Publications 2008

@article{su_probing_2008,
	title = {Probing {Mode} and {Site} of {Substrate} {Water} {Binding} to the {Oxygen}-{Evolving} {Complex} in the {S2} {State} of {Photosystem} {II} by {17O}-{HYSCORE} {Spectroscopy}},
	volume = {130},
	issn = {0002-7863},
	url = {https://doi.org/10.1021/ja076620i},
	doi = {10.1021/ja076620i},
	abstract = {In the oxygen-evolving complex (OEC) of photosystem II (PSII) molecular oxygen is formed from two substrate water molecules that are ligated to a μ-oxo bridged cluster containing four Mn ions and one Ca ion (Mn4OxCa cluster; Ox symbolizes the unknown number of μ-oxo bridges; x ≥ 5). There is a long-standing enigma as to when, where, and how the two substrate water molecules bind to the Mn4OxCa cluster during the cyclic water-splitting reaction, which involves five distinct redox intermediates (Si-states; i = 0,...,4). To address this question we employed hyperfine sublevel correlation (HYSCORE) spectroscopy on H217O-enriched PSII samples poised in the paramagnetic S2 state. This approach allowed us to resolve the magnetic interaction between one solvent exchangeable 17O that is directly ligated to one or more Mn ions of the Mn4OxCa cluster in the S2 state of PSII. Direct coordination of 17O to Mn is supported by the strong (A ≈ 10 MHz) hyperfine coupling. Because these are properties expected from a substrate water molecule, this spectroscopic signature holds the potential for gaining long-sought information about the binding mode and site of one of the two substrate water molecules in the S2 state of PSII.},
	number = {3},
	urldate = {2024-12-12},
	journal = {Journal of the American Chemical Society},
	author = {Su, Ji-Hu and Lubitz, Wolfgang and Messinger, Johannes},
	month = jan,
	year = {2008},
	note = {Publisher: American Chemical Society},
	pages = {786--787},
}

In the oxygen-evolving complex (OEC) of photosystem II (PSII) molecular oxygen is formed from two substrate water molecules that are ligated to a μ-oxo bridged cluster containing four Mn ions and one Ca ion (Mn4OxCa cluster; Ox symbolizes the unknown number of μ-oxo bridges; x ≥ 5). There is a long-standing enigma as to when, where, and how the two substrate water molecules bind to the Mn4OxCa cluster during the cyclic water-splitting reaction, which involves five distinct redox intermediates (Si-states; i = 0,...,4). To address this question we employed hyperfine sublevel correlation (HYSCORE) spectroscopy on H217O-enriched PSII samples poised in the paramagnetic S2 state. This approach allowed us to resolve the magnetic interaction between one solvent exchangeable 17O that is directly ligated to one or more Mn ions of the Mn4OxCa cluster in the S2 state of PSII. Direct coordination of 17O to Mn is supported by the strong (A ≈ 10 MHz) hyperfine coupling. Because these are properties expected from a substrate water molecule, this spectroscopic signature holds the potential for gaining long-sought information about the binding mode and site of one of the two substrate water molecules in the S2 state of PSII.

@inproceedings{yano_electronic_2008,
	address = {Dordrecht},
	title = {Electronic {Structure} and {Oxidation} {State} {Changes} in the {Mn4Ca} {Cluster} of {Photosystem} {II}},
	isbn = {978-1-4020-6709-9},
	doi = {10.1007/978-1-4020-6709-9_120},
	abstract = {Oxygen-evolving complex (Mn4Ca cluster) of Photosystem II cycles through five intermediate states (Si-states, i = 0–4) before a molecule of dioxygen is released. During the Sstate transitions, electrons are extracted from the OEC, either from Mn or alternatively from an oxo ligand. The oxidation state of Mn is widely accepted as Mn4(III2,IV2) and Mn4(III,IV3) for S1 and S2 states, while it is still controversial for the S0 and S3 states. We used resonant inelastic X-ray scattering (RIXS) to study the electronic structure of Mn4Ca complex in the OEC. The RIXS data yield two- dimensional plots that provide a significant advantage by obtaining both K-edge pre-edge (charge density sensitive) and L-edge-like spectra (metal spin state sensitive) simultaneously. The spectral changes in the Mn 1s2p3/2 RIXS spectra between the S-states were compared to those of the Mn oxides and coordination complexes. The results indicate strong covalency for the electronic configuration in the OEC, and we conclude that the electron is transferred from a strongly delocalized orbital, compared to those in Mn oxides or coordination complexes. The magnitude for the S0 to S1, and S1 to S2 transitions is twice as large as that during the S2 to S3 transition, indicating that the electron for this transition is extracted from a highly delocalized orbital with little change in charge density at the Mn atoms.},
	language = {en},
	booktitle = {Photosynthesis. {Energy} from the {Sun}},
	publisher = {Springer Netherlands},
	author = {Yano, Junko and Pushkar, Yulia and Messinger, Johannes and Bergmann, Uwe and Glatzel, Pieter and Yachandra, Vittal K.},
	editor = {Allen, John F. and Gantt, Elisabeth and Golbeck, John H. and Osmond, Barry},
	year = {2008},
	keywords = {Electronic structure, Mn4Ca cluster, RIXS, X-ray spectroscopy, oxygen-evolving complex, photosystem II},
	pages = {529--532},
}

Oxygen-evolving complex (Mn4Ca cluster) of Photosystem II cycles through five intermediate states (Si-states, i = 0–4) before a molecule of dioxygen is released. During the Sstate transitions, electrons are extracted from the OEC, either from Mn or alternatively from an oxo ligand. The oxidation state of Mn is widely accepted as Mn4(III2,IV2) and Mn4(III,IV3) for S1 and S2 states, while it is still controversial for the S0 and S3 states. We used resonant inelastic X-ray scattering (RIXS) to study the electronic structure of Mn4Ca complex in the OEC. The RIXS data yield two- dimensional plots that provide a significant advantage by obtaining both K-edge pre-edge (charge density sensitive) and L-edge-like spectra (metal spin state sensitive) simultaneously. The spectral changes in the Mn 1s2p3/2 RIXS spectra between the S-states were compared to those of the Mn oxides and coordination complexes. The results indicate strong covalency for the electronic configuration in the OEC, and we conclude that the electron is transferred from a strongly delocalized orbital, compared to those in Mn oxides or coordination complexes. The magnitude for the S0 to S1, and S1 to S2 transitions is twice as large as that during the S2 to S3 transition, indicating that the electron for this transition is extracted from a highly delocalized orbital with little change in charge density at the Mn atoms.

@inproceedings{yano_structure_2008,
	address = {Dordrecht},
	title = {Structure of the {Photosynthetic} {Mn4Ca} {Cluster} {Using} {X}-ray {Spectroscopy}},
	isbn = {978-1-4020-6709-9},
	doi = {10.1007/978-1-4020-6709-9_121},
	abstract = {Single crystals of Photosystem II (PSII) isolated from thermophilic cyanobacteria have been studied by X-ray diffraction (XRD) with resolutions between 3 and 3.8 Å (Ferreira et al. 2004; Loll et al. 2005). These studies have localized electron density associated with the wateroxidizing Mn4Ca cluster within the large complex of PSII peptides, but the limited resolution is short of what is needed to place individual metal atoms precisely in the cluster. Examination of the orientation dependence of the EXAFS of single crystals of PSII can provide structural information about the Mn sites at a resolution higher than that is presently available from single-crystal X-ray diffraction. We have successfully collected single crystal XANES and EXAFS data from the native S1 state with the X-ray e-vector parallel to the a, b, and c axes of the crystal, under non-damaging conditions by monitoring the Mn K-edge for any X-ray induced Mn reduction. The EXAFS spectra show that the Fourier peaks are clearly dichroic, demonstrating an asymmetric Mn cluster. We have used the EXAFS dichroism to evaluate the Mn cluster geometry. Three Mn4Ca models which satisfy the trend of EXAFS dichroism were further fit into the ligand environment obtained from XRD, in order to discriminate between the several symmetry-related orientations which arise from the crystal symmetry. Furthermore, single crystals in the S1 state were illuminated either by continuous illumination or by laser flashes to create intermediate S-states (S2 and S3). Polarized XANES and EXAFS spectra from these crystals show unique orientational dependence. Additionally, a review of how the resolution of traditional EXAFS techniques can be improved, using methods such as rangeextended EXAFS, is presented.},
	language = {en},
	booktitle = {Photosynthesis. {Energy} from the {Sun}},
	publisher = {Springer Netherlands},
	author = {Yano, Junko and Kern, Jan and Sauer, Kenneth and Pushkar, Yulia and Bergmann, Uwe and Glatzel, Pieter and Messinger, Johannes and Zouni, Athina and Yachandra, Vittal K.},
	editor = {Allen, John F. and Gantt, Elisabeth and Golbeck, John H. and Osmond, Barry},
	year = {2008},
	keywords = {Mn4Ca cluster, X-ray spectroscopy, oxygen-evolving complex, photosystem II},
	pages = {533--538},
}

Single crystals of Photosystem II (PSII) isolated from thermophilic cyanobacteria have been studied by X-ray diffraction (XRD) with resolutions between 3 and 3.8 Å (Ferreira et al. 2004; Loll et al. 2005). These studies have localized electron density associated with the wateroxidizing Mn4Ca cluster within the large complex of PSII peptides, but the limited resolution is short of what is needed to place individual metal atoms precisely in the cluster. Examination of the orientation dependence of the EXAFS of single crystals of PSII can provide structural information about the Mn sites at a resolution higher than that is presently available from single-crystal X-ray diffraction. We have successfully collected single crystal XANES and EXAFS data from the native S1 state with the X-ray e-vector parallel to the a, b, and c axes of the crystal, under non-damaging conditions by monitoring the Mn K-edge for any X-ray induced Mn reduction. The EXAFS spectra show that the Fourier peaks are clearly dichroic, demonstrating an asymmetric Mn cluster. We have used the EXAFS dichroism to evaluate the Mn cluster geometry. Three Mn4Ca models which satisfy the trend of EXAFS dichroism were further fit into the ligand environment obtained from XRD, in order to discriminate between the several symmetry-related orientations which arise from the crystal symmetry. Furthermore, single crystals in the S1 state were illuminated either by continuous illumination or by laser flashes to create intermediate S-states (S2 and S3). Polarized XANES and EXAFS spectra from these crystals show unique orientational dependence. Additionally, a review of how the resolution of traditional EXAFS techniques can be improved, using methods such as rangeextended EXAFS, is presented.

@inproceedings{su_substrate_2008,
	address = {Dordrecht},
	title = {Substrate {Water} {Bound} to the {S2}-{State} of the {Mn4OxCa} {Cluster} in {Photosystem} {II} {Studied} by {Advanced} {Pulse} {EPR} {Spectroscopy}},
	isbn = {978-1-4020-6709-9},
	doi = {10.1007/978-1-4020-6709-9_114},
	abstract = {In The Present Study, We Employed Several Advanced Pulse Epr Techniques To Detect Weak Hyperfine Couplings To Study Substrate Water Binding To The Mn4OXCa Cluster In The S2, State Of Photosystem Ii. Our Data Show That The Hyperfine Coupling Between The 2H And The Mn4OXCa Cluster Is Too Weak To Be Resolved. We Propose That The Information Does Not Allow Make Precise Conclusions About The Mode Of Substrate Water Binding To The Mn4OXCa Cluster. Our Preliminary Data Suggest That More Detailed Information Can Be Obtained From The H216O/ H217O Exchange Experiments.},
	language = {en},
	booktitle = {Photosynthesis. {Energy} from the {Sun}},
	publisher = {Springer Netherlands},
	author = {Su, Ji-Hu and Lubitz, Wolfgang and Messinger, Johannes},
	editor = {Allen, John F. and Gantt, Elisabeth and Golbeck, John H. and Osmond, Barry},
	year = {2008},
	keywords = {ESEEM, HYSCORE, Mims ENDOR, PSII, Water binding, pulse EPR},
	pages = {503--507},
}

In The Present Study, We Employed Several Advanced Pulse Epr Techniques To Detect Weak Hyperfine Couplings To Study Substrate Water Binding To The Mn4OXCa Cluster In The S2, State Of Photosystem Ii. Our Data Show That The Hyperfine Coupling Between The 2H And The Mn4OXCa Cluster Is Too Weak To Be Resolved. We Propose That The Information Does Not Allow Make Precise Conclusions About The Mode Of Substrate Water Binding To The Mn4OXCa Cluster. Our Preliminary Data Suggest That More Detailed Information Can Be Obtained From The H216O/ H217O Exchange Experiments.

@article{shevela_hydrogencarbonate_2008,
	title = {Hydrogencarbonate is not a tightly bound constituent of the water-oxidizing complex in photosystem {II}},
	volume = {1777},
	issn = {0005-2728},
	url = {https://www.sciencedirect.com/science/article/pii/S0005272808000650},
	doi = {10.1016/j.bbabio.2008.03.031},
	abstract = {Since the end of the 1950s hydrogencarbonate (‘bicarbonate’) is discussed as a possible cofactor of photosynthetic water-splitting, and in a recent X-ray crystallography model of photosystem II (PSII) it was displayed as a ligand of the Mn4OxCa cluster. Employing membrane-inlet mass spectrometry (MIMS) and isotope labelling we confirm the release of less than one (≈0.3) HCO3− per PSII upon addition of formate. The same amount of HCO3− release is observed upon formate addition to Mn-depleted PSII samples. This suggests that formate does not replace HCO3− from the donor side, but only from the non-heme iron at the acceptor side of PSII. The absence of a firmly bound HCO3− is corroborated by showing that a reductive destruction of the Mn4OxCa cluster inside the MIMS cell by NH2OH addition does not lead to any CO2/HCO3− release. We note that even after an essentially complete HCO3−/CO2 removal from the sample medium by extensive degassing in the MIMS cell the PSII samples retain ≥75\% of their initial flash-induced O2-evolving capacity. We therefore conclude that HCO3− has only ‘indirect’ effects on water-splitting in PSII, possibly by being part of a proton relay network and/or by participating in assembly and stabilization of the water-oxidizing complex.},
	number = {6},
	urldate = {2024-11-29},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Shevela, Dmitriy and Su, Ji-Hu and Klimov, Vyacheslav and Messinger, Johannes},
	month = jun,
	year = {2008},
	keywords = {Bicarbonate, Hydrogencarbonate, Membrane-inlet mass spectrometry (MIMS), Photosystem II, Water oxidation, Water-splitting},
	pages = {532--539},
}

Since the end of the 1950s hydrogencarbonate (‘bicarbonate’) is discussed as a possible cofactor of photosynthetic water-splitting, and in a recent X-ray crystallography model of photosystem II (PSII) it was displayed as a ligand of the Mn4OxCa cluster. Employing membrane-inlet mass spectrometry (MIMS) and isotope labelling we confirm the release of less than one (≈0.3) HCO3− per PSII upon addition of formate. The same amount of HCO3− release is observed upon formate addition to Mn-depleted PSII samples. This suggests that formate does not replace HCO3− from the donor side, but only from the non-heme iron at the acceptor side of PSII. The absence of a firmly bound HCO3− is corroborated by showing that a reductive destruction of the Mn4OxCa cluster inside the MIMS cell by NH2OH addition does not lead to any CO2/HCO3− release. We note that even after an essentially complete HCO3−/CO2 removal from the sample medium by extensive degassing in the MIMS cell the PSII samples retain ≥75% of their initial flash-induced O2-evolving capacity. We therefore conclude that HCO3− has only ‘indirect’ effects on water-splitting in PSII, possibly by being part of a proton relay network and/or by participating in assembly and stabilization of the water-oxidizing complex.

@inproceedings{shevela_formate-induced_2008,
	address = {Dordrecht},
	title = {Formate-{Induced} {Release} of {Carbon} {Dioxide}/ {Hydrogencarbonate} from {Photosystem} {II}},
	isbn = {978-1-4020-6709-9},
	doi = {10.1007/978-1-4020-6709-9_112},
	abstract = {Using Membrane-Inlet Mass Spectrometry (Mims) We Confirm That Injections Of High Concentrations (100 Mm Final Concentration) Of Formate Into The Psii Samples Induce A Slow Release Of Carbon Dioxide/Hydrogencarbonate (Co2/ Hco3 -) (Govindjee Et Al. 1997). The Amount Of The Released Inorganic Carbon (CI) Is Proportional Tothe Concentration Of The Bby Samples. Hydrazinepre- Treated Bby, Leading To An ̃90\% Inhibition Of The Overall Oxygen Evolution Activity, Release After Formate Injection Practically The Same Amount Of CI As Non-Treated Control Samples. These Results Indicate That The Released CI Originates From The Acceptor Side Of Psii And Evidently None From The Mn4OXCa Cluster. Thus, No Evidence Was Found In This Study For Hydrogencarbonate Being Tight Ligand Of The Mn4OXCa Cluster, Which Can Be Released By Formate Injection. The Possibility Of Hco3 - Release From Psii During Degassation In The Mass Spec Cell Is Discussed.},
	language = {en},
	booktitle = {Photosynthesis. {Energy} from the {Sun}},
	publisher = {Springer Netherlands},
	author = {Shevela, Dmitriy and Klimov, Vyacheslav and Messinger, Johannes},
	editor = {Allen, John F. and Gantt, Elisabeth and Golbeck, John H. and Osmond, Barry},
	year = {2008},
	keywords = {Membrane-inlet mass spectrometry (MIMS), bicarbonate, formate, hydrogencarbonate, photosystem II (PSII)},
	pages = {495--498},
}

Using Membrane-Inlet Mass Spectrometry (Mims) We Confirm That Injections Of High Concentrations (100 Mm Final Concentration) Of Formate Into The Psii Samples Induce A Slow Release Of Carbon Dioxide/Hydrogencarbonate (Co2/ Hco3 -) (Govindjee Et Al. 1997). The Amount Of The Released Inorganic Carbon (CI) Is Proportional Tothe Concentration Of The Bby Samples. Hydrazinepre- Treated Bby, Leading To An ̃90% Inhibition Of The Overall Oxygen Evolution Activity, Release After Formate Injection Practically The Same Amount Of CI As Non-Treated Control Samples. These Results Indicate That The Released CI Originates From The Acceptor Side Of Psii And Evidently None From The Mn4OXCa Cluster. Thus, No Evidence Was Found In This Study For Hydrogencarbonate Being Tight Ligand Of The Mn4OXCa Cluster, Which Can Be Released By Formate Injection. The Possibility Of Hco3 - Release From Psii During Degassation In The Mass Spec Cell Is Discussed.

@article{pecoraro_structure_2008,
	title = {The structure of the {Mn}$_{\textrm{4}}${Ca}{\textless}{SUP}{\textgreater}2+{\textless}/{SUP}{\textgreater} cluster of photosystem {II} and its protein environment as revealed by {X}-ray crystallography -: {Discussion}},
	volume = {363},
	issn = {0962-8436},
	language = {English},
	number = {1494},
	journal = {PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES},
	author = {Pecoraro, V. L. and Barber, J. and Dau, H. and Brudvig, G. and Siegbahn, P. and Messinger, J.},
	month = mar,
	year = {2008},
	note = {Num Pages: 2
Place: London
Publisher: Royal Soc
Web of Science ID: WOS:000253117000003},
	pages = {1137--1138},
}

@article{pecoraro_water_2008,
	title = {Water oxidation chemistry of photosystem {II} - {Discussion}},
	volume = {363},
	issn = {0962-8436},
	language = {English},
	number = {1494},
	journal = {PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES},
	author = {Pecoraro, V. and Brudvig, G. and Dau, H. and Aukauloo, A. and Nocera, D. and Siegbalm, P. and Messinger, J.},
	month = mar,
	year = {2008},
	note = {Num Pages: 2
Place: London
Publisher: Royal Soc
Web of Science ID: WOS:000253117000021},
	pages = {1218--1219},
}

@article{pace_focusing_2008,
	title = {Focusing the view on nature's water-splitting catalyst - {Discussion}},
	volume = {363},
	issn = {0962-8436},
	language = {English},
	number = {1494},
	journal = {PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES},
	author = {Pace, R. and Messinger, J. and Boussac, A. and Britt, R. D. and Dismukes, C.},
	month = mar,
	year = {2008},
	note = {Num Pages: 1
Place: London
Publisher: Royal Soc
Web of Science ID: WOS:000253117000011},
	keywords = {COMPLEX, PHOTOSYSTEM-II, S-0 STATE, SIGNAL},
	pages = {1177--1177},
}

@article{noring_effects_2008,
	title = {Effects of methanol on the {Si}-state transitions in photosynthetic water-splitting},
	volume = {98},
	issn = {1573-5079},
	url = {https://doi.org/10.1007/s11120-008-9364-4},
	doi = {10.1007/s11120-008-9364-4},
	abstract = {From a chemical point of view methanol is one of the closest analogues of water. Consistent with this idea EPR spectroscopy studies have shown that methanol binds at—or at least very close to—the Mn4OxCa cluster of photosystem II (PSII). In contrast, Clark-type oxygen rate measurements demonstrate that the O2 evolving activity of PSII is surprisingly unaffected by methanol concentrations of up to 10\%. Here we study for the first time in detail the effect of methanol on photosynthetic water-splitting by employing a Joliot-type bare platinum electrode. We demonstrate a linear dependence of the miss parameter for Sistate advancement on the methanol concentrations in the range of 0–10\% (v/v). This finding is consistent with the idea that methanol binds in PSII with similar affinity as water to one or both substrate binding sites at the Mn4OxCa cluster. The possibility is discussed that the two substrate water molecules bind at different stages of the cycle, one during the S4 → S0 and the other during the S2 → S3 transition.},
	language = {en},
	number = {1},
	urldate = {2024-11-29},
	journal = {Photosynthesis Research},
	author = {Nöring, Birgit and Shevela, Dmitriy and Renger, Gernot and Messinger, Johannes},
	month = oct,
	year = {2008},
	keywords = {Manganese cluster, Methanol, Oxygen evolution, Photosystem II, Water-splitting},
	pages = {251--260},
}

From a chemical point of view methanol is one of the closest analogues of water. Consistent with this idea EPR spectroscopy studies have shown that methanol binds at—or at least very close to—the Mn4OxCa cluster of photosystem II (PSII). In contrast, Clark-type oxygen rate measurements demonstrate that the O2 evolving activity of PSII is surprisingly unaffected by methanol concentrations of up to 10%. Here we study for the first time in detail the effect of methanol on photosynthetic water-splitting by employing a Joliot-type bare platinum electrode. We demonstrate a linear dependence of the miss parameter for Sistate advancement on the methanol concentrations in the range of 0–10% (v/v). This finding is consistent with the idea that methanol binds in PSII with similar affinity as water to one or both substrate binding sites at the Mn4OxCa cluster. The possibility is discussed that the two substrate water molecules bind at different stages of the cycle, one during the S4 → S0 and the other during the S2 → S3 transition.

@article{lubitz_solar_2008,
	title = {Solar water-splitting into {H2} and {O2}: design principles of photosystem {II} and hydrogenases},
	volume = {1},
	issn = {1754-5706},
	shorttitle = {Solar water-splitting into {H2} and {O2}},
	url = {https://pubs.rsc.org/en/content/articlelanding/2008/ee/b808792j},
	doi = {10.1039/B808792J},
	abstract = {This review aims at presenting the principles of water-oxidation in photosystem II and of hydrogen production by the two major classes of hydrogenases in order to facilitate application for the design of artificial catalysts for solar fuel production.},
	language = {en},
	number = {1},
	urldate = {2024-11-29},
	journal = {Energy \& Environmental Science},
	author = {Lubitz, Wolfgang and Reijerse, Edward J. and Messinger, Johannes},
	month = jul,
	year = {2008},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {15--31},
}

This review aims at presenting the principles of water-oxidation in photosystem II and of hydrogen production by the two major classes of hydrogenases in order to facilitate application for the design of artificial catalysts for solar fuel production.

@incollection{konermann_mass_2008,
	address = {Dordrecht},
	title = {Mass {Spectrometry}-{Based} {Methods} for {Studying} {Kinetics} and {Dynamics} in {Biological} {Systems}},
	isbn = {978-1-4020-8250-4},
	url = {https://doi.org/10.1007/978-1-4020-8250-4_9},
	abstract = {In recent years, mass spectrometry (MS) has become one of the most widely used analytical techniques. MS allows studies on compounds ranging in size from single atoms to mega-Dalton biomolecular assemblies. This chapter provides an overview of recent MS applications in biophysical chemistry. The focus of our discussion is on ‘time-resolved’ techniques for tracking changes in complex biological reaction mixtures on time scales of milliseconds to days, thereby providing important structural and mechanistic insights. After a general introduction to biological MS, we discuss practical aspects of time-resolved membrane inlet mass spectrometry (MIMS), such as membrane properties and the use of different sample chambers. The MIMS technique allows online detection of dissolved gases and volatile compounds. It is particularly useful for resolving competing biochemical reactions involving common reactants, because isotopic labeling of substrates can be performed. As examples we present mechanistic studies on Photosystem II, carbonic anhydrase and hydrogenase. In the third part of this chapter we discuss the kinetics and mechanisms of protein folding and unfolding in solution, which can be explored via electrospray ionization mass spectrometry (ESI-MS). On-line coupling of ESI-MS with continuous-flow rapid mixing devices allows monitoring conformational changes of polypeptide chains with millisecond time resolution, as well as the detection and characterization of (un)folding intermediates. Due to its ‘softness’ the ESI process retains even weakly bound noncovalent complexes during the transition into the gas phase, such that protein-protein and protein-ligand interactions can be monitored directly. Additional insights into the conformational dynamics of proteins can be obtained by using time-resolved ESI-MS in conjunction with hydrogen/deuterium exchange methods. It is hoped that this chapter will stimulate the application of time-resolved MS techniques to a wide range of hitherto unexplored research areas.},
	language = {en},
	urldate = {2024-11-29},
	booktitle = {Biophysical {Techniques} in {Photosynthesis}},
	publisher = {Springer Netherlands},
	author = {Konermann, Lars and Messinger, Johannes and Hillier, Warwick},
	editor = {Aartsma, Thijs J. and Matysik, Jörg},
	year = {2008},
	doi = {10.1007/978-1-4020-8250-4_9},
	keywords = {Electrospray Ionization Mass Spectrometry, Electrospray Mass Spectrometry, Oxygen Evolve Complex, Phys Chem Chem Phys, Sample Chamber},
	pages = {167--190},
}

In recent years, mass spectrometry (MS) has become one of the most widely used analytical techniques. MS allows studies on compounds ranging in size from single atoms to mega-Dalton biomolecular assemblies. This chapter provides an overview of recent MS applications in biophysical chemistry. The focus of our discussion is on ‘time-resolved’ techniques for tracking changes in complex biological reaction mixtures on time scales of milliseconds to days, thereby providing important structural and mechanistic insights. After a general introduction to biological MS, we discuss practical aspects of time-resolved membrane inlet mass spectrometry (MIMS), such as membrane properties and the use of different sample chambers. The MIMS technique allows online detection of dissolved gases and volatile compounds. It is particularly useful for resolving competing biochemical reactions involving common reactants, because isotopic labeling of substrates can be performed. As examples we present mechanistic studies on Photosystem II, carbonic anhydrase and hydrogenase. In the third part of this chapter we discuss the kinetics and mechanisms of protein folding and unfolding in solution, which can be explored via electrospray ionization mass spectrometry (ESI-MS). On-line coupling of ESI-MS with continuous-flow rapid mixing devices allows monitoring conformational changes of polypeptide chains with millisecond time resolution, as well as the detection and characterization of (un)folding intermediates. Due to its ‘softness’ the ESI process retains even weakly bound noncovalent complexes during the transition into the gas phase, such that protein-protein and protein-ligand interactions can be monitored directly. Additional insights into the conformational dynamics of proteins can be obtained by using time-resolved ESI-MS in conjunction with hydrogen/deuterium exchange methods. It is hoped that this chapter will stimulate the application of time-resolved MS techniques to a wide range of hitherto unexplored research areas.

@article{dau_ftir_2008,
	title = {{FTIR} detection of water reactions in the oxygen-evolving centre of photosystem {II} - {Discussion}},
	volume = {363},
	issn = {0962-8436},
	url = {https://www.webofscience.com/wos/woscc/full-record/WOS:000253117000015},
	language = {English},
	number = {1494},
	urldate = {2024-11-29},
	journal = {PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES},
	author = {Dau, H. and Noguchi, T. and Messinger, J. and Moran, K. and Hillier, W.},
	month = mar,
	year = {2008},
	note = {Num Pages: 2
Place: London
Publisher: Royal Soc
Web of Science ID: WOS:000253117000015},
	pages = {1194--1195},
}

@article{barber_using_2008,
	title = {Using small molecule complexes to elucidate features of photosynthetic water oxidation - {Discussion}},
	volume = {363},
	issn = {0962-8436, 1471-2970},
	language = {English},
	number = {1494},
	journal = {PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES},
	author = {Barber, J. and Pecoraro, V. and Brudvig, G. and Aukauloo, A. and Messinger, J.},
	month = mar,
	year = {2008},
	note = {Num Pages: 3
Place: London
Publisher: Royal Soc
Web of Science ID: WOS:000253117000034},
	keywords = {S-3 STATE},
	pages = {1279--1281},
}

@article{beckmann_formation_2008,
	title = {Formation of stoichiometrically {18O}-labelled oxygen from the oxidation of {18O}-enriched water mediated by a dinuclear manganese complex—a mass spectrometry and {EPR} study},
	volume = {1},
	issn = {1754-5706},
	url = {https://pubs.rsc.org/en/content/articlelanding/2008/ee/b811806j},
	doi = {10.1039/B811806J},
	abstract = {Oxygen formation was detected for the oxidations of various multinuclear manganese complexes by oxone (HSO5−) in aqueous solution. To determine to what extent water was the source of the evolved O2, H218O isotope-labelling experiments coupled with membrane inlet mass spectrometry (MIMS) were carried out. We discovered that during the reaction of oxone with [Mn2(OAc)2(bpmp)]+ (1), stoichiometrically labelled oxygen (18O2) was formed. This is the first example of a homogeneous reaction mediated by a synthetic manganese complex where the addition of a strong chemical oxidant yields 18O2 with labelling percentages matching the theoretically expected values for the case of both O-atoms originating from water. Experiments using lead acetate as an alternative oxidant supported this finding. A detailed investigation of the reaction by EPR spectroscopy, MIMS and Clark-type oxygen detection enabled us to propose potential reaction pathways.},
	language = {en},
	number = {6},
	urldate = {2024-11-29},
	journal = {Energy \& Environmental Science},
	author = {Beckmann, Katrin and Uchtenhagen, Hannes and Berggren, Gustav and Anderlund, Magnus F. and Thapper, Anders and Messinger, Johannes and Styring, Stenbjörn and Kurz, Philipp},
	month = dec,
	year = {2008},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {668--676},
}

Oxygen formation was detected for the oxidations of various multinuclear manganese complexes by oxone (HSO5−) in aqueous solution. To determine to what extent water was the source of the evolved O2, H218O isotope-labelling experiments coupled with membrane inlet mass spectrometry (MIMS) were carried out. We discovered that during the reaction of oxone with [Mn2(OAc)2(bpmp)]+ (1), stoichiometrically labelled oxygen (18O2) was formed. This is the first example of a homogeneous reaction mediated by a synthetic manganese complex where the addition of a strong chemical oxidant yields 18O2 with labelling percentages matching the theoretically expected values for the case of both O-atoms originating from water. Experiments using lead acetate as an alternative oxidant supported this finding. A detailed investigation of the reaction by EPR spectroscopy, MIMS and Clark-type oxygen detection enabled us to propose potential reaction pathways.

@inproceedings{beckmann_effects_2008,
	address = {Dordrecht},
	title = {Effects of {Chloride}/{Bromide} {Substitution} on {Substrate} {Water} {Exchange} {Rates} in {Photosystem} {II}},
	isbn = {978-1-4020-6709-9},
	doi = {10.1007/978-1-4020-6709-9_83},
	abstract = {The role of chloride in photosynthetic water oxidation is still under discussion since both its precise function and possible binding site are unresolved. In the present study the effects of Cl− on substrate water binding was investigated by monitoring the substrate water exchange kinetics in the S3-state. This was measured with time-resolved membrane-inlet mass spectrometry in thylakoids isolated from Thermosynechococcus elongatus grown in either CaCl2- or CaBr2-containing media. The results show that the exchange rate of the slowly exchangeable substrate water molecule is accelerated by replacement of Cl− by Br−.},
	language = {en},
	booktitle = {Photosynthesis. {Energy} from the {Sun}},
	publisher = {Springer Netherlands},
	author = {Beckmann, Katrin and Ishida, Naoko and Boussac, Alain and Messinger, Johannes},
	editor = {Allen, John F. and Gantt, Elisabeth and Golbeck, John H. and Osmond, Barry},
	year = {2008},
	keywords = {Bromide, chloride, isotope exchange, membrane-inlet mass spectrometry, oxygen evolving complex, photosystem II, substrate water},
	pages = {369--371},
}

The role of chloride in photosynthetic water oxidation is still under discussion since both its precise function and possible binding site are unresolved. In the present study the effects of Cl− on substrate water binding was investigated by monitoring the substrate water exchange kinetics in the S3-state. This was measured with time-resolved membrane-inlet mass spectrometry in thylakoids isolated from Thermosynechococcus elongatus grown in either CaCl2- or CaBr2-containing media. The results show that the exchange rate of the slowly exchangeable substrate water molecule is accelerated by replacement of Cl− by Br−.

@incollection{yang_signaling_2008,
	address = {Oxford, UK},
	title = {Signaling between the {Organelles} and the {Nucleus}},
	isbn = {978-1-4443-0238-7 978-1-4051-6002-5},
	url = {http://doi.wiley.com/10.1002/9781444302387.ch11},
	language = {en},
	urldate = {2021-06-10},
	booktitle = {Intracellular {Signaling} in {Plants}},
	publisher = {Wiley-Blackwell},
	author = {Fernández, Aurora Pias and Strand, Åsa},
	editor = {Yang, Zhenbiao},
	month = jun,
	year = {2008},
	doi = {10.1002/9781444302387.ch11},
	pages = {307--335},
}

@misc{minhas_r_minhas_2008,
	title = {Minhas: {Genetics} of some fiber quality traits among... - {Google} {Scholar}},
	url = {https://scholar.google.com/scholar_lookup?&title=Genetics%20of%20some%20fiber%20quality%20traits%20among%20intraspecific%20crosses%20of%20American%20cotton%20%28Gossypium%20hirsutum%20L.%29&journal=Int%20J%20Agric%20Biol&volume=10&issue=2&pages=196-200&publication_year=2008&author=Minhas%2CR&author=Khan%2CIA&author=Anjam%2CMS&author=Ali%2CK},
	abstract = {Five American cotton (Gossypium hirsutum L.) varieties namely Coker-4601, MNH-552, S-14, Stoneville and Allepo-41 were crossed in a complete diallel fashion and evaluated in randomized complete block design. Gene action and combining ability effects were estimated for the fiber quality its fineness, staple length, uniformity ratio and strength. Fiber fineness, staple length and fiber strength were found to be controlled by additive type of gene action with partial dominance while fiber uniformity ratio with over dominance type of gene action. For fiber fineness and staple length genotype Coker-4601 was a good general combiner whereas S-14 and Stoneville were good combiner for fiber uniformity ratio and its strength. The cross combinations, Coker-4601 X Stoneville showed better SCA for staple length and fiber strength while Coker-4601 X Allepo-41 and Coker-4601 X S-14 showed good SCA for fiber fineness and fiber uniformity ratio.},
	urldate = {2024-08-30},
	author = {{Minhas R} and {Khan IA} and {Anjam MS} and {Ali K}},
	year = {2008},
}

Five American cotton (Gossypium hirsutum L.) varieties namely Coker-4601, MNH-552, S-14, Stoneville and Allepo-41 were crossed in a complete diallel fashion and evaluated in randomized complete block design. Gene action and combining ability effects were estimated for the fiber quality its fineness, staple length, uniformity ratio and strength. Fiber fineness, staple length and fiber strength were found to be controlled by additive type of gene action with partial dominance while fiber uniformity ratio with over dominance type of gene action. For fiber fineness and staple length genotype Coker-4601 was a good general combiner whereas S-14 and Stoneville were good combiner for fiber uniformity ratio and its strength. The cross combinations, Coker-4601 X Stoneville showed better SCA for staple length and fiber strength while Coker-4601 X Allepo-41 and Coker-4601 X S-14 showed good SCA for fiber fineness and fiber uniformity ratio.

@article{jang_arabidopsis_2008,
	title = {Arabidopsis {COP1} shapes the temporal pattern of {CO} accumulation conferring a photoperiodic flowering response},
	volume = {27},
	issn = {0261-4189},
	url = {https://www.embopress.org/doi/full/10.1038/emboj.2008.68},
	doi = {10.1038/emboj.2008.68},
	abstract = {The transcriptional regulator CONSTANS (CO) promotes flowering of Arabidopsis under long summer days (LDs) but not under short winter days (SDs). Post-translational regulation of CO is crucial for this response by stabilizing the protein at the end of a LD, whereas promoting its degradation throughout the night under LD and SD. We show that mutations in CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), a component of a ubiquitin ligase, cause extreme early flowering under SDs, and that this is largely dependent on CO activity. Furthermore, transcription of the CO target gene FT is increased in cop1 mutants and decreased in plants overexpressing COP1 in phloem companion cells. COP1 and CO interact in vivo and in vitro through the C-terminal region of CO. COP1 promotes CO degradation mainly in the dark, so that in cop1 mutants CO protein but not CO mRNA abundance is dramatically increased during the night. However, in the morning CO degradation occurs independently of COP1 by a phytochrome B-dependent mechanism. Thus, COP1 contributes to day length perception by reducing the abundance of CO during the night and thereby delaying flowering under SDs.},
	number = {8},
	urldate = {2022-11-30},
	journal = {The EMBO Journal},
	author = {Jang, Seonghoe and Marchal, Virginie and Panigrahi, Kishore C S and Wenkel, Stephan and Soppe, Wim and Deng, Xing-Wang and Valverde, Federico and Coupland, George},
	month = apr,
	year = {2008},
	keywords = {CONSTANS, flowering, photomorphogenesis, ubiquitin ligase},
	pages = {1277--1288},
}

The transcriptional regulator CONSTANS (CO) promotes flowering of Arabidopsis under long summer days (LDs) but not under short winter days (SDs). Post-translational regulation of CO is crucial for this response by stabilizing the protein at the end of a LD, whereas promoting its degradation throughout the night under LD and SD. We show that mutations in CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), a component of a ubiquitin ligase, cause extreme early flowering under SDs, and that this is largely dependent on CO activity. Furthermore, transcription of the CO target gene FT is increased in cop1 mutants and decreased in plants overexpressing COP1 in phloem companion cells. COP1 and CO interact in vivo and in vitro through the C-terminal region of CO. COP1 promotes CO degradation mainly in the dark, so that in cop1 mutants CO protein but not CO mRNA abundance is dramatically increased during the night. However, in the morning CO degradation occurs independently of COP1 by a phytochrome B-dependent mechanism. Thus, COP1 contributes to day length perception by reducing the abundance of CO during the night and thereby delaying flowering under SDs.

@article{gapare_genetics_2008,
	title = {Genetics of {Shrinkage} in {Juvenile} {Trees} of {Pinus} radiata {D}. {Don} {From} {Two} {Test} {Sites} in {Australia}},
	volume = {57},
	url = {https://www.sciendo.com/article/10.1515/sg-2008-0022},
	doi = {10/gnj3pf},
	abstract = {To examine the genetic control of wood shrinkage (radial, tangential and longitudinal) in juvenile wood of radiata pine (Pinus radiata D. Don), we assessed samples collected at breast height in two related progeny tests of age 8 and 9 years, established at two different sites in Australia. Green to oven-dry tangential and radial shrinkage for the outer-rings was similar at both sites. Similarly, mean longitudinal shrinkage for the outer-rings was similar at both sites (0.3\%, ranging from 0.1 to 1.9 at Flynn and 0.4\%, ranging from 0.02 to 1.6, at Kromelite). Mean longitudinal shrinkage for the inner-rings was 4 times greater than that of the outerrings at both sites. The magnitude of the gradient of longitudinal shrinkage from pith to bark (0.001 to 2.9\%) is large enough to cause distortion problems including twist and warp, during drying of sawn boards. These values also suggest that shrinkage in the juvenile core of radiata pine is of major economic importance and therefore should be improved either through genetics or silviculture. Individual-tree narrow-sense individual heritability for tangential and radial shrinkage in the outer-rings (4-6) was moderate at Flynn (0.24 ± 0.09 and 0.26±0.07, respectively). There was a lack of significant genetic variation},
	language = {en},
	number = {1-6},
	urldate = {2021-11-22},
	journal = {Silvae Genetica},
	author = {Gapare, W. J. and Ivković, M. and Powell, M. B. and McRae, T. A. and Wu, H. X.},
	month = dec,
	year = {2008},
	pages = {145--151},
}

To examine the genetic control of wood shrinkage (radial, tangential and longitudinal) in juvenile wood of radiata pine (Pinus radiata D. Don), we assessed samples collected at breast height in two related progeny tests of age 8 and 9 years, established at two different sites in Australia. Green to oven-dry tangential and radial shrinkage for the outer-rings was similar at both sites. Similarly, mean longitudinal shrinkage for the outer-rings was similar at both sites (0.3%, ranging from 0.1 to 1.9 at Flynn and 0.4%, ranging from 0.02 to 1.6, at Kromelite). Mean longitudinal shrinkage for the inner-rings was 4 times greater than that of the outerrings at both sites. The magnitude of the gradient of longitudinal shrinkage from pith to bark (0.001 to 2.9%) is large enough to cause distortion problems including twist and warp, during drying of sawn boards. These values also suggest that shrinkage in the juvenile core of radiata pine is of major economic importance and therefore should be improved either through genetics or silviculture. Individual-tree narrow-sense individual heritability for tangential and radial shrinkage in the outer-rings (4-6) was moderate at Flynn (0.24 ± 0.09 and 0.26±0.07, respectively). There was a lack of significant genetic variation

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

The CONSTITUTIVE PHOTOMORPHOGENIC9 (COP9) signalosome (CSN) is an evolutionarily conserved multiprotein complex that interacts with cullin-RING type E3 ubiquitin ligases (CRLs). CSN subunit 5 (CSN5), which, when incorporated into CSN, can deconjugate the NEDD8 modification from the cullin subunit of CRLs, is essential for CSN's role in controlling CRL activity. Whether the CSN5 monomer, which is maintained in csn mutants such as csn3 or csn4, has a functional role, remains to be established. We performed a comparative gene expression-profiling experiment with Arabidopsis (Arabidopsis thaliana) csn3, csn4, and csn5 mutants, and we show here that these mutants cannot be distinguished at the transcriptional level. Furthermore, we show that csn3 csn5 mutants are morphologically indistinguishable from csn3 or csn5 mutants. Taken together, these data suggest that the CSN5 monomer does not have a function that leads to transcriptional or morphological changes in the csn mutants. We further examined auxin responses in csn mutants. Whereas CSN had previously been shown to be required for the auxin response-regulatory E3 complexes, specifically SCFTIR1, the csn mutant phenotype suggests that CSN is not essential for auxin responses. We present physiological and genetic data that indicate that auxin responses are indeed only partially impaired in csn mutants and that this is not the result of maternally contributed CSN. Finally, we discuss these findings in the context of the current understanding of the role of neddylation and CSN-mediated deneddylation for CRL activity.

@article{nieminen_cytokinin_2008,
	title = {Cytokinin signaling regulates cambial development in poplar},
	volume = {105},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0805617106},
	doi = {10/cv6jmj},
	language = {en},
	number = {50},
	urldate = {2021-06-10},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Nieminen, K. and Immanen, J. and Laxell, M. and Kauppinen, L. and Tarkowski, P. and Dolezal, K. and Tahtiharju, S. and Elo, A. and Decourteix, M. and Ljung, K. and Bhalerao, Rishikesh P. and Keinonen, K. and Albert, V. A. and Helariutta, Y.},
	month = dec,
	year = {2008},
	pages = {20032--20037},
}

@article{ubeda-tomas_root_2008,
	title = {Root growth in {Arabidopsis} requires gibberellin/{DELLA} signalling in the endodermis},
	volume = {10},
	issn = {1465-7392, 1476-4679},
	url = {http://www.nature.com/articles/ncb1726},
	doi = {10/fj897f},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {Nature Cell Biology},
	author = {Ubeda-Tomás, Susana and Swarup, Ranjan and Coates, Juliet and Swarup, Kamal and Laplaze, Laurent and Beemster, Gerrit T.S. and Hedden, Peter and Bhalerao, Rishikesh P. and Bennett, Malcolm J.},
	month = may,
	year = {2008},
	pages = {625--628},
}

@article{ding_mm_application_2008,
	title = {Application of {GGE} biplot analysis to evaluate genotype ({G}), environment ({E}) and {GxE} interaction on {Pinus} radiata: a case study},
	number = {38},
	urldate = {2021-06-10},
	journal = {N.Z.J. For. Sci.},
	author = {{Ding MM} and {Tier B} and {Yan W} and {Wu HX}},
	year = {2008},
	keywords = {⛔ No DOI found},
	pages = {132--142},
}

@article{ding_multi-environment_2008,
	title = {Multi-environment trial analysis for {Pinus} radiata},
	volume = {38},
	abstract = {A stem-diameter data set of five combined trials of Pinus radiata D. Don was used to identify and determine the nature of genetics by environment (GxE) interaction. The restricted maximum likelihood approach was applied to handle the main issues of the multi-environment trial analysis: (1) Testing sources of heterogeneity of variance and lack of between-sites genetic correlation; (2) Modelling the heterogeneity of error variance among trials and micro-environmental variation within each trial; and (3) Selecting the best model for prediction of breeding values. Model comparison was based on the criterion of log-likelihood. The significance of variance components was tested by the likelihood ratio test which showed that all sources of GxE interactions were highly significant, indicating that GxE interactions occurred in these five trials due to both the heterogeneity of variances and the lack of correlation. Estimates of Type B genetic correlations were increased slightly by correcting for the heterogeneity of variances. The full model, which accommodated heterogeneity of error variances between trials, spatial variation within trials, and fitting a separate GxE interaction variance for each trial, was superior to other models for this multi-environment trial.},
	journal = {New Zealand Journal of Forestry Science},
	author = {Ding, M. and Tier, Bruce and Dutkowski, G.W. and Wu, Harry and Powell, Michael and McRae, T.A.},
	month = jan,
	year = {2008},
	keywords = {⛔ No DOI found},
	pages = {143--159},
}

A stem-diameter data set of five combined trials of Pinus radiata D. Don was used to identify and determine the nature of genetics by environment (GxE) interaction. The restricted maximum likelihood approach was applied to handle the main issues of the multi-environment trial analysis: (1) Testing sources of heterogeneity of variance and lack of between-sites genetic correlation; (2) Modelling the heterogeneity of error variance among trials and micro-environmental variation within each trial; and (3) Selecting the best model for prediction of breeding values. Model comparison was based on the criterion of log-likelihood. The significance of variance components was tested by the likelihood ratio test which showed that all sources of GxE interactions were highly significant, indicating that GxE interactions occurred in these five trials due to both the heterogeneity of variances and the lack of correlation. Estimates of Type B genetic correlations were increased slightly by correcting for the heterogeneity of variances. The full model, which accommodated heterogeneity of error variances between trials, spatial variation within trials, and fitting a separate GxE interaction variance for each trial, was superior to other models for this multi-environment trial.

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

The COP9 signalosome (CSN) is required for the full activity of cullin-RING E3 ubiquitin ligases (CRLs) in eukaryotes. CSN exerts its function on CRLs by removing the ubiquitin-related NEDD8 conjugate from the cullin subunit of CRLs. CSN seems, thereby, to control CRL disassembly or CRL subunit stability. In Arabidopsis thaliana, loss of CSN function leads to constitutive photomorphogenic (cop) seedling development and a post-germination growth arrest. The underlying molecular cause of this growth arrest is currently unknown. Here, we show that Arabidopsis csn mutants are delayed in G2 phase progression. This cell cycle arrest correlates with the induction of the DNA damage response pathway and is suggestive of the activation of a DNA damage checkpoint. In support of this hypothesis, we detected gene conversion events in csn mutants that are indicative of DNA double-strand breaks. DNA damage is also apparent in mutants of the NEDD8 conjugation pathway and in mutants of the E3 ligase subunits CULLIN4, COP1 and DET1, which share phenotypes with csn mutants. In summary, our data suggest that Arabidopsis csn mutants undergo DNA damage, which might be the cause of the delay in G2 cell cycle progression.

@article{hanson_sucrose_2008,
	title = {The sucrose regulated transcription factor {bZIP11} affects amino acid metabolism by regulating the expression of {ASPARAGINE} {SYNTHETASE1} and {PROLINE} {DEHYDROGENASE2}},
	volume = {53},
	copyright = {© 2008 The Authors},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2007.03385.x},
	doi = {10/cqhtc6},
	abstract = {Translation of the transcription factor bZIP11 is repressed by sucrose in a process that involves a highly conserved peptide encoded by the 5′ leaders of bZIP11 and other plant basic region leucine zipper (bZip) genes. It is likely that a specific signaling pathway operating at physiological sucrose concentrations controls metabolism via a feedback mechanism. In this paper bZIP11 target processes are identified using transiently increased nuclear bZIP11 levels and genome-wide expression analysis. bZIP11 affects the expression of hundreds of genes with proposed functions in biochemical pathways and signal transduction. The expression levels of approximately 80\% of the genes tested are not affected by bZIP11 promoter-mediated overexpression of bZIP11. This suggests that {\textless}20\% of the identified genes appear to be physiologically relevant targets of bZIP11. ASPARAGINE SYNTHETASE1 and PROLINE DEHYDROGENASE2 are among the rapidly activated bZIP11 targets, whose induction is independent of protein translation. Transient expression experiments in Arabidopsis protoplasts show that the bZIP11-dependent activation of the ASPARAGINE SYNTHETASE1 gene is dependent on a G-box element present in the promoter. Increased bZIP11 expression leads to decreased proline and increased phenylalanine levels. A model is proposed in which sugar signals control amino acid levels via the bZIP11 transcription factor.},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Hanson, Johannes and Hanssen, Micha and Wiese, Anika and Hendriks, Margriet M. W. B. and Smeekens, Sjef},
	year = {2008},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2007.03385.x},
	keywords = {ATB2, nitrogen metabolism, sucrose, sugar signaling, target gene},
	pages = {935--949},
}

Translation of the transcription factor bZIP11 is repressed by sucrose in a process that involves a highly conserved peptide encoded by the 5′ leaders of bZIP11 and other plant basic region leucine zipper (bZip) genes. It is likely that a specific signaling pathway operating at physiological sucrose concentrations controls metabolism via a feedback mechanism. In this paper bZIP11 target processes are identified using transiently increased nuclear bZIP11 levels and genome-wide expression analysis. bZIP11 affects the expression of hundreds of genes with proposed functions in biochemical pathways and signal transduction. The expression levels of approximately 80% of the genes tested are not affected by bZIP11 promoter-mediated overexpression of bZIP11. This suggests that \textless20% of the identified genes appear to be physiologically relevant targets of bZIP11. ASPARAGINE SYNTHETASE1 and PROLINE DEHYDROGENASE2 are among the rapidly activated bZIP11 targets, whose induction is independent of protein translation. Transient expression experiments in Arabidopsis protoplasts show that the bZIP11-dependent activation of the ASPARAGINE SYNTHETASE1 gene is dependent on a G-box element present in the promoter. Increased bZIP11 expression leads to decreased proline and increased phenylalanine levels. A model is proposed in which sugar signals control amino acid levels via the bZIP11 transcription factor.

@article{s_arabinogalactan_2008,
	title = {Arabinogalactan proteins ({AGPs}) related to pollen tube guidance into the embryo sac in {Arabidopsis}.},
	volume = {3},
	issn = {1559-2316, 1559-2324},
	url = {https://europepmc.org/article/PMC/2634427},
	doi = {10/fkvbwk},
	abstract = {Europe PMC is an archive of life sciences journal literature., Arabinogalactan proteins (AGPs) related to pollen tube guidance into the embryo sac in Arabidopsis.},
	language = {English},
	number = {7},
	urldate = {2021-06-10},
	journal = {Plant Signaling \& Behavior},
	author = {S, Coimbra and B, Jones and Lg, Pereira},
	month = jul,
	year = {2008},
	pmid = {19704483},
	pages = {455--456},
}

Europe PMC is an archive of life sciences journal literature., Arabinogalactan proteins (AGPs) related to pollen tube guidance into the embryo sac in Arabidopsis.

@article{endo_transient_2008,
	title = {Transient transformation and {RNA} silencing in {Zinnia} tracheary element differentiating cell cultures},
	volume = {53},
	issn = {0960-7412, 1365-313X},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2007.03377.x},
	doi = {10/fr9hdc},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Endo, Satoshi and Pesquet, Edouard and Tashiro, Gen and Kuriyama, Hideo and Goffner, Deborah and Fukuda, Hiroo and Demura, Taku},
	month = mar,
	year = {2008},
	pages = {864--875},
}

@article{robert_endosidin1_2008,
	title = {Endosidin1 defines a compartment involved in endocytosis of the brassinosteroid receptor {BRI1} and the auxin transporters {PIN2} and {AUX1}},
	volume = {105},
	copyright = {© 2008 by The National Academy of Sciences of the USA},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/105/24/8464},
	doi = {10/ck5x78},
	abstract = {Although it is known that proteins are delivered to and recycled from the plasma membrane (PM) via endosomes, the nature of the compartments and pathways responsible for cargo and vesicle sorting and cellular signaling is poorly understood. To define and dissect specific recycling pathways, chemical effectors of proteins involved in vesicle trafficking, especially through endosomes, would be invaluable. Thus, we identified chemicals affecting essential steps in PM/endosome trafficking, using the intensely localized PM transport at the tips of germinating pollen tubes. The basic mechanisms of this localized growth are likely similar to those of non-tip growing cells in seedlings. The compound endosidin 1 (ES1) interfered selectively with endocytosis in seedlings, providing a unique tool to dissect recycling pathways. ES1 treatment induced the rapid agglomeration of the auxin translocators PIN2 and AUX1 and the brassinosteroid receptor BRI1 into distinct endomembrane compartments termed “endosidin bodies”; however, the markers PIN1, PIN7, and other PM proteins were unaffected. Endosidin bodies were defined by the syntaxin SYP61 and the V-ATPase subunit VHA-a1, two trans-Golgi network (TGN)/endosomal proteins. Interestingly, brassinosteroid (BR)-induced gene expression was inhibited by ES1 and treated seedlings displayed a brassinolide (BL)-insensitive phenotype similar to a bri1 loss-of-function mutant. No effect was detected in auxin signaling. Thus, PIN2, AUX1, and BRI1 use interactive pathways involving an early SYP61/VHA-a1 endosomal compartment.},
	language = {en},
	number = {24},
	urldate = {2021-06-10},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Robert, Stéphanie and Chary, S. Narasimha and Drakakaki, Georgia and Li, Shundai and Yang, Zhenbiao and Raikhel, Natasha V. and Hicks, Glenn R.},
	month = jun,
	year = {2008},
	pmid = {18550817},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {Arabidopsis, chemical genomics, endosome, prieurianin},
	pages = {8464--8469},
}

Although it is known that proteins are delivered to and recycled from the plasma membrane (PM) via endosomes, the nature of the compartments and pathways responsible for cargo and vesicle sorting and cellular signaling is poorly understood. To define and dissect specific recycling pathways, chemical effectors of proteins involved in vesicle trafficking, especially through endosomes, would be invaluable. Thus, we identified chemicals affecting essential steps in PM/endosome trafficking, using the intensely localized PM transport at the tips of germinating pollen tubes. The basic mechanisms of this localized growth are likely similar to those of non-tip growing cells in seedlings. The compound endosidin 1 (ES1) interfered selectively with endocytosis in seedlings, providing a unique tool to dissect recycling pathways. ES1 treatment induced the rapid agglomeration of the auxin translocators PIN2 and AUX1 and the brassinosteroid receptor BRI1 into distinct endomembrane compartments termed “endosidin bodies”; however, the markers PIN1, PIN7, and other PM proteins were unaffected. Endosidin bodies were defined by the syntaxin SYP61 and the V-ATPase subunit VHA-a1, two trans-Golgi network (TGN)/endosomal proteins. Interestingly, brassinosteroid (BR)-induced gene expression was inhibited by ES1 and treated seedlings displayed a brassinolide (BL)-insensitive phenotype similar to a bri1 loss-of-function mutant. No effect was detected in auxin signaling. Thus, PIN2, AUX1, and BRI1 use interactive pathways involving an early SYP61/VHA-a1 endosomal compartment.

@article{ingvarsson_molecular_2008,
	title = {Molecular evolution of synonymous codon usage in {Populus}},
	volume = {8},
	issn = {1471-2148},
	url = {https://doi.org/10.1186/1471-2148-8-307},
	doi = {10/fqhpcm},
	abstract = {Evolution of synonymous codon usage is thought to be determined by a balance between mutation, genetic drift and natural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes.},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Evolutionary Biology},
	author = {Ingvarsson, Pär K.},
	month = nov,
	year = {2008},
	keywords = {Codon, Codon Usage, Effective Population Size, Gene Length, Synonymous Codon},
	pages = {307},
}

Evolution of synonymous codon usage is thought to be determined by a balance between mutation, genetic drift and natural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes.

@article{strengbom_commercial_2008,
	title = {Commercial forest fertilization causes long-term residual effects in ground vegetation of boreal forests},
	volume = {256},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378112708006178},
	doi = {10/ch24fw},
	language = {en},
	number = {12},
	urldate = {2021-06-10},
	journal = {Forest Ecology and Management},
	author = {Strengbom, Joachim and Nordin, Annika},
	month = dec,
	year = {2008},
	pages = {2175--2181},
}

@article{forsum_nitrogen_2008,
	title = {Nitrogen uptake by \textit{{Hylocomium} splendens} during snowmelt in a boreal forest},
	volume = {15},
	issn = {1195-6860, 2376-7626},
	url = {https://www.tandfonline.com/doi/full/10.2980/15-3-3141},
	doi = {10/bp7d7w},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Écoscience},
	author = {Forsum, Åsa and Laudon, Hjalmar and Nordin, Annika},
	month = sep,
	year = {2008},
	pages = {315--319},
}

@article{rieu_genetic_2008,
	title = {Genetic {Analysis} {Reveals} {That} {C19}-{GA} 2-{Oxidation} {Is} a {Major} {Gibberellin} {Inactivation} {Pathway} in \textit{{Arabidopsis}}},
	volume = {20},
	issn = {1532-298X},
	url = {https://academic.oup.com/plcell/article/20/9/2420/6092501},
	doi = {10/bb7kzv},
	abstract = {Abstract
            Bioactive hormone concentrations are regulated both at the level of hormone synthesis and through controlled inactivation. Based on the ubiquitous presence of 2β-hydroxylated gibberellins (GAs), a major inactivating pathway for the plant hormone GA seems to be via GA 2-oxidation. In this study, we used various approaches to determine the role of C19-GA 2-oxidation in regulating GA concentration and GA-responsive plant growth and development. We show that Arabidopsis thaliana has five C19-GA 2-oxidases, transcripts for one or more of which are present in all organs and at all stages of development examined. Expression of four of the five genes is subject to feed-forward regulation. By knocking out all five Arabidopsis C19-GA 2-oxidases, we show that C19-GA 2-oxidation limits bioactive GA content and regulates plant development at various stages during the plant life cycle: C19-GA 2-oxidases prevent seed germination in the absence of light and cold stimuli, delay the vegetative and floral phase transitions, limit the number of flowers produced per inflorescence, and suppress elongation of the pistil prior to fertilization. Under GA-limited conditions, further roles are revealed, such as limiting elongation of the main stem and side shoots. We conclude that C19-GA 2-oxidation is a major GA inactivation pathway regulating development in Arabidopsis.},
	language = {en},
	number = {9},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Rieu, Ivo and Eriksson, Sven and Powers, Stephen J. and Gong, Fan and Griffiths, Jayne and Woolley, Lindsey and Benlloch, Reyes and Nilsson, Ove and Thomas, Stephen G. and Hedden, Peter and Phillips, Andrew L.},
	month = oct,
	year = {2008},
	pages = {2420--2436},
}

Abstract Bioactive hormone concentrations are regulated both at the level of hormone synthesis and through controlled inactivation. Based on the ubiquitous presence of 2β-hydroxylated gibberellins (GAs), a major inactivating pathway for the plant hormone GA seems to be via GA 2-oxidation. In this study, we used various approaches to determine the role of C19-GA 2-oxidation in regulating GA concentration and GA-responsive plant growth and development. We show that Arabidopsis thaliana has five C19-GA 2-oxidases, transcripts for one or more of which are present in all organs and at all stages of development examined. Expression of four of the five genes is subject to feed-forward regulation. By knocking out all five Arabidopsis C19-GA 2-oxidases, we show that C19-GA 2-oxidation limits bioactive GA content and regulates plant development at various stages during the plant life cycle: C19-GA 2-oxidases prevent seed germination in the absence of light and cold stimuli, delay the vegetative and floral phase transitions, limit the number of flowers produced per inflorescence, and suppress elongation of the pistil prior to fertilization. Under GA-limited conditions, further roles are revealed, such as limiting elongation of the main stem and side shoots. We conclude that C19-GA 2-oxidation is a major GA inactivation pathway regulating development in Arabidopsis.

@article{rajangam_map20_2008,
	title = {{MAP20}, a {Microtubule}-{Associated} {Protein} in the {Secondary} {Cell} {Walls} of {Hybrid} {Aspen}, {Is} a {Target} of the {Cellulose} {Synthesis} {Inhibitor} 2,6-{Dichlorobenzonitrile}},
	volume = {148},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/148/3/1283/6107546},
	doi = {10/cfbvtp},
	abstract = {Abstract
            We have identified a gene, denoted PttMAP20, which is strongly up-regulated during secondary cell wall synthesis and tightly coregulated with the secondary wall-associated CESA genes in hybrid aspen (Populus tremula × tremuloides). Immunolocalization studies with affinity-purified antibodies specific for PttMAP20 revealed that the protein is found in all cell types in developing xylem and that it is most abundant in cells forming secondary cell walls. This PttMAP20 protein sequence contains a highly conserved TPX2 domain first identified in a microtubule-associated protein (MAP) in Xenopus laevis. Overexpression of PttMAP20 in Arabidopsis (Arabidopsis  thaliana) leads to helical twisting of epidermal cells, frequently associated with MAPs. In addition, a PttMAP20-yellow fluorescent protein fusion protein expressed in tobacco (Nicotiana tabacum) leaves localizes to microtubules in leaf epidermal pavement cells. Recombinant PttMAP20 expressed in Escherichia coli also binds specifically to in vitro-assembled, taxol-stabilized bovine microtubules. Finally, the herbicide 2,6-dichlorobenzonitrile, which inhibits cellulose synthesis in plants, was found to bind specifically to PttMAP20. Together with the known function of cortical microtubules in orienting cellulose microfibrils, these observations suggest that PttMAP20 has a role in cellulose biosynthesis.},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Plant Physiology},
	author = {Rajangam, Alex S. and Kumar, Manoj and Aspeborg, Henrik and Guerriero, Gea and Arvestad, Lars and Pansri, Podjamas and Brown, Christian J.-L. and Hober, Sophia and Blomqvist, Kristina and Divne, Christina and Ezcurra, Ines and Mellerowicz, Ewa and Sundberg, Björn and Bulone, Vincent and Teeri, Tuula T.},
	month = nov,
	year = {2008},
	pages = {1283--1294},
}

Abstract We have identified a gene, denoted PttMAP20, which is strongly up-regulated during secondary cell wall synthesis and tightly coregulated with the secondary wall-associated CESA genes in hybrid aspen (Populus tremula × tremuloides). Immunolocalization studies with affinity-purified antibodies specific for PttMAP20 revealed that the protein is found in all cell types in developing xylem and that it is most abundant in cells forming secondary cell walls. This PttMAP20 protein sequence contains a highly conserved TPX2 domain first identified in a microtubule-associated protein (MAP) in Xenopus laevis. Overexpression of PttMAP20 in Arabidopsis (Arabidopsis  thaliana) leads to helical twisting of epidermal cells, frequently associated with MAPs. In addition, a PttMAP20-yellow fluorescent protein fusion protein expressed in tobacco (Nicotiana tabacum) leaves localizes to microtubules in leaf epidermal pavement cells. Recombinant PttMAP20 expressed in Escherichia coli also binds specifically to in vitro-assembled, taxol-stabilized bovine microtubules. Finally, the herbicide 2,6-dichlorobenzonitrile, which inhibits cellulose synthesis in plants, was found to bind specifically to PttMAP20. Together with the known function of cortical microtubules in orienting cellulose microfibrils, these observations suggest that PttMAP20 has a role in cellulose biosynthesis.

@article{bjurhager_mechanical_2008,
	title = {Mechanical characterization of juvenile {European} aspen ({Populus} tremula) and hybrid aspen ({Populus} tremula × {Populus} tremuloides) using full-field strain measurements},
	volume = {54},
	issn = {1435-0211, 1611-4663},
	url = {http://link.springer.com/10.1007/s10086-008-0960-x},
	doi = {10/bw2n5t},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {Journal of Wood Science},
	author = {Bjurhager, Ingela and Berglund, Lars A. and Bardage, Stig L. and Sundberg, Björn},
	month = oct,
	year = {2008},
	pages = {349--355},
}

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

@article{storm_small_2008,
	title = {The small {CAB}-like proteins of {Synechocystis} sp. {PCC} 6803 bind chlorophyll: {In} vitro pigment reconstitution studies on one-helix light-harvesting-like proteins},
	volume = {98},
	issn = {0166-8595, 1573-5079},
	shorttitle = {The small {CAB}-like proteins of {Synechocystis} sp. {PCC} 6803 bind chlorophyll},
	url = {http://link.springer.com/10.1007/s11120-008-9368-0},
	doi = {10/fhrvq9},
	language = {en},
	number = {1-3},
	urldate = {2021-06-10},
	journal = {Photosynthesis Research},
	author = {Storm, Patrik and Hernandez-Prieto, Miguel A. and Eggink, Laura L. and Hoober, J. Kenneth and Funk, Christiane},
	month = oct,
	year = {2008},
	pages = {479--488},
}

@article{goue_microgenomic_2008,
	title = {Microgenomic analysis reveals cell type‐specific gene expression patterns between ray and fusiform initials within the cambial meristem of \textit{{Populus}}},
	volume = {180},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02556.x},
	doi = {10/cpqv9f},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Goué, Nadia and Lesage‐Descauses, Marie‐Claude and Mellerowicz, Ewa J. and Magel, Elisabeth and Label, Philippe and Sundberg, Björn},
	month = oct,
	year = {2008},
	pages = {45--56},
}

@article{mouillon_mimicking_2008,
	title = {Mimicking the {Plant} {Cell} {Interior} under {Water} {Stress} by {Macromolecular} {Crowding}: {Disordered} {Dehydrin} {Proteins} {Are} {Highly} {Resistant} to {Structural} {Collapse}},
	volume = {148},
	issn = {1532-2548},
	shorttitle = {Mimicking the {Plant} {Cell} {Interior} under {Water} {Stress} by {Macromolecular} {Crowding}},
	url = {https://academic.oup.com/plphys/article/148/4/1925/6107608},
	doi = {10/dmnsk2},
	abstract = {Abstract
            The dehydrins are a class of drought-induced proteins in plants that lack a fixed three-dimensional structure. Their specific molecular action, as well as the reason for their disordered character, is as yet poorly understood. It has been speculated, however, that the dehydrins are tuned to acquire a biologically active structure only under the conditions in which they normally function (i.e. upon dehydration). To test this hypothesis, we here investigate the effect of reduced water content and macromolecular crowding on three dehydrins from Arabidopsis (Arabidopsis thaliana). As a simplistic model for mimicking cellular dehydration, we used polyethylene glycol, glycerol, and sugars that plants naturally employ as compatible solutes (i.e. sucrose and glucose). Macromolecular crowding was induced by the large polysaccharides Ficoll and dextran. The results show that the dehydrins are remarkably stable in their disordered state and are only modestly affected by the solvent alterations. A notable exception is the dehydrin Cor47, which shows a small, intrinsic increase in helical structure at high concentrations of osmolytes. We also examined the effect of phosphorylation but found no evidence that such posttranslational modifications of the dehydrin sequences modulate their structural response to osmolytes and crowding agents. These results suggest that the dehydrins are highly specialized proteins that have evolved to maintain their disordered character under conditions in which unfolded states of several globular proteins would tend to collapse.},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Plant Physiology},
	author = {Mouillon, Jean-Marie and Eriksson, Sylvia K. and Harryson, Pia},
	month = dec,
	year = {2008},
	pages = {1925--1937},
}

Abstract The dehydrins are a class of drought-induced proteins in plants that lack a fixed three-dimensional structure. Their specific molecular action, as well as the reason for their disordered character, is as yet poorly understood. It has been speculated, however, that the dehydrins are tuned to acquire a biologically active structure only under the conditions in which they normally function (i.e. upon dehydration). To test this hypothesis, we here investigate the effect of reduced water content and macromolecular crowding on three dehydrins from Arabidopsis (Arabidopsis thaliana). As a simplistic model for mimicking cellular dehydration, we used polyethylene glycol, glycerol, and sugars that plants naturally employ as compatible solutes (i.e. sucrose and glucose). Macromolecular crowding was induced by the large polysaccharides Ficoll and dextran. The results show that the dehydrins are remarkably stable in their disordered state and are only modestly affected by the solvent alterations. A notable exception is the dehydrin Cor47, which shows a small, intrinsic increase in helical structure at high concentrations of osmolytes. We also examined the effect of phosphorylation but found no evidence that such posttranslational modifications of the dehydrin sequences modulate their structural response to osmolytes and crowding agents. These results suggest that the dehydrins are highly specialized proteins that have evolved to maintain their disordered character under conditions in which unfolded states of several globular proteins would tend to collapse.

@article{bylesjo_k-opls_2008,
	title = {K-{OPLS} package: {Kernel}-based orthogonal projections to latent structures for prediction and interpretation in feature space},
	volume = {9},
	issn = {1471-2105},
	shorttitle = {K-{OPLS} package},
	url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-106},
	doi = {10/b3k8qs},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Bioinformatics},
	author = {Bylesjö, Max and Rantalainen, Mattias and Nicholson, Jeremy K and Holmes, Elaine and Trygg, Johan},
	year = {2008},
	pages = {106},
}

@article{rantalainen_piecewise_2008,
	title = {Piecewise multivariate modelling of sequential metabolic profiling data},
	volume = {9},
	issn = {1471-2105},
	url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-105},
	doi = {10/d3swj2},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Bioinformatics},
	author = {Rantalainen, Mattias and Cloarec, Olivier and Ebbels, Timothy M D and Lundstedt, Torbjorn and Nicholson, Jeremy K and Holmes, Elaine and Trygg, Johan},
	year = {2008},
	pages = {105},
}

@article{stone_disruptions_2008,
	title = {Disruptions in {AUX1}-{Dependent} {Auxin} {Influx} {Alter} {Hypocotyl} {Phototropism} in {Arabidopsis}},
	volume = {1},
	issn = {16742052},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1674205214603324},
	doi = {10/d6wcw6},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Molecular Plant},
	author = {Stone, Bethany B. and Stowe-Evans, Emily L. and Harper, Reneé M. and Celaya, R. Brandon and Ljung, Karin and Sandberg, Göran and Liscum, Emmanuel},
	month = jan,
	year = {2008},
	pages = {129--144},
}

@article{strombergsson_interaction_2008,
	title = {Interaction {Model} {Based} on {Local} {Protein} {Substructures} {Generalizes} to the {Entire} {Structural} {Enzyme}-{Ligand} {Space}},
	volume = {48},
	issn = {1549-9596, 1549-960X},
	url = {https://pubs.acs.org/doi/10.1021/ci800200e},
	doi = {10/cbdhmz},
	language = {en},
	number = {11},
	urldate = {2021-06-10},
	journal = {Journal of Chemical Information and Modeling},
	author = {Strömbergsson, Helena and Daniluk, Pawel and Kryshtafovych, Andriy and Fidelis, Krzysztof and Wikberg, Jarl E. S. and Kleywegt, Gerard J. and Hvidsten, Torgeir R.},
	month = nov,
	year = {2008},
	pages = {2278--2288},
}

@article{ibanez_overall_2008,
	title = {Overall {Alteration} of {Circadian} {Clock} {Gene} {Expression} in the {Chestnut} {Cold} {Response}},
	volume = {3},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0003567},
	doi = {10/fh92nj},
	language = {en},
	number = {10},
	urldate = {2021-06-10},
	journal = {PLoS ONE},
	author = {Ibañez, Cristian and Ramos, Alberto and Acebo, Paloma and Contreras, Angela and Casado, Rosa and Allona, Isabel and Aragoncillo, Cipriano},
	editor = {Baxter, Ivan},
	month = oct,
	year = {2008},
	pages = {e3567},
}

@article{stenlund_orthogonal_2008,
	title = {Orthogonal {Projections} to {Latent} {Structures} {Discriminant} {Analysis} {Modeling} on in {Situ} {FT}-{IR} {Spectral} {Imaging} of {Liver} {Tissue} for {Identifying} {Sources} of {Variability}},
	volume = {80},
	issn = {0003-2700, 1520-6882},
	url = {https://pubs.acs.org/doi/10.1021/ac8005318},
	doi = {10/drkhn3},
	language = {en},
	number = {18},
	urldate = {2021-06-10},
	journal = {Analytical Chemistry},
	author = {Stenlund, Hans and Gorzsás, András and Persson, Per and Sundberg, Björn and Trygg, Johan},
	month = sep,
	year = {2008},
	pages = {6898--6906},
}

@article{ivkovic_prediction_2008,
	title = {Prediction of wood stiffness, strength, and shrinkage in juvenile wood of radiata pine},
	volume = {43},
	issn = {1432-5225},
	url = {https://doi.org/10.1007/s00226-008-0232-3},
	doi = {10/bsmjjc},
	abstract = {Development of optimal ways to predict juvenile wood stiffness, strength, and stability using wood properties that can be measured with relative ease and low cost is a priority for tree breeding and silviculture. Wood static modulus of elasticity (MOE), modulus of rupture (MOR), radial, tangential, and longitudinal shrinkage (RS, TS, LS), wood density (DEN), sound wave velocity (SWV), spiral grain (SLG), and microfibril angle (MFA) were measured on juvenile wood samples from lower stem sections in two radiata pine test plantations. Variation between inner (rings 1–2 from pith) and outer (rings 3–6 from pith) rings was generally larger than that among trees. MOE and MOR were lower (50\%) in inner-rings than in outer-rings. RS and TS were higher (30–50\%) for outer-rings than inner-rings, but LS decreased rapidly ({\textgreater}200\%) from inner-rings to outer-rings. DEN had a higher correlation with MOR than with MOE, while MFA had a higher correlation with dry wood MOE than with MOR. SLG had higher significant correlation with MOE than with MOR. DEN and MOE had a weak, significant linear relationship with RS and TS, while MOE had a strong negative non-linear relationship with LS. Multiple regressions had a good potential as a method for predicting billet stiffness (R2 {\textgreater} 0.42), but had only a weak potential to predict wood strength and shrinkage (R2 {\textless} 0.22). For wood stiffness acoustic velocity measurements seemed to be the most practical, and for wood strength and stability acoustic velocity plus core density seemed to be the most practical measurements for predicting lower stem average in young trees.},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Wood Science and Technology},
	author = {Ivković, Miloš and Gapare, Washington J. and Abarquez, Aljoy and Ilic, Jugo and Powell, Michael B. and Wu, Harry X.},
	month = oct,
	year = {2008},
	pages = {237},
}

Development of optimal ways to predict juvenile wood stiffness, strength, and stability using wood properties that can be measured with relative ease and low cost is a priority for tree breeding and silviculture. Wood static modulus of elasticity (MOE), modulus of rupture (MOR), radial, tangential, and longitudinal shrinkage (RS, TS, LS), wood density (DEN), sound wave velocity (SWV), spiral grain (SLG), and microfibril angle (MFA) were measured on juvenile wood samples from lower stem sections in two radiata pine test plantations. Variation between inner (rings 1–2 from pith) and outer (rings 3–6 from pith) rings was generally larger than that among trees. MOE and MOR were lower (50%) in inner-rings than in outer-rings. RS and TS were higher (30–50%) for outer-rings than inner-rings, but LS decreased rapidly (\textgreater200%) from inner-rings to outer-rings. DEN had a higher correlation with MOR than with MOE, while MFA had a higher correlation with dry wood MOE than with MOR. SLG had higher significant correlation with MOE than with MOR. DEN and MOE had a weak, significant linear relationship with RS and TS, while MOE had a strong negative non-linear relationship with LS. Multiple regressions had a good potential as a method for predicting billet stiffness (R2 \textgreater 0.42), but had only a weak potential to predict wood strength and shrinkage (R2 \textless 0.22). For wood stiffness acoustic velocity measurements seemed to be the most practical, and for wood strength and stability acoustic velocity plus core density seemed to be the most practical measurements for predicting lower stem average in young trees.

@article{street_cross-species_2008,
	title = {A cross-species transcriptomics approach to identify genes involved in leaf development},
	volume = {9},
	issn = {1471-2164},
	url = {http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-589},
	doi = {10/d5c8qb},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Genomics},
	author = {Street, Nathaniel and Sjödin, Andreas and Bylesjö, Max and Gustafsson, Petter and Trygg, Johan and Jansson, Stefan},
	year = {2008},
	pages = {589},
}

@article{mellerowicz_xyloglucan_2008,
	title = {Xyloglucan: {The} {Molecular} {Muscle} of {Trees}},
	volume = {102},
	issn = {1095-8290, 0305-7364},
	shorttitle = {Xyloglucan},
	url = {https://academic.oup.com/aob/article-lookup/doi/10.1093/aob/mcn170},
	doi = {10/d76fhs},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {Annals of Botany},
	author = {Mellerowicz, Ewa J. and Immerzeel, Peter and Hayashi, Takahisa},
	month = nov,
	year = {2008},
	pages = {659--665},
}

@article{staldal_auxin_2008,
	title = {Auxin can act independently of \textit{{CRC}} , \textit{{LUG}} , \textit{{SEU}} , \textit{{SPT}} and \textit{{STY1}} in style development but not apical-basal patterning of the \textit{{Arabidopsis}} gynoecium},
	volume = {180},
	issn = {0028646X, 14698137},
	url = {http://doi.wiley.com/10.1111/j.1469-8137.2008.02625.x},
	doi = {10/dbpq5p},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Ståldal, Veronika and Sohlberg, Joel J. and Eklund, D. Magnus and Ljung, Karin and Sundberg, Eva},
	month = dec,
	year = {2008},
	pages = {798--808},
}

@article{ivanov_photosystem_2008,
	title = {Photosystem {II} reaction centre quenching: mechanisms and physiological role},
	volume = {98},
	issn = {0166-8595, 1573-5079},
	shorttitle = {Photosystem {II} reaction centre quenching},
	url = {http://link.springer.com/10.1007/s11120-008-9365-3},
	doi = {10/b9ssbn},
	language = {en},
	number = {1-3},
	urldate = {2021-06-10},
	journal = {Photosynthesis Research},
	author = {Ivanov, Alexander G. and Sane, Prafullachandra V. and Hurry, Vaughan and Öquist, Gunnar and Huner, Norman P. A.},
	month = oct,
	year = {2008},
	pages = {565--574},
}

@article{nguyen_transcriptome_2008,
	title = {Transcriptome for {Photobiological} {Hydrogen} {Production} {Induced} by {Sulfur} {Deprivation} in the {Green} {Alga} \textit{{Chlamydomonas} reinhardtii}},
	volume = {7},
	issn = {1535-9778, 1535-9786},
	url = {https://journals.asm.org/doi/10.1128/EC.00418-07},
	doi = {10/bv32ft},
	abstract = {ABSTRACT
            
              Photobiological hydrogen production using microalgae is being developed into a promising clean fuel stream for the future. In this study, microarray analyses were used to obtain global expression profiles of mRNA abundance in the green alga
              Chlamydomonas reinhardtii
              at different time points before the onset and during the course of sulfur-depleted hydrogen production. These studies were followed by real-time quantitative reverse transcription-PCR and protein analyses. The present work provides new insights into photosynthesis, sulfur acquisition strategies, and carbon metabolism-related gene expression during sulfur-induced hydrogen production. A general trend toward repression of transcripts encoding photosynthetic genes was observed. In contrast to all other
              LHCBM
              genes, the abundance of the
              LHCBM9
              transcript (encoding a major light-harvesting polypeptide) and its protein was strongly elevated throughout the experiment. This suggests a major remodeling of the photosystem II light-harvesting complex as well as an important function of
              LHCBM9
              under sulfur starvation and photobiological hydrogen production. This paper presents the first global transcriptional analysis of
              C. reinhardtii
              before, during, and after photobiological hydrogen production under sulfur deprivation.},
	language = {en},
	number = {11},
	urldate = {2021-06-10},
	journal = {Eukaryotic Cell},
	author = {Nguyen, Anh Vu and Thomas-Hall, Skye R. and Malnoë, Alizée and Timmins, Matthew and Mussgnug, Jan H. and Rupprecht, Jens and Kruse, Olaf and Hankamer, Ben and Schenk, Peer M.},
	month = nov,
	year = {2008},
	pages = {1965--1979},
}

ABSTRACT Photobiological hydrogen production using microalgae is being developed into a promising clean fuel stream for the future. In this study, microarray analyses were used to obtain global expression profiles of mRNA abundance in the green alga Chlamydomonas reinhardtii at different time points before the onset and during the course of sulfur-depleted hydrogen production. These studies were followed by real-time quantitative reverse transcription-PCR and protein analyses. The present work provides new insights into photosynthesis, sulfur acquisition strategies, and carbon metabolism-related gene expression during sulfur-induced hydrogen production. A general trend toward repression of transcripts encoding photosynthetic genes was observed. In contrast to all other LHCBM genes, the abundance of the LHCBM9 transcript (encoding a major light-harvesting polypeptide) and its protein was strongly elevated throughout the experiment. This suggests a major remodeling of the photosystem II light-harvesting complex as well as an important function of LHCBM9 under sulfur starvation and photobiological hydrogen production. This paper presents the first global transcriptional analysis of C. reinhardtii before, during, and after photobiological hydrogen production under sulfur deprivation.

@article{li_single_2008,
	title = {Single nucleotide polymorphism discovery of {Pinus} radiata with chromosome walking {PCR} method},
	volume = {3},
	issn = {1673-3630},
	url = {https://doi.org/10.1007/s11461-008-0055-2},
	doi = {10/djzr4f},
	abstract = {In this paper, the basic principle of chromosome walking is presented and we used an actin gene of radiata pine (Pinus radiata) as an example to conduct upstream and downstream chromosome walking for EST sequences. The full genomic sequence (2154 bp) of the actin gene, including promoters 5′ UTR, CDS and 3′ UTR, was identified by chromosome walking. PCR amplification and DNA band sequencing from 200 unrelated radiata pine trees revealed a total of 21 SNPs for the actin gene, three in the promoter region, 15 in CDS and 4 in 3′ UTR. The results of this experiment provide a technical framework for SNPs discovery in none coding regions of candidate genes.},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Frontiers of Forestry in China},
	author = {Li, Wei and Li, Hui and Chen, Xiaoyang and Wu, Harry},
	month = sep,
	year = {2008},
	pages = {352--356},
}

In this paper, the basic principle of chromosome walking is presented and we used an actin gene of radiata pine (Pinus radiata) as an example to conduct upstream and downstream chromosome walking for EST sequences. The full genomic sequence (2154 bp) of the actin gene, including promoters 5′ UTR, CDS and 3′ UTR, was identified by chromosome walking. PCR amplification and DNA band sequencing from 200 unrelated radiata pine trees revealed a total of 21 SNPs for the actin gene, three in the promoter region, 15 in CDS and 4 in 3′ UTR. The results of this experiment provide a technical framework for SNPs discovery in none coding regions of candidate genes.

@article{wu_breeding_2008,
	title = {Breeding for {Wood} {Quality} and {Profit} in {Radiata} {Pine}: {A} {Review} of {Genetic} {Parameters}},
	volume = {38},
	shorttitle = {Breeding for {Wood} {Quality} and {Profit} in {Radiata} {Pine}},
	author = {Wu, Harry and Ivković, Miloš and Gapare, Washington and Matheson, Alastair and Baltunis, Brian and Powell, Michael and McRae, T.},
	month = jan,
	year = {2008},
}

@article{fey_isolation_2008,
	title = {Isolation of highly active photosystem {II} core complexes with a {His}-tagged {Cyt} b559 subunit from transplastomic tobacco plants},
	volume = {1777},
	issn = {00052728},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272808006907},
	doi = {10/bpz97h},
	language = {en},
	number = {12},
	urldate = {2021-06-10},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Fey, Holger and Piano, Dario and Horn, Ruth and Fischer, David and Schmidt, Matthias and Ruf, Stephanie and Schröder, Wolfgang P. and Bock, Ralph and Büchel, Claudia},
	month = dec,
	year = {2008},
	pages = {1501--1509},
}

@article{atkin_using_2008,
	title = {Using temperature-dependent changes in leaf scaling relationships to quantitatively account for thermal acclimation of respiration in a coupled global climate-vegetation model: {THERMAL} {HISTORY} {AND} {RESPIRATORY} {ACCLIMATION}},
	volume = {14},
	issn = {13541013},
	shorttitle = {Using temperature-dependent changes in leaf scaling relationships to quantitatively account for thermal acclimation of respiration in a coupled global climate-vegetation model},
	url = {http://doi.wiley.com/10.1111/j.1365-2486.2008.01664.x},
	doi = {10/fk2hwr},
	language = {en},
	number = {11},
	urldate = {2021-06-10},
	journal = {Global Change Biology},
	author = {Atkin, Owen K. and Atkinson, Lindsey J. and Fisher, Rosie A. and Campbell, Catherine D. and Zaragoza-Castells, Joana and Pitchford, Jon W. and Woodward, F. Ian and Hurry, Vaughan},
	month = nov,
	year = {2008},
	pages = {2709--2726},
}

@article{timm_cytosolic_2008,
	title = {A {Cytosolic} {Pathway} for the {Conversion} of {Hydroxypyruvate} to {Glycerate} during {Photorespiration} in \textit{{Arabidopsis}}},
	volume = {20},
	issn = {1532-298X},
	url = {https://academic.oup.com/plcell/article/20/10/2848/6093042},
	doi = {10/cxddm5},
	abstract = {Abstract
            Deletion of any of the core enzymes of the photorespiratory cycle, one of the major pathways of plant primary metabolism, results in severe air-sensitivity of the respective mutants. The peroxisomal enzyme hydroxypyruvate reductase (HPR1) represents the only exception to this rule. This indicates the presence of extraperoxisomal reactions of photorespiratory hydroxypyruvate metabolism. We have identified a second hydroxypyruvate reductase, HPR2, and present genetic and biochemical evidence that the enzyme provides a cytosolic bypass to the photorespiratory core cycle in Arabidopsis thaliana. Deletion of HPR2 results in elevated levels of hydroxypyruvate and other metabolites in leaves. Photosynthetic gas exchange is slightly altered, especially under long-day conditions. Otherwise, the mutant closely resembles wild-type plants. The combined deletion of both HPR1 and HPR2, however, results in distinct air-sensitivity and a dramatic reduction in photosynthetic performance. These results suggest that photorespiratory metabolism is not confined to chloroplasts, peroxisomes, and mitochondria but also extends to the cytosol. The extent to which cytosolic reactions contribute to the operation of the photorespiratory cycle in varying natural environments is not yet known, but it might be dynamically regulated by the availability of NADH in the context of peroxisomal redox homeostasis.},
	language = {en},
	number = {10},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Timm, Stefan and Nunes-Nesi, Adriano and Pärnik, Tiit and Morgenthal, Katja and Wienkoop, Stefanie and Keerberg, Olav and Weckwerth, Wolfram and Kleczkowski, Leszek A. and Fernie, Alisdair R. and Bauwe, Hermann},
	month = dec,
	year = {2008},
	pages = {2848--2859},
}

Abstract Deletion of any of the core enzymes of the photorespiratory cycle, one of the major pathways of plant primary metabolism, results in severe air-sensitivity of the respective mutants. The peroxisomal enzyme hydroxypyruvate reductase (HPR1) represents the only exception to this rule. This indicates the presence of extraperoxisomal reactions of photorespiratory hydroxypyruvate metabolism. We have identified a second hydroxypyruvate reductase, HPR2, and present genetic and biochemical evidence that the enzyme provides a cytosolic bypass to the photorespiratory core cycle in Arabidopsis thaliana. Deletion of HPR2 results in elevated levels of hydroxypyruvate and other metabolites in leaves. Photosynthetic gas exchange is slightly altered, especially under long-day conditions. Otherwise, the mutant closely resembles wild-type plants. The combined deletion of both HPR1 and HPR2, however, results in distinct air-sensitivity and a dramatic reduction in photosynthetic performance. These results suggest that photorespiratory metabolism is not confined to chloroplasts, peroxisomes, and mitochondria but also extends to the cytosol. The extent to which cytosolic reactions contribute to the operation of the photorespiratory cycle in varying natural environments is not yet known, but it might be dynamically regulated by the availability of NADH in the context of peroxisomal redox homeostasis.

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

Abstract The biotrophic actinomycete Rhodococcus fascians has a profound impact on plant development and a common aspect of the symptomatology is the deformation of infected leaves. In Arabidopsis (Arabidopsis thaliana), the serrated leaf margins formed upon infection resemble the leaf phenotype of transgenic plants with ectopic expression of KNOTTED-like homeobox (KNOX) genes. Through transcript profiling, we demonstrate that class-I KNOX genes are transcribed in symptomatic leaves. Functional analysis revealed that BREVIPEDICELLUS/KNOTTED-LIKE1 and mainly SHOOT MERISTEMLESS were essential for the observed leaf dissection. However, these results also positioned the KNOX genes downstream in the signaling cascade triggered by R. fascians infection. The much faster activation of ARABIDOPSIS RESPONSE REGULATOR5 and the establishment of homeostatic and feedback mechanisms to control cytokinin (CK) levels support the overrepresentation of this hormone in infected plants due to the secretion by the pathogen, thereby placing the CK response high up in the cascade. Hormone measurements show a net decrease of tested CKs, indicating either that secretion by the bacterium and degradation by the plant are in balance, or, as suggested by the strong reaction of 35S:CKX plants, that other CKs are at play. At early time points of the interaction, activation of gibberellin 2-oxidase presumably installs a local hormonal setting favorable for meristematic activity that provokes leaf serrations. The results are discussed in the context of symptom development, evasion of plant defense, and the establishment of a specific niche by R. fascians.

@article{fernandez_retrograde_2008,
	title = {Retrograde signaling and plant stress: plastid signals initiate cellular stress responses},
	volume = {11},
	issn = {13695266},
	shorttitle = {Retrograde signaling and plant stress},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526608001052},
	doi = {10/bf6bbr},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {Current Opinion in Plant Biology},
	author = {Fernández, Aurora Piñas and Strand, Åsa},
	month = oct,
	year = {2008},
	pages = {509--513},
}

@article{garcia-gil_evolutionary_2008,
	title = {Evolutionary {Aspects} of {Functional} and {Pseudogene} {Members} of the {Phytochrome} {Gene} {Family} in {Scots} {Pine}},
	volume = {67},
	issn = {0022-2844, 1432-1432},
	url = {http://link.springer.com/10.1007/s00239-008-9135-z},
	doi = {10/dmzkqj},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Journal of Molecular Evolution},
	author = {García-Gil, Maria Rosario},
	month = aug,
	year = {2008},
	pages = {222--232},
}

@article{koh_atypical_2008,
	title = {An {Atypical} {Catalytic} {Mechanism} {Involving} {Three} {Cysteines} of {Thioredoxin}},
	volume = {283},
	issn = {00219258},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925819493629},
	doi = {10/df4v82},
	language = {en},
	number = {34},
	urldate = {2021-06-10},
	journal = {Journal of Biological Chemistry},
	author = {Koh, Cha San and Navrot, Nicolas and Didierjean, Claude and Rouhier, Nicolas and Hirasawa, Masakazu and Knaff, David B. and Wingsle, Gunnar and Samian, Razip and Jacquot, Jean-Pierre and Corbier, Catherine and Gelhaye, Eric},
	month = aug,
	year = {2008},
	pages = {23062--23072},
}

@article{svennerstam_root_2008,
	title = {Root uptake of cationic amino acids by {Arabidopsis} depends on functional expression of amino acid permease 5},
	volume = {180},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02589.x},
	doi = {10/dtpjgf},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Svennerstam, Henrik and Ganeteg, Ulrika and Näsholm, Torgny},
	month = nov,
	year = {2008},
	pages = {620--630},
}

@article{nikitina_importance_2008,
	title = {Importance of a single disulfide bond for the {PsbO} protein of photosystem {II}: protein structure stability and soluble overexpression in {Escherichia} coli},
	volume = {98},
	issn = {0166-8595, 1573-5079},
	shorttitle = {Importance of a single disulfide bond for the {PsbO} protein of photosystem {II}},
	url = {http://link.springer.com/10.1007/s11120-008-9327-9},
	doi = {10/dbwmrh},
	language = {en},
	number = {1-3},
	urldate = {2021-06-10},
	journal = {Photosynthesis Research},
	author = {Nikitina, Julia and Shutova, Tatiana and Melnik, Bogdan and Chernyshov, Sergey and Marchenkov, Victor and Semisotnov, Gennady and Klimov, Vyacheslav and Samuelsson, Göran},
	month = oct,
	year = {2008},
	pages = {391--403},
}

@article{overmyer_complex_2008,
	title = {Complex phenotypic profiles leading to ozone sensitivity in \textit{{Arabidopsis} thaliana} mutants},
	volume = {31},
	issn = {01407791, 13653040},
	url = {http://doi.wiley.com/10.1111/j.1365-3040.2008.01837.x},
	doi = {10/bvqtdg},
	language = {en},
	number = {9},
	urldate = {2021-06-10},
	journal = {Plant, Cell \& Environment},
	author = {Overmyer, Kirk and Kollist, Hannes and Tuominen, Hannele and Betz, Christian and Langebartels, Christian and Wingsle, Gunnar and Kangasjärvi, Saijaliisa and Brader, Günter and Mullineaux, Phil and Kangasjärvi, Jaakko},
	month = sep,
	year = {2008},
	pages = {1237--1249},
}

@article{bylesjo_lamina_2008,
	title = {{LAMINA}: a tool for rapid quantification of leaf size and shape parameters},
	volume = {8},
	issn = {1471-2229},
	shorttitle = {{LAMINA}},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-8-82},
	doi = {10/dg9gsg},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Plant Biology},
	author = {Bylesjö, Max and Segura, Vincent and Soolanayakanahally, Raju Y and Rae, Anne M and Trygg, Johan and Gustafsson, Petter and Jansson, Stefan and Street, Nathaniel R},
	year = {2008},
	pages = {82},
}

@article{swarup_auxin_2008,
	title = {The auxin influx carrier {LAX3} promotes lateral root emergence},
	volume = {10},
	issn = {1465-7392, 1476-4679},
	url = {http://www.nature.com/articles/ncb1754},
	doi = {10/cc9bgf},
	language = {en},
	number = {8},
	urldate = {2021-06-10},
	journal = {Nature Cell Biology},
	author = {Swarup, Kamal and Benková, Eva and Swarup, Ranjan and Casimiro, Ilda and Péret, Benjamin and Yang, Yaodong and Parry, Geraint and Nielsen, Erik and De Smet, Ive and Vanneste, Steffen and Levesque, Mitch P. and Carrier, David and James, Nicholas and Calvo, Vanessa and Ljung, Karin and Kramer, Eric and Roberts, Rebecca and Graham, Neil and Marillonnet, Sylvestre and Patel, Kanu and Jones, Jonathan D.G. and Taylor, Christopher G. and Schachtman, Daniel P. and May, Sean and Sandberg, Goran and Benfey, Philip and Friml, Jiri and Kerr, Ian and Beeckman, Tom and Laplaze, Laurent and Bennett, Malcolm J.},
	month = aug,
	year = {2008},
	pages = {946--954},
}

@article{ingvarsson_multilocus_2008,
	title = {Multilocus {Patterns} of {Nucleotide} {Polymorphism} and the {Demographic} {History} of \textit{{Populus} tremula}},
	volume = {180},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/180/1/329/6105097},
	doi = {10/bg9v54},
	abstract = {Abstract
            I have studied nucleotide polymorphism and linkage disequilibrium using multilocus data from 77 fragments, with an average length of fragments of 550 bp, in the deciduous tree Populus tremula (Salicaceae). The frequency spectrum across loci showed a modest excess of mutations segregating at low frequency and a marked excess of high-frequency derived mutations at silent sites, relative to neutral expectations. These excesses were also seen at replacement sites, but were not so pronounced for high-frequency derived mutations. There was a marked excess of low-frequency mutations at replacement sites, likely indicating deleterious amino acid-changing mutations that segregate at low frequencies in P. tremula. I used approximate Bayesian computation (ABC) to evaluate a number of different demographic scenarios and to estimate parameters for the best-fitting model. The data were found to be consistent with a historical reduction in the effective population size of P. tremula through a bottleneck. The timing inferred for this bottleneck is largely consistent with geological data and with data from several other long-lived plant species. The results show that P. tremula harbors substantial levels of nucleotide polymorphism with the posterior mode of the scaled mutation rate, θ = 0.0177 across loci. The ABC analyses also provided an estimate of the scaled recombination rate that indicates that recombination rates in P. tremula are likely to be 2–10 times higher than the mutation rate. This study reinforces the notion that linkage disequilibrium is low and decays to negligible levels within a few hundred base pairs in P. tremula.},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Genetics},
	author = {Ingvarsson, Pär K},
	month = sep,
	year = {2008},
	pages = {329--340},
}

Abstract I have studied nucleotide polymorphism and linkage disequilibrium using multilocus data from 77 fragments, with an average length of fragments of 550 bp, in the deciduous tree Populus tremula (Salicaceae). The frequency spectrum across loci showed a modest excess of mutations segregating at low frequency and a marked excess of high-frequency derived mutations at silent sites, relative to neutral expectations. These excesses were also seen at replacement sites, but were not so pronounced for high-frequency derived mutations. There was a marked excess of low-frequency mutations at replacement sites, likely indicating deleterious amino acid-changing mutations that segregate at low frequencies in P. tremula. I used approximate Bayesian computation (ABC) to evaluate a number of different demographic scenarios and to estimate parameters for the best-fitting model. The data were found to be consistent with a historical reduction in the effective population size of P. tremula through a bottleneck. The timing inferred for this bottleneck is largely consistent with geological data and with data from several other long-lived plant species. The results show that P. tremula harbors substantial levels of nucleotide polymorphism with the posterior mode of the scaled mutation rate, θ = 0.0177 across loci. The ABC analyses also provided an estimate of the scaled recombination rate that indicates that recombination rates in P. tremula are likely to be 2–10 times higher than the mutation rate. This study reinforces the notion that linkage disequilibrium is low and decays to negligible levels within a few hundred base pairs in P. tremula.

@article{muniz_acaulis5_2008,
	title = {{ACAULIS5} controls \textit{{Arabidopsis}} xylem specification through the prevention of premature cell death},
	volume = {135},
	issn = {1477-9129, 0950-1991},
	url = {https://journals.biologists.com/dev/article/135/15/2573/64801/ACAULIS5-controls-Arabidopsis-xylem-specification},
	doi = {10/bktf62},
	abstract = {Cell size and secondary cell wall patterning are crucial for the proper functioning of xylem vessel elements in the vascular tissues of plants. Through detailed anatomical characterization of Arabidopsis thalianahypocotyls, we observed that mutations in the putative spermine biosynthetic gene ACL5 severely affected xylem specification: the xylem vessel elements of the acl5 mutant were small and mainly of the spiral type,and the normally predominant pitted vessels as well as the xylem fibers were completely missing. The cell-specific expression of ACL5 in the early developing vessel elements, as detected by in situ hybridization and reporter gene analyses, suggested that the observed xylem vessel defects were caused directly by the acl5 mutation. Exogenous spermine prolonged xylem element differentiation and stimulated cell expansion and cell wall elaboration in xylogenic cell cultures of Zinnia elegans, suggesting that ACL5 prevents premature death of the developing vessel elements to allow complete expansion and secondary cell wall patterning. This was further supported by our observations that the vessel elements of acl5 seemed to initiate the cell death program too early and that the xylem defects associated with acl5 could be largely phenocopied by induction of premature, diphtheria toxin-mediated cell death in the ACL5-expressing vessel elements. We therefore provide, for the first time, mechanistic evidence for the function of ACL5 in xylem specification through its action on the duration of xylem element differentiation.},
	language = {en},
	number = {15},
	urldate = {2021-06-10},
	journal = {Development},
	author = {Muñiz, Luis and Minguet, Eugenio G. and Singh, Sunil Kumar and Pesquet, Edouard and Vera-Sirera, Francisco and Moreau-Courtois, Charleen L. and Carbonell, Juan and Blázquez, Miguel A. and Tuominen, Hannele},
	month = aug,
	year = {2008},
	pages = {2573--2582},
}

Cell size and secondary cell wall patterning are crucial for the proper functioning of xylem vessel elements in the vascular tissues of plants. Through detailed anatomical characterization of Arabidopsis thalianahypocotyls, we observed that mutations in the putative spermine biosynthetic gene ACL5 severely affected xylem specification: the xylem vessel elements of the acl5 mutant were small and mainly of the spiral type,and the normally predominant pitted vessels as well as the xylem fibers were completely missing. The cell-specific expression of ACL5 in the early developing vessel elements, as detected by in situ hybridization and reporter gene analyses, suggested that the observed xylem vessel defects were caused directly by the acl5 mutation. Exogenous spermine prolonged xylem element differentiation and stimulated cell expansion and cell wall elaboration in xylogenic cell cultures of Zinnia elegans, suggesting that ACL5 prevents premature death of the developing vessel elements to allow complete expansion and secondary cell wall patterning. This was further supported by our observations that the vessel elements of acl5 seemed to initiate the cell death program too early and that the xylem defects associated with acl5 could be largely phenocopied by induction of premature, diphtheria toxin-mediated cell death in the ACL5-expressing vessel elements. We therefore provide, for the first time, mechanistic evidence for the function of ACL5 in xylem specification through its action on the duration of xylem element differentiation.

@article{stenbaek_nadph-dependent_2008,
	title = {{NADPH}-dependent thioredoxin reductase and 2-{Cys} peroxiredoxins are needed for the protection of {Mg}-protoporphyrin monomethyl ester cyclase},
	volume = {582},
	issn = {00145793},
	url = {http://doi.wiley.com/10.1016/j.febslet.2008.07.006},
	doi = {10/df6ctd},
	language = {en},
	number = {18},
	urldate = {2021-06-10},
	journal = {FEBS Letters},
	author = {Stenbaek, Anne and Hansson, Andreas and Wulff, Ragna Peterson and Hansson, Mats and Dietz, Karl-Josef and Jensen, Poul Erik},
	month = aug,
	year = {2008},
	pages = {2773--2778},
}

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

@article{hedenstrom_visualization_2008,
	title = {Visualization and interpretation of {OPLS} models based on {2D} {NMR} data},
	volume = {92},
	issn = {01697439},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0169743908000142},
	doi = {10/fwnw6q},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Chemometrics and Intelligent Laboratory Systems},
	author = {Hedenström, Mattias and Wiklund, Susanne and Sundberg, Björn and Edlund, Ulf},
	month = jul,
	year = {2008},
	pages = {110--117},
}

@article{holmgren_identification_2008,
	title = {Identification of white-rot and soft-rot fungi increasing ethanol production from spent sulfite liquor in co-culture with \textit{{Saccharomyces} cerevisiae}},
	volume = {105},
	issn = {13645072, 13652672},
	url = {http://doi.wiley.com/10.1111/j.1365-2672.2008.03724.x},
	doi = {10/cb236h},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Journal of Applied Microbiology},
	author = {Holmgren, M. and Sellstedt, A.},
	month = jul,
	year = {2008},
	pages = {134--140},
}

@article{frenkel_illustrated_2008,
	title = {An illustrated gardener's guide to transgenic \textit{{Arabidopsis}} field experiments},
	volume = {180},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02591.x},
	doi = {10/ds43gk},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Frenkel, Martin and Johansson Jänkänpää, Hanna and Moen, Jon and Jansson, Stefan},
	month = oct,
	year = {2008},
	pages = {545--555},
}

@article{christensen_functional_2008,
	title = {Functional {Characterization} of {Arabidopsis} {Calreticulin1a}: {A} {Key} {Alleviator} of {Endoplasmic} {Reticulum} {Stress}},
	volume = {49},
	issn = {0032-0781, 1471-9053},
	shorttitle = {Functional {Characterization} of {Arabidopsis} {Calreticulin1a}},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcn065},
	doi = {10/cf9k5g},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {Plant and Cell Physiology},
	author = {Christensen, A. and Svensson, K. and Persson, S. and Jung, J. and Michalak, M. and Widell, S. and Sommarin, M.},
	month = apr,
	year = {2008},
	pages = {912--924},
}

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

@article{forsum_capacities_2008,
	title = {Capacities and constraints of amino acid utilization in \textit{{Arabidopsis}}},
	volume = {179},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02546.x},
	doi = {10/ctn242},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Forsum, Oskar and Svennerstam, Henrik and Ganeteg, Ulrika and Näsholm, Torgny},
	month = sep,
	year = {2008},
	pages = {1058--1069},
}

@article{sjodin_global_2008,
	title = {Global expression profiling in leaves of free-growing aspen},
	volume = {8},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-8-61},
	doi = {10/dsf6k8},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Plant Biology},
	author = {Sjodin, Andreas and Wissel, Kirsten and Bylesjo, Max and Trygg, Johan and Jansson, Stefan},
	year = {2008},
	pages = {61},
}

@article{wadenback_lignin_2008,
	title = {Lignin biosynthesis in transgenic {Norway} spruce plants harboring an antisense construct for cinnamoyl {CoA} reductase ({CCR})},
	volume = {17},
	issn = {0962-8819, 1573-9368},
	url = {http://link.springer.com/10.1007/s11248-007-9113-z},
	doi = {10/cr7v44},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Transgenic Research},
	author = {Wadenbäck, Johan and von Arnold, Sara and Egertsdotter, Ulrika and Walter, Michael H. and Grima-Pettenati, Jacqueline and Goffner, Deborah and Gellerstedt, Göran and Gullion, Terry and Clapham, David},
	month = jun,
	year = {2008},
	pages = {379--392},
}

@article{gutierrez_towards_2008,
	title = {Towards a {Systematic} {Validation} of {References} in {Real}-{Time} {RT}-{PCR}},
	volume = {20},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/20/7/1734-1735/6092386},
	doi = {10/drh6vn},
	language = {en},
	number = {7},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Gutierrez, Laurent and Mauriat, Mélanie and Pelloux, Jérôme and Bellini, Catherine and Van Wuytswinkel, Olivier},
	month = jul,
	year = {2008},
	pages = {1734--1735},
}

@article{crutsinger_ecosystem_2008,
	title = {Ecosystem retrogression leads to increased insect abundance and herbivory across an island chronosequence},
	volume = {22},
	issn = {02698463, 13652435},
	url = {http://doi.wiley.com/10.1111/j.1365-2435.2008.01435.x},
	doi = {10/b3g3tc},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {Functional Ecology},
	author = {Crutsinger, G. M. and Sanders, N. J. and Albrectsen, B. R. and Abreu, I. N. and Wardle, D. A.},
	month = oct,
	year = {2008},
	pages = {816--823},
}

@article{varghese_fertility_2008,
	title = {Fertility variation and its impact on seed crops in seed production areas and a natural stand of teak in southern {India}},
	volume = {160},
	issn = {0014-2336, 1573-5060},
	url = {http://link.springer.com/10.1007/s10681-007-9591-3},
	doi = {10/cs27v7},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Euphytica},
	author = {Varghese, M. and Kamalakannan, R. and Nicodemus, A. and Lindgren, D.},
	month = mar,
	year = {2008},
	pages = {131--141},
}

@article{bilir_variation_2008,
	title = {Variation in cone and seed characters in clonal seed orchards of {Pinus} sylvestris},
	volume = {36},
	issn = {0169-4286, 1573-5095},
	url = {http://link.springer.com/10.1007/s11056-008-9092-9},
	doi = {10/fkbk7b},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {New Forests},
	author = {Bilir, Nebi and Prescher, Finnvid and Lindgren, Dag and Kroon, Johan},
	month = sep,
	year = {2008},
	pages = {187--199},
}

@article{waldmann_efficient_2008,
	title = {Efficient {Markov} {Chain} {Monte} {Carlo} {Implementation} of {Bayesian} {Analysis} of {Additive} and {Dominance} {Genetic} {Variances} in {Noninbred} {Pedigrees}},
	volume = {179},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/179/2/1101/6064669},
	doi = {10/ctwbh5},
	abstract = {Abstract
            Accurate and fast computation of quantitative genetic variance parameters is of great importance in both natural and breeding populations. For experimental designs with complex relationship structures it can be important to include both additive and dominance variance components in the statistical model. In this study, we introduce a Bayesian Gibbs sampling approach for estimation of additive and dominance genetic variances in the traditional infinitesimal model. The method can handle general pedigrees without inbreeding. To optimize between computational time and good mixing of the Markov chain Monte Carlo (MCMC) chains, we used a hybrid Gibbs sampler that combines a single site and a blocked Gibbs sampler. The speed of the hybrid sampler and the mixing of the single-site sampler were further improved by the use of pretransformed variables. Two traits (height and trunk diameter) from a previously published diallel progeny test of Scots pine (Pinus sylvestris L.) and two large simulated data sets with different levels of dominance variance were analyzed. We also performed Bayesian model comparison on the basis of the posterior predictive loss approach. Results showed that models with both additive and dominance components had the best fit for both height and diameter and for the simulated data with high dominance. For the simulated data with low dominance, we needed an informative prior to avoid the dominance variance component becoming overestimated. The narrow-sense heritability estimates in the Scots pine data were lower compared to the earlier results, which is not surprising because the level of dominance variance was rather high, especially for diameter. In general, the hybrid sampler was considerably faster than the blocked sampler and displayed better mixing properties than the single-site sampler.},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Genetics},
	author = {Waldmann, Patrik and Hallander, Jon and Hoti, Fabian and Sillanpää, Mikko J},
	month = jun,
	year = {2008},
	pages = {1101--1112},
}

Abstract Accurate and fast computation of quantitative genetic variance parameters is of great importance in both natural and breeding populations. For experimental designs with complex relationship structures it can be important to include both additive and dominance variance components in the statistical model. In this study, we introduce a Bayesian Gibbs sampling approach for estimation of additive and dominance genetic variances in the traditional infinitesimal model. The method can handle general pedigrees without inbreeding. To optimize between computational time and good mixing of the Markov chain Monte Carlo (MCMC) chains, we used a hybrid Gibbs sampler that combines a single site and a blocked Gibbs sampler. The speed of the hybrid sampler and the mixing of the single-site sampler were further improved by the use of pretransformed variables. Two traits (height and trunk diameter) from a previously published diallel progeny test of Scots pine (Pinus sylvestris L.) and two large simulated data sets with different levels of dominance variance were analyzed. We also performed Bayesian model comparison on the basis of the posterior predictive loss approach. Results showed that models with both additive and dominance components had the best fit for both height and diameter and for the simulated data with high dominance. For the simulated data with low dominance, we needed an informative prior to avoid the dominance variance component becoming overestimated. The narrow-sense heritability estimates in the Scots pine data were lower compared to the earlier results, which is not surprising because the level of dominance variance was rather high, especially for diameter. In general, the hybrid sampler was considerably faster than the blocked sampler and displayed better mixing properties than the single-site sampler.

@article{jansson_senescence_2008,
	title = {Senescence: developmental program or timetable?},
	volume = {179},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Senescence},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02471.x},
	doi = {10/drc9xn},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Jansson, Stefan and Thomas, Howard},
	month = aug,
	year = {2008},
	pages = {575--579},
}

@article{le_hir_gene_2008,
	title = {Gene expression profiling: keys for investigating phloem functions},
	volume = {13},
	issn = {13601385},
	shorttitle = {Gene expression profiling},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138508001301},
	doi = {10/b4c2q3},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {Trends in Plant Science},
	author = {Le Hir, Rozenn and Beneteau, Julie and Bellini, Catherine and Vilaine, Françoise and Dinant, Sylvie},
	month = jun,
	year = {2008},
	pages = {273--280},
}

@article{vaultier_hydrophobic_2008,
	title = {The hydrophobic segment of \textit{{Arabidopsis} thaliana} cluster {I} diacylglycerol kinases is sufficient to target the proteins to cell membranes},
	volume = {582},
	issn = {00145793},
	url = {http://doi.wiley.com/10.1016/j.febslet.2008.04.042},
	doi = {10/ckpr43},
	language = {en},
	number = {12},
	urldate = {2021-06-10},
	journal = {FEBS Letters},
	author = {Vaultier, Marie-Noëlle and Cantrel, Catherine and Guerbette, Françoise and Boutté, Yohann and Vergnolle, Chantal and Çiçek, Dominique and Bolte, Susanne and Zachowski, Alain and Ruelland, Eric},
	month = may,
	year = {2008},
	pages = {1743--1748},
}

@article{gronlund_dynamic_2008,
	title = {Dynamic scaling regimes of collective decision making},
	volume = {81},
	issn = {0295-5075, 1286-4854},
	url = {https://iopscience.iop.org/article/10.1209/0295-5075/81/28003},
	doi = {10/c3khnq},
	number = {2},
	urldate = {2021-06-10},
	journal = {EPL (Europhysics Letters)},
	author = {Grönlund, A. and Holme, P. and Minnhagen, P.},
	month = jan,
	year = {2008},
	pages = {28003},
}

@article{jamtgard_characteristics_2008,
	title = {Characteristics of amino acid uptake in barley},
	volume = {302},
	issn = {0032-079X, 1573-5036},
	url = {http://link.springer.com/10.1007/s11104-007-9473-4},
	doi = {10/fn54kb},
	language = {en},
	number = {1-2},
	urldate = {2021-06-10},
	journal = {Plant and Soil},
	author = {Jämtgård, Sandra and Näsholm, Torgny and Huss-Danell, Kerstin},
	month = jan,
	year = {2008},
	pages = {221--231},
}

@article{gonzalez_baro_speciation_2008,
	title = {Speciation in the aqueous peroxovanadate–maltol and (peroxo)vanadate–uridine systems},
	issn = {1477-9226, 1477-9234},
	url = {http://xlink.rsc.org/?DOI=b717119f},
	doi = {10/d893kx},
	language = {en},
	number = {8},
	urldate = {2021-06-10},
	journal = {Dalton Transactions},
	author = {González Baró, Ana and Andersson, Ingegärd and Pettersson, Lage and Gorzsás, András},
	year = {2008},
	pages = {1095},
}

@article{hund_cold_2008,
	title = {Cold tolerance of maize seedlings as determined by root morphology and photosynthetic traits},
	volume = {28},
	issn = {11610301},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1161030107000883},
	doi = {10/dpstgw},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {European Journal of Agronomy},
	author = {Hund, Andreas and Fracheboud, Yvan and Soldati, Alberto and Stamp, Peter},
	month = apr,
	year = {2008},
	pages = {178--185},
}

@article{boberg_glucose_2008,
	title = {Glucose and ammonium additions affect needle decomposition and carbon allocation by the litter degrading fungus {Mycena} epipterygia},
	volume = {40},
	issn = {00380717},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0038071707004464},
	doi = {10/bdg3pf},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Soil Biology and Biochemistry},
	author = {Boberg, J and Finlay, R and Stenlid, J and Nasholm, T and Lindahl, B},
	month = apr,
	year = {2008},
	pages = {995--999},
}

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

@article{singh_insight_2008,
	title = {Insight into the early steps of root hair formation revealed by the procuste1 cellulose synthase mutant of {Arabidopsis} thaliana},
	volume = {8},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-8-57},
	doi = {10/dk7r27},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Plant Biology},
	author = {Singh, Sunil K and Fischer, Urs and Singh, Manoj and Grebe, Markus and Marchant, Alan},
	year = {2008},
	pages = {57},
}

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

KDEL-tailed cysteine endopeptidases are a group of papain-type peptidases found in senescing tissue undergoing programmed cell death (PCD). Their genes have so far been cloned and analyzed in 12 angiosperms. They are synthesized as proenzymes with a C-terminal KDEL endoplasmatic reticulum retention signal, which is removed with the prosequence to activate enzyme activity. We previously identified three genes for KDEL-tailed cysteine endopeptidases (AtCEP1, AtCEP2, AtCEP3) in Arabidopsis thaliana. Transgenic plants of A. thaliana expressing β-glucuronidase (GUS) under the control of the promoters for the three genes were produced and analyzed histochemically. GUS activity was promoter- and tissue-specific GUS activity during seedling, flower, and root development, especially in tissues that collapse during final stages of PCD, and in the course of lateral root formation. KDEL-tailed cysteine endopeptidases are unique in being able to digest the extensins that form the basic scaffold for cell wall formation. The broad substrate specificity is due to the structure of the active site cleft of the KDEL-tailed cysteine endopeptidase that accepts a wide variety of amino acids, including proline and glycosylated hydroxyproline of the hydroxyproline rich glycoproteins of the cell wall.

@article{gutierrez_possible_2008,
	title = {A possible role of prolyl oligopeptidase during {Linum} usitatissimum (flax) seed development},
	volume = {10},
	issn = {1435-8603, 1438-8677},
	url = {http://doi.wiley.com/10.1111/j.1438-8677.2008.00038.x},
	doi = {10/dcbbfm},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Plant Biology},
	author = {Gutierrez, L. and Castelain, M. and Verdeil, J.-L. and Conejero, G. and Van Wuytswinkel, O.},
	month = may,
	year = {2008},
	pages = {398--402},
}

@article{nilsson_dissecting_2008,
	title = {Dissecting the {Molecular} {Basis} of the {Regulation} of {Wood} {Formation} by {Auxin} in {Hybrid} {Aspen}},
	volume = {20},
	issn = {1532-298X},
	url = {https://academic.oup.com/plcell/article/20/4/843/6092327},
	doi = {10/c7bg45},
	abstract = {Abstract
            Indole acetic acid (auxin) is a key regulator of wood formation, and an observed overlap between auxin concentration gradient and developing secondary xylem cells has led to the hypothesis that auxin regulates wood formation by acting as a morphogen. We dissected the role of auxin in wood formation by identifying the auxin-responsive transcriptome in wood-forming tissues and investigating alterations in wood formation in transgenic hybrid aspen plants (Populus tremula × Populus tremuloides) with perturbed auxin signaling. We showed that auxin-responsive genes in wood-forming tissues respond dynamically to changes in cellular auxin levels. However, the expression patterns of most of the auxin-responsive genes displayed limited correlation with the auxin concentration across this developmental zone. Perturbing auxin signaling by reducing auxin responsiveness reduced the cambial cell division activity, caused spatial deregulation of cell division of the cambial initials, and led to reductions in not only radial but also axial dimensions of fibers and vessels. We propose that, instead of acting as a morphogen, changes in auxin concentration in developing secondary xylem cells may provide important regulatory cues that modulate the expression of a few key regulators; these, in turn, may control the global gene expression patterns that are essential for normal secondary xylem development.},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Nilsson, Jeanette and Karlberg, Anna and Antti, Henrik and Lopez-Vernaza, Manuel and Mellerowicz, Ewa and Perrot-Rechenmann, Catherine and Sandberg, Göran and Bhalerao, Rishikesh P.},
	month = may,
	year = {2008},
	pages = {843--855},
}

Abstract Indole acetic acid (auxin) is a key regulator of wood formation, and an observed overlap between auxin concentration gradient and developing secondary xylem cells has led to the hypothesis that auxin regulates wood formation by acting as a morphogen. We dissected the role of auxin in wood formation by identifying the auxin-responsive transcriptome in wood-forming tissues and investigating alterations in wood formation in transgenic hybrid aspen plants (Populus tremula × Populus tremuloides) with perturbed auxin signaling. We showed that auxin-responsive genes in wood-forming tissues respond dynamically to changes in cellular auxin levels. However, the expression patterns of most of the auxin-responsive genes displayed limited correlation with the auxin concentration across this developmental zone. Perturbing auxin signaling by reducing auxin responsiveness reduced the cambial cell division activity, caused spatial deregulation of cell division of the cambial initials, and led to reductions in not only radial but also axial dimensions of fibers and vessels. We propose that, instead of acting as a morphogen, changes in auxin concentration in developing secondary xylem cells may provide important regulatory cues that modulate the expression of a few key regulators; these, in turn, may control the global gene expression patterns that are essential for normal secondary xylem development.

@article{mellerowicz_wood_2008,
	title = {Wood cell walls: biosynthesis, developmental dynamics and their implications for wood properties},
	volume = {11},
	issn = {13695266},
	shorttitle = {Wood cell walls},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526608000435},
	doi = {10/bjwt68},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Current Opinion in Plant Biology},
	author = {Mellerowicz, E and Sundberg, B},
	month = jun,
	year = {2008},
	pages = {293--300},
}

@article{siedlecka_pectin_2008,
	title = {Pectin {Methyl} {Esterase} {Inhibits} {Intrusive} and {Symplastic} {Cell} {Growth} in {Developing} {Wood} {Cells} of \textit{{Populus}}},
	volume = {146},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/146/2/323/6107207},
	doi = {10/bz7b7b},
	abstract = {Abstract
            Wood cells, unlike most other cells in plants, grow by a unique combination of intrusive and symplastic growth. Fibers grow in diameter by diffuse symplastic growth, but they elongate solely by intrusive apical growth penetrating the pectin-rich middle lamella that cements neighboring cells together. In contrast, vessel elements grow in diameter by a combination of intrusive and symplastic growth. We demonstrate that an abundant pectin methyl esterase (PME; EC 3.1.1.11) from wood-forming tissues of hybrid aspen (Populus tremula × tremuloides) acts as a negative regulator of both symplastic and intrusive growth of developing wood cells. When PttPME1 expression was up- and down-regulated in transgenic aspen trees, the PME activity in wood-forming tissues was correspondingly altered. PME removes methyl ester groups from homogalacturonan (HG) and transgenic trees had modified HG methylesterification patterns, as demonstrated by two-dimensional nuclear magnetic resonance and immunostaining using PAM1 and LM7 antibodies. In situ distributions of PAM1 and LM7 epitopes revealed changes in pectin methylesterification in transgenic trees that were specifically localized in expanding wood cells. The results show that en block deesterification of HG by PttPME1 inhibits both symplastic growth and intrusive growth. PttPME1 is therefore involved in mechanisms determining fiber width and length in the wood of aspen trees.},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Plant Physiology},
	author = {Siedlecka, Anna and Wiklund, Susanne and Péronne, Marie-Amélie and Micheli, Fabienne and Leśniewska, Joanna and Sethson, Ingmar and Edlund, Ulf and Richard, Luc and Sundberg, Björn and Mellerowicz, Ewa J.},
	month = feb,
	year = {2008},
	pages = {323--324},
}

Abstract Wood cells, unlike most other cells in plants, grow by a unique combination of intrusive and symplastic growth. Fibers grow in diameter by diffuse symplastic growth, but they elongate solely by intrusive apical growth penetrating the pectin-rich middle lamella that cements neighboring cells together. In contrast, vessel elements grow in diameter by a combination of intrusive and symplastic growth. We demonstrate that an abundant pectin methyl esterase (PME; EC 3.1.1.11) from wood-forming tissues of hybrid aspen (Populus tremula × tremuloides) acts as a negative regulator of both symplastic and intrusive growth of developing wood cells. When PttPME1 expression was up- and down-regulated in transgenic aspen trees, the PME activity in wood-forming tissues was correspondingly altered. PME removes methyl ester groups from homogalacturonan (HG) and transgenic trees had modified HG methylesterification patterns, as demonstrated by two-dimensional nuclear magnetic resonance and immunostaining using PAM1 and LM7 antibodies. In situ distributions of PAM1 and LM7 epitopes revealed changes in pectin methylesterification in transgenic trees that were specifically localized in expanding wood cells. The results show that en block deesterification of HG by PttPME1 inhibits both symplastic growth and intrusive growth. PttPME1 is therefore involved in mechanisms determining fiber width and length in the wood of aspen trees.

@article{ingvarsson_nucleotide_2008,
	title = {Nucleotide {Polymorphism} and {Phenotypic} {Associations} {Within} and {Around} the \textit{phytochrome {B2}} {Locus} in {European} {Aspen} ( \textit{{Populus} tremula} , {Salicaceae})},
	volume = {178},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/178/4/2217/6073872},
	doi = {10/bd8hh3},
	abstract = {Abstract
            We investigated the utility of association mapping to dissect the genetic basis of naturally occurring variation in bud phenology in European aspen (Populus tremula). With this aim, we surveyed nucleotide polymorphism in 13 fragments spanning an 80-kb region surrounding the phytochrome B2 (phyB2) locus. Although polymorphism varies substantially across the phyB2 region, we detected no signs for deviations from neutral expectations. We also identified a total of 41 single nucleotide polymorphisms (SNPs) that were subsequently scored in a mapping population consisting of 120 trees. We identified two nonsynonymous SNPs in the phytochrome B2 gene that were independently associated with variation in the timing of bud set and that explained between 1.5 and 5\% of the observed phenotypic variation in bud set. Earlier studies have shown that the frequencies of both these SNPs vary clinally with latitude. Linkage disequilibrium across the region was low, suggesting that the SNPs we identified are strong candidates for being causally linked to variation in bud set in our mapping populations. One of the SNPs (T608N) is located in the “hinge region,” close to the chromophore binding site of the phyB2 protein. The other SNP (L1078P) is located in a region supposed to mediate downstream signaling from the phyB2 locus. The lack of population structure, combined with low levels of linkage disequilibrium, suggests that association mapping is a fruitful method for dissecting naturally occurring variation in Populus tremula.},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Genetics},
	author = {Ingvarsson, Pär K and Garcia, M Victoria and Luquez, Virginia and Hall, David and Jansson, Stefan},
	month = apr,
	year = {2008},
	pages = {2217--2226},
}

Abstract We investigated the utility of association mapping to dissect the genetic basis of naturally occurring variation in bud phenology in European aspen (Populus tremula). With this aim, we surveyed nucleotide polymorphism in 13 fragments spanning an 80-kb region surrounding the phytochrome B2 (phyB2) locus. Although polymorphism varies substantially across the phyB2 region, we detected no signs for deviations from neutral expectations. We also identified a total of 41 single nucleotide polymorphisms (SNPs) that were subsequently scored in a mapping population consisting of 120 trees. We identified two nonsynonymous SNPs in the phytochrome B2 gene that were independently associated with variation in the timing of bud set and that explained between 1.5 and 5% of the observed phenotypic variation in bud set. Earlier studies have shown that the frequencies of both these SNPs vary clinally with latitude. Linkage disequilibrium across the region was low, suggesting that the SNPs we identified are strong candidates for being causally linked to variation in bud set in our mapping populations. One of the SNPs (T608N) is located in the “hinge region,” close to the chromophore binding site of the phyB2 protein. The other SNP (L1078P) is located in a region supposed to mediate downstream signaling from the phyB2 locus. The lack of population structure, combined with low levels of linkage disequilibrium, suggests that association mapping is a fruitful method for dissecting naturally occurring variation in Populus tremula.

@article{moriguchi_optimum_2008,
	title = {Optimum lifetime for {Swedish} {Picea} abies seed orchards},
	volume = {35},
	issn = {0169-4286, 1573-5095},
	url = {http://link.springer.com/10.1007/s11056-007-9068-1},
	doi = {10/dp8s65},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {New Forests},
	author = {Moriguchi, Yoshinari and Prescher, Finnvid and Lindgren, Dag},
	month = mar,
	year = {2008},
	pages = {147--157},
}

@article{augusti_deriving_2008,
	title = {Deriving correlated climate and physiological signals from deuterium isotopomers in tree rings},
	volume = {252},
	issn = {00092541},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0009254108000193},
	doi = {10/cqxzgr},
	language = {en},
	number = {1-2},
	urldate = {2021-06-10},
	journal = {Chemical Geology},
	author = {Augusti, Angela and Betson, Tatiana R. and Schleucher, Jürgen},
	month = jun,
	year = {2008},
	pages = {1--8},
}

@article{ivanov_reaction_2008,
	title = {Reaction centre quenching of excess light energy and photoprotection of photosystem {II}},
	volume = {51},
	issn = {1867-0725},
	url = {https://doi.org/10.1007/BF03030716},
	doi = {10/frvq84},
	abstract = {In addition to the energy dissipation of excess light occurring in PSII antenna via the xanthophyll cycle, there is mounting evidence of a zeaxanthin-independent pathway for non-photochemical quenching based within the PSII reaction centre (reaction centre quenching) that may also play a significant role in photoprotection. It has been demonstrated that acclimation of higher plants, green algae and cyanobacteria to low temperature or high light conditions which potentially induce an imbalance between energy supply and energy utilization is accompanied by the development of higher reduction state of QA and higher resistance to photoinhibition (Huner et al., 1998). Although this is a fundamental feature of all photoautotrophs, and the acquisition of increased tolerance to photoinhibition has been ascribed to growth and development under high PSII excitation pressure, the precise mechanism controlling the redox state of QA and its physiological significance in developing higher resistance to photoinhibition has not been fully elucidated. In this review we summarize recent data indicating that the increased resistance to high light in a broad spectrum of photosynthetic organisms acclimated to high excitation pressure conditions is associated with an increase probability for alternative non-radiative P680+QA- radical pair recombination pathway for energy dissipation within the reaction centre of PSII. The various molecular mechanisms that could account for non-photochemical quenching through PSII reaction centre are also discussed.},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Journal of Plant Biology},
	author = {Ivanov, Alexander G. and Hurry, Vaughan and Sane, Prafullachandra V. and Öquist, Gunnar and Huner, Norman P. A.},
	month = mar,
	year = {2008},
	pages = {85},
}

In addition to the energy dissipation of excess light occurring in PSII antenna via the xanthophyll cycle, there is mounting evidence of a zeaxanthin-independent pathway for non-photochemical quenching based within the PSII reaction centre (reaction centre quenching) that may also play a significant role in photoprotection. It has been demonstrated that acclimation of higher plants, green algae and cyanobacteria to low temperature or high light conditions which potentially induce an imbalance between energy supply and energy utilization is accompanied by the development of higher reduction state of QA and higher resistance to photoinhibition (Huner et al., 1998). Although this is a fundamental feature of all photoautotrophs, and the acquisition of increased tolerance to photoinhibition has been ascribed to growth and development under high PSII excitation pressure, the precise mechanism controlling the redox state of QA and its physiological significance in developing higher resistance to photoinhibition has not been fully elucidated. In this review we summarize recent data indicating that the increased resistance to high light in a broad spectrum of photosynthetic organisms acclimated to high excitation pressure conditions is associated with an increase probability for alternative non-radiative P680+QA- radical pair recombination pathway for energy dissipation within the reaction centre of PSII. The various molecular mechanisms that could account for non-photochemical quenching through PSII reaction centre are also discussed.

@article{tao_rapid_2008,
	title = {Rapid {Synthesis} of {Auxin} via a {New} {Tryptophan}-{Dependent} {Pathway} {Is} {Required} for {Shade} {Avoidance} in {Plants}},
	volume = {133},
	issn = {00928674},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0092867408002146},
	doi = {10/frnv64},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Cell},
	author = {Tao, Yi and Ferrer, Jean-Luc and Ljung, Karin and Pojer, Florence and Hong, Fangxin and Long, Jeff A. and Li, Lin and Moreno, Javier E. and Bowman, Marianne E. and Ivans, Lauren J. and Cheng, Youfa and Lim, Jason and Zhao, Yunde and Ballaré, Carlos L. and Sandberg, Göran and Noel, Joseph P. and Chory, Joanne},
	month = apr,
	year = {2008},
	pages = {164--176},
}

@article{albrectsen_nutrient_2008,
	title = {Nutrient addition extends flowering display, which gets tracked by seed predators, but not by their parasitoids},
	volume = {117},
	issn = {00301299},
	url = {http://doi.wiley.com/10.1111/j.2008.0030-1299.16381.x},
	doi = {10/dp76wq},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Oikos},
	author = {Albrectsen, Benedicte Riber and Ericson, Lars and Lundberg, Per},
	month = mar,
	year = {2008},
	pages = {473--480},
}

@article{neale_population_2008,
	title = {Population, quantitative and comparative genomics of adaptation in forest trees},
	volume = {11},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S136952660700177X},
	doi = {10/d45npq},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Current Opinion in Plant Biology},
	author = {Neale, David B and Ingvarsson, Pär K},
	month = apr,
	year = {2008},
	pages = {149--155},
}

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

@article{shutova_photosystem_2008,
	title = {The photosystem {II}-associated {Cah3} in {Chlamydomonas} enhances the {O2} evolution rate by proton removal},
	volume = {27},
	issn = {0261-4189, 1460-2075},
	url = {http://emboj.embopress.org/cgi/doi/10.1038/emboj.2008.12},
	doi = {10/dmmd7c},
	number = {5},
	urldate = {2021-06-10},
	journal = {The EMBO Journal},
	author = {Shutova, Tatiana and Kenneweg, Hella and Buchta, Joachim and Nikitina, Julia and Terentyev, Vasily and Chernyshov, Sergey and Andersson, Bertil and Allakhverdiev, Suleyman I and Klimov, Vyacheslav V and Dau, Holger and Junge, Wolfgang and Samuelsson, Göran},
	month = mar,
	year = {2008},
	pages = {782--791},
}

@article{meng_molecular_2008,
	title = {Molecular and kinetic characterization of two {UDP}-glucose pyrophosphorylases, products of distinct genes, from {Arabidopsis}},
	volume = {1784},
	issn = {15709639},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1570963908000794},
	doi = {10/bvzvzf},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics},
	author = {Meng, Meng and Wilczynska, Malgorzata and Kleczkowski, Leszek A.},
	month = jun,
	year = {2008},
	pages = {967--972},
}

@article{szal_changes_2008,
	title = {Changes in energy status of leaf cells as a consequence of mitochondrial genome rearrangement},
	volume = {227},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-007-0652-6},
	doi = {10/fjnnh7},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Planta},
	author = {Szal, Bożena and Dąbrowska, Zofia and Malmberg, Gunilla and Gardeström, Per and Rychter, Anna M.},
	month = feb,
	year = {2008},
	pages = {697--706},
}

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

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

@article{larsson_inhibited_2008,
	title = {Inhibited polar auxin transport results in aberrant embryo development in {Norway} spruce},
	volume = {177},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2007.02289.x},
	doi = {10/fcmjzj},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Larsson, Emma and Sitbon, Folke and Ljung, Karin and Von Arnold, Sara},
	month = jan,
	year = {2008},
	pages = {356--366},
}

@article{andersen_requirement_2008,
	title = {Requirement of {B2}-{Type} \textit{{Cyclin}-{Dependent} {Kinases}} for {Meristem} {Integrity} in \textit{{Arabidopsis} thaliana}},
	volume = {20},
	issn = {1532-298X},
	url = {https://academic.oup.com/plcell/article/20/1/88/6091364},
	doi = {10/djf5gv},
	abstract = {Abstract
            To maintain proper meristem function, cell division and differentiation must be coordinately regulated in distinct subdomains of the meristem. Although a number of regulators necessary for the correct organization of the shoot apical meristem (SAM) have been identified, it is still largely unknown how their function is integrated with the cell cycle machinery to translate domain identity into correct cellular behavior. We show here that the cyclin-dependent kinases CDKB2;1 and CDKB2;2 are required both for normal cell cycle progression and for meristem organization. Consistently, the CDKB2 genes are highly expressed in the SAM in a cell cycle–dependent fashion, and disruption of CDKB2 function leads to severe meristematic defects. In addition, strong alterations in hormone signaling both at the level of active hormones and with respect to transcriptional and physiological outputs were observed in plants with disturbed CDKB2 activity.},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Andersen, Stig Uggerhøj and Buechel, Sabine and Zhao, Zhong and Ljung, Karin and Novák, Ondřej and Busch, Wolfgang and Schuster, Christoph and Lohmann, Jan U.},
	month = feb,
	year = {2008},
	pages = {88--100},
}

Abstract To maintain proper meristem function, cell division and differentiation must be coordinately regulated in distinct subdomains of the meristem. Although a number of regulators necessary for the correct organization of the shoot apical meristem (SAM) have been identified, it is still largely unknown how their function is integrated with the cell cycle machinery to translate domain identity into correct cellular behavior. We show here that the cyclin-dependent kinases CDKB2;1 and CDKB2;2 are required both for normal cell cycle progression and for meristem organization. Consistently, the CDKB2 genes are highly expressed in the SAM in a cell cycle–dependent fashion, and disruption of CDKB2 function leads to severe meristematic defects. In addition, strong alterations in hormone signaling both at the level of active hormones and with respect to transcriptional and physiological outputs were observed in plants with disturbed CDKB2 activity.

@article{szilagyi_laurdan_2008,
	title = {Laurdan fluorescence spectroscopy in the thylakoid bilayer: {The} effect of violaxanthin to zeaxanthin conversion on the galactolipid dominated lipid environment},
	volume = {1778},
	issn = {00052736},
	shorttitle = {Laurdan fluorescence spectroscopy in the thylakoid bilayer},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005273607003963},
	doi = {10/bhvt6n},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Biochimica et Biophysica Acta (BBA) - Biomembranes},
	author = {Szilágyi, Anna and Selstam, Eva and Åkerlund, Hans-Erik},
	month = jan,
	year = {2008},
	pages = {348--355},
}

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

@article{luquez_natural_2008,
	title = {Natural phenological variation in aspen ({Populus} tremula): the {SwAsp} collection},
	volume = {4},
	issn = {1614-2942, 1614-2950},
	shorttitle = {Natural phenological variation in aspen ({Populus} tremula)},
	url = {http://link.springer.com/10.1007/s11295-007-0108-y},
	doi = {10/bwk27s},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Tree Genetics \& Genomes},
	author = {Luquez, Virginia and Hall, David and Albrectsen, Benedicte R. and Karlsson, Jan and Ingvarsson, Pär and Jansson, Stefan},
	month = apr,
	year = {2008},
	pages = {279--292},
}

@article{hogberg_high_2008,
	title = {High temporal resolution tracing of photosynthate carbon from the tree canopy to forest soil microorganisms},
	volume = {177},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2007.02238.x},
	doi = {10/d2q3v2},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Högberg, P. and Högberg, M. N. and Göttlicher, S. G. and Betson, N. R. and Keel, S. G. and Metcalfe, D. B. and Campbell, C. and Schindlbacher, A. and Hurry, V. and Lundmark, T. and Linder, S. and Näsholm, T.},
	month = jan,
	year = {2008},
	pages = {220--228},
}

@article{prescher_genetic_2008,
	title = {Genetic thinning of clonal seed orchards using linear deployment may improve both gain and diversity},
	volume = {254},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378112707005671},
	doi = {10/b2vf8c},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Forest Ecology and Management},
	author = {Prescher, Finnvid and Lindgren, Dag and Karlsson, Bo},
	month = jan,
	year = {2008},
	pages = {188--192},
}

@article{kufryk_association_2008,
	title = {Association of small {CAB}-like proteins ({SCPs}) of {Synechocystis} sp. {PCC} 6803 with {Photosystem} {II}},
	volume = {95},
	issn = {0166-8595, 1573-5079},
	url = {http://link.springer.com/10.1007/s11120-007-9244-3},
	doi = {10/dftf99},
	language = {en},
	number = {2-3},
	urldate = {2021-06-10},
	journal = {Photosynthesis Research},
	author = {Kufryk, Galyna and Hernandez-Prieto, Miguel A. and Kieselbach, Thomas and Miranda, Helder and Vermaas, Wim and Funk, Christiane},
	month = feb,
	year = {2008},
	pages = {135--145},
}