},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Pacurar, Daniel Ioan and Perrone, Irene and Bellini, Catherine},
	month = may,
	year = {2014},
	pages = {83--96},
}

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

@incollection{staiger_perennial_2014,
	address = {New York, NY},
	title = {The {Perennial} {Clock} {Is} an {Essential} {Timer} for {Seasonal} {Growth} {Events} and {Cold} {Hardiness}},
	volume = {1158},
	isbn = {978-1-4939-0699-4 978-1-4939-0700-7},
	url = {http://link.springer.com/10.1007/978-1-4939-0700-7_20},
	urldate = {2021-06-08},
	booktitle = {Plant {Circadian} {Networks}},
	publisher = {Springer New York},
	author = {Johansson, Mikael and Ibáñez, Cristian and Takata, Naoki and Eriksson, Maria E.},
	editor = {Staiger, Dorothee},
	year = {2014},
	doi = {10.1007/978-1-4939-0700-7_20},
	note = {Series Title: Methods in Molecular Biology},
	pages = {297--311},
}

@incollection{staiger_monitoring_2014,
	address = {New York, NY},
	title = {Monitoring {Seasonal} {Bud} {Set}, {Bud} {Burst}, and {Cold} {Hardiness} in {Populus}},
	volume = {1158},
	isbn = {978-1-4939-0699-4 978-1-4939-0700-7},
	url = {http://link.springer.com/10.1007/978-1-4939-0700-7_21},
	urldate = {2021-06-08},
	booktitle = {Plant {Circadian} {Networks}},
	publisher = {Springer New York},
	author = {Johansson, Mikael and Takata, Naoki and Ibáñez, Cristian and Eriksson, Maria E.},
	editor = {Staiger, Dorothee},
	year = {2014},
	doi = {10.1007/978-1-4939-0700-7_21},
	note = {Series Title: Methods in Molecular Biology},
	pages = {313--324},
}

@article{bykova_function_2014,
	series = {Plant {Mitochondria} in {Mitochondrion}},
	title = {The function of glycine decarboxylase complex is optimized to maintain high photorespiratory flux via buffering of its reaction products},
	volume = {19},
	issn = {1567-7249},
	url = {https://www.sciencedirect.com/science/article/pii/S1567724914000026},
	doi = {10/f3nszc},
	abstract = {Oxidation of glycine in photorespiratory pathway is the major flux through mitochondria of C3 plants in the light. It sustains increased intramitochondrial concentrations of NADH and NADPH, which are required to engage the internal rotenone-insensitive NAD(P)H dehydrogenases and the alternative oxidase. We discuss here possible mechanisms of high photorespiratory flux maintenance in mitochondria and suggest that it is fulfilled under conditions where the concentrations of glycine decarboxylase reaction products NADH and CO2 achieve an equilibrium provided by malate dehydrogenase and carbonic anhydrase, respectively. This results in the removal of these products from the glycine decarboxylase multienzyme active sites and in the maintenance of their concentrations at levels sufficiently low to prevent substrate inhibition of the reaction.},
	language = {en},
	urldate = {2021-06-08},
	journal = {Mitochondrion},
	author = {Bykova, Natalia V. and Møller, Ian M. and Gardeström, Per and Igamberdiev, Abir U.},
	month = nov,
	year = {2014},
	keywords = {Carbonic anhydrase, Glycine decarboxylase, Malate dehydrogenase, Non-coupled electron transport, Photorespiration},
	pages = {357--364},
}

Oxidation of glycine in photorespiratory pathway is the major flux through mitochondria of C3 plants in the light. It sustains increased intramitochondrial concentrations of NADH and NADPH, which are required to engage the internal rotenone-insensitive NAD(P)H dehydrogenases and the alternative oxidase. We discuss here possible mechanisms of high photorespiratory flux maintenance in mitochondria and suggest that it is fulfilled under conditions where the concentrations of glycine decarboxylase reaction products NADH and CO2 achieve an equilibrium provided by malate dehydrogenase and carbonic anhydrase, respectively. This results in the removal of these products from the glycine decarboxylase multienzyme active sites and in the maintenance of their concentrations at levels sufficiently low to prevent substrate inhibition of the reaction.

@article{netotea_complex_2014,
	title = {{ComPlEx}: conservation and divergence of co-expression networks in {A}. thaliana, {Populus} and {O}. sativa},
	volume = {15},
	issn = {1471-2164},
	shorttitle = {{ComPlEx}},
	url = {http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-106},
	doi = {10/f23r6f},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Genomics},
	author = {Netotea, Sergiu and Sundell, David and Street, Nathaniel R and Hvidsten, Torgeir R},
	year = {2014},
	pages = {106},
}

@article{lastdrager_sugar_2014,
	title = {Sugar signals and the control of plant growth and development},
	volume = {65},
	issn = {1460-2431, 0022-0957},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/ert474},
	doi = {10/f239qn},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Lastdrager, Jeroen and Hanson, Johannes and Smeekens, Sjef},
	month = mar,
	year = {2014},
	pages = {799--807},
}

@article{viotti_er_2014,
	title = {{ER} and vacuoles: never been closer},
	volume = {5},
	issn = {1664-462X},
	shorttitle = {{ER} and vacuoles},
	url = {http://journal.frontiersin.org/article/10.3389/fpls.2014.00020/abstract},
	doi = {10/f23557},
	urldate = {2021-06-08},
	journal = {Frontiers in Plant Science},
	author = {Viotti, Corrado},
	year = {2014},
}

@article{kami_reduced_2014,
	title = {Reduced phototropism in \textit{pks} mutants may be due to altered auxin-regulated gene expression or reduced lateral auxin transport},
	volume = {77},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.12395},
	doi = {10/f25d98},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Kami, Chitose and Allenbach, Laure and Zourelidou, Melina and Ljung, Karin and Schütz, Frédéric and Isono, Erika and Watahiki, Masaaki K. and Yamamoto, Kotaro T. and Schwechheimer, Claus and Fankhauser, Christian},
	month = feb,
	year = {2014},
	pages = {393--403},
}

@article{keefover-ring_2-z-cinnamoylsalicortin_2014,
	title = {2′-({Z})-{Cinnamoylsalicortin}: {A} novel salicinoid isolated from {Populus} tremula},
	volume = {7},
	issn = {18743900},
	shorttitle = {2′-({Z})-{Cinnamoylsalicortin}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1874390013002085},
	doi = {10/f22wct},
	language = {en},
	urldate = {2021-06-08},
	journal = {Phytochemistry Letters},
	author = {Keefover-Ring, Ken and Carlsson, Marcus and Albrectsen, Benedicte Riber},
	month = feb,
	year = {2014},
	pages = {212--216},
}

@article{malnoe_thylakoid_2014,
	title = {Thylakoid {FtsH} {Protease} {Contributes} to {Photosystem} {II} and {Cytochrome} \textit{b} 6 \textit{f} {Remodeling} in \textit{{Chlamydomonas} reinhardtii} under {Stress} {Conditions}},
	volume = {26},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/26/1/373/6102321},
	doi = {10/f5vk82},
	abstract = {Abstract
            FtsH is the major thylakoid membrane protease found in organisms performing oxygenic photosynthesis. Here, we show that FtsH from Chlamydomonas reinhardtii forms heterooligomers comprising two subunits, FtsH1 and FtsH2. We characterized this protease using FtsH mutants that we identified through a genetic suppressor approach that restored phototrophic growth of mutants originally defective for cytochrome b  6  f accumulation. We thus extended the spectrum of FtsH substrates in the thylakoid membranes beyond photosystem II, showing the susceptibility of cytochrome b  6  f complexes (and proteins involved in the c  i heme binding pathway to cytochrome b  6) to FtsH. We then show how FtsH is involved in the response of C. reinhardtii to macronutrient stress. Upon phosphorus starvation, photosynthesis inactivation results from an FtsH-sensitive photoinhibition process. In contrast, we identified an FtsH-dependent loss of photosystem II and cytochrome b  6  f complexes in darkness upon sulfur deprivation. The D1 fragmentation pattern observed in the latter condition was similar to that observed in photoinhibitory conditions, which points to a similar degradation pathway in these two widely different environmental conditions. Our experiments thus provide extensive evidence that FtsH plays a major role in the quality control of thylakoid membrane proteins and in the response of C. reinhardtii to light and macronutrient stress.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Malnoë, Alizée and Wang, Fei and Girard-Bascou, Jacqueline and Wollman, Francis-André and de Vitry, Catherine},
	month = feb,
	year = {2014},
	pages = {373--390},
}

Abstract FtsH is the major thylakoid membrane protease found in organisms performing oxygenic photosynthesis. Here, we show that FtsH from Chlamydomonas reinhardtii forms heterooligomers comprising two subunits, FtsH1 and FtsH2. We characterized this protease using FtsH mutants that we identified through a genetic suppressor approach that restored phototrophic growth of mutants originally defective for cytochrome b  6  f accumulation. We thus extended the spectrum of FtsH substrates in the thylakoid membranes beyond photosystem II, showing the susceptibility of cytochrome b  6  f complexes (and proteins involved in the c  i heme binding pathway to cytochrome b  6) to FtsH. We then show how FtsH is involved in the response of C. reinhardtii to macronutrient stress. Upon phosphorus starvation, photosynthesis inactivation results from an FtsH-sensitive photoinhibition process. In contrast, we identified an FtsH-dependent loss of photosystem II and cytochrome b  6  f complexes in darkness upon sulfur deprivation. The D1 fragmentation pattern observed in the latter condition was similar to that observed in photoinhibitory conditions, which points to a similar degradation pathway in these two widely different environmental conditions. Our experiments thus provide extensive evidence that FtsH plays a major role in the quality control of thylakoid membrane proteins and in the response of C. reinhardtii to light and macronutrient stress.

@article{wei_nitric_2014,
	title = {Nitric {Oxide}–{Triggered} {Remodeling} of {Chloroplast} {Bioenergetics} and {Thylakoid} {Proteins} upon {Nitrogen} {Starvation} in \textit{{Chlamydomonas} reinhardtii}},
	volume = {26},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/26/1/353/6102308},
	doi = {10/gj6zmv},
	abstract = {Abstract
            Starving microalgae for nitrogen sources is commonly used as a biotechnological tool to boost storage of reduced carbon into starch granules or lipid droplets, but the accompanying changes in bioenergetics have been little studied so far. Here, we report that the selective depletion of Rubisco and cytochrome b  6  f complex that occurs when Chlamydomonas reinhardtii is starved for nitrogen in the presence of acetate and under normoxic conditions is accompanied by a marked increase in chlororespiratory enzymes, which converts the photosynthetic thylakoid membrane into an intracellular matrix for oxidative catabolism of reductants. Cytochrome b  6  f subunits and most proteins specifically involved in their biogenesis are selectively degraded, mainly by the FtsH and Clp chloroplast proteases. This regulated degradation pathway does not require light, active photosynthesis, or state transitions but is prevented when respiration is impaired or under phototrophic conditions. We provide genetic and pharmacological evidence that NO production from intracellular nitrite governs this degradation pathway: Addition of a NO scavenger and of two distinct NO producers decrease and increase, respectively, the rate of cytochrome b  6  f degradation; NO-sensitive fluorescence probes, visualized by confocal microscopy, demonstrate that nitrogen-starved cells produce NO only when the cytochrome b  6  f degradation pathway is activated.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Wei, Lili and Derrien, Benoit and Gautier, Arnaud and Houille-Vernes, Laura and Boulouis, Alix and Saint-Marcoux, Denis and Malnoë, Alizée and Rappaport, Fabrice and de Vitry, Catherine and Vallon, Olivier and Choquet, Yves and Wollman, Francis-André},
	month = feb,
	year = {2014},
	pages = {353--372},
}

Abstract Starving microalgae for nitrogen sources is commonly used as a biotechnological tool to boost storage of reduced carbon into starch granules or lipid droplets, but the accompanying changes in bioenergetics have been little studied so far. Here, we report that the selective depletion of Rubisco and cytochrome b  6  f complex that occurs when Chlamydomonas reinhardtii is starved for nitrogen in the presence of acetate and under normoxic conditions is accompanied by a marked increase in chlororespiratory enzymes, which converts the photosynthetic thylakoid membrane into an intracellular matrix for oxidative catabolism of reductants. Cytochrome b  6  f subunits and most proteins specifically involved in their biogenesis are selectively degraded, mainly by the FtsH and Clp chloroplast proteases. This regulated degradation pathway does not require light, active photosynthesis, or state transitions but is prevented when respiration is impaired or under phototrophic conditions. We provide genetic and pharmacological evidence that NO production from intracellular nitrite governs this degradation pathway: Addition of a NO scavenger and of two distinct NO producers decrease and increase, respectively, the rate of cytochrome b  6  f degradation; NO-sensitive fluorescence probes, visualized by confocal microscopy, demonstrate that nitrogen-starved cells produce NO only when the cytochrome b  6  f degradation pathway is activated.

@incollection{hicks_using_2014,
	address = {Totowa, NJ},
	title = {Using a {Reverse} {Genetics} {Approach} to {Investigate} {Small}-{Molecule} {Activity}},
	volume = {1056},
	isbn = {978-1-62703-591-0 978-1-62703-592-7},
	url = {http://link.springer.com/10.1007/978-1-62703-592-7_6},
	urldate = {2021-06-08},
	booktitle = {Plant {Chemical} {Genomics}},
	publisher = {Humana Press},
	author = {Doyle, Siamsa M. and Robert, Stéphanie},
	editor = {Hicks, Glenn R and Robert, Stéphanie},
	year = {2014},
	doi = {10.1007/978-1-62703-592-7_6},
	note = {Series Title: Methods in Molecular Biology},
	pages = {51--62},
}