Publications 2005

@article{wu_genotype_2005,
	title = {Genotype by environment interactions in an {Australia}-wide radiata pine diallel mating experiment: implications for regionalized breeding},
	volume = {51},
	issn = {0015-749X},
	shorttitle = {Genotype by environment interactions in an {Australia}-wide radiata pine diallel mating experiment},
	abstract = {Genotype by site interactions were studied in an Australia-wide diallel experiment covering 10 testing sites for stem dbh, stem straightness, branch angle and size, and number of branch clusters on the stem at age 10.5 to 11.5 years. The size and practical importance of genotype by site interactions were examined by four approaches: (1) the ratio of interaction variance to general combining ability (GCA) variance; (2) additive genetic correlations among sites; (3) testing whether the interaction was a result of a few families reacting more than others; and (4) by the size of genetic gains through a proposed regionalization. The genotype by site interaction for dbh observed in this experiment was larger than reported earlier for radiata pine because two high-elevation sites were included. There were more interactions between the two high-elevation sites and other lower elevation sites than interactions between lower elevation sites. The large genotype by region interaction was attributed to the extensive snow loading at the two higher elevation sites. Gain predictions from five regionalization schemes in this experiment favor regionalization of radiata pine breeding into two main regions: higher elevation and lower elevation sites. FOR. SCI. 51(1):29-40.},
	language = {eng},
	number = {1},
	journal = {Forest science.},
	author = {Wu, H. X. and Matheson, A. C.},
	month = feb,
	year = {2005},
	keywords = {⛔ No DOI found},
	pages = {29--40},
}

Genotype by site interactions were studied in an Australia-wide diallel experiment covering 10 testing sites for stem dbh, stem straightness, branch angle and size, and number of branch clusters on the stem at age 10.5 to 11.5 years. The size and practical importance of genotype by site interactions were examined by four approaches: (1) the ratio of interaction variance to general combining ability (GCA) variance; (2) additive genetic correlations among sites; (3) testing whether the interaction was a result of a few families reacting more than others; and (4) by the size of genetic gains through a proposed regionalization. The genotype by site interaction for dbh observed in this experiment was larger than reported earlier for radiata pine because two high-elevation sites were included. There were more interactions between the two high-elevation sites and other lower elevation sites than interactions between lower elevation sites. The large genotype by region interaction was attributed to the extensive snow loading at the two higher elevation sites. Gain predictions from five regionalization schemes in this experiment favor regionalization of radiata pine breeding into two main regions: higher elevation and lower elevation sites. FOR. SCI. 51(1):29-40.

@article{robert_arabidopsis_2005,
	title = {An {Arabidopsis} {Endo}-1,4-β-d-{Glucanase} {Involved} in {Cellulose} {Synthesis} {Undergoes} {Regulated} {Intracellular} {Cycling}},
	volume = {17},
	issn = {1040-4651},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1315376/},
	doi = {10.1105/tpc.105.036228},
	abstract = {The synthesis of cellulose microfibrils requires the presence of a membrane-bound endo-1,4-β-d-glucanase, KORRIGAN1 (KOR1). Although the exact biochemical role of KOR1 in cellulose synthesis is unknown, we used the protein as a marker to explore the potential involvement of subcellular transport processes in cellulose synthesis. Using immunofluorescence and a green fluorescent protein (GFP)–KOR1 fusion that complemented the phenotype conferred by the kor1-1 mutant, we investigated the distribution of KOR1 in epidermal cells in the root meristem. KOR1 was localized in intracellular compartments corresponding to a heterogeneous population of organelles, which comprised the Golgi apparatus, FM4-64–labeled compartments referred to as early endosomes, and, in the case of GFP-KOR1, the tonoplast. Inhibition of cellulose synthesis by isoxaben promoted a net redistribution of GFP-KOR1 toward a homogeneous population of compartments, distinct from early endosomes, which were concentrated close to the plasma membrane facing the root surface. A redistribution of GFP-KOR1 away from early endosomes was also observed in the same cells at later stages of cell elongation. A subpopulation of GFP-KOR1–containing compartments followed trajectories along the plasma membrane, and this motility required intact microtubules. These observations demonstrate that the deposition of cellulose, like chitin synthesis in yeast, involves the regulated intracellular cycling of at least one enzyme required for its synthesis.},
	number = {12},
	urldate = {2021-10-21},
	journal = {The Plant Cell},
	author = {Robert, Stéphanie and Bichet, Adeline and Grandjean, Olivier and Kierzkowski, Daniel and Satiat-Jeunemaître, Béatrice and Pelletier, Sandra and Hauser, Marie-Theres and Höfte, Herman and Vernhettes, Samantha},
	month = dec,
	year = {2005},
	pmid = {16284310},
	pmcid = {PMC1315376},
	pages = {3378--3389},
}

The synthesis of cellulose microfibrils requires the presence of a membrane-bound endo-1,4-β-d-glucanase, KORRIGAN1 (KOR1). Although the exact biochemical role of KOR1 in cellulose synthesis is unknown, we used the protein as a marker to explore the potential involvement of subcellular transport processes in cellulose synthesis. Using immunofluorescence and a green fluorescent protein (GFP)–KOR1 fusion that complemented the phenotype conferred by the kor1-1 mutant, we investigated the distribution of KOR1 in epidermal cells in the root meristem. KOR1 was localized in intracellular compartments corresponding to a heterogeneous population of organelles, which comprised the Golgi apparatus, FM4-64–labeled compartments referred to as early endosomes, and, in the case of GFP-KOR1, the tonoplast. Inhibition of cellulose synthesis by isoxaben promoted a net redistribution of GFP-KOR1 toward a homogeneous population of compartments, distinct from early endosomes, which were concentrated close to the plasma membrane facing the root surface. A redistribution of GFP-KOR1 away from early endosomes was also observed in the same cells at later stages of cell elongation. A subpopulation of GFP-KOR1–containing compartments followed trajectories along the plasma membrane, and this motility required intact microtubules. These observations demonstrate that the deposition of cellulose, like chitin synthesis in yeast, involves the regulated intracellular cycling of at least one enzyme required for its synthesis.

@article{fulop_arabidopsis_2005,
	title = {Arabidopsis {Anaphase}-{Promoting} {Complexes}: {Multiple} {Activators} and {Wide} {Range} of {Substrates} {Might} {Keep} {APC} {Perpetually} {Busy}},
	volume = {4},
	issn = {1538-4101},
	shorttitle = {Arabidopsis {Anaphase}-{Promoting} {Complexes}},
	url = {https://doi.org/10.4161/cc.4.8.1856},
	doi = {10.4161/cc.4.8.1856},
	abstract = {The anaphase-promoting complex (APC), a multisubunit E3 ubiquitin ligase, is anessential regulator of the cell cycle from metaphase until S phase in yeast and metazoans.APC mediates degradation of numerous cell cycle-related proteins, including mitoticcyclins and its activation and substrate-specificity are determined by two adaptor proteins,Cdc20 and Cdh1. Plants have multiple APC activators and the Cdh1-type proteins, inaddition, are represented by two subclasses, known as Ccs52A and Ccs52B. TheArabidopsis genome contains five cdc20 genes as well as ccs52A1, ccs52A2 and ccs52B. InSchizosaccharomyces pombe, expression of the three Atccs52 genes elicited distinctphenotypes supporting non-redundant function of the AtCcs52 proteins. Consistent withthese activities, the AtCcs52 proteins were able to bind both to the yeast and theArabidopsis APCs. In synchronized Arabidopsis cell cultures the cdc20 transcripts werepresent from early G2 until the M-phase exit, ccs52B from G2/M to M while ccs52A1 andccs52A2 were from late M until early G2, suggesting consecutive action of these APCactivators in the plant cell cycle. The AtCcs52 proteins interacted with different subsets ofmitotic cyclins, in accordance with their expression profiles, either in free- or CDK-boundforms. Expression of most APC subunits was constitutive, whereas cdc27a and cdc27b,corresponding to two forms of apc3, and ubc19 and ubc20 encoding E2-C type ubiquitinconjugatingenzymes displayed differences in their cell cycle regulation. These dataindicate the existence of numerous APCCdc20/Ccs52/Cdc27 forms in Arabidopsis, which inconjunction with different E2 enzymes might have distinct or complementary functions atdistinct stages of the cell cycle.},
	number = {8},
	urldate = {2021-10-14},
	journal = {Cell Cycle},
	author = {Fülöp, Katalin and Tarayre, Sylvie and Kelemen, Zsolt and Horváth, Gábor and Kevei, Zoltán and Nikovics, Krisztina and Bakó, László and Brown, Spencer and Kondorosi, Adam and Kondorosi, Eva},
	month = aug,
	year = {2005},
	pages = {4084--4092},
}

The anaphase-promoting complex (APC), a multisubunit E3 ubiquitin ligase, is anessential regulator of the cell cycle from metaphase until S phase in yeast and metazoans.APC mediates degradation of numerous cell cycle-related proteins, including mitoticcyclins and its activation and substrate-specificity are determined by two adaptor proteins,Cdc20 and Cdh1. Plants have multiple APC activators and the Cdh1-type proteins, inaddition, are represented by two subclasses, known as Ccs52A and Ccs52B. TheArabidopsis genome contains five cdc20 genes as well as ccs52A1, ccs52A2 and ccs52B. InSchizosaccharomyces pombe, expression of the three Atccs52 genes elicited distinctphenotypes supporting non-redundant function of the AtCcs52 proteins. Consistent withthese activities, the AtCcs52 proteins were able to bind both to the yeast and theArabidopsis APCs. In synchronized Arabidopsis cell cultures the cdc20 transcripts werepresent from early G2 until the M-phase exit, ccs52B from G2/M to M while ccs52A1 andccs52A2 were from late M until early G2, suggesting consecutive action of these APCactivators in the plant cell cycle. The AtCcs52 proteins interacted with different subsets ofmitotic cyclins, in accordance with their expression profiles, either in free- or CDK-boundforms. Expression of most APC subunits was constitutive, whereas cdc27a and cdc27b,corresponding to two forms of apc3, and ubc19 and ubc20 encoding E2-C type ubiquitinconjugatingenzymes displayed differences in their cell cycle regulation. These dataindicate the existence of numerous APCCdc20/Ccs52/Cdc27 forms in Arabidopsis, which inconjunction with different E2 enzymes might have distinct or complementary functions atdistinct stages of the cell cycle.

@article{schauer_gcms_2005,
	title = {{GC}–{MS} libraries for the rapid identification of metabolites in complex biological samples},
	volume = {579},
	issn = {1873-3468},
	url = {https://febs.onlinelibrary.wiley.com/doi/abs/10.1016/j.febslet.2005.01.029},
	doi = {10/fg7786},
	abstract = {Gas chromatography–mass spectrometry based metabolite profiling of biological samples is rapidly becoming one of the cornerstones of functional genomics and systems biology. Thus, the technology needs to be available to many laboratories and open exchange of information is required such as those achieved for transcript and protein data. The key-step in metabolite profiling is the unambiguous identification of metabolites in highly complex metabolite preparations with composite structure. Collections of mass spectra, which comprise frequently observed identified and non-identified metabolites, represent the most effective means to pool the identification efforts currently performed in many laboratories around the world. Here, we describe a platform for mass spectral and retention time index libraries that will enable this process (MSRI; www.csbdb.mpimp-golm.mpg.de/gmd.html). This resource should ameliorate many of the problems that each laboratory will face both for the initial establishment of metabolome analysis and for its maintenance at a constant sample throughput.},
	language = {en},
	number = {6},
	urldate = {2021-08-31},
	journal = {FEBS Letters},
	author = {Schauer, Nicolas and Steinhauser, Dirk and Strelkov, Sergej and Schomburg, Dietmar and Allison, Gordon and Moritz, Thomas and Lundgren, Krister and Roessner-Tunali, Ute and Forbes, Megan G. and Willmitzer, Lothar and Fernie, Alisdair R. and Kopka, Joachim},
	year = {2005},
	keywords = {GC, GC–MS, Gas chromatography–mass spectrometry, MS, MST, Mass spectral library, Metabolite profiling, Metabolomics, RI, Retention time index, TOF, gas chromatography, mass spectral metabolite tag, mass spectrometry, retention time index, time of flight},
	pages = {1332--1337},
}

Gas chromatography–mass spectrometry based metabolite profiling of biological samples is rapidly becoming one of the cornerstones of functional genomics and systems biology. Thus, the technology needs to be available to many laboratories and open exchange of information is required such as those achieved for transcript and protein data. The key-step in metabolite profiling is the unambiguous identification of metabolites in highly complex metabolite preparations with composite structure. Collections of mass spectra, which comprise frequently observed identified and non-identified metabolites, represent the most effective means to pool the identification efforts currently performed in many laboratories around the world. Here, we describe a platform for mass spectral and retention time index libraries that will enable this process (MSRI; www.csbdb.mpimp-golm.mpg.de/gmd.html). This resource should ameliorate many of the problems that each laboratory will face both for the initial establishment of metabolome analysis and for its maintenance at a constant sample throughput.

@article{atkin_hot_2005,
	title = {The hot and the cold: unravelling the variable response of plant respiration to temperature},
	volume = {32},
	issn = {1445-4408},
	shorttitle = {The hot and the cold},
	doi = {10.1071/FP03176},
	abstract = {When predicting the effects of climate change, global carbon circulation models that include a positive feedback effect of climate warming on the carbon cycle often assume that ( 1) plant respiration increases exponentially with temperature ( with a constant Q(10)) and ( 2) that there is no acclimation of respiration to long-term changes in temperature. In this review, we show that these two assumptions are incorrect. While Q(10) does not respond systematically to elevated atmospheric CO2 concentrations, other factors such as temperature, light, and water availability all have the potential to influence the temperature sensitivity of respiratory CO2 efflux. Roots and leaves can also differ in their Q(10) values, as can upper and lower canopy leaves. The consequences of such variable Q(10) values need to be fully explored in carbon modelling. Here, we consider the extent of variability in the degree of thermal acclimation of respiration, and discuss in detail the biochemical mechanisms underpinning this variability; the response of respiration to long-term changes in temperature is highly dependent on the effect of temperature on plant development, and on interactive effects of temperature and other abiotic factors ( e. g. irradiance, drought and nutrient availability). Rather than acclimating to the daily mean temperature, recent studies suggest that other components of the daily temperature regime can be important ( e. g. daily minimum and / or night temperature). In some cases, acclimation may simply reflect a passive response to changes in respiratory substrate availability, whereas in others acclimation may be critical in helping plants grow and survive at contrasting temperatures. We also consider the impact of acclimation on the balance between respiration and photosynthesis; although environmental factors such as water availability can alter the balance between these two processes, the available data suggests that temperature-mediated differences in dark leaf respiration are closely linked to concomitant differences in leaf photosynthesis. We conclude by highlighting the need for a greater process-based understanding of thermal acclimation of respiration if we are to successfully predict future ecosystem CO2 fluxes and potential feedbacks on atmospheric CO2 concentrations.},
	language = {English},
	number = {2},
	journal = {Functional Plant Biology},
	author = {Atkin, O. K. and Bruhn, D. and Hurry, Vaughan and Tjoelker, M. G.},
	year = {2005},
	note = {Place: Clayton
Publisher: Csiro Publishing
WOS:000227247600001},
	keywords = {alternative oxidase, arabidopsis-thaliana leaves, atmospheric co2 concentration, carbon fluxes, carbon-dioxide concentration, climate change, leaf dark respiration, long-term, relative growth-rate, respiration, ribulose-1,5-bisphosphate carboxylase oxygenase, root respiration, secale-cereale l, temperature},
	pages = {87--105},
}

When predicting the effects of climate change, global carbon circulation models that include a positive feedback effect of climate warming on the carbon cycle often assume that ( 1) plant respiration increases exponentially with temperature ( with a constant Q(10)) and ( 2) that there is no acclimation of respiration to long-term changes in temperature. In this review, we show that these two assumptions are incorrect. While Q(10) does not respond systematically to elevated atmospheric CO2 concentrations, other factors such as temperature, light, and water availability all have the potential to influence the temperature sensitivity of respiratory CO2 efflux. Roots and leaves can also differ in their Q(10) values, as can upper and lower canopy leaves. The consequences of such variable Q(10) values need to be fully explored in carbon modelling. Here, we consider the extent of variability in the degree of thermal acclimation of respiration, and discuss in detail the biochemical mechanisms underpinning this variability; the response of respiration to long-term changes in temperature is highly dependent on the effect of temperature on plant development, and on interactive effects of temperature and other abiotic factors ( e. g. irradiance, drought and nutrient availability). Rather than acclimating to the daily mean temperature, recent studies suggest that other components of the daily temperature regime can be important ( e. g. daily minimum and / or night temperature). In some cases, acclimation may simply reflect a passive response to changes in respiratory substrate availability, whereas in others acclimation may be critical in helping plants grow and survive at contrasting temperatures. We also consider the impact of acclimation on the balance between respiration and photosynthesis; although environmental factors such as water availability can alter the balance between these two processes, the available data suggests that temperature-mediated differences in dark leaf respiration are closely linked to concomitant differences in leaf photosynthesis. We conclude by highlighting the need for a greater process-based understanding of thermal acclimation of respiration if we are to successfully predict future ecosystem CO2 fluxes and potential feedbacks on atmospheric CO2 concentrations.

@article{swarup_root_2005,
	title = {Root gravitropism requires lateral root cap and epidermal cells for transport and response to a mobile auxin signal},
	volume = {7},
	copyright = {2005 Nature Publishing Group},
	issn = {1476-4679},
	url = {https://www.nature.com/articles/ncb1316},
	doi = {10.1038/ncb1316},
	abstract = {Re-orientation of Arabidopsis seedlings induces a rapid, asymmetric release of the growth regulator auxin from gravity-sensing columella cells at the root apex. The resulting lateral auxin gradient is hypothesized to drive differential cell expansion in elongation-zone tissues. We mapped those root tissues that function to transport or respond to auxin during a gravitropic response. Targeted expression of the auxin influx facilitator AUX1 demonstrated that root gravitropism requires auxin to be transported via the lateral root cap to all elongating epidermal cells. A three-dimensional model of the root elongation zone predicted that AUX1 causes the majority of auxin to accumulate in the epidermis. Selectively disrupting the auxin responsiveness of expanding epidermal cells by expressing a mutant form of the AUX/IAA17 protein, axr3-1, abolished root gravitropism. We conclude that gravitropic curvature in Arabidopsis roots is primarily driven by the differential expansion of epidermal cells in response to an influx-carrier-dependent auxin gradient.},
	language = {en},
	number = {11},
	urldate = {2021-06-11},
	journal = {Nature Cell Biology},
	author = {Swarup, Ranjan and Kramer, Eric M. and Perry, Paula and Knox, Kirsten and Leyser, H. M. Ottoline and Haseloff, Jim and Beemster, Gerrit T. S. and Bhalerao, Rishikesh P. and Bennett, Malcolm J.},
	month = nov,
	year = {2005},
	note = {Number: 11
Publisher: Nature Publishing Group},
	pages = {1057--1065},
}

Re-orientation of Arabidopsis seedlings induces a rapid, asymmetric release of the growth regulator auxin from gravity-sensing columella cells at the root apex. The resulting lateral auxin gradient is hypothesized to drive differential cell expansion in elongation-zone tissues. We mapped those root tissues that function to transport or respond to auxin during a gravitropic response. Targeted expression of the auxin influx facilitator AUX1 demonstrated that root gravitropism requires auxin to be transported via the lateral root cap to all elongating epidermal cells. A three-dimensional model of the root elongation zone predicted that AUX1 causes the majority of auxin to accumulate in the epidermis. Selectively disrupting the auxin responsiveness of expanding epidermal cells by expressing a mutant form of the AUX/IAA17 protein, axr3-1, abolished root gravitropism. We conclude that gravitropic curvature in Arabidopsis roots is primarily driven by the differential expansion of epidermal cells in response to an influx-carrier-dependent auxin gradient.

@article{villarejo_evidence_2005,
	title = {Evidence for a protein transported through the secretory pathway en route to the higher plant chloroplast},
	volume = {7},
	copyright = {2005 Nature Publishing Group},
	issn = {1476-4679},
	url = {https://www.nature.com/articles/ncb1330},
	doi = {10/fmrqwn},
	abstract = {In contrast to animal and fungal cells, green plant cells contain one or multiple chloroplasts, the organelle(s) in which photosynthetic reactions take place. Chloroplasts are believed to have originated from an endosymbiotic event and contain DNA that codes for some of their proteins. Most chloroplast proteins are encoded by the nuclear genome and imported with the help of sorting signals that are intrinsic parts of the polypeptides. Here, we show that a chloroplast-located protein in higher plants takes an alternative route through the secretory pathway, and becomes N-glycosylated before entering the chloroplast.},
	language = {en},
	number = {12},
	urldate = {2021-06-11},
	journal = {Nature Cell Biology},
	author = {Villarejo, Arsenio and Burén, Stefan and Larsson, Susanne and Déjardin, Annabelle and Monné, Magnus and Rudhe, Charlotta and Karlsson, Jan and Jansson, Stefan and Lerouge, Patrice and Rolland, Norbert and von Heijne, Gunnar and Grebe, Markus and Bakó, Laszlo and Samuelsson, Göran},
	month = dec,
	year = {2005},
	note = {Number: 12
Publisher: Nature Publishing Group},
	pages = {1224--1231},
}

In contrast to animal and fungal cells, green plant cells contain one or multiple chloroplasts, the organelle(s) in which photosynthetic reactions take place. Chloroplasts are believed to have originated from an endosymbiotic event and contain DNA that codes for some of their proteins. Most chloroplast proteins are encoded by the nuclear genome and imported with the help of sorting signals that are intrinsic parts of the polypeptides. Here, we show that a chloroplast-located protein in higher plants takes an alternative route through the secretory pathway, and becomes N-glycosylated before entering the chloroplast.

@article{wu_predicting_2005,
	title = {Predicting site productivity and pest hazard in lodgepole pine using biogeoclimatic system and geographic variables in {British} {Columbia}},
	volume = {62},
	copyright = {INRA, EDP Sciences},
	issn = {1286-4560, 1297-966X},
	url = {http://dx.doi.org/10.1051/forest:2004089},
	doi = {10/d2rsm7},
	abstract = {Annals of Forest Science, is a source of information about current developments and trends in forest research and forestry},
	language = {en},
	number = {1},
	urldate = {2021-06-15},
	journal = {Annals of Forest Science},
	author = {Wu, Harry X. and Ying, Cheng C. and Ju, Hong-Bo},
	month = jan,
	year = {2005},
	note = {Publisher: EDP Sciences},
	pages = {31--42},
}

Annals of Forest Science, is a source of information about current developments and trends in forest research and forestry

@article{ishikawa_functional_2005,
	title = {Functional analysis of the {PsbP}-like protein (sll1418) in {Synechocystis} sp. {PCC} 6803},
	volume = {84},
	issn = {1573-5079},
	url = {https://doi.org/10.1007/s11120-005-0477-8},
	doi = {10/dnrhzh},
	abstract = {A recent proteomic analysis of the thylakoid lumen of Arabidopsis thaliana revealed the presence of several PsbP-like proteins, and a homologue to this gene family was detected in the genome of the cyanobacterium Synechocystis sp. PCC 6803 (Schubert M, Petersson UA, Haas BJ, Funk C, Schröder WP, Kieselbach T (2002) J Biol Chem 277, 8354–8365). Using a peptide-directed antibody against this cyanobacterial PsbP-like protein (sll1418) we could show that it was localized in the thylakoid membrane and associated with Photosystem II. While salt washes did not remove the PsbP-like protein from the thylakoid membrane, it was partially lost during the detergent-based isolation of PSII membrane fractions. In total cell extracts this protein is present in the same amount as the extrinsic PsbO protein. We did not see any significant functional difference between the wild-type and a PsbP-like insertion mutant.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {Photosynthesis Research},
	author = {Ishikawa, Yasuo and Schröder, Wolfgang P. and Funk, Christiane},
	month = jun,
	year = {2005},
	pages = {257--262},
}

A recent proteomic analysis of the thylakoid lumen of Arabidopsis thaliana revealed the presence of several PsbP-like proteins, and a homologue to this gene family was detected in the genome of the cyanobacterium Synechocystis sp. PCC 6803 (Schubert M, Petersson UA, Haas BJ, Funk C, Schröder WP, Kieselbach T (2002) J Biol Chem 277, 8354–8365). Using a peptide-directed antibody against this cyanobacterial PsbP-like protein (sll1418) we could show that it was localized in the thylakoid membrane and associated with Photosystem II. While salt washes did not remove the PsbP-like protein from the thylakoid membrane, it was partially lost during the detergent-based isolation of PSII membrane fractions. In total cell extracts this protein is present in the same amount as the extrinsic PsbO protein. We did not see any significant functional difference between the wild-type and a PsbP-like insertion mutant.

@article{chow_photoinactivation_2005,
	title = {Photoinactivation of {Photosystem} {II} in leaves},
	volume = {84},
	issn = {1573-5079},
	url = {https://doi.org/10.1007/s11120-005-0410-1},
	doi = {10/dm64r6},
	abstract = {Photoinactivation of Photosystem II (PS II), the light-induced loss of ability to evolve oxygen, inevitably occurs under any light environment in nature, counteracted by repair. Under certain conditions, the extent of photoinactivation of PS II depends on the photon exposure (light dosage, x), rather than the irradiance or duration of illumination per se, thus obeying the law of reciprocity of irradiance and duration of illumination, namely, that equal photon exposure produces an equal effect. If the probability of photoinactivation (p) of PS II is directly proportional to an increment in photon exposure (p = kΔx, where k is the probability per unit photon exposure), it can be deduced that the number of active PS II complexes decreases exponentially as a function of photon exposure: N = Noexp(−kx). Further, since a photon exposure is usually achieved by varying the illumination time (t) at constant irradiance (I), N = Noexp(−kI t), i.e., N decreases exponentially with time, with a rate coefficient of photoinactivation kI, where the product kI is obviously directly proportional to I. Given that N = Noexp(−kx), the quantum yield of photoinactivation of PS II can be defined as −dN/dx = kN, which varies with the number of active PS II complexes remaining. Typically, the quantum yield of photoinactivation of PS II is ca. 0.1μmol PS II per mol photons at low photon exposure when repair is inhibited. That is, when about 107 photons have been received by leaf tissue, one PS II complex is inactivated. Some species such as grapevine have a much lower quantum yield of photoinactivation of PS II, even at a chilling temperature. Examination of the longer-term time course of photoinactivation of PS II in capsicum leaves reveals that the decrease in N deviates from a single-exponential decay when the majority of the PS II complexes are inactivated in the absence of repair. This can be attributed to the formation of strong quenchers in severely-photoinactivated PS II complexes, able to dissipate excitation energy efficiently and to protect the remaining active neighbours against damage by light.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {Photosynthesis Research},
	author = {Chow, Wah Soon and Lee, Hae-Youn and He, Jie and Hendrickson, Luke and Hong, Young-Nam and Matsubara, Shizue},
	month = jun,
	year = {2005},
	pages = {35--41},
}

Photoinactivation of Photosystem II (PS II), the light-induced loss of ability to evolve oxygen, inevitably occurs under any light environment in nature, counteracted by repair. Under certain conditions, the extent of photoinactivation of PS II depends on the photon exposure (light dosage, x), rather than the irradiance or duration of illumination per se, thus obeying the law of reciprocity of irradiance and duration of illumination, namely, that equal photon exposure produces an equal effect. If the probability of photoinactivation (p) of PS II is directly proportional to an increment in photon exposure (p = kΔx, where k is the probability per unit photon exposure), it can be deduced that the number of active PS II complexes decreases exponentially as a function of photon exposure: N = Noexp(−kx). Further, since a photon exposure is usually achieved by varying the illumination time (t) at constant irradiance (I), N = Noexp(−kI t), i.e., N decreases exponentially with time, with a rate coefficient of photoinactivation kI, where the product kI is obviously directly proportional to I. Given that N = Noexp(−kx), the quantum yield of photoinactivation of PS II can be defined as −dN/dx = kN, which varies with the number of active PS II complexes remaining. Typically, the quantum yield of photoinactivation of PS II is ca. 0.1μmol PS II per mol photons at low photon exposure when repair is inhibited. That is, when about 107 photons have been received by leaf tissue, one PS II complex is inactivated. Some species such as grapevine have a much lower quantum yield of photoinactivation of PS II, even at a chilling temperature. Examination of the longer-term time course of photoinactivation of PS II in capsicum leaves reveals that the decrease in N deviates from a single-exponential decay when the majority of the PS II complexes are inactivated in the absence of repair. This can be attributed to the formation of strong quenchers in severely-photoinactivated PS II complexes, able to dissipate excitation energy efficiently and to protect the remaining active neighbours against damage by light.

@article{akesson_overexpression_2005,
	title = {Overexpression of the {Ca2}+-binding protein calreticulin in the endoplasmic reticulum improves growth of tobacco cell suspensions ({Nicotiana} tabacum) in high-{Ca2}+ medium},
	volume = {123},
	issn = {0031-9317},
	doi = {10/c9bnr5},
	abstract = {Calreticulin (CRT) is a eukaryotic, highly conserved, Ca2+-binding protein predominantly located in the endoplasmic reticulum (ER) lumen. In addition to being involved in the regulation of cellular Ca2+, calreticulin is a key quality control element during protein folding in the ER lumen. Tobacco (Nicotiana tabacum L.) suspension cells overexpressing a maize CRT (CRT1a) were used here to examine the properties of CRT in growing plant cells with respect to stress exposure. The endogenous CRT gene was induced rapidly after subculturing of the cells to new medium. In accordance, the CRT protein levels increased, peaking at days 3-4. At day 5, when the CRT transcript levels had levelled off, a further increase in endogenous CRT expression was obtained when the cells were treated with excess Ca2+ or the N-linked glycosylation inhibitor tunicamycin. Whereas the response to Ca2+ occurred within 30 min, the induction by tunicamycin took several hours to be established. Transforming tobacco cells with maize CRT1a, under a constitutive mannopine synthase promoter, resulted in a stable level of expressed CRT1a during the growth cycle compared with endogenous CRT. The CRTs showed differences in attached glycans, but both contained the high mannose-rich-type glycans characteristic of ER proteins. In agreement with an ER location, both tobacco CRT and the transgene product CRT1a codistributed with the ER marker NADH cytochrome c reductase after density gradient centrifugation of microsomal fractions from tobacco cells. Increased production of CRT, as was obtained in the transgenic tobacco cell lines, made cells more tolerant than wild-type cells to high Ca2+ during growth. These data suggest that overexpression of CRT1a in plant cells results in a more efficient calcium buffering capacity in the ER.},
	language = {English},
	number = {1},
	journal = {Physiologia Plantarum},
	author = {Akesson, A. and Persson, S. and Love, J. and Boss, W. F. and Widell, S. and Sommarin, M.},
	month = jan,
	year = {2005},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000226428300011},
	keywords = {ca2+, calcium, expression, glycosylation, identification, plants, release},
	pages = {92--99},
}

Calreticulin (CRT) is a eukaryotic, highly conserved, Ca2+-binding protein predominantly located in the endoplasmic reticulum (ER) lumen. In addition to being involved in the regulation of cellular Ca2+, calreticulin is a key quality control element during protein folding in the ER lumen. Tobacco (Nicotiana tabacum L.) suspension cells overexpressing a maize CRT (CRT1a) were used here to examine the properties of CRT in growing plant cells with respect to stress exposure. The endogenous CRT gene was induced rapidly after subculturing of the cells to new medium. In accordance, the CRT protein levels increased, peaking at days 3-4. At day 5, when the CRT transcript levels had levelled off, a further increase in endogenous CRT expression was obtained when the cells were treated with excess Ca2+ or the N-linked glycosylation inhibitor tunicamycin. Whereas the response to Ca2+ occurred within 30 min, the induction by tunicamycin took several hours to be established. Transforming tobacco cells with maize CRT1a, under a constitutive mannopine synthase promoter, resulted in a stable level of expressed CRT1a during the growth cycle compared with endogenous CRT. The CRTs showed differences in attached glycans, but both contained the high mannose-rich-type glycans characteristic of ER proteins. In agreement with an ER location, both tobacco CRT and the transgene product CRT1a codistributed with the ER marker NADH cytochrome c reductase after density gradient centrifugation of microsomal fractions from tobacco cells. Increased production of CRT, as was obtained in the transgenic tobacco cell lines, made cells more tolerant than wild-type cells to high Ca2+ during growth. These data suggest that overexpression of CRT1a in plant cells results in a more efficient calcium buffering capacity in the ER.

@article{strengbom_multitrophic_2005,
	title = {Do multitrophic interactions override {N} fertilization effects on {Operophtera} larvae?},
	volume = {143},
	issn = {1432-1939},
	url = {https://doi.org/10.1007/s00442-004-1799-5},
	doi = {10/fqbq2g},
	abstract = {We examined how performance of Operophtera brumata (Lepidoptera) larvae was affected by nitrogen (N) fertilization of boreal forest understorey vegetation. We monitored larval densities on Vaccinium myrtillus plants for a period of 7 years in a field experiment. Preliminary results indicated that the N effect on larval densities was weak. To examine if this was due to indirect interactions with a plant pathogen, Valdensia heterodoxa, that share the same host plant, or due to top-down effects of predation, we performed both a laboratory feeding experiment (individual level) and a bird exclusion experiment (population level) in the field. At the individual level, altered food plant quality (changes in plant concentration of carbon, N, phenolics, or condensed tannins) due to repeated infection by the pathogen had no effect on larval performance, but both survival to the adult stage and adult weight were positively affected by N fertilization. Exclusion of insectivorous birds increased the frequency of larval damage on V. myrtillus shoots, indicating higher larval densities. This effect was stronger in fertilized than in unfertilized plots, indicating higher bird predation in fertilized plots. Predation may thus explain the lack of fertilization effect on larval densities in the field experiment. Our results suggest that top-down effects are more important for larval densities than bottom-up effects, and that bird predation may play an important role in population regulation of O. brumata in boreal forests.},
	language = {en},
	number = {2},
	urldate = {2021-06-11},
	journal = {Oecologia},
	author = {Strengbom, Joachim and Witzell, Johanna and Nordin, Annika and Ericson, Lars},
	month = mar,
	year = {2005},
	pages = {241--250},
}

We examined how performance of Operophtera brumata (Lepidoptera) larvae was affected by nitrogen (N) fertilization of boreal forest understorey vegetation. We monitored larval densities on Vaccinium myrtillus plants for a period of 7 years in a field experiment. Preliminary results indicated that the N effect on larval densities was weak. To examine if this was due to indirect interactions with a plant pathogen, Valdensia heterodoxa, that share the same host plant, or due to top-down effects of predation, we performed both a laboratory feeding experiment (individual level) and a bird exclusion experiment (population level) in the field. At the individual level, altered food plant quality (changes in plant concentration of carbon, N, phenolics, or condensed tannins) due to repeated infection by the pathogen had no effect on larval performance, but both survival to the adult stage and adult weight were positively affected by N fertilization. Exclusion of insectivorous birds increased the frequency of larval damage on V. myrtillus shoots, indicating higher larval densities. This effect was stronger in fertilized than in unfertilized plots, indicating higher bird predation in fertilized plots. Predation may thus explain the lack of fertilization effect on larval densities in the field experiment. Our results suggest that top-down effects are more important for larval densities than bottom-up effects, and that bird predation may play an important role in population regulation of O. brumata in boreal forests.

@article{sterck_est_2005,
	title = {{EST} data suggest that poplar is an ancient polyploid},
	volume = {167},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/j.1469-8137.2005.01378.x},
	doi = {10/c6wh5d},
	abstract = {• We analysed the publicly available expressed sequence tag (EST) collections for the genus Populus to examine whether evidence can be found for large-scale gene-duplication events in the evolutionary past of this genus. • The ESTs were clustered into unigenes for each poplar species examined. Gene families were constructed for all proteins deduced from these unigenes, and KS dating was performed on all paralogs within a gene family. The fraction of paralogs was then plotted against the KS values, which resulted in a distribution reflecting the age of duplicated genes in poplar. • Sufficient EST data were available for seven different poplar species spanning four of the six sections of the genus Populus. For all these species, there was evidence that a large-scale gene-duplication event had occurred. • From our analysis it is clear that all poplar species have shared the same large-scale gene-duplication event, suggesting that this event must have occurred in the ancestor of poplar, or at least very early in the evolution of the Populus genus.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {New Phytologist},
	author = {Sterck, Lieven and Rombauts, Stephane and Jansson, Stefan and Sterky, Fredrik and Rouzé, Pierre and Peer, Yves Van de},
	year = {2005},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2005.01378.x},
	keywords = {EST (expressed sequence tag) data, KS dating, Populus (poplar), evolution, fossil record, genome duplication, polyploidy},
	pages = {165--170},
}

• We analysed the publicly available expressed sequence tag (EST) collections for the genus Populus to examine whether evidence can be found for large-scale gene-duplication events in the evolutionary past of this genus. • The ESTs were clustered into unigenes for each poplar species examined. Gene families were constructed for all proteins deduced from these unigenes, and KS dating was performed on all paralogs within a gene family. The fraction of paralogs was then plotted against the KS values, which resulted in a distribution reflecting the age of duplicated genes in poplar. • Sufficient EST data were available for seven different poplar species spanning four of the six sections of the genus Populus. For all these species, there was evidence that a large-scale gene-duplication event had occurred. • From our analysis it is clear that all poplar species have shared the same large-scale gene-duplication event, suggesting that this event must have occurred in the ancestor of poplar, or at least very early in the evolution of the Populus genus.

@article{klenell_involvement_2005,
	title = {Involvement of the chloroplast signal recognition particle {cpSRP43} in acclimation to photooxidative stress condition in {Arabidopsis}},
	volume = {46},
	issn = {0032-0781},
	doi = {10/bv6cqv},
	language = {English},
	journal = {Plant and Cell Physiology},
	author = {Klenell, M. and Morita, S. and Tiemblo-Olmo, M. and Muhlenbock, P. and Karpinski, S. and Karpinska, B.},
	year = {2005},
	note = {Place: Oxford
Publisher: Oxford Univ Press
WOS:000228104101182},
	pages = {S170--S170},
}

@article{keech_preparation_2005,
	title = {Preparation of leaf mitochondria from {Arabidopsis} thaliana},
	volume = {124},
	issn = {0031-9317},
	doi = {10/d7jvrz},
	abstract = {Arabidopsis thaliana is, perhaps, the most important model species in modern plant biology. However, the isolation of organelles from leaves of this plant has been difficult. Here, we present two different protocols for the isolation of mitochondria, yielding either highly functional crude mitochondria or highly purified mitochondria. The crude mitochondria were well coupled with the substrates tested (malate + glutamate, glycine and NADH), exhibiting respiratory control ratios of 2.1-3.9. Purified mitochondria with very low levels of chlorophyll contamination were obtained by Percoll gradient centrifugation, yielding 1.2 mg of mitochondrial protein from 50 g of leaves.},
	language = {English},
	number = {4},
	journal = {Physiologia Plantarum},
	author = {Keech, O. and Dizengremel, P. and Gardestrom, P.},
	month = aug,
	year = {2005},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000230573300001},
	keywords = {chloroplasts, criteria, dehydrogenase, expression, metabolism, oxidation, photosynthesis, respiration, spinach, tissue},
	pages = {403--409},
}

Arabidopsis thaliana is, perhaps, the most important model species in modern plant biology. However, the isolation of organelles from leaves of this plant has been difficult. Here, we present two different protocols for the isolation of mitochondria, yielding either highly functional crude mitochondria or highly purified mitochondria. The crude mitochondria were well coupled with the substrates tested (malate + glutamate, glycine and NADH), exhibiting respiratory control ratios of 2.1-3.9. Purified mitochondria with very low levels of chlorophyll contamination were obtained by Percoll gradient centrifugation, yielding 1.2 mg of mitochondrial protein from 50 g of leaves.

@article{gardestrom_new_2005,
	title = {New in {Physiologia} {Plantarum}},
	volume = {124},
	issn = {0031-9317},
	doi = {10/cfjjkc},
	language = {English},
	number = {1},
	journal = {Physiologia Plantarum},
	author = {Gardestrom, P. and Hurry, V.},
	month = may,
	year = {2005},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000228975000001},
	keywords = {chloroplasts, gene-expression, photosynthesis, redox regulation, responses, stress, tolerance},
	pages = {1--3},
}

@article{bennett_integrative_2005,
	title = {Integrative biology: dissecting cross-talk between plant signalling pathways},
	volume = {123},
	issn = {0031-9317},
	shorttitle = {Integrative biology},
	doi = {10/bwb463},
	language = {English},
	number = {2},
	journal = {Physiologia Plantarum},
	author = {Bennett, M. and Bellini, C. and Van Der Straeten, D.},
	month = feb,
	year = {2005},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000226966400001},
	keywords = {ethylene, gene, growth},
	pages = {109--110},
}

@article{kulheim_what_2005,
	title = {What leads to reduced fitness in non-photochemical quenching mutants?},
	volume = {125},
	issn = {0031-9317},
	doi = {10/djtwsp},
	abstract = {Feedback de-excitation (FDE) is a process that protects photosystem II from damage during short periods of overexcitation. Arabidopsis thaliana mutants lacking this mechanism have reduced fitness in environments with variable light intensities. We have assayed the physiological consequences of mutations resulting in the lack of FDE and analysed the differences between field-grown plants and plants grown under fluctuating light in the laboratory. We show that FDE is an important mechanism in short-term responses to fluctuating light. Anthocyanin and carbohydrate levels indicated that the mutant plants were stressed to a higher degree than wild-type (WT) plants. Field-grown mutants were photo-inactivated to a greater degree than WT, whereas mutant plants in the fluctuating light environment in the laboratory seemed to downregulate the photosynthetic quantum yield, thereby avoiding photo-damage but resulting in impaired growth in the case of one mutant. Finally, we provide evidence that FDE is most important under conditions when photosynthesis limits plant growth, for example during flower and seed development.},
	language = {English},
	number = {2},
	journal = {Physiologia Plantarum},
	author = {Kulheim, C. and Jansson, S.},
	month = oct,
	year = {2005},
	note = {Place: Oxford
Publisher: Blackwell Publishing
WOS:000231677000006},
	keywords = {arabidopsis-thaliana, chlorophyll fluorescence, cold-acclimation, energy-dissipation, light-harvesting complex, low-temperature, photoinhibition, photosynthesis, plants, xanthophyll cycle},
	pages = {202--211},
}

Feedback de-excitation (FDE) is a process that protects photosystem II from damage during short periods of overexcitation. Arabidopsis thaliana mutants lacking this mechanism have reduced fitness in environments with variable light intensities. We have assayed the physiological consequences of mutations resulting in the lack of FDE and analysed the differences between field-grown plants and plants grown under fluctuating light in the laboratory. We show that FDE is an important mechanism in short-term responses to fluctuating light. Anthocyanin and carbohydrate levels indicated that the mutant plants were stressed to a higher degree than wild-type (WT) plants. Field-grown mutants were photo-inactivated to a greater degree than WT, whereas mutant plants in the fluctuating light environment in the laboratory seemed to downregulate the photosynthetic quantum yield, thereby avoiding photo-damage but resulting in impaired growth in the case of one mutant. Finally, we provide evidence that FDE is most important under conditions when photosynthesis limits plant growth, for example during flower and seed development.

@article{sorin_auxin_2005,
	title = {Auxin and {Light} {Control} of {Adventitious} {Rooting} in {Arabidopsis} {Require} {ARGONAUTE1}},
	volume = {17},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.105.031625},
	doi = {10/bsmnt5},
	abstract = {Adventitious rooting is a quantitative genetic trait regulated by both environmental and endogenous factors. To better understand the physiological and molecular basis of adventitious rooting, we took advantage of two classes of Arabidopsis thaliana mutants altered in adventitious root formation: the superroot mutants, which spontaneously make adventitious roots, and the argonaute1 (ago1) mutants, which unlike superroot are barely able to form adventitious roots. The defect in adventitious rooting observed in ago1 correlated with light hypersensitivity and the deregulation of auxin homeostasis specifically in the apical part of the seedlings. In particular, a clear reduction in endogenous levels of free indoleacetic acid (IAA) and IAA conjugates was shown. This was correlated with a downregulation of the expression of several auxin-inducible GH3 genes in the hypocotyl of the ago1-3 mutant. We also found that the Auxin Response Factor17 (ARF17) gene, a potential repressor of auxin-inducible genes, was overexpressed in ago1-3 hypocotyls. The characterization of an ARF17-overexpressing line showed that it produced fewer adventitious roots than the wild type and retained a lower expression of GH3 genes. Thus, we suggest that ARF17 negatively regulates adventitious root formation in ago1 mutants by repressing GH3 genes and therefore perturbing auxin homeostasis in a light-dependent manner. These results suggest that ARF17 could be a major regulator of adventitious rooting in Arabidopsis.},
	number = {5},
	urldate = {2021-06-11},
	journal = {The Plant Cell},
	author = {Sorin, Céline and Bussell, John D. and Camus, Isabelle and Ljung, Karin and Kowalczyk, Mariusz and Geiss, Gaia and McKhann, Heather and Garcion, Christophe and Vaucheret, Hervé and Sandberg, Göran and Bellini, Catherine},
	month = may,
	year = {2005},
	pages = {1343--1359},
}

Adventitious rooting is a quantitative genetic trait regulated by both environmental and endogenous factors. To better understand the physiological and molecular basis of adventitious rooting, we took advantage of two classes of Arabidopsis thaliana mutants altered in adventitious root formation: the superroot mutants, which spontaneously make adventitious roots, and the argonaute1 (ago1) mutants, which unlike superroot are barely able to form adventitious roots. The defect in adventitious rooting observed in ago1 correlated with light hypersensitivity and the deregulation of auxin homeostasis specifically in the apical part of the seedlings. In particular, a clear reduction in endogenous levels of free indoleacetic acid (IAA) and IAA conjugates was shown. This was correlated with a downregulation of the expression of several auxin-inducible GH3 genes in the hypocotyl of the ago1-3 mutant. We also found that the Auxin Response Factor17 (ARF17) gene, a potential repressor of auxin-inducible genes, was overexpressed in ago1-3 hypocotyls. The characterization of an ARF17-overexpressing line showed that it produced fewer adventitious roots than the wild type and retained a lower expression of GH3 genes. Thus, we suggest that ARF17 negatively regulates adventitious root formation in ago1 mutants by repressing GH3 genes and therefore perturbing auxin homeostasis in a light-dependent manner. These results suggest that ARF17 could be a major regulator of adventitious rooting in Arabidopsis.

@article{wiklund_new_2005,
	title = {A new metabonomic strategy for analysing the growth process of the poplar tree},
	volume = {3},
	issn = {1467-7652},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1467-7652.2005.00129.x},
	doi = {10/dhs8p7},
	abstract = {High-resolution, magic angle spinning, proton nuclear magnetic resonance (1H HR/MAS NMR) spectroscopy and multivariate data analysis using batch processing (BP) were applied to the analysis of two different genotypes of poplar tree (Populus tremula L. x tremuloides Michx.) containing an antisense construct of PttMYB76 and control (wild-type). A gene encoding a MYB transcription factor, with unknown function, PttMYB76, was selected from a cambial expressed sequence tag (EST) library of poplar tree (Populus tremula L. x tremuloides Michx.) for metabonomic characterization. The PttMYB76 gene is believed to affect different paths in the phenyl propanoid synthetic pathway. This pathway leads to the formation of S- and G-lignin, flavonoids and sinapate esters. Milled poplar samples collected at the internodes of the tree were analysed using 1H HR/MAS NMR spectroscopy. The application of multivariate BP of the NMR results revealed a growth-related gradient in the plant internode direction, as well as the discrimination between the trees with down-regulated PttMYB76 expression and wild-type populations. This paper focuses on the potential of a new analytical multivariate approach for analysing time-related plant metabonomic data. The techniques used could, with the aid of suitable model compounds, be of high relevance to the detection and understanding of the different lignification processes within the two types of poplar tree. Additionally, the findings highlight the importance of applying robust and organized multivariate data analysis approaches to facilitate the modelling and interpretation of complex biological data sets.},
	language = {en},
	number = {3},
	urldate = {2021-06-11},
	journal = {Plant Biotechnology Journal},
	author = {Wiklund, Susanne and Karlsson, Marlene and Antti, Henrik and Johnels, Dan and Sjöström, Michael and Wingsle, Gunnar and Edlund, Ulf},
	year = {2005},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1467-7652.2005.00129.x},
	keywords = {1H HR/MAS NMR, batch process, partial least squares projections to latent structures, poplar tree, principal components analysis, wood formation},
	pages = {353--362},
}

High-resolution, magic angle spinning, proton nuclear magnetic resonance (1H HR/MAS NMR) spectroscopy and multivariate data analysis using batch processing (BP) were applied to the analysis of two different genotypes of poplar tree (Populus tremula L. x tremuloides Michx.) containing an antisense construct of PttMYB76 and control (wild-type). A gene encoding a MYB transcription factor, with unknown function, PttMYB76, was selected from a cambial expressed sequence tag (EST) library of poplar tree (Populus tremula L. x tremuloides Michx.) for metabonomic characterization. The PttMYB76 gene is believed to affect different paths in the phenyl propanoid synthetic pathway. This pathway leads to the formation of S- and G-lignin, flavonoids and sinapate esters. Milled poplar samples collected at the internodes of the tree were analysed using 1H HR/MAS NMR spectroscopy. The application of multivariate BP of the NMR results revealed a growth-related gradient in the plant internode direction, as well as the discrimination between the trees with down-regulated PttMYB76 expression and wild-type populations. This paper focuses on the potential of a new analytical multivariate approach for analysing time-related plant metabonomic data. The techniques used could, with the aid of suitable model compounds, be of high relevance to the detection and understanding of the different lignification processes within the two types of poplar tree. Additionally, the findings highlight the importance of applying robust and organized multivariate data analysis approaches to facilitate the modelling and interpretation of complex biological data sets.

@article{magyar_role_2005,
	title = {The {Role} of the {Arabidopsis} {E2FB} {Transcription} {Factor} in {Regulating} {Auxin}-{Dependent} {Cell} {Division}},
	volume = {17},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.105.033761},
	doi = {10/dtpwks},
	abstract = {The molecular mechanisms by which the phytohormone auxin coordinates cell division with cell growth and differentiation are largely unknown. Here, we show that in Arabidopsis thaliana E2FB, accumulation and stability are positively regulated by auxin. Coexpression of E2FB, but not of E2FA, with its dimerization partner A, stimulated cell proliferation in the absence of auxin in tobacco (Nicotiana tabacum) Bright Yellow-2 cells. E2FB regulated the entry into both S- and M-phases, the latter corresponding to the activation of a plant-specific mitotic regulator, CDKB1;1. Increased E2FB levels led to shortened cell cycle duration, elevated cell numbers, and extremely small cell sizes. In the absence of auxin, cells elongated with concomitant increase in their ploidy level, but both were strongly inhibited by E2FB. We conclude that E2FB is one of the key targets for auxin to determine whether cells proliferate or whether they exit the cell cycle, enlarge, and endoreduplicate their DNA.},
	number = {9},
	urldate = {2021-06-11},
	journal = {The Plant Cell},
	author = {Magyar, Zoltán and De Veylder, Lieven and Atanassova, Ana and Bakó, László and Inzé, Dirk and Bögre, László},
	month = sep,
	year = {2005},
	pages = {2527--2541},
}

The molecular mechanisms by which the phytohormone auxin coordinates cell division with cell growth and differentiation are largely unknown. Here, we show that in Arabidopsis thaliana E2FB, accumulation and stability are positively regulated by auxin. Coexpression of E2FB, but not of E2FA, with its dimerization partner A, stimulated cell proliferation in the absence of auxin in tobacco (Nicotiana tabacum) Bright Yellow-2 cells. E2FB regulated the entry into both S- and M-phases, the latter corresponding to the activation of a plant-specific mitotic regulator, CDKB1;1. Increased E2FB levels led to shortened cell cycle duration, elevated cell numbers, and extremely small cell sizes. In the absence of auxin, cells elongated with concomitant increase in their ploidy level, but both were strongly inhibited by E2FB. We conclude that E2FB is one of the key targets for auxin to determine whether cells proliferate or whether they exit the cell cycle, enlarge, and endoreduplicate their DNA.

@article{ljung_sites_2005,
	title = {Sites and {Regulation} of {Auxin} {Biosynthesis} in {Arabidopsis} {Roots}},
	volume = {17},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.104.029272},
	doi = {10/bccfh4},
	abstract = {Auxin has been shown to be important for many aspects of root development, including initiation and emergence of lateral roots, patterning of the root apical meristem, gravitropism, and root elongation. Auxin biosynthesis occurs in both aerial portions of the plant and in roots; thus, the auxin required for root development could come from either source, or both. To monitor putative internal sites of auxin synthesis in the root, a method for measuring indole-3-acetic acid (IAA) biosynthesis with tissue resolution was developed. We monitored IAA synthesis in 0.5- to 2-mm sections of Arabidopsis thaliana roots and were able to identify an important auxin source in the meristematic region of the primary root tip as well as in the tips of emerged lateral roots. Lower but significant synthesis capacity was observed in tissues upward from the tip, showing that the root contains multiple auxin sources. Root-localized IAA synthesis was diminished in a cyp79B2 cyp79B3 double knockout, suggesting an important role for Trp-dependent IAA synthesis pathways in the root. We present a model for how the primary root is supplied with auxin during early seedling development.},
	number = {4},
	urldate = {2021-06-11},
	journal = {The Plant Cell},
	author = {Ljung, Karin and Hull, Anna K. and Celenza, John and Yamada, Masashi and Estelle, Mark and Normanly, Jennifer and Sandberg, Göran},
	month = apr,
	year = {2005},
	pages = {1090--1104},
}

Auxin has been shown to be important for many aspects of root development, including initiation and emergence of lateral roots, patterning of the root apical meristem, gravitropism, and root elongation. Auxin biosynthesis occurs in both aerial portions of the plant and in roots; thus, the auxin required for root development could come from either source, or both. To monitor putative internal sites of auxin synthesis in the root, a method for measuring indole-3-acetic acid (IAA) biosynthesis with tissue resolution was developed. We monitored IAA synthesis in 0.5- to 2-mm sections of Arabidopsis thaliana roots and were able to identify an important auxin source in the meristematic region of the primary root tip as well as in the tips of emerged lateral roots. Lower but significant synthesis capacity was observed in tissues upward from the tip, showing that the root contains multiple auxin sources. Root-localized IAA synthesis was diminished in a cyp79B2 cyp79B3 double knockout, suggesting an important role for Trp-dependent IAA synthesis pathways in the root. We present a model for how the primary root is supplied with auxin during early seedling development.

@article{vanneste_cell_2005,
	title = {Cell cycle progression in the pericycle is not sufficient for {SOLITARY} {ROOT}/{IAA14}-mediated lateral root initiation in {Arabidopsis} thaliana},
	volume = {17},
	issn = {1040-4651},
	doi = {10/dwzcgw},
	abstract = {To study the mechanisms behind auxin-induced cell division, lateral root initiation was used as a model system. By means of microarray analysis, genome-wide transcriptional changes were monitored during the early steps of lateral root initiation. Inclusion of the dominant auxin signaling mutant solitary root1 (slr1) identified genes involved in lateral root initiation that act downstream of the auxin/indole-3-acetic acid (AUX/IAA) signaling pathway. Interestingly, key components of the cell cycle machinery were strongly defective in slr1, suggesting a direct link between AUX/IAA signaling and core cell cycle regulation. However, induction of the cell cycle in the mutant background by overexpression of the D-type cyclin (CYCD3;1) was able to trigger complete rounds of cell division in the pericycle that did not result in lateral root formation. Therefore, lateral root initiation can only take place when cell cycle activation is accompanied by cell fate respecification of pericycle cells. The microarray data also yielded evidence for the existence of both negative and positive feedback mechanisms that regulate auxin homeostasis and signal transduction in the pericycle, thereby fine-tuning the process of lateral root initiation.},
	language = {English},
	number = {11},
	journal = {Plant Cell},
	author = {Vanneste, S. and De Rybel, B. and Beemster, G. T. S. and Ljung, K. and De Smet, I. and Van Isterdael, G. and Naudts, M. and Iida, R. and Gruissem, W. and Tasaka, M. and Inze, D. and Fukaki, H. and Beeckman, T.},
	month = nov,
	year = {2005},
	note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000232991700017},
	keywords = {amino-acids, aux/iaa   proteins, box protein tir1, dependent kinase, domain-ii, family, gene-expression, microarray, plant development, polar auxin transport},
	pages = {3035--3050},
}

To study the mechanisms behind auxin-induced cell division, lateral root initiation was used as a model system. By means of microarray analysis, genome-wide transcriptional changes were monitored during the early steps of lateral root initiation. Inclusion of the dominant auxin signaling mutant solitary root1 (slr1) identified genes involved in lateral root initiation that act downstream of the auxin/indole-3-acetic acid (AUX/IAA) signaling pathway. Interestingly, key components of the cell cycle machinery were strongly defective in slr1, suggesting a direct link between AUX/IAA signaling and core cell cycle regulation. However, induction of the cell cycle in the mutant background by overexpression of the D-type cyclin (CYCD3;1) was able to trigger complete rounds of cell division in the pericycle that did not result in lateral root formation. Therefore, lateral root initiation can only take place when cell cycle activation is accompanied by cell fate respecification of pericycle cells. The microarray data also yielded evidence for the existence of both negative and positive feedback mechanisms that regulate auxin homeostasis and signal transduction in the pericycle, thereby fine-tuning the process of lateral root initiation.

@article{fulop_medicago_2005,
	title = {The {Medicago} {CDKC};1-{CYCLINT};1 kinase complex phosphorylates the carboxy-terminal domain of {RNA} polymerase {II} and promotes transcription},
	volume = {42},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2005.02421.x},
	doi = {10/fmbqpx},
	abstract = {The Ms;CDKC;1 kinase is structurally similar to those cyclin-dependent kinases (CDKs) that are not involved directly in cell cycle regulation. The presence of a PITAIRE motif in Ms;CDKC;1 suggests that it interacts with cyclins different from known PSTAIRE/PPTALRE kinase regulatory subunits. Here we demonstrate that a Medicago CYCLINT (CYCT) protein is a specific interactor of Ms;CDKC;1 and the interaction between these two proteins gives rise to an active kinase complex that localizes to the nucleus and phosphorylates the carboxy-terminal YSPTSPS heptapeptide repeat domain (CTD) of the largest subunit of RNA polymerase II in vitro. Mutation of Ser to Ala at position 5 within the heptapeptide repeat abolishes substrate phosphorylation by the Ms;CDKC;1 kinase complex. Furthermore, our data show that addition of the Medicago CDKC;1-CYCT;1 heterodimer completely restored the transcriptional activity of a HeLa nuclear extract depleted of endogeneous CDK9 kinase complexes. Together, these results indicate that the Medicago CDKC;1-CYCT;1 complex is a positive regulator of transcription in plants and has a role similar to the CDK9/cyclin T complex of human positive transcription elongation factor P-TEFb.},
	language = {en},
	number = {6},
	urldate = {2021-06-11},
	journal = {The Plant Journal},
	author = {Fülöp, Katalin and Pettkó-Szandtner, Aladàr and Magyar, Zoltán and Miskolczi, Pál and Kondorosi, Éva and Dudits, Dénes and Bakó, László},
	year = {2005},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2005.02421.x},
	keywords = {CDK-cyclin complex, CTD kinase, Medicago, P-TEFb, cell cycle, transcription},
	pages = {810--820},
}

The Ms;CDKC;1 kinase is structurally similar to those cyclin-dependent kinases (CDKs) that are not involved directly in cell cycle regulation. The presence of a PITAIRE motif in Ms;CDKC;1 suggests that it interacts with cyclins different from known PSTAIRE/PPTALRE kinase regulatory subunits. Here we demonstrate that a Medicago CYCLINT (CYCT) protein is a specific interactor of Ms;CDKC;1 and the interaction between these two proteins gives rise to an active kinase complex that localizes to the nucleus and phosphorylates the carboxy-terminal YSPTSPS heptapeptide repeat domain (CTD) of the largest subunit of RNA polymerase II in vitro. Mutation of Ser to Ala at position 5 within the heptapeptide repeat abolishes substrate phosphorylation by the Ms;CDKC;1 kinase complex. Furthermore, our data show that addition of the Medicago CDKC;1-CYCT;1 heterodimer completely restored the transcriptional activity of a HeLa nuclear extract depleted of endogeneous CDK9 kinase complexes. Together, these results indicate that the Medicago CDKC;1-CYCT;1 complex is a positive regulator of transcription in plants and has a role similar to the CDK9/cyclin T complex of human positive transcription elongation factor P-TEFb.

@article{klenell_involvement_2005,
	title = {Involvement of the {Chloroplast} {Signal} {Recognition} {Particle} {cpSRP43} in {Acclimation} to {Conditions} {Promoting} {Photooxidative} {Stress} in {Arabidopsis}},
	volume = {46},
	issn = {0032-0781},
	url = {https://doi.org/10.1093/pcp/pci010},
	doi = {10/bv6cqv},
	abstract = {In this study, we have investigated the role of the CAO gene (coding for the chloroplast recognition particle cpSRP43) in the protection against and acclimation to environmental conditions that promote photooxidative stress. Deficiency of cpSRP43 in the Arabidopsis mutant chaos has been shown previously to lead to partial loss of a number of proteins of the photosystem II (PSII) antennae. In addition, as reported here, mutant plants have lower growth rates and reduced lignin contents under laboratory conditions. However, chaos seedlings showed significantly higher tolerance to photooxidative stress under both tightly controlled laboratory conditions and highly variable conditions in the field. This greater tolerance of chaos plants was manifested in less photooxidative damage together with faster growth recovery in young seedlings. It was also associated with a lower production of H2O2, lower ascorbate levels and less induction of ascorbate peroxidases. Under field conditions, chaos exhibited better overall photosynthetic performance and had higher survival rates. Expression of the CAO gene may be regulated by a light-dependent chloroplastic redox signalling pathway, and was inhibited during acclimation to high light and chilling temperatures, simultaneously with induction of ascorbate peroxidases. It is concluded that the presence/absence of the CAO gene has an impact on photo-produced H2O2, lignification in the hypocotyls and on the plant’s susceptibility to photooxidative stress. Therefore, regulation of the CAO gene may be part of the plant’s system for acclimation to high light and chilling temperatures.},
	number = {1},
	urldate = {2021-06-11},
	journal = {Plant and Cell Physiology},
	author = {Klenell, Markus and Morita, Shigeto and Tiemblo-Olmo, Mercedes and Mühlenbock, Per and Karpinski, Stanislaw and Karpinska, Barbara},
	month = jan,
	year = {2005},
	pages = {118--129},
}

In this study, we have investigated the role of the CAO gene (coding for the chloroplast recognition particle cpSRP43) in the protection against and acclimation to environmental conditions that promote photooxidative stress. Deficiency of cpSRP43 in the Arabidopsis mutant chaos has been shown previously to lead to partial loss of a number of proteins of the photosystem II (PSII) antennae. In addition, as reported here, mutant plants have lower growth rates and reduced lignin contents under laboratory conditions. However, chaos seedlings showed significantly higher tolerance to photooxidative stress under both tightly controlled laboratory conditions and highly variable conditions in the field. This greater tolerance of chaos plants was manifested in less photooxidative damage together with faster growth recovery in young seedlings. It was also associated with a lower production of H2O2, lower ascorbate levels and less induction of ascorbate peroxidases. Under field conditions, chaos exhibited better overall photosynthetic performance and had higher survival rates. Expression of the CAO gene may be regulated by a light-dependent chloroplastic redox signalling pathway, and was inhibited during acclimation to high light and chilling temperatures, simultaneously with induction of ascorbate peroxidases. It is concluded that the presence/absence of the CAO gene has an impact on photo-produced H2O2, lignification in the hypocotyls and on the plant’s susceptibility to photooxidative stress. Therefore, regulation of the CAO gene may be part of the plant’s system for acclimation to high light and chilling temperatures.

@article{bechtold_influence_2005,
	title = {The influence of the light environment and photosynthesis on oxidative signalling responses in plant-biotrophic pathogen interactions},
	volume = {28},
	issn = {0140-7791},
	doi = {10/b2mf4v},
	abstract = {Plants grow in a constantly fluctuating environment, which has driven the evolution of a highly flexible metabolism and development necessary for their sessile lifestyle. In contrast to the situation in the natural world, the detailed dissection of the regulatory networks that govern plants' responses to abiotic insults and their interaction with pathogens have been studied almost exclusively in controlled environments where a single challenge has been applied. However, the question arises of how such pathways operate when the plant is subjected to multiple stresses, especially where the expression of overlapping gene sets and common signalling molecules, such as reactive oxygen species (ROS), are implicated. This review will focus on the responsiveness of leaves to their light environment and how this might influence both basal and induced resistance to infection by biotrophic pathogens. While several signalling pathways operate in a complex network of defence responses, the functioning of the salicylic acid (SA) signalling pathway will receive specific consideration. This is because information is becoming available of its role in abiotic stress responses and it dependency on light. This article covers several topics, some of which formerly have received scant attention. These include the effects of infection on photosynthetic performance and carbohydrate metabolism, the parallels between the induction of acclimation to high light and immunity to pathogens, the role of light in the functioning of the SA signalling pathway and the light sensitivity of lesion formation and the use of lesion mimic mutants and transgenic plants. Finally, a model is proposed that attempts to extrapolate these controlled environment-based studies to the functioning of defences against pathogens in a field-grown crop.},
	language = {English},
	number = {8},
	journal = {Plant Cell and Environment},
	author = {Bechtold, U. and Karpinski, S. and Mullineaux, P. M.},
	month = aug,
	year = {2005},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000230432100008},
	keywords = {arabidopsis-thaliana, cell-death, cucumber mosaic-virus, disease resistance, excitation energy, hydrogen-peroxide, lesion mimic mutants, light, photosynthesis, plant-pathogen interactions, reactive oxygen species, salicylic acid pathway, salicylic-acid, signalling, systemic acquired-resistance, transgenic tobacco plants, yeast-derived   invertase},
	pages = {1046--1055},
}

Plants grow in a constantly fluctuating environment, which has driven the evolution of a highly flexible metabolism and development necessary for their sessile lifestyle. In contrast to the situation in the natural world, the detailed dissection of the regulatory networks that govern plants' responses to abiotic insults and their interaction with pathogens have been studied almost exclusively in controlled environments where a single challenge has been applied. However, the question arises of how such pathways operate when the plant is subjected to multiple stresses, especially where the expression of overlapping gene sets and common signalling molecules, such as reactive oxygen species (ROS), are implicated. This review will focus on the responsiveness of leaves to their light environment and how this might influence both basal and induced resistance to infection by biotrophic pathogens. While several signalling pathways operate in a complex network of defence responses, the functioning of the salicylic acid (SA) signalling pathway will receive specific consideration. This is because information is becoming available of its role in abiotic stress responses and it dependency on light. This article covers several topics, some of which formerly have received scant attention. These include the effects of infection on photosynthetic performance and carbohydrate metabolism, the parallels between the induction of acclimation to high light and immunity to pathogens, the role of light in the functioning of the SA signalling pathway and the light sensitivity of lesion formation and the use of lesion mimic mutants and transgenic plants. Finally, a model is proposed that attempts to extrapolate these controlled environment-based studies to the functioning of defences against pathogens in a field-grown crop.

@article{weijers_maintenance_2005,
	title = {Maintenance of {Embryonic} {Auxin} {Distribution} for {Apical}-{Basal} {Patterning} by {PIN}-{FORMED}–{Dependent} {Auxin} {Transport} in {Arabidopsis}},
	volume = {17},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.105.034637},
	doi = {10/b3g9nd},
	abstract = {Molecular mechanisms of pattern formation in the plant embryo are not well understood. Recent molecular and cellular studies, in conjunction with earlier microsurgical, physiological, and genetic work, are now starting to define the outlines of a model where gradients of the signaling molecule auxin play a central role in embryo patterning. It is relatively clear how these gradients are established and interpreted, but how they are maintained is still unresolved. Here, we have studied the contributions of auxin biosynthesis, conjugation, and transport pathways to the maintenance of embryonic auxin gradients. Auxin homeostasis in the embryo was manipulated by region-specific conditional expression of indoleacetic acid-tryptophan monooxygenase or indoleacetic acid-lysine synthetase, bacterial enzymes for auxin biosynthesis or conjugation. Neither manipulation of auxin biosynthesis nor of auxin conjugation interfered with auxin gradients and patterning in the embryo. This result suggests a compensatory mechanism for buffering auxin gradients in the embryo. Chemical and genetic inhibition revealed that auxin transport activity, in particular that of the PIN-FORMED1 (PIN1) and PIN4 proteins, is a major factor in the maintenance of these gradients.},
	number = {9},
	urldate = {2021-06-11},
	journal = {The Plant Cell},
	author = {Weijers, Dolf and Sauer, Michael and Meurette, Olivier and Friml, Jiří and Ljung, Karin and Sandberg, Göran and Hooykaas, Paul and Offringa, Remko},
	month = sep,
	year = {2005},
	pages = {2517--2526},
}

Molecular mechanisms of pattern formation in the plant embryo are not well understood. Recent molecular and cellular studies, in conjunction with earlier microsurgical, physiological, and genetic work, are now starting to define the outlines of a model where gradients of the signaling molecule auxin play a central role in embryo patterning. It is relatively clear how these gradients are established and interpreted, but how they are maintained is still unresolved. Here, we have studied the contributions of auxin biosynthesis, conjugation, and transport pathways to the maintenance of embryonic auxin gradients. Auxin homeostasis in the embryo was manipulated by region-specific conditional expression of indoleacetic acid-tryptophan monooxygenase or indoleacetic acid-lysine synthetase, bacterial enzymes for auxin biosynthesis or conjugation. Neither manipulation of auxin biosynthesis nor of auxin conjugation interfered with auxin gradients and patterning in the embryo. This result suggests a compensatory mechanism for buffering auxin gradients in the embryo. Chemical and genetic inhibition revealed that auxin transport activity, in particular that of the PIN-FORMED1 (PIN1) and PIN4 proteins, is a major factor in the maintenance of these gradients.

@article{israelsson_tissue-specific_2005,
	title = {Tissue-specific localization of gibberellins and expression of gibberellin-biosynthetic and signaling genes in wood-forming tissues in aspen},
	volume = {44},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2005.02547.x},
	doi = {10/b9g6dq},
	abstract = {Bioactive gibberellins (GAs) are known regulators of shoot growth and development in plants. In an attempt to identify where GAs are formed, we have analyzed the expression patterns of six GA biosynthesis genes and two genes with predicted roles in GA signaling and responses in relation to measured levels of GAs. The analysis was based on tangential sections, giving tissue-specific resolution across the cambial region of aspen trees (Populus tremula). Gibberellin quantification by GC/MS-SRM showed that the bioactive GA1 and GA4 were predominantly located in the zone of expansion of xylem cells. Based on co-localization of the expression of the late GA biosynthesis gene GA 20-oxidase 1 and bioactive GAs, we suggest that de novo GA biosynthesis occurs in the expanding xylem. However, expression levels of the first committed GA biosynthesis enzyme, ent-copalyl diphosphate synthase, were high in the phloem, suggesting that a GA precursor(s) may be transported to the xylem. The expression of the GA signaling and response genes DELLA-like1 and GIP-like1 coincided well with sites of high bioactive GA levels. We therefore suggest that the main role of GA during wood formation is to regulate early stages of xylem differentiation, including cell elongation.},
	language = {en},
	number = {3},
	urldate = {2021-06-11},
	journal = {The Plant Journal},
	author = {Israelsson, Maria and Sundberg, Björn and Moritz, Thomas},
	year = {2005},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2005.02547.x},
	keywords = {DELLA, Populus, fiber, gibberellin-biosynthetic genes, gibberellins, wood formation},
	pages = {494--504},
}

Bioactive gibberellins (GAs) are known regulators of shoot growth and development in plants. In an attempt to identify where GAs are formed, we have analyzed the expression patterns of six GA biosynthesis genes and two genes with predicted roles in GA signaling and responses in relation to measured levels of GAs. The analysis was based on tangential sections, giving tissue-specific resolution across the cambial region of aspen trees (Populus tremula). Gibberellin quantification by GC/MS-SRM showed that the bioactive GA1 and GA4 were predominantly located in the zone of expansion of xylem cells. Based on co-localization of the expression of the late GA biosynthesis gene GA 20-oxidase 1 and bioactive GAs, we suggest that de novo GA biosynthesis occurs in the expanding xylem. However, expression levels of the first committed GA biosynthesis enzyme, ent-copalyl diphosphate synthase, were high in the phloem, suggesting that a GA precursor(s) may be transported to the xylem. The expression of the GA signaling and response genes DELLA-like1 and GIP-like1 coincided well with sites of high bioactive GA levels. We therefore suggest that the main role of GA during wood formation is to regulate early stages of xylem differentiation, including cell elongation.

@article{singh_cell_2005,
	title = {Cell adhesion in {Arabidopsis} thaliana is mediated by {ECTOPICALLY} {PARTING} {CELLS} 1 – a glycosyltransferase ({GT64}) related to the animal exostosins},
	volume = {43},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2005.02455.x},
	doi = {10/dnqqxd},
	abstract = {Despite the fact that several hundred glycosyltransferases have been identified from sequencing of plant genomes, the biological functions of only a handful have been established to date. A Poplar glycosyltransferase 64 (GT64) family member that is differentially expressed during the cell division and elongation phases of cambial growth was identified from previously generated transcript profiling of cambium tissues. The predicted Poplar GT64 protein has a closely related Arabidopsis homolog ECTOPICALLY PARTING CELLS (EPC1). Mutation of the EPC1 gene, one of three Arabidopsis GT64 family members, results in plants with a dramatically reduced growth habit, defects in vascular formation and reduced cell–cell adhesion properties in hypocotyl and cotyledon tissues. Secondary growth is enhanced in epc1 hypocotyl tissues and it is proposed that this results from the abnormal cell–cell adhesion within the cortical parenchyma cell layers. Loss of cell–cell contacts within cotyledon and leaf tissues is also proposed to account for vascular patterning defects and the fragile nature of epc1 tissues. The EPC1 protein thus plays a critical role during plant development in maintaining the integrity of organs via cell–cell adhesion, thereby providing mechanical strength and facilitating the movement of metabolites throughout the plant.},
	language = {en},
	number = {3},
	urldate = {2021-06-11},
	journal = {The Plant Journal},
	author = {Singh, Sunil Kumar and Eland, Cathlene and Harholt, Jesper and Scheller, Henrik Vibe and Marchant, Alan},
	year = {2005},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2005.02455.x},
	keywords = {Arabidopsis, cell adhesion, cell walls, glycosyltransferase},
	pages = {384--397},
}

Despite the fact that several hundred glycosyltransferases have been identified from sequencing of plant genomes, the biological functions of only a handful have been established to date. A Poplar glycosyltransferase 64 (GT64) family member that is differentially expressed during the cell division and elongation phases of cambial growth was identified from previously generated transcript profiling of cambium tissues. The predicted Poplar GT64 protein has a closely related Arabidopsis homolog ECTOPICALLY PARTING CELLS (EPC1). Mutation of the EPC1 gene, one of three Arabidopsis GT64 family members, results in plants with a dramatically reduced growth habit, defects in vascular formation and reduced cell–cell adhesion properties in hypocotyl and cotyledon tissues. Secondary growth is enhanced in epc1 hypocotyl tissues and it is proposed that this results from the abnormal cell–cell adhesion within the cortical parenchyma cell layers. Loss of cell–cell contacts within cotyledon and leaf tissues is also proposed to account for vascular patterning defects and the fragile nature of epc1 tissues. The EPC1 protein thus plays a critical role during plant development in maintaining the integrity of organs via cell–cell adhesion, thereby providing mechanical strength and facilitating the movement of metabolites throughout the plant.

@article{pineau_hca_2005,
	title = {hca: an {Arabidopsis} mutant exhibiting unusual cambial activity and altered vascular patterning},
	volume = {44},
	issn = {1365-313X},
	shorttitle = {hca},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2005.02526.x},
	doi = {10/c4jjf5},
	abstract = {By screening a T-DNA population of Arabidopsis mutants for alterations in inflorescence stem vasculature, we have isolated a mutant with a dramatic increase in vascular tissue development, characterized by a continuous ring of xylem/phloem. This phenotype is the consequence of premature and numerous cambial cell divisions in both the fascicular and interfascicular regions that result in the loss of the alternate vascular bundle/fiber organization typically observed in Arabidopsis stems. The mutant was therefore designated high cambial activity (hca). The hca mutation also resulted in pleiotropic effects including stunting and a delay in developmental events such as flowering and senescence. The physiological characterization of hca seedlings in vitro revealed an altered auxin and cytokinin response and, most strikingly, an enhanced sensitivity to cytokinin. These results were substantiated by comparative microarray analysis between hca and wild-type plants. The genetic analysis of hca indicated that the mutant phenotype was not tagged by the T-DNA and that the hca mutation segregated as a single recessive locus, mapping to the long arm of chromosome 4. We propose that hca is involved in mechanisms controlling the arrangement of vascular bundles throughout the plant by regulating the auxin–cytokinin sensitivity of vascular cambial cells. Thus, the hca mutant is a useful model for examining the genetic and hormonal control of cambial growth and differentiation.},
	language = {en},
	number = {2},
	urldate = {2021-06-11},
	journal = {The Plant Journal},
	author = {Pineau, Christophe and Freydier, Amandine and Ranocha, Philippe and Jauneau, Alain and Turner, Simon and Lemonnier, Gaëtan and Renou, Jean-Pierre and Tarkowski, Petr and Sandberg, Göran and Jouanin, Lise and Sundberg, Björn and Boudet, Alain-Michel and Goffner, Deborah and Pichon, Magalie},
	year = {2005},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2005.02526.x},
	keywords = {Arabidopsis thaliana, Complete Arabidopsis Transcriptome MicroArray (CATMA), cambium, cytokinin hypersensitivity, secondary xylem, vascular patterning},
	pages = {271--289},
}

By screening a T-DNA population of Arabidopsis mutants for alterations in inflorescence stem vasculature, we have isolated a mutant with a dramatic increase in vascular tissue development, characterized by a continuous ring of xylem/phloem. This phenotype is the consequence of premature and numerous cambial cell divisions in both the fascicular and interfascicular regions that result in the loss of the alternate vascular bundle/fiber organization typically observed in Arabidopsis stems. The mutant was therefore designated high cambial activity (hca). The hca mutation also resulted in pleiotropic effects including stunting and a delay in developmental events such as flowering and senescence. The physiological characterization of hca seedlings in vitro revealed an altered auxin and cytokinin response and, most strikingly, an enhanced sensitivity to cytokinin. These results were substantiated by comparative microarray analysis between hca and wild-type plants. The genetic analysis of hca indicated that the mutant phenotype was not tagged by the T-DNA and that the hca mutation segregated as a single recessive locus, mapping to the long arm of chromosome 4. We propose that hca is involved in mechanisms controlling the arrangement of vascular bundles throughout the plant by regulating the auxin–cytokinin sensitivity of vascular cambial cells. Thus, the hca mutant is a useful model for examining the genetic and hormonal control of cambial growth and differentiation.

@article{erikson_dsda_2005,
	title = {The {dsdA} gene from {Escherichia} coli provides a novel selectable marker for plant transformation},
	volume = {57},
	issn = {1573-5028},
	url = {https://doi.org/10.1007/s11103-004-7902-9},
	doi = {10/dzwnws},
	abstract = {Plants are sensitive to D-serine, but functional expression of the dsdA gene, encoding D-serine ammonia lyase, from Escherichia coli can alleviate this toxicity. Plants, in contrast to many other organisms, lack the common pathway for oxidative deamination of D-amino acids. This difference in metabolism has major consequences for plant responses to D-amino acids, since several D-amino acids are toxic to plants even at relatively low concentrations. Therefore, introducing an enzyme specific for a phytotoxic D-amino acid should generate a selectable characteristic that can be screened. Here we present the use of the dsdA gene as a selectable marker for transformation of Arabidopsis. D-serine ammonia lyase catalyses the deamination of D-serine into pyruvate, water and ammonium. dsdA transgenic seedlings can be clearly distinguished from wild type, having an unambiguous phenotype immediately following germination when selected on D-serine containing medium. The dsdA marker allows flexibility in application of the selective agent: it can be applied in sterile plates, in foliar sprays or in liquid culture. Selection with D-serine resistance was compared with selection based on kanamycin resistance, and was found to generate similar transformation frequencies but also to be more unambiguous, more rapid and more versatile with respect to the way the selective agent can be supplied.},
	language = {en},
	number = {3},
	urldate = {2021-06-11},
	journal = {Plant Molecular Biology},
	author = {Erikson, Oskar and Hertzberg, Magnus and Näsholm, Torgny},
	month = feb,
	year = {2005},
	pages = {425--433},
}

Plants are sensitive to D-serine, but functional expression of the dsdA gene, encoding D-serine ammonia lyase, from Escherichia coli can alleviate this toxicity. Plants, in contrast to many other organisms, lack the common pathway for oxidative deamination of D-amino acids. This difference in metabolism has major consequences for plant responses to D-amino acids, since several D-amino acids are toxic to plants even at relatively low concentrations. Therefore, introducing an enzyme specific for a phytotoxic D-amino acid should generate a selectable characteristic that can be screened. Here we present the use of the dsdA gene as a selectable marker for transformation of Arabidopsis. D-serine ammonia lyase catalyses the deamination of D-serine into pyruvate, water and ammonium. dsdA transgenic seedlings can be clearly distinguished from wild type, having an unambiguous phenotype immediately following germination when selected on D-serine containing medium. The dsdA marker allows flexibility in application of the selective agent: it can be applied in sterile plates, in foliar sprays or in liquid culture. Selection with D-serine resistance was compared with selection based on kanamycin resistance, and was found to generate similar transformation frequencies but also to be more unambiguous, more rapid and more versatile with respect to the way the selective agent can be supplied.

@article{keskitalo_cellular_2005,
	title = {A {Cellular} {Timetable} of {Autumn} {Senescence}},
	volume = {139},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.105.066845},
	doi = {10/cdw8rv},
	abstract = {We have studied autumn leaf senescence in a free-growing aspen (Populus tremula) by following changes in pigment, metabolite and nutrient content, photosynthesis, and cell and organelle integrity. The senescence process started on September 11, 2003, apparently initiated solely by the photoperiod, and progressed steadily without any obvious influence of other environmental signals. For example, after this date, senescing leaves accumulated anthocyanins in response to conditions inducing photooxidative stress, but at the beginning of September the leaves did not. Degradation of leaf constituents took place over an 18-d period, and, although the cells in each leaf did not all senesce in parallel, senescence in the tree as a whole was synchronous. Lutein and β-carotene were degraded in parallel with chlorophyll, whereas neoxanthin and the xanthophyll cycle pigments were retained longer. Chloroplasts in each cell were rapidly converted to gerontoplasts and many, although not all, cells died. From September 19, when chlorophyll levels had dropped by 50\%, mitochondrial respiration provided the energy for nutrient remobilization. Remobilization seemed to stop on September 29, probably due to the cessation of phloem transport, but, up to abscission of the last leaves (over 1 week later), some cells were metabolically active and had chlorophyll-containing gerontoplasts. About 80\% of the nitrogen and phosphorus was remobilized, and on September 29 a sudden change occurred in the δ15n of the cellular content, indicating that volatile compounds may have been released.},
	number = {4},
	urldate = {2021-06-11},
	journal = {Plant Physiology},
	author = {Keskitalo, Johanna and Bergquist, Gustaf and Gardeström, Per and Jansson, Stefan},
	month = dec,
	year = {2005},
	pages = {1635--1648},
}

We have studied autumn leaf senescence in a free-growing aspen (Populus tremula) by following changes in pigment, metabolite and nutrient content, photosynthesis, and cell and organelle integrity. The senescence process started on September 11, 2003, apparently initiated solely by the photoperiod, and progressed steadily without any obvious influence of other environmental signals. For example, after this date, senescing leaves accumulated anthocyanins in response to conditions inducing photooxidative stress, but at the beginning of September the leaves did not. Degradation of leaf constituents took place over an 18-d period, and, although the cells in each leaf did not all senesce in parallel, senescence in the tree as a whole was synchronous. Lutein and β-carotene were degraded in parallel with chlorophyll, whereas neoxanthin and the xanthophyll cycle pigments were retained longer. Chloroplasts in each cell were rapidly converted to gerontoplasts and many, although not all, cells died. From September 19, when chlorophyll levels had dropped by 50%, mitochondrial respiration provided the energy for nutrient remobilization. Remobilization seemed to stop on September 29, probably due to the cessation of phloem transport, but, up to abscission of the last leaves (over 1 week later), some cells were metabolically active and had chlorophyll-containing gerontoplasts. About 80% of the nitrogen and phosphorus was remobilized, and on September 29 a sudden change occurred in the δ15n of the cellular content, indicating that volatile compounds may have been released.

@article{aspeborg_carbohydrate-active_2005,
	title = {Carbohydrate-{Active} {Enzymes} {Involved} in the {Secondary} {Cell} {Wall} {Biogenesis} in {Hybrid} {Aspen}},
	volume = {137},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.104.055087},
	doi = {10/fk2nz4},
	abstract = {Wood formation is a fundamental biological process with significant economic interest. While lignin biosynthesis is currently relatively well understood, the pathways leading to the synthesis of the key structural carbohydrates in wood fibers remain obscure. We have used a functional genomics approach to identify enzymes involved in carbohydrate biosynthesis and remodeling during xylem development in the hybrid aspen Populus tremula × tremuloides. Microarrays containing cDNA clones from different tissue-specific libraries were hybridized with probes obtained from narrow tissue sections prepared by cryosectioning of the developing xylem. Bioinformatic analyses using the sensitive tools developed for carbohydrate-active enzymes allowed the identification of 25 xylem-specific glycosyltransferases belonging to the Carbohydrate-Active EnZYme families GT2, GT8, GT14, GT31, GT43, GT47, and GT61 and nine glycosidases (or transglycosidases) belonging to the Carbohydrate-Active EnZYme families GH9, GH10, GH16, GH17, GH19, GH28, GH35, and GH51. While no genes encoding either polysaccharide lyases or carbohydrate esterases were found among the secondary wall-specific genes, one putative O-acetyltransferase was identified. These wood-specific enzyme genes constitute a valuable resource for future development of engineered fibers with improved performance in different applications.},
	number = {3},
	urldate = {2021-06-11},
	journal = {Plant Physiology},
	author = {Aspeborg, Henrik and Schrader, Jarmo and Coutinho, Pedro M. and Stam, Mark and Kallas, Åsa and Djerbi, Soraya and Nilsson, Peter and Denman, Stuart and Amini, Bahram and Sterky, Fredrik and Master, Emma and Sandberg, Göran and Mellerowicz, Ewa and Sundberg, Björn and Henrissat, Bernard and Teeri, Tuula T.},
	month = mar,
	year = {2005},
	pages = {983--997},
}

Wood formation is a fundamental biological process with significant economic interest. While lignin biosynthesis is currently relatively well understood, the pathways leading to the synthesis of the key structural carbohydrates in wood fibers remain obscure. We have used a functional genomics approach to identify enzymes involved in carbohydrate biosynthesis and remodeling during xylem development in the hybrid aspen Populus tremula × tremuloides. Microarrays containing cDNA clones from different tissue-specific libraries were hybridized with probes obtained from narrow tissue sections prepared by cryosectioning of the developing xylem. Bioinformatic analyses using the sensitive tools developed for carbohydrate-active enzymes allowed the identification of 25 xylem-specific glycosyltransferases belonging to the Carbohydrate-Active EnZYme families GT2, GT8, GT14, GT31, GT43, GT47, and GT61 and nine glycosidases (or transglycosidases) belonging to the Carbohydrate-Active EnZYme families GH9, GH10, GH16, GH17, GH19, GH28, GH35, and GH51. While no genes encoding either polysaccharide lyases or carbohydrate esterases were found among the secondary wall-specific genes, one putative O-acetyltransferase was identified. These wood-specific enzyme genes constitute a valuable resource for future development of engineered fibers with improved performance in different applications.

@article{marin_stand_2005,
	title = {Stand dynamics and basal area change in a tropical dry forest reserve in {Nicaragua}},
	volume = {208},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112704008278},
	doi = {10/ck4828},
	abstract = {Stand dynamics and basal area change were determined in deciduous and gallery forest types at the Chacocente Wildlife Reserve, Nicaragua. All stems ≥10cmdbh in 4ha were tagged and identified by species and measured in 1993 and 2000. In year 2000 totally 519 stemsha−1 with a basal area of 15.62m2ha−1 were recorded in the deciduous forest type and corresponding figures were 308 stemsha−1 and 23.13m2ha−1 for the gallery forest type. Comparison of stem diameter and basal area distribution during this study period revealed no changes. Both forests types had a reversed J-shape diameter distribution dominated ({\textgreater}80\%) by small stems ({\textless}30cmdbh). In the deciduous forest small stems contributed to more than half of the basal area, whereas in the gallery forest large stems ({\textgreater}70cmdbh) contributed to almost half the basal area. Based on a logarithmic model the mortality and recruitment rates were calculated at 4.5 and 2.5\%year−1, respectively, in the deciduous forest type and 4.2 and 4.0\% in the gallery forest type. The decrease in stand density in the deciduous forest type was significant whereas it was not the case for the gallery forest type. There was also a significant decrease in basal area of 1.2\%year−1 in the deciduous forest and no change in the gallery forest. The recorded median diameter (dbh) increment was 0.14cmyear−1 with a range of 1.21cmyear−1 in the deciduous forest type and corresponding figures for the gallery forest were 0.24cmyear−1 and 0.71cmyear−1. Three of the five most common species in the deciduous forest, Lonchocarpus minimiflorus, Gyrocarpus americanus and Stemmadenia ovovata had mortality rates above 9\%. Although L. minimiflorus and S. ovovata had recruitment rates above average the net balance was negative. Among the five most common species only Tabebuia ochracea a timber species had an annual recruitment higher than its mortality rate. Non-timber species as a group had the largest calculated negative balance between mortality and recruitment as well as between loss and gain of basal area indicating a possible anthropogenic influence. In the gallery forest Capparis pachaca was the only species, out of the most common, with a positive annual balance. In both forest types there was a higher than average calculated recruitment and basal area growth for species with no local use.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {Forest Ecology and Management},
	author = {Marín, Guillermo Castro and Nygård, Robert and Rivas, Benigno Gonzales and Oden, Per Christer},
	month = apr,
	year = {2005},
	keywords = {Chacocente Wildlife Reserve, Diameter increment, Dry deciduous forest, Gain, Gallery forest, Ingrowth, Loss, Mortality, Recruitment},
	pages = {63--75},
}

Stand dynamics and basal area change were determined in deciduous and gallery forest types at the Chacocente Wildlife Reserve, Nicaragua. All stems ≥10cmdbh in 4ha were tagged and identified by species and measured in 1993 and 2000. In year 2000 totally 519 stemsha−1 with a basal area of 15.62m2ha−1 were recorded in the deciduous forest type and corresponding figures were 308 stemsha−1 and 23.13m2ha−1 for the gallery forest type. Comparison of stem diameter and basal area distribution during this study period revealed no changes. Both forests types had a reversed J-shape diameter distribution dominated (\textgreater80%) by small stems (\textless30cmdbh). In the deciduous forest small stems contributed to more than half of the basal area, whereas in the gallery forest large stems (\textgreater70cmdbh) contributed to almost half the basal area. Based on a logarithmic model the mortality and recruitment rates were calculated at 4.5 and 2.5%year−1, respectively, in the deciduous forest type and 4.2 and 4.0% in the gallery forest type. The decrease in stand density in the deciduous forest type was significant whereas it was not the case for the gallery forest type. There was also a significant decrease in basal area of 1.2%year−1 in the deciduous forest and no change in the gallery forest. The recorded median diameter (dbh) increment was 0.14cmyear−1 with a range of 1.21cmyear−1 in the deciduous forest type and corresponding figures for the gallery forest were 0.24cmyear−1 and 0.71cmyear−1. Three of the five most common species in the deciduous forest, Lonchocarpus minimiflorus, Gyrocarpus americanus and Stemmadenia ovovata had mortality rates above 9%. Although L. minimiflorus and S. ovovata had recruitment rates above average the net balance was negative. Among the five most common species only Tabebuia ochracea a timber species had an annual recruitment higher than its mortality rate. Non-timber species as a group had the largest calculated negative balance between mortality and recruitment as well as between loss and gain of basal area indicating a possible anthropogenic influence. In the gallery forest Capparis pachaca was the only species, out of the most common, with a positive annual balance. In both forest types there was a higher than average calculated recruitment and basal area growth for species with no local use.

@article{lindgren_optimal_2005,
	title = {Optimal clone number for seed orchards with tested clones},
	volume = {54},
	issn = {0037-5349},
	doi = {10/gkj9xs},
	abstract = {The optimal number of clones in seed orchards is discussed. A model is constructed to maximize a goodness criterion ("benefit") for seed orchards. This criterion is a function of. 1) the number of tested genotypes available for selection and planted in seed orchard; 2) the contribution to pollination from: a) the ramet itself; b) the closest neighbors; c) the rest of the orchard and sources outside the orchard (contamination); 3) variation among genotypes for fertility; 4) frequency of selfing; 5) production of selfed genotypes; 6) gene diversity (=status number); 7) influence of contamination; 8) genetic variation among candidates; 9) correlation between selection criterion (e.g. height in progeny test) and value for forestry (e.g. production in forests from the orchard); and 10) the number of clones harvested. Numeric values of the entries are discussed, and values were chosen to be relevant for scenarios with Swedish conifers (focusing on Scots pine) and for loblolly pine. Benefit was maximized considering the number of clones. The optimum was 16 clones for the Swedish scenario, while less for the loblolly pine scenario. The optimum was rather broad, thus it is not essential to deploy the exact optimum, and an approximate optimum will do. A sensitivity analyses was performed to evaluate the importance of the likely uncertainty and variation in different entries. Quantification of the benefit of gene diversity is important. Other significant considerations are the genetic variance in the goal character and the ability to predict it, as well as the impact of selfing and the variation in reproductive success between clones. Twenty clones is suggested as a thumb rule for Swedish conifers.},
	language = {English},
	number = {2},
	journal = {Silvae Genetica},
	author = {Lindgren, D. and Prescher, F.},
	year = {2005},
	note = {Place: Warsaw
Publisher: Sciendo
WOS:000231705900007},
	keywords = {clone number, depression, diversity, gene diversity, genetic gain, pollination, relatedness, seed   orchard, selfing, tree},
	pages = {80--92},
}

The optimal number of clones in seed orchards is discussed. A model is constructed to maximize a goodness criterion ("benefit") for seed orchards. This criterion is a function of. 1) the number of tested genotypes available for selection and planted in seed orchard; 2) the contribution to pollination from: a) the ramet itself; b) the closest neighbors; c) the rest of the orchard and sources outside the orchard (contamination); 3) variation among genotypes for fertility; 4) frequency of selfing; 5) production of selfed genotypes; 6) gene diversity (=status number); 7) influence of contamination; 8) genetic variation among candidates; 9) correlation between selection criterion (e.g. height in progeny test) and value for forestry (e.g. production in forests from the orchard); and 10) the number of clones harvested. Numeric values of the entries are discussed, and values were chosen to be relevant for scenarios with Swedish conifers (focusing on Scots pine) and for loblolly pine. Benefit was maximized considering the number of clones. The optimum was 16 clones for the Swedish scenario, while less for the loblolly pine scenario. The optimum was rather broad, thus it is not essential to deploy the exact optimum, and an approximate optimum will do. A sensitivity analyses was performed to evaluate the importance of the likely uncertainty and variation in different entries. Quantification of the benefit of gene diversity is important. Other significant considerations are the genetic variance in the goal character and the ability to predict it, as well as the impact of selfing and the variation in reproductive success between clones. Twenty clones is suggested as a thumb rule for Swedish conifers.

@article{gelhaye_specific_2005,
	title = {A specific form of thioredoxin h occurs in plant mitochondria and regulates the alternative oxidase (vol 101, pg 14545, 2004)},
	volume = {102},
	issn = {0027-8424},
	doi = {10/drv3tz},
	language = {English},
	number = {10},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Gelhaye, E. and Rouhier, N. and Gerard, J. and Jolivet, Y. and Gualberto, J. and Navrot, N. and Ohlsson, P. I. and Wingsle, G. and Hirasawa, M. and Knaff, D. B. and Wang, H. M. and Dizengremel, P. and Meyer, Y. and Jacquot, J. P.},
	month = mar,
	year = {2005},
	note = {Place: Washington
Publisher: Natl Acad Sciences
WOS:000227533100066},
	pages = {3886--3886},
}

@article{bykova_interaction_2005,
	title = {Interaction between photorespiration and respiration in transgenic potato plants with antisense reduction in glycine decarboxylase},
	volume = {222},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s00425-005-1505-9},
	doi = {10/dxgd5p},
	abstract = {Potato (Solanum tuberosum L. cv. Désirée) plants with an antisense reduction in the P-protein of the glycine decarboxylase complex (GDC) were used to study the interaction between respiration and photorespiration. Mitochondria isolated from transgenic plants had a decreased capacity for glycine oxidation and glycine accumulated in the leaves. Malate consumption increased in leaves of GDC deficient plants and the capacity for malate and NADH oxidation increased in isolated mitochondria. A lower level of alternative oxidase protein and decreased partitioning of electrons to the alternative pathway was found in these plants. The adenylate status was altered in protoplasts from transgenic plants, most notably the chloroplastic ATP/ADP ratio increased. The lower capacity for photorespiration in leaves of GDC deficient plants was compensated for by increased respiratory decarboxylations in the light. This is interpreted as a decreased light suppression of the tricarboxylic acid cycle in GDC deficient plants in comparison to wild-type plants. The results support the view that respiratory decarboxylations in the light are restricted at the level of the pyruvate dehydrogenase complex and/or isocitrate dehydrogenase and that this effect is likely to be mediated by mitochondrial photorespiratory products.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {Planta},
	author = {Bykova, Natalia V. and Keerberg, Olav and Pärnik, Tiit and Bauwe, Hermann and Gardeström, Per},
	month = sep,
	year = {2005},
	pages = {130--140},
}

Potato (Solanum tuberosum L. cv. Désirée) plants with an antisense reduction in the P-protein of the glycine decarboxylase complex (GDC) were used to study the interaction between respiration and photorespiration. Mitochondria isolated from transgenic plants had a decreased capacity for glycine oxidation and glycine accumulated in the leaves. Malate consumption increased in leaves of GDC deficient plants and the capacity for malate and NADH oxidation increased in isolated mitochondria. A lower level of alternative oxidase protein and decreased partitioning of electrons to the alternative pathway was found in these plants. The adenylate status was altered in protoplasts from transgenic plants, most notably the chloroplastic ATP/ADP ratio increased. The lower capacity for photorespiration in leaves of GDC deficient plants was compensated for by increased respiratory decarboxylations in the light. This is interpreted as a decreased light suppression of the tricarboxylic acid cycle in GDC deficient plants in comparison to wild-type plants. The results support the view that respiratory decarboxylations in the light are restricted at the level of the pyruvate dehydrogenase complex and/or isocitrate dehydrogenase and that this effect is likely to be mediated by mitochondrial photorespiratory products.

@article{overmyer_ozone-induced_2005,
	title = {Ozone-{Induced} {Programmed} {Cell} {Death} in the {Arabidopsis} radical-induced cell death1 {Mutant}},
	volume = {137},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.104.055681},
	doi = {10/dqjtb3},
	abstract = {Short, high-concentration peaks of the atmospheric pollutant ozone (O3) cause the formation of cell death lesions on the leaves of sensitive plants. Numerous similarities between the plant responses to O3 and pathogens suggest that O3 triggers hypersensitive response-like programmed cell death (PCD). We examined O3 and superoxide-induced cell death in the O3-sensitive radical-induced cell death1 (rcd1) mutant. Dying cells in O3-exposed rcd1 exhibited several of the typical morphological characteristics of the hypersensitive response and PCD. Double-mutant analyses indicated a requirement for salicylic acid and the function of the cyclic nucleotide-gated ion channel AtCNGC2 in cell death. Furthermore, a requirement for ATPases, kinases, transcription, Ca2+ flux, caspase-like proteolytic activity, and also one or more phenylmethylsulfonyl fluoride-sensitive protease activities was shown for the development of cell death lesions in rcd1. Furthermore, mitogen-activated protein kinases showed differential activation patterns in rcd1 and Columbia. Taken together, these results directly demonstrate the induction of PCD by O3.},
	number = {3},
	urldate = {2021-06-11},
	journal = {Plant Physiology},
	author = {Overmyer, Kirk and Brosché, Mikael and Pellinen, Riikka and Kuittinen, Tero and Tuominen, Hannele and Ahlfors, Reetta and Keinänen, Markku and Saarma, Mart and Scheel, Dierk and Kangasjärvi, Jaakko},
	month = mar,
	year = {2005},
	pages = {1092--1104},
}

Short, high-concentration peaks of the atmospheric pollutant ozone (O3) cause the formation of cell death lesions on the leaves of sensitive plants. Numerous similarities between the plant responses to O3 and pathogens suggest that O3 triggers hypersensitive response-like programmed cell death (PCD). We examined O3 and superoxide-induced cell death in the O3-sensitive radical-induced cell death1 (rcd1) mutant. Dying cells in O3-exposed rcd1 exhibited several of the typical morphological characteristics of the hypersensitive response and PCD. Double-mutant analyses indicated a requirement for salicylic acid and the function of the cyclic nucleotide-gated ion channel AtCNGC2 in cell death. Furthermore, a requirement for ATPases, kinases, transcription, Ca2+ flux, caspase-like proteolytic activity, and also one or more phenylmethylsulfonyl fluoride-sensitive protease activities was shown for the development of cell death lesions in rcd1. Furthermore, mitogen-activated protein kinases showed differential activation patterns in rcd1 and Columbia. Taken together, these results directly demonstrate the induction of PCD by O3.

@article{zida_germination_2005,
	title = {Germination requirements of seeds of four woody species from the {Sudanian} savanna in {Burkina} {Faso}, {West} {Africa}},
	volume = {33},
	doi = {10/f3p6db},
	abstract = {The germination requirements of seeds of four savanna tree species, Burkea africana, Detarium microcarpum, Entada africana and Pterocarpus erinaceus, were investigated. Seeds of all species except P. erinaceus were subjected to mechanical scarification,
sulphuric acid or hot water treatments. Seeds of all four species were incubated under different constant temperatures of 20°C to 40°C, in light or darkness, or exposed to various dry heat treatments. The results show that mechanical scarification and exposure to sulphuric acid for
15 and 20 minutes resulted in significantly higher germination of B. africana seeds. Scarified and non-scarified seeds of D. microcarpum and E. africana germinated close to 100\%; confirming that seeds of these species are not dormant and dispersed seeds can readily germinate
provided that favorable germination conditions exist. Seeds of all species germinated equally well in light and darkness and the optimal germination temperature ranged between 25 and 35°C except E. africana seeds that germinated well at all temperature regimes. For all dry heat
treatments, germination was high for E. africana followed by D. microcarpum, P. erinaceus and the lowest being for B. africana seeds. High temperature heat shock (90 and 100°C) was found detrimental to the germination of seeds of all species.},
	number = {3},
	journal = {Seed Science and Technology},
	author = {Zida, D. and Tigabu, M. and Sawadogo, L. and Oden, P.C.},
	month = oct,
	year = {2005},
	pages = {581--593},
}

The germination requirements of seeds of four savanna tree species, Burkea africana, Detarium microcarpum, Entada africana and Pterocarpus erinaceus, were investigated. Seeds of all species except P. erinaceus were subjected to mechanical scarification, sulphuric acid or hot water treatments. Seeds of all four species were incubated under different constant temperatures of 20°C to 40°C, in light or darkness, or exposed to various dry heat treatments. The results show that mechanical scarification and exposure to sulphuric acid for 15 and 20 minutes resulted in significantly higher germination of B. africana seeds. Scarified and non-scarified seeds of D. microcarpum and E. africana germinated close to 100%; confirming that seeds of these species are not dormant and dispersed seeds can readily germinate provided that favorable germination conditions exist. Seeds of all species germinated equally well in light and darkness and the optimal germination temperature ranged between 25 and 35°C except E. africana seeds that germinated well at all temperature regimes. For all dry heat treatments, germination was high for E. africana followed by D. microcarpum, P. erinaceus and the lowest being for B. africana seeds. High temperature heat shock (90 and 100°C) was found detrimental to the germination of seeds of all species.

@article{tigabu_identification_2005,
	title = {Identification of seed sources and parents of {Pinus} sylvestris {L}. using visible–near infrared reflectance spectra and multivariate analysis},
	volume = {19},
	issn = {1432-2285},
	url = {https://doi.org/10.1007/s00468-005-0408-5},
	doi = {10/dnnsgc},
	abstract = {The potential of visible (VIS) and near infrared (NIR) spectroscopy for identifying seed sources and parents of Pinus sylvestris L. was studied. Seeds of a single family (clones AC1005 × BD1178) collected from three localities in Sweden—Sävar (north), Röskär (central) and Degeberga (south)—and seeds from four maternal (clone no. BD1032, AC1014, BD1178 and AC1005) and four paternal (Y3020, BD1178, AC1014 and BD1032) parents were used to evaluate the method. VIS and NIR reflectance spectra were recorded on individual seeds using a NIRSystems Model 6500 spectrometer from 400 to 2,498 nm with a resolution of 2 nm. The VIS + NIR spectroscopic data were pre-treated with multiplicative signal correction, and analysed by soft independent modelling of class analogy (SIMCA) and partial least squares-discriminant analysis (PLS-DA). The computed models were later applied to classify samples in the external test sets. The results show that seed sources were identified with 100\% classification accuracy using PLS-DA models in the VIS + NIR, VIS and NIR regions. The average classification accuracy for maternal parents ranged from 92\% to 96\%, while paternal parents were identified with 91.2–96\% accuracies. The classification accuracy using the SIMCA approach was relatively low for seed sources as well as maternal and paternal parents. It can be concluded that VIS + NIR spectroscopy could be employed as a rapid and non-destructive method for monitoring putative seed sources. The result underscores the prospect of the technique for characterizing seeds based on genotype, thereby serving as a tool in tree improvement and breeding.},
	language = {en},
	number = {4},
	urldate = {2021-06-11},
	journal = {Trees},
	author = {Tigabu, Mulualem and Oden, Per Christer and Lindgren, Dag},
	month = jun,
	year = {2005},
	pages = {468--476},
}

The potential of visible (VIS) and near infrared (NIR) spectroscopy for identifying seed sources and parents of Pinus sylvestris L. was studied. Seeds of a single family (clones AC1005 × BD1178) collected from three localities in Sweden—Sävar (north), Röskär (central) and Degeberga (south)—and seeds from four maternal (clone no. BD1032, AC1014, BD1178 and AC1005) and four paternal (Y3020, BD1178, AC1014 and BD1032) parents were used to evaluate the method. VIS and NIR reflectance spectra were recorded on individual seeds using a NIRSystems Model 6500 spectrometer from 400 to 2,498 nm with a resolution of 2 nm. The VIS + NIR spectroscopic data were pre-treated with multiplicative signal correction, and analysed by soft independent modelling of class analogy (SIMCA) and partial least squares-discriminant analysis (PLS-DA). The computed models were later applied to classify samples in the external test sets. The results show that seed sources were identified with 100% classification accuracy using PLS-DA models in the VIS + NIR, VIS and NIR regions. The average classification accuracy for maternal parents ranged from 92% to 96%, while paternal parents were identified with 91.2–96% accuracies. The classification accuracy using the SIMCA approach was relatively low for seed sources as well as maternal and paternal parents. It can be concluded that VIS + NIR spectroscopy could be employed as a rapid and non-destructive method for monitoring putative seed sources. The result underscores the prospect of the technique for characterizing seeds based on genotype, thereby serving as a tool in tree improvement and breeding.

@article{bollard_comparative_2005,
	title = {Comparative metabonomics of differential hydrazine toxicity in the rat and mouse},
	volume = {204},
	issn = {0041-008X},
	url = {https://www.sciencedirect.com/science/article/pii/S0041008X04004119},
	doi = {10/d7wn4p},
	abstract = {Interspecies variation between rats and mice has been studied for hydrazine toxicity using a novel metabonomics approach. Hydrazine hydrochloride was administered to male Sprague–Dawley rats (30 mg/kg, n = 10 and 90 mg/kg, n = 10) and male B6C3F mice (100 mg/kg, n = 8 and 250 mg/kg, n = 8) by oral gavage. In each species, the high dose was selected to produce the major histopathologic effect, hepatocellular lipid accumulation. Urine samples were collected at sequential time points up to 168 h post dose and analyzed by 1H NMR spectroscopy. The metabolites of hydrazine, namely diacetyl hydrazine and 1,4,5,6-tetrahydro-6-oxo-3-pyridazine carboxylic acid (THOPC), were detected in both the rat and mouse urine samples. Monoacetyl hydrazine was detected only in urine samples from the rat and its absence in the urine of the mouse was attributed to a higher activity of N-acetyl transferases in the mouse compared with the rat. Differential metabolic effects observed between the two species included elevated urinary β-alanine, 3-d-hydroxybutyrate, citrulline, N-acetylcitrulline, and reduced trimethylamine-N-oxide excretion unique to the rat. Metabolic principal component (PC) trajectories highlighted the greater degree of toxic response in the rat. A data scaling method, scaled to maximum aligned and reduced trajectories (SMART) analysis, was used to remove the differences between the metabolic starting positions of the rat and mouse and varying magnitudes of effect, to facilitate comparison of the response geometries between the rat and mouse. Mice followed “biphasic” open PC trajectories, with incomplete recovery 7 days after dosing, whereas rats followed closed “hairpin” time profiles, indicating functional reversibility. The greater magnitude of metabolic effects observed in the rat was supported by the more pronounced effect on liver pathology in the rat when compared with the mouse.},
	language = {en},
	number = {2},
	urldate = {2021-06-11},
	journal = {Toxicology and Applied Pharmacology},
	author = {Bollard, Mary E. and Keun, Hector C. and Beckonert, Olaf and Ebbels, Tim M. D. and Antti, Henrik and Nicholls, Andrew W. and Shockcor, John P. and Cantor, Glenn H. and Stevens, Greg and Lindon, John C. and Holmes, Elaine and Nicholson, Jeremy K.},
	month = apr,
	year = {2005},
	keywords = {Hydrazine toxicity, Metabonomic analysis, Mouse, Rat},
	pages = {135--151},
}

Interspecies variation between rats and mice has been studied for hydrazine toxicity using a novel metabonomics approach. Hydrazine hydrochloride was administered to male Sprague–Dawley rats (30 mg/kg, n = 10 and 90 mg/kg, n = 10) and male B6C3F mice (100 mg/kg, n = 8 and 250 mg/kg, n = 8) by oral gavage. In each species, the high dose was selected to produce the major histopathologic effect, hepatocellular lipid accumulation. Urine samples were collected at sequential time points up to 168 h post dose and analyzed by 1H NMR spectroscopy. The metabolites of hydrazine, namely diacetyl hydrazine and 1,4,5,6-tetrahydro-6-oxo-3-pyridazine carboxylic acid (THOPC), were detected in both the rat and mouse urine samples. Monoacetyl hydrazine was detected only in urine samples from the rat and its absence in the urine of the mouse was attributed to a higher activity of N-acetyl transferases in the mouse compared with the rat. Differential metabolic effects observed between the two species included elevated urinary β-alanine, 3-d-hydroxybutyrate, citrulline, N-acetylcitrulline, and reduced trimethylamine-N-oxide excretion unique to the rat. Metabolic principal component (PC) trajectories highlighted the greater degree of toxic response in the rat. A data scaling method, scaled to maximum aligned and reduced trajectories (SMART) analysis, was used to remove the differences between the metabolic starting positions of the rat and mouse and varying magnitudes of effect, to facilitate comparison of the response geometries between the rat and mouse. Mice followed “biphasic” open PC trajectories, with incomplete recovery 7 days after dosing, whereas rats followed closed “hairpin” time profiles, indicating functional reversibility. The greater magnitude of metabolic effects observed in the rat was supported by the more pronounced effect on liver pathology in the rat when compared with the mouse.

@article{wigge_integration_2005,
	title = {Integration of spatial and temporal information during floral induction in {Arabidopsis}},
	volume = {309},
	issn = {1095-9203},
	doi = {10/c6nzdx},
	abstract = {Flowering of Arabidopsis is regulated by several environmental and endogenous signals. An important integrator of these inputs is the FLOWERING LOCUS T (FT) gene, which encodes a small, possibly mobile protein. A primary response to floral induction is the activation of FT RNA expression in leaves. Because flowers form at a distant site, the shoot apex, these data suggest that FT primarily controls the timing of flowering. Integration of temporal and spatial information is mediated in part by the bZIP transcription factor FD, which is already expressed at the shoot apex before floral induction. A complex of FT and FD proteins in turn can activate floral identity genes such as APETALA1 (AP1).},
	language = {eng},
	number = {5737},
	journal = {Science (New York, N.Y.)},
	author = {Wigge, Philip A. and Kim, Min Chul and Jaeger, Katja E. and Busch, Wolfgang and Schmid, Markus and Lohmann, Jan U. and Weigel, Detlef},
	month = aug,
	year = {2005},
	pmid = {16099980},
	keywords = {Arabidopsis, Arabidopsis Proteins, Chromatin Immunoprecipitation, DNA-Binding Proteins, Flowers, Gene Expression Regulation, Plant, Homeodomain Proteins, MADS Domain Proteins, Models, Biological, Mutation, Oligonucleotide Array Sequence Analysis, Phenotype, Plant Leaves, Plant Proteins, Plant Shoots, Protein Interaction Mapping, Recombinant Fusion Proteins, Signal Transduction, Time Factors, Transcription Factors, Transcription, Genetic, Two-Hybrid System Techniques},
	pages = {1056--1059},
}

Flowering of Arabidopsis is regulated by several environmental and endogenous signals. An important integrator of these inputs is the FLOWERING LOCUS T (FT) gene, which encodes a small, possibly mobile protein. A primary response to floral induction is the activation of FT RNA expression in leaves. Because flowers form at a distant site, the shoot apex, these data suggest that FT primarily controls the timing of flowering. Integration of temporal and spatial information is mediated in part by the bZIP transcription factor FD, which is already expressed at the shoot apex before floral induction. A complex of FT and FD proteins in turn can activate floral identity genes such as APETALA1 (AP1).

@article{wadenback_comparison_2005,
	title = {Comparison of standard exponential and linear techniques to amplify small {cDNA} samples for microarrays},
	volume = {6},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/1471-2164-6-61},
	doi = {10/fmgwt5},
	abstract = {The need to perform microarray experiments with small amounts of tissue has led to the development of several protocols for amplifying the target transcripts. The use of different amplification protocols could affect the comparability of microarray experiments.},
	number = {1},
	urldate = {2021-06-11},
	journal = {BMC Genomics},
	author = {Wadenbäck, Johan and Clapham, David H. and Craig, Deborah and Sederoff, Ronald and Peter, Gary F. and von Arnold, Sara and Egertsdotter, Ulrika},
	month = may,
	year = {2005},
	keywords = {Amplification Method, Linear Amplification, Percentage Unit, Pinus Taeda, Technical Repeat},
	pages = {61},
}

The need to perform microarray experiments with small amounts of tissue has led to the development of several protocols for amplifying the target transcripts. The use of different amplification protocols could affect the comparability of microarray experiments.

@article{taylor_transcriptome_2005,
	title = {The transcriptome of {Populus} in elevated {CO2}},
	volume = {167},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/j.1469-8137.2005.01450.x},
	doi = {10/d7g7mz},
	abstract = {• The consequences of increasing atmospheric carbon dioxide for long-term adaptation of forest ecosystems remain uncertain, with virtually no studies undertaken at the genetic level. A global analysis using cDNA microarrays was conducted following 6 yr exposure of Populus × euramericana (clone I-214) to elevated [CO2] in a FACE (free-air CO2 enrichment) experiment. • Gene expression was sensitive to elevated [CO2] but the response depended on the developmental age of the leaves, and {\textless} 50 transcripts differed significantly between different CO2 environments. For young leaves most differentially expressed genes were upregulated in elevated [CO2], while in semimature leaves most were downregulated in elevated [CO2]. • For transcripts related only to the small subunit of Rubisco, upregulation in LPI 3 and downregulation in LPI 6 leaves in elevated CO2 was confirmed by anova. Similar patterns of gene expression for young leaves were also confirmed independently across year 3 and year 6 microarray data, and using real-time RT–PCR. • This study provides the first clues to the long-term genetic expression changes that may occur during long-term plant response to elevated CO2.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {New Phytologist},
	author = {Taylor, Gail and Street, Nathaniel R. and Tricker, Penny J. and Sjödin, Andreas and Graham, Laura and Skogström, Oskar and Calfapietra, Carlo and Scarascia-Mugnozza, Giuseppe and Jansson, Stefan},
	year = {2005},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2005.01450.x},
	keywords = {FACE (free-air CO2 enrichment), Populus, elevated CO2, gene expression, leaf development, microarray},
	pages = {143--154},
}

• The consequences of increasing atmospheric carbon dioxide for long-term adaptation of forest ecosystems remain uncertain, with virtually no studies undertaken at the genetic level. A global analysis using cDNA microarrays was conducted following 6 yr exposure of Populus × euramericana (clone I-214) to elevated [CO2] in a FACE (free-air CO2 enrichment) experiment. • Gene expression was sensitive to elevated [CO2] but the response depended on the developmental age of the leaves, and \textless 50 transcripts differed significantly between different CO2 environments. For young leaves most differentially expressed genes were upregulated in elevated [CO2], while in semimature leaves most were downregulated in elevated [CO2]. • For transcripts related only to the small subunit of Rubisco, upregulation in LPI 3 and downregulation in LPI 6 leaves in elevated CO2 was confirmed by anova. Similar patterns of gene expression for young leaves were also confirmed independently across year 3 and year 6 microarray data, and using real-time RT–PCR. • This study provides the first clues to the long-term genetic expression changes that may occur during long-term plant response to elevated CO2.

@article{klimmek_structure_2005,
	title = {Structure of the {Higher} {Plant} {Light} {Harvesting} {Complex} {I}:  {In} {Vivo} {Characterization} and {Structural} {Interdependence} of the {Lhca} {Proteins}},
	volume = {44},
	issn = {0006-2960},
	shorttitle = {Structure of the {Higher} {Plant} {Light} {Harvesting} {Complex} {I}},
	url = {https://doi.org/10.1021/bi047873g},
	doi = {10/dfnxgm},
	abstract = {We have investigated the structure of the higher plant light harvesting complex of photosystem I (LHCI) by analyzing PSI−LHCI particles isolated from a set of Arabidopsis plant lines, each lacking a specific Lhca (Lhca1−4) polypeptide. Functional antenna size measurements support the recent finding that there are four Lhca proteins per PSI in the crystal structure [Ben-Shem, A., Frolow, F., and Nelson, N. (2003) Nature 426, 630−635]. According to HPLC analyses the number of pigment molecules bound within the LHCI is higher than expected from reconstitution studies or analyses of isolated native LHCI. Comparison of the spectra of the particles from the different lines reveals chlorophyll absorption bands peaking at 696, 688, 665, and 655 nm that are not present in isolated PSI or LHCI. These bands presumably originate from “gap” or “linker” pigments that are cooperatively coordinated by the Lhca and/or PSI proteins, which we have tentatively localized in the PSI−LHCI complex.},
	number = {8},
	urldate = {2021-06-11},
	journal = {Biochemistry},
	author = {Klimmek, Frank and Ganeteg, Ulrika and Ihalainen, Janne A. and van Roon, Henny and Jensen, Poul E. and Scheller, Henrik V. and Dekker, Jan P. and Jansson, Stefan},
	month = mar,
	year = {2005},
	note = {Publisher: American Chemical Society},
	pages = {3065--3073},
}

We have investigated the structure of the higher plant light harvesting complex of photosystem I (LHCI) by analyzing PSI−LHCI particles isolated from a set of Arabidopsis plant lines, each lacking a specific Lhca (Lhca1−4) polypeptide. Functional antenna size measurements support the recent finding that there are four Lhca proteins per PSI in the crystal structure [Ben-Shem, A., Frolow, F., and Nelson, N. (2003) Nature 426, 630−635]. According to HPLC analyses the number of pigment molecules bound within the LHCI is higher than expected from reconstitution studies or analyses of isolated native LHCI. Comparison of the spectra of the particles from the different lines reveals chlorophyll absorption bands peaking at 696, 688, 665, and 655 nm that are not present in isolated PSI or LHCI. These bands presumably originate from “gap” or “linker” pigments that are cooperatively coordinated by the Lhca and/or PSI proteins, which we have tentatively localized in the PSI−LHCI complex.

@article{waldmann_comparing_2005,
	title = {Comparing {Bayesian} estimates of genetic differentiation of molecular markers and quantitative traits: an application to {Pinus} sylvestris},
	volume = {94},
	copyright = {2005 The Genetics Society},
	issn = {1365-2540},
	shorttitle = {Comparing {Bayesian} estimates of genetic differentiation of molecular markers and quantitative traits},
	url = {https://www.nature.com/articles/6800672},
	doi = {10.1038/sj.hdy.6800672},
	abstract = {Comparison of the level of differentiation at neutral molecular markers (estimated as FST or GST) with the level of differentiation at quantitative traits (estimated as QST) has become a standard tool for inferring that there is differential selection between populations. We estimated QST of timing of bud set from a latitudinal cline of Pinus sylvestris with a Bayesian hierarchical variance component method utilizing the information on the pre-estimated population structure from neutral molecular markers. Unfortunately, the between-family variances differed substantially between populations that resulted in a bimodal posterior of QST that could not be compared in any sensible way with the unimodal posterior of the microsatellite FST. In order to avoid publishing studies with flawed QST estimates, we recommend that future studies should present heritability estimates for each trait and population. Moreover, to detect variance heterogeneity in frequentist methods (ANOVA and REML), it is of essential importance to check also that the residuals are normally distributed and do not follow any systematically deviating trends.},
	language = {en},
	number = {6},
	urldate = {2021-06-11},
	journal = {Heredity},
	author = {Waldmann, P. and García-Gil, M. R. and Sillanpää, M. J.},
	month = jun,
	year = {2005},
	note = {Number: 6
Publisher: Nature Publishing Group},
	pages = {623--629},
}

Comparison of the level of differentiation at neutral molecular markers (estimated as FST or GST) with the level of differentiation at quantitative traits (estimated as QST) has become a standard tool for inferring that there is differential selection between populations. We estimated QST of timing of bud set from a latitudinal cline of Pinus sylvestris with a Bayesian hierarchical variance component method utilizing the information on the pre-estimated population structure from neutral molecular markers. Unfortunately, the between-family variances differed substantially between populations that resulted in a bimodal posterior of QST that could not be compared in any sensible way with the unimodal posterior of the microsatellite FST. In order to avoid publishing studies with flawed QST estimates, we recommend that future studies should present heritability estimates for each trait and population. Moreover, to detect variance heterogeneity in frequentist methods (ANOVA and REML), it is of essential importance to check also that the residuals are normally distributed and do not follow any systematically deviating trends.

@article{kleczkowski_factors_2005,
	title = {Factors affecting oligomerization status of {UDP}-glucose pyrophosphorylase},
	volume = {66},
	issn = {0031-9422},
	url = {https://www.sciencedirect.com/science/article/pii/S0031942205004607},
	doi = {10.1016/j.phytochem.2005.09.034},
	abstract = {UDP-glucose pyrophosphorylase (UGPase) is involved in the production of UDP-glucose, a key precursor to polysaccharide synthesis in all organisms. UGPase activity has recently been proposed to be regulated by oligomerization, with monomer as the active species. In the present study, we investigated factors affecting oligomerization status of the enzyme, using purified recombinant barley UGPase. Incubation of wild-type (wt) UGPase with phosphate or Tris buffers promoted oligomerization, whereas Mops and Hepes completely dissociated the oligomers to monomers (the active form). Similar buffer effects were observed for KK127-128LL and C99S mutants of UGPase; however, the buffers had a relatively small effect on the oligomerization status of the LIV135-137NIN mutant, impaired in deoligomerization ability and showing only 6–9\% activity of the wt. Buffer composition had no effect on UGPase activity at UGPase protein concentrations below ca. 20ng/ml. However, at higher protein concentration the activity in Tris, but not Mops nor Hepes, underestimated the amount of the enzyme. The data suggest that oligomerization status of UGPase can be controlled by subtle changes in an immediate environment (buffers) and by protein dilution. The evidence is discussed in relation to our recent model of UGPase structure/function, and with respect to earlier reports on the oligomeric integrity/activity of UGPases from eukaryotic tissues.},
	language = {en},
	number = {24},
	urldate = {2021-06-11},
	journal = {Phytochemistry},
	author = {Kleczkowski, Leszek A. and Martz, Françoise and Wilczynska, Malgorzata},
	month = dec,
	year = {2005},
	keywords = {Cellulose, Protein oligomerization, Sucrose, UDP-glucose synthesis},
	pages = {2815--2821},
}

UDP-glucose pyrophosphorylase (UGPase) is involved in the production of UDP-glucose, a key precursor to polysaccharide synthesis in all organisms. UGPase activity has recently been proposed to be regulated by oligomerization, with monomer as the active species. In the present study, we investigated factors affecting oligomerization status of the enzyme, using purified recombinant barley UGPase. Incubation of wild-type (wt) UGPase with phosphate or Tris buffers promoted oligomerization, whereas Mops and Hepes completely dissociated the oligomers to monomers (the active form). Similar buffer effects were observed for KK127-128LL and C99S mutants of UGPase; however, the buffers had a relatively small effect on the oligomerization status of the LIV135-137NIN mutant, impaired in deoligomerization ability and showing only 6–9% activity of the wt. Buffer composition had no effect on UGPase activity at UGPase protein concentrations below ca. 20ng/ml. However, at higher protein concentration the activity in Tris, but not Mops nor Hepes, underestimated the amount of the enzyme. The data suggest that oligomerization status of UGPase can be controlled by subtle changes in an immediate environment (buffers) and by protein dilution. The evidence is discussed in relation to our recent model of UGPase structure/function, and with respect to earlier reports on the oligomeric integrity/activity of UGPases from eukaryotic tissues.

@article{cloarec_statistical_2005,
	title = {Statistical total correlation spectroscopy: {An} exploratory approach for latent biomarker identification from metabolic {H}-1 {NMR} data sets},
	volume = {77},
	issn = {0003-2700},
	shorttitle = {Statistical total correlation spectroscopy},
	doi = {10.1021/ac048630x},
	abstract = {We describe here the implementation of the statistical total correlation spectroscopy (STOCSY) analysis method for aiding the identification of potential biomarker molecules in metabonomic studies based on NMR spectroscopic data. STOCSY takes advantage of the multicollinearity of the intensity variables in a set of spectra (in this case H-1 NMR spectra) to generate a pseudo-two-dimensional NMR spectrum that displays the correlation among the intensities of the various peaks across the whole sample. This method is not limited to the usual connectivities that are deducible from more standard two-dimensional NMR spectroscopic methods, such as TOCSY. Moreover, two or more molecules involved in the same pathway can also present high intermolecular correlations because of biological covariance or can even be anticorrelated. This combination of STOCSY with supervised pattern recognition and particularly orthogonal projection on latent structure-discriminant analysis (O-PLS-DA) offers a new powerful framework for analysis of metabonomic data. In a first step O-PLS-DA extracts the part of NMR spectra related to discrimination. This information is then cross-combined with the STOCSY results to help identify the molecules responsible for the metabolic variation. To illustrate the applicability of the method, it has been applied to 114 NMR spectra of urine from a metabonomic study of a model of insulin resistance based on the administration of a carbohydrate diet to three different mice strains (C57BL/60xjr, BAIB/cOxjr, and 129S6/SvEvOxjr) in which a series of metabolites of biological importance can be conclusively assigned and identified by use of the STOCSY approach.},
	language = {English},
	number = {5},
	journal = {Analytical Chemistry},
	author = {Cloarec, O. and Dumas, M. E. and Craig, A. and Barton, R. H. and Trygg, J. and Hudson, J. and Blancher, C. and Gauguier, D. and Lindon, J. C. and Holmes, E. and Nicholson, J.},
	month = mar,
	year = {2005},
	note = {Place: Washington
Publisher: Amer Chemical Soc
WOS:000227409800019},
	keywords = {automatic data reduction, disease, metabonomics, nmr-spectra, o2-pls, urine},
	pages = {1282--1289},
}

We describe here the implementation of the statistical total correlation spectroscopy (STOCSY) analysis method for aiding the identification of potential biomarker molecules in metabonomic studies based on NMR spectroscopic data. STOCSY takes advantage of the multicollinearity of the intensity variables in a set of spectra (in this case H-1 NMR spectra) to generate a pseudo-two-dimensional NMR spectrum that displays the correlation among the intensities of the various peaks across the whole sample. This method is not limited to the usual connectivities that are deducible from more standard two-dimensional NMR spectroscopic methods, such as TOCSY. Moreover, two or more molecules involved in the same pathway can also present high intermolecular correlations because of biological covariance or can even be anticorrelated. This combination of STOCSY with supervised pattern recognition and particularly orthogonal projection on latent structure-discriminant analysis (O-PLS-DA) offers a new powerful framework for analysis of metabonomic data. In a first step O-PLS-DA extracts the part of NMR spectra related to discrimination. This information is then cross-combined with the STOCSY results to help identify the molecules responsible for the metabolic variation. To illustrate the applicability of the method, it has been applied to 114 NMR spectra of urine from a metabonomic study of a model of insulin resistance based on the administration of a carbohydrate diet to three different mice strains (C57BL/60xjr, BAIB/cOxjr, and 129S6/SvEvOxjr) in which a series of metabolites of biological importance can be conclusively assigned and identified by use of the STOCSY approach.

@article{schwab_specific_2005,
	title = {Specific effects of {microRNAs} on the plant transcriptome},
	volume = {8},
	issn = {1534-5807},
	doi = {10.1016/j.devcel.2005.01.018},
	abstract = {Most plant microRNAs (miRNAs) have perfect or near-perfect complementarity with their targets. This is consistent with their primary mode of action being cleavage of target mRNAs, similar to that induced by perfectly complementary small interfering RNAs (siRNAs). However, there are natural targets with up to five mismatches. Furthermore, artificial siRNAs can have substantial effects on so-called off-targets, to which they have only limited complementarity. By analyzing the transcriptome of plants overexpressing different miRNAs, we have deduced a set of empirical parameters for target recognition. Compared to artificial siRNAs, authentic plant miRNAs appear to have much higher specificity, which may reflect their coevolution with the remainder of the transcriptome. We also demonstrate that miR172, previously thought to act primarily by translational repression, can efficiently guide mRNA cleavage, although the effects on steady-state levels of target transcripts are obscured by strong feedback regulation. This finding unifies the view of plant miRNA action.},
	language = {eng},
	number = {4},
	journal = {Developmental Cell},
	author = {Schwab, Rebecca and Palatnik, Javier F. and Riester, Markus and Schommer, Carla and Schmid, Markus and Weigel, Detlef},
	month = apr,
	year = {2005},
	pmid = {15809034},
	keywords = {Base Pairing, Base Sequence, Gene Expression Profiling, Gene Expression Regulation, Plant, MicroRNAs, Nucleic Acid Conformation, Oligonucleotide Array Sequence Analysis, Phenotype, Plant Proteins, Plants, Genetically Modified, RNA, Plant, Reproducibility of Results, Transcription, Genetic},
	pages = {517--527},
}

Most plant microRNAs (miRNAs) have perfect or near-perfect complementarity with their targets. This is consistent with their primary mode of action being cleavage of target mRNAs, similar to that induced by perfectly complementary small interfering RNAs (siRNAs). However, there are natural targets with up to five mismatches. Furthermore, artificial siRNAs can have substantial effects on so-called off-targets, to which they have only limited complementarity. By analyzing the transcriptome of plants overexpressing different miRNAs, we have deduced a set of empirical parameters for target recognition. Compared to artificial siRNAs, authentic plant miRNAs appear to have much higher specificity, which may reflect their coevolution with the remainder of the transcriptome. We also demonstrate that miR172, previously thought to act primarily by translational repression, can efficiently guide mRNA cleavage, although the effects on steady-state levels of target transcripts are obscured by strong feedback regulation. This finding unifies the view of plant miRNA action.

@article{schmid_gene_2005,
	title = {A gene expression map of {Arabidopsis} thaliana development},
	volume = {37},
	issn = {1061-4036},
	doi = {10.1038/ng1543},
	abstract = {Regulatory regions of plant genes tend to be more compact than those of animal genes, but the complement of transcription factors encoded in plant genomes is as large or larger than that found in those of animals. Plants therefore provide an opportunity to study how transcriptional programs control multicellular development. We analyzed global gene expression during development of the reference plant Arabidopsis thaliana in samples covering many stages, from embryogenesis to senescence, and diverse organs. Here, we provide a first analysis of this data set, which is part of the AtGenExpress expression atlas. We observed that the expression levels of transcription factor genes and signal transduction components are similar to those of metabolic genes. Examining the expression patterns of large gene families, we found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.},
	language = {eng},
	number = {5},
	journal = {Nature Genetics},
	author = {Schmid, Markus and Davison, Timothy S. and Henz, Stefan R. and Pape, Utz J. and Demar, Monika and Vingron, Martin and Schölkopf, Bernhard and Weigel, Detlef and Lohmann, Jan U.},
	month = may,
	year = {2005},
	pmid = {15806101},
	keywords = {Arabidopsis, Gene Expression, Gene Expression Profiling, Genetic Markers},
	pages = {501--506},
}

Regulatory regions of plant genes tend to be more compact than those of animal genes, but the complement of transcription factors encoded in plant genomes is as large or larger than that found in those of animals. Plants therefore provide an opportunity to study how transcriptional programs control multicellular development. We analyzed global gene expression during development of the reference plant Arabidopsis thaliana in samples covering many stages, from embryogenesis to senescence, and diverse organs. Here, we provide a first analysis of this data set, which is part of the AtGenExpress expression atlas. We observed that the expression levels of transcription factor genes and signal transduction components are similar to those of metabolic genes. Examining the expression patterns of large gene families, we found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.

@article{lempe_diversity_2005,
	title = {Diversity of flowering responses in wild {Arabidopsis} thaliana strains},
	volume = {1},
	issn = {1553-7390},
	doi = {10.1371/journal.pgen.0010006},
	abstract = {Although multiple environmental cues regulate the transition to flowering in Arabidopsis thaliana, previous studies have suggested that wild A. thaliana accessions fall primarily into two classes, distinguished by their requirement for vernalization (extended winter-like temperatures), which enables rapid flowering under long days. Much of the difference in vernalization response is apparently due to variation at two epistatically acting loci, FRI and FLC. We present the response of over 150 wild accessions to three different environmental variables. In long days, FLC is among those genes whose expression is most highly correlated with flowering. In short days, FRI and FLC are less important, although their contribution is still significant. In addition, there is considerable variation not only in vernalization response, but also in the response to differences in day length or ambient growth temperature. The identification of accessions that flower relatively early or late in specific environments suggests that many of the flowering-time pathways identified by mutagenesis, such as those that respond to day length, contribute to flowering-time variation in the wild. In contrast to differences in vernalization requirement, which are mainly mediated by FRI and FLC, it seems that variation in these other pathways is due to allelic effects at several different loci.},
	language = {eng},
	number = {1},
	journal = {PLoS genetics},
	author = {Lempe, Janne and Balasubramanian, Sureshkumar and Sureshkumar, Sridevi and Singh, Anandita and Schmid, Markus and Weigel, Detlef},
	month = jul,
	year = {2005},
	pmid = {16103920},
	pmcid = {PMC1183525},
	pages = {109--118},
}

Although multiple environmental cues regulate the transition to flowering in Arabidopsis thaliana, previous studies have suggested that wild A. thaliana accessions fall primarily into two classes, distinguished by their requirement for vernalization (extended winter-like temperatures), which enables rapid flowering under long days. Much of the difference in vernalization response is apparently due to variation at two epistatically acting loci, FRI and FLC. We present the response of over 150 wild accessions to three different environmental variables. In long days, FLC is among those genes whose expression is most highly correlated with flowering. In short days, FRI and FLC are less important, although their contribution is still significant. In addition, there is considerable variation not only in vernalization response, but also in the response to differences in day length or ambient growth temperature. The identification of accessions that flower relatively early or late in specific environments suggests that many of the flowering-time pathways identified by mutagenesis, such as those that respond to day length, contribute to flowering-time variation in the wild. In contrast to differences in vernalization requirement, which are mainly mediated by FRI and FLC, it seems that variation in these other pathways is due to allelic effects at several different loci.

@article{keech_adsorption_2005,
	title = {Adsorption of allelopathic compounds by wood-derived charcoal: the role of wood porosity},
	volume = {272},
	issn = {1573-5036},
	shorttitle = {Adsorption of allelopathic compounds by wood-derived charcoal},
	url = {https://doi.org/10.1007/s11104-004-5485-5},
	doi = {10.1007/s11104-004-5485-5},
	abstract = {In Swedish boreal forests, areas dominated by the dwarf shrub Empetrum hermaphroditum Hagerup are known for their poor regeneration of trees and one of the causes of this poor regeneration has been attributed to allelopathy (i.e. chemical interferences) by E. hermaphroditum. Fire-produced charcoal is suggested to play an important role in rejuvenating those ecosystems by adsorbing allelopathic compounds, such as phenols, released by E. hermaphroditum. In this study, we firstly investigated whether the adsorption capacity of charcoal of different plant species varies according to the wood anatomical structures of these, and secondly we tried to relate the adsorption capacity to wood anatomical structure. Charcoal was produced from eight boreal and one temperate woody plant species and the adsorption capacity of charcoal was tested by bioassays technique. Seed germination was used as a measurement of the ability of charcoal to adsorb allelochemicals. The charcoal porosity was estimated and the pore size distribution was then calculated in order to relate the wood anatomical features to the adsorption capacity. The results showed that the adsorption capacity of charcoal was significantly different between plant species and that deciduous trees had a significantly higher adsorption capacity than conifers and ericaceous species. The presence of macro-pores rather than a high porosity appears to be the most important for the adsorption capacity. These results suggest that fire-produced charcoal has different ability to adsorb phenols in boreal forest soil, and therefore may have differing effects on the germination of seeds of establishing tree seedlings.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {Plant and Soil},
	author = {Keech, Olivier and Carcaillet, Christopher and Nilsson, Marie-Charlotte},
	month = may,
	year = {2005},
	pages = {291--300},
}

In Swedish boreal forests, areas dominated by the dwarf shrub Empetrum hermaphroditum Hagerup are known for their poor regeneration of trees and one of the causes of this poor regeneration has been attributed to allelopathy (i.e. chemical interferences) by E. hermaphroditum. Fire-produced charcoal is suggested to play an important role in rejuvenating those ecosystems by adsorbing allelopathic compounds, such as phenols, released by E. hermaphroditum. In this study, we firstly investigated whether the adsorption capacity of charcoal of different plant species varies according to the wood anatomical structures of these, and secondly we tried to relate the adsorption capacity to wood anatomical structure. Charcoal was produced from eight boreal and one temperate woody plant species and the adsorption capacity of charcoal was tested by bioassays technique. Seed germination was used as a measurement of the ability of charcoal to adsorb allelochemicals. The charcoal porosity was estimated and the pore size distribution was then calculated in order to relate the wood anatomical features to the adsorption capacity. The results showed that the adsorption capacity of charcoal was significantly different between plant species and that deciduous trees had a significantly higher adsorption capacity than conifers and ericaceous species. The presence of macro-pores rather than a high porosity appears to be the most important for the adsorption capacity. These results suggest that fire-produced charcoal has different ability to adsorb phenols in boreal forest soil, and therefore may have differing effects on the germination of seeds of establishing tree seedlings.

@article{pesquet_novel_2005,
	title = {Novel {Markers} of {Xylogenesis} in {Zinnia} {Are} {Differentially} {Regulated} by {Auxin} and {Cytokinin}},
	volume = {139},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.105.064337},
	doi = {10.1104/pp.105.064337},
	abstract = {The characterization of in vitro xylogenic cultures of zinnia (Zinnia elegans) has led to major discoveries in the understanding of xylem formation in plants. We have constructed and characterized a subtractive library from zinnia cultures enriched in genes that are specifically expressed at the onset of secondary wall deposition and tracheary element (TE) programmed cell death. This Late Xylogenesis Library (LXL) consisted of 236 nonredundant cDNAs, 77\% of which encoded novel sequences in comparison with the 17,622 expressed sequence tag sequences publicly available. cDNA arrays were constructed to examine dynamic global gene expression during the course of TE formation. As a first step in dissecting auxin and cytokinin signaling during TE differentiation, macroarrays were probed with cDNAs from cells cultured in different hormonal conditions. Fifty-one percent of the LXL genes were induced by either auxin or cytokinin individually, the large majority by auxin. To determine the potential involvement of these categories of genes in TE differentiation, multiplex in situ-reverse transcription-PCR was performed on cells for two genes encoding putative cell wall proteins: Gibberellin stimulated transcript-1, induced by auxin alone, and expansin 5, induced by cytokinin alone. All transcriptionally active TEs expressed both genes, indicating that, although these genes may not be considered as specific markers for TE differentiation per se, they are nevertheless an integral part of TE differentiation program. Among the non-TE population, four different gene expression-based cell types could be distinguished. Together, these results demonstrate the underlying complexity of hormonal perception and the existence of several different cell types in in vitro TE cell cultures.},
	number = {4},
	urldate = {2021-06-11},
	journal = {Plant Physiology},
	author = {Pesquet, Edouard and Ranocha, Philippe and Legay, Sylvain and Digonnet, Catherine and Barbier, Odile and Pichon, Magalie and Goffner, Deborah},
	month = dec,
	year = {2005},
	pages = {1821--1839},
}

The characterization of in vitro xylogenic cultures of zinnia (Zinnia elegans) has led to major discoveries in the understanding of xylem formation in plants. We have constructed and characterized a subtractive library from zinnia cultures enriched in genes that are specifically expressed at the onset of secondary wall deposition and tracheary element (TE) programmed cell death. This Late Xylogenesis Library (LXL) consisted of 236 nonredundant cDNAs, 77% of which encoded novel sequences in comparison with the 17,622 expressed sequence tag sequences publicly available. cDNA arrays were constructed to examine dynamic global gene expression during the course of TE formation. As a first step in dissecting auxin and cytokinin signaling during TE differentiation, macroarrays were probed with cDNAs from cells cultured in different hormonal conditions. Fifty-one percent of the LXL genes were induced by either auxin or cytokinin individually, the large majority by auxin. To determine the potential involvement of these categories of genes in TE differentiation, multiplex in situ-reverse transcription-PCR was performed on cells for two genes encoding putative cell wall proteins: Gibberellin stimulated transcript-1, induced by auxin alone, and expansin 5, induced by cytokinin alone. All transcriptionally active TEs expressed both genes, indicating that, although these genes may not be considered as specific markers for TE differentiation per se, they are nevertheless an integral part of TE differentiation program. Among the non-TE population, four different gene expression-based cell types could be distinguished. Together, these results demonstrate the underlying complexity of hormonal perception and the existence of several different cell types in in vitro TE cell cultures.

@article{van_raemdonck_molecular_2005,
	title = {Molecular changes associated with the setting up of secondary growth in aspen},
	volume = {56},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/eri221},
	doi = {10.1093/jxb/eri221},
	abstract = {Vascular secondary growth results from the activity of the vascular cambium, which produces secondary phloem and secondary xylem. By means of cDNA-amplified fragment length polymorphism (cDNA-AFLP) analysis along aspen stems, several potential regulatory genes involved in the progressive transition from primary to secondary growth were identified. A total of 83 unique transcript-derived fragments (TDFs) was found to be differentiated between the top and the bottom of the stem. An independent RT-PCR expression analysis validated the cDNA-AFLP profiles for 19 of the TDFs. Among these, seven correspond to new genes encoding putative regulatory proteins. Emphasis was laid upon two genes encoding, respectively, an AP2/ERF-like transcription factor (PtaERF1) and a RING finger protein (PtaRHE1); their differential expression was further confirmed by reverse northern analysis. In situ RT-PCR revealed that PtaERF1 was expressed in phloem tissue and that PtaRHE1 had a pronounced expression in ray initials and their derivatives within the cambial zone. These results suggest that these genes have a potential role in vascular tissue development and/or functioning.},
	number = {418},
	urldate = {2021-06-11},
	journal = {Journal of Experimental Botany},
	author = {van Raemdonck, Damien and Pesquet, Edouard and Cloquet, Sophie and Beeckman, Hans and Boerjan, Wout and Goffner, Deborah and El Jaziri, Mondher and Baucher, Marie},
	month = aug,
	year = {2005},
	pages = {2211--2227},
}

Vascular secondary growth results from the activity of the vascular cambium, which produces secondary phloem and secondary xylem. By means of cDNA-amplified fragment length polymorphism (cDNA-AFLP) analysis along aspen stems, several potential regulatory genes involved in the progressive transition from primary to secondary growth were identified. A total of 83 unique transcript-derived fragments (TDFs) was found to be differentiated between the top and the bottom of the stem. An independent RT-PCR expression analysis validated the cDNA-AFLP profiles for 19 of the TDFs. Among these, seven correspond to new genes encoding putative regulatory proteins. Emphasis was laid upon two genes encoding, respectively, an AP2/ERF-like transcription factor (PtaERF1) and a RING finger protein (PtaRHE1); their differential expression was further confirmed by reverse northern analysis. In situ RT-PCR revealed that PtaERF1 was expressed in phloem tissue and that PtaRHE1 had a pronounced expression in ray initials and their derivatives within the cambial zone. These results suggest that these genes have a potential role in vascular tissue development and/or functioning.

@article{unneberg_analysis_2005,
	title = {Analysis of 70,000 {EST} sequences to study divergence between two closely related {Populus} species},
	volume = {1},
	issn = {1614-2950},
	url = {https://doi.org/10.1007/s11295-005-0014-0},
	doi = {10.1007/s11295-005-0014-0},
	abstract = {The Populus genus has evolved as the model organism for forest tree genomics, which has been further emphasised with the sequencing of the Populus trichocarpa genome. Populus species are widely spread over the Northern Hemisphere and provide a great source of genetic diversity, which can be used for mapping of quantitative trait loci, positional cloning, association mapping and studies in environmental adaptation. Collections of expressed sequence tags (ESTs) are rich sources in studies of genetic diversity. Here, we report on an in-depth analysis of 70,000 ESTs from two Populus species, Populus tremula and Populus trichocarpa. We present data on the level of conservation in transcript sequences and supply a collection of potential single nucleotide polymorphisms.},
	language = {en},
	number = {3},
	urldate = {2021-06-11},
	journal = {Tree Genetics \& Genomes},
	author = {Unneberg, Per and Strömberg, Michael and Lundeberg, Joakim and Jansson, Stefan and Sterky, Fredrik},
	month = nov,
	year = {2005},
	pages = {109--115},
}

The Populus genus has evolved as the model organism for forest tree genomics, which has been further emphasised with the sequencing of the Populus trichocarpa genome. Populus species are widely spread over the Northern Hemisphere and provide a great source of genetic diversity, which can be used for mapping of quantitative trait loci, positional cloning, association mapping and studies in environmental adaptation. Collections of expressed sequence tags (ESTs) are rich sources in studies of genetic diversity. Here, we report on an in-depth analysis of 70,000 ESTs from two Populus species, Populus tremula and Populus trichocarpa. We present data on the level of conservation in transcript sequences and supply a collection of potential single nucleotide polymorphisms.

@article{garcia-lorenzo_degradation_2005,
	title = {Degradation of the main {Photosystem} {II} light-harvesting complex},
	volume = {4},
	issn = {1474-9092},
	url = {https://pubs.rsc.org/en/content/articlelanding/2005/pp/b506625e},
	doi = {10.1039/B506625E},
	abstract = {Many factors trigger the degradation of proteins, including changes in environmental conditions, genetic mutations, and limitations in the availability of cofactors. Despite the importance for viability, still very little is known about protein degradation and its regulation. The degradation of the most abundant membrane protein on Earth, the light-harvesting complex of Photosystem II (LHC II), is highly regulated under different environmental conditions, e.g. light stress, to prevent photochemical damage of the reaction center. However, despite major effort to identify the protease/proteases involved in the degradation of the apoproteins of LHC II the molecular details of this important process remain obscure. LHC II belongs to the family of chlorophyll a/b binding proteins (CAB proteins) and is located in the thylakoid membrane of the plant chloroplast. The results of biochemical experiments to isolate and characterize the protease degrading LHC II are summarized here and compared to our own recent finding indicating that a metalloprotease of the FtsH family is involved in this process.},
	language = {en},
	number = {12},
	urldate = {2021-06-11},
	journal = {Photochemical \& Photobiological Sciences},
	author = {García-Lorenzo, Maribel and Żelisko, Agnieszka and Jackowski, Grzegorz and Funk, Christiane},
	month = nov,
	year = {2005},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {1065--1071},
}

Many factors trigger the degradation of proteins, including changes in environmental conditions, genetic mutations, and limitations in the availability of cofactors. Despite the importance for viability, still very little is known about protein degradation and its regulation. The degradation of the most abundant membrane protein on Earth, the light-harvesting complex of Photosystem II (LHC II), is highly regulated under different environmental conditions, e.g. light stress, to prevent photochemical damage of the reaction center. However, despite major effort to identify the protease/proteases involved in the degradation of the apoproteins of LHC II the molecular details of this important process remain obscure. LHC II belongs to the family of chlorophyll a/b binding proteins (CAB proteins) and is located in the thylakoid membrane of the plant chloroplast. The results of biochemical experiments to isolate and characterize the protease degrading LHC II are summarized here and compared to our own recent finding indicating that a metalloprotease of the FtsH family is involved in this process.

@incollection{hurry_respiration_2005,
	address = {Dordrecht},
	series = {Advances in {Photosynthesis} and {Respiration}},
	title = {Respiration in {Photosynthetic} {Cells}: {Gas} {Exchange} {Components}, {Interactions} with {Photorespiration} and the {Operation} of {Mitochondria} in the {Light}},
	isbn = {978-1-4020-3589-0},
	shorttitle = {Respiration in {Photosynthetic} {Cells}},
	url = {https://doi.org/10.1007/1-4020-3589-6_4},
	abstract = {SummaryAccording to gas exchange measurements, mitochondrial oxygen consumption in the light is always fast, while respiratory CO2 evolution is markedly decreased (compared with rates in darkness). We analyze the metabolic events that lead to such contrasting responses. In the light, the generation of NADH in mitochondria, both in the glycine decarboxylase reaction and in the tricarboxylic acid cycle, leads to increased NAD(P)H levels, which may increase the activity of the rotenone-insensitive NAD(P)H dehydrogenases. The resulting increase of the reduction level of ubiquinone activates the alternative oxidase. Stabilization of (photo)respiratory flux during the transition from darkness to light takes place at higher NADH/NAD+ and ATP/ADP ratios. Maintenance of fast rates of mitochondrial electron transport in the light is facilitated by the import of oxaloacetate (OAA) from the cytosol to remove NADH, and by the export of citrate to the cytosol. This reduces the flow of metabolites in the tricarboxylic acid cycle, decreasing decarboxylation rates, while the rate of oxygen consumption reactions remain fast.},
	language = {en},
	urldate = {2021-06-11},
	booktitle = {Plant {Respiration}: {From} {Cell} to {Ecosystem}},
	publisher = {Springer Netherlands},
	author = {Hurry, Vaughan and Igamberdiev, Abir U. and Keerberg, Olav and Pärnik, Tiit and Atkin, Owen K. and Zaragoza-Castells, Joana and Gardeström, Per},
	editor = {Lambers, Hans and Ribas-Carbo, Miquel},
	year = {2005},
	doi = {10.1007/1-4020-3589-6_4},
	keywords = {Alternative Oxidase, Comp LETE, Glycine Decarboxylase, Leaf Respiration, PHOTORESPIRATORY Condition},
	pages = {43--61},
}

SummaryAccording to gas exchange measurements, mitochondrial oxygen consumption in the light is always fast, while respiratory CO2 evolution is markedly decreased (compared with rates in darkness). We analyze the metabolic events that lead to such contrasting responses. In the light, the generation of NADH in mitochondria, both in the glycine decarboxylase reaction and in the tricarboxylic acid cycle, leads to increased NAD(P)H levels, which may increase the activity of the rotenone-insensitive NAD(P)H dehydrogenases. The resulting increase of the reduction level of ubiquinone activates the alternative oxidase. Stabilization of (photo)respiratory flux during the transition from darkness to light takes place at higher NADH/NAD+ and ATP/ADP ratios. Maintenance of fast rates of mitochondrial electron transport in the light is facilitated by the import of oxaloacetate (OAA) from the cytosol to remove NADH, and by the export of citrate to the cytosol. This reduces the flow of metabolites in the tricarboxylic acid cycle, decreasing decarboxylation rates, while the rate of oxygen consumption reactions remain fast.

@article{huang_mrna_2005,
	title = {The {mRNA} of the {Arabidopsis} {Gene} {FT} {Moves} from {Leaf} to {Shoot} {Apex} and {Induces} {Flowering}},
	volume = {309},
	copyright = {American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {https://science.sciencemag.org/content/309/5741/1694},
	doi = {10.1126/science.1117768},
	abstract = {Day length controls flowering time in many plants. The day-length signal is perceived in the leaf, but how this signal is transduced to the shoot apex, where floral initiation occurs, is not known. In Arabidopsis, the day-length response depends on the induction of the FLOWERING LOCUS T (FT) gene. We show here that local induction of FT in a single Arabidopsis leaf is sufficient to trigger flowering. The FT messenger RNA is transported to the shoot apex, where downstream genes are activated. These data suggest that the FT mRNA is an important component of the elusive “florigen” signal that moves from leaf to shoot apex.
The long-sought "florigen" that moves from leaf to shoot and induces flowering as days lengthen is the messenger RNA for the Flowering Locus T gene FT.
The long-sought "florigen" that moves from leaf to shoot and induces flowering as days lengthen is the messenger RNA for the Flowering Locus T gene FT.},
	language = {en},
	number = {5741},
	urldate = {2021-06-11},
	journal = {Science},
	author = {Huang, Tao and Böhlenius, Henrik and Eriksson, Sven and Parcy, François and Nilsson, Ove},
	month = sep,
	year = {2005},
	pmid = {16099949},
	note = {Publisher: American Association for the Advancement of Science
Section: Research Article},
	pages = {1694--1696},
}

Day length controls flowering time in many plants. The day-length signal is perceived in the leaf, but how this signal is transduced to the shoot apex, where floral initiation occurs, is not known. In Arabidopsis, the day-length response depends on the induction of the FLOWERING LOCUS T (FT) gene. We show here that local induction of FT in a single Arabidopsis leaf is sufficient to trigger flowering. The FT messenger RNA is transported to the shoot apex, where downstream genes are activated. These data suggest that the FT mRNA is an important component of the elusive “florigen” signal that moves from leaf to shoot apex. The long-sought "florigen" that moves from leaf to shoot and induces flowering as days lengthen is the messenger RNA for the Flowering Locus T gene FT. The long-sought "florigen" that moves from leaf to shoot and induces flowering as days lengthen is the messenger RNA for the Flowering Locus T gene FT.

@article{grebe_growth_2005,
	title = {Growth by {Auxin}: {When} a {Weed} {Needs} {Acid}},
	volume = {310},
	copyright = {© 2005 American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	shorttitle = {Growth by {Auxin}},
	url = {https://science.sciencemag.org/content/310/5745/60},
	doi = {10.1126/science.1119735},
	abstract = {{\textless}p{\textgreater} In his Perspective, Grebe discusses how a plant proton pump residing in intracellular compartments, rather than in the plasma membrane of the cell surface, regulates growth and development. The pump modulates the expression at the plasma membrane of both a transporter for the hormone auxin and another proton pump. These findings open new views on how plants regulate cell wall acidity and hormone transport during development. {\textless}/p{\textgreater}},
	language = {en},
	number = {5745},
	urldate = {2021-06-11},
	journal = {Science},
	author = {Grebe, Markus},
	month = oct,
	year = {2005},
	pmid = {16210521},
	note = {Publisher: American Association for the Advancement of Science
Section: Perspective},
	pages = {60--61},
}

\textlessp\textgreater In his Perspective, Grebe discusses how a plant proton pump residing in intracellular compartments, rather than in the plasma membrane of the cell surface, regulates growth and development. The pump modulates the expression at the plasma membrane of both a transporter for the hormone auxin and another proton pump. These findings open new views on how plants regulate cell wall acidity and hormone transport during development. \textless/p\textgreater

@article{danusevicius_optimization_2005,
	title = {Optimization of breeding population size for long-term breeding},
	volume = {20},
	issn = {0282-7581},
	doi = {10.1080/02827580410019517},
	abstract = {A model for optimization of the long-term breeding population size by considering genetic gain, relatedness, time and cost components was developed for the optimum allocation of resources between the breeding and testing populations. The group coancestry and the average breeding value for the breeding population were merged into a joint index, known as group merit. The size of the breeding population was regarded optimal when the annual increase in group merit was maximized at a budget constraint. A study scenario with a balanced selection and parameters suitable to northerly conifers bred in a multipopulation design was applied. The optimum breeding population size ranged between 30 and 70. High heritability, more efficient breeding strategy, high additive variance at mature age, low annual budget, expensive testing method and a low value assigned to gene diversity favoured a small breeding population size.},
	language = {English},
	number = {1},
	journal = {Scandinavian Journal of Forest Research},
	author = {Danusevicius, D. and Lindgren, D.},
	year = {2005},
	note = {Place: Oslo
Publisher: Taylor \& Francis As
WOS:000227176600007},
	keywords = {economic efficiency, efficiency, gain, gene diversity, genetic gain, genetic-parameters, group merit, heritability, optimization, pinus-sylvestris, relatedness, selection, simulation, time trends, traits, tree},
	pages = {18--25},
}

A model for optimization of the long-term breeding population size by considering genetic gain, relatedness, time and cost components was developed for the optimum allocation of resources between the breeding and testing populations. The group coancestry and the average breeding value for the breeding population were merged into a joint index, known as group merit. The size of the breeding population was regarded optimal when the annual increase in group merit was maximized at a budget constraint. A study scenario with a balanced selection and parameters suitable to northerly conifers bred in a multipopulation design was applied. The optimum breeding population size ranged between 30 and 70. High heritability, more efficient breeding strategy, high additive variance at mature age, low annual budget, expensive testing method and a low value assigned to gene diversity favoured a small breeding population size.

@article{louis_remote_2005,
	title = {Remote sensing of sunlight-induced chlorophyll fluorescence and reflectance of {Scots} pine in the boreal forest during spring recovery},
	volume = {96},
	issn = {0034-4257},
	doi = {10.1016/j.rse.2005.01.013},
	abstract = {A measurement campaign to assess the feasibility of remote sensing of sunlight-induced chlorophyll fluorescence (ChlF) from a coniferous canopy was conducted in a boreal forest study site (Finland). A Passive Multi-wavelength Fluorescence Detector (PMFD) sensor, developed in the LURE laboratory, was used to obtain simultaneous measurements of ChlF in the oxygen absorption bands, at 687 and 760 nm, and a reflectance index, the PRI (Physiological Reflectance Index), for a month during spring recovery. When these data were compared with active fluorescence measurements performed on needles they revealed the same trend. During sunny days fluorescence and reflectance signals were found to be strongly influenced by shadows associated with the canopy structure. Moreover, chlorophyll fluorescence variations induced by rapid light changes (due to transient cloud shadows) were found to respond more quickly and with larger amplitude under summer conditions compared to those obtained under cold acclimation conditions. In addition, ChlF at 760 nm was observed to increase with the chlorophyll content. During this campaign, the CO2 assimilation was measured at the forest canopy level and was found remarkably well correlated with the PRI index. (c) 2005 Elsevier Inc. All rights reserved.},
	language = {English},
	number = {1},
	journal = {Remote Sensing of Environment},
	author = {Louis, J. and Ounis, A. and Ducruet, J. M. and Evain, S. and Laurila, T. and Thum, T. and Aurela, M. and Wingsle, G. and Alonso, L. and Pedros, R. and Moya, I.},
	month = may,
	year = {2005},
	note = {Place: New York
Publisher: Elsevier Science Inc
WOS:000229355100003},
	keywords = {CO2 flux, FLD   principle, Scots pine, airborne, boreal forest, diurnal cycle, instrument, leaves, oxygen absorption band, passive remote sensing, photoprotection, photosynthesis, photosystem-ii, pri, responses, state, sunlight-induced chlorophyll fluorescence, water-stress, xanthophyll cycle},
	pages = {37--48},
}

A measurement campaign to assess the feasibility of remote sensing of sunlight-induced chlorophyll fluorescence (ChlF) from a coniferous canopy was conducted in a boreal forest study site (Finland). A Passive Multi-wavelength Fluorescence Detector (PMFD) sensor, developed in the LURE laboratory, was used to obtain simultaneous measurements of ChlF in the oxygen absorption bands, at 687 and 760 nm, and a reflectance index, the PRI (Physiological Reflectance Index), for a month during spring recovery. When these data were compared with active fluorescence measurements performed on needles they revealed the same trend. During sunny days fluorescence and reflectance signals were found to be strongly influenced by shadows associated with the canopy structure. Moreover, chlorophyll fluorescence variations induced by rapid light changes (due to transient cloud shadows) were found to respond more quickly and with larger amplitude under summer conditions compared to those obtained under cold acclimation conditions. In addition, ChlF at 760 nm was observed to increase with the chlorophyll content. During this campaign, the CO2 assimilation was measured at the forest canopy level and was found remarkably well correlated with the PRI index. (c) 2005 Elsevier Inc. All rights reserved.

@article{zelisko_atftsh6_2005,
	title = {{AtFtsH6} is involved in the degradation of the light-harvesting complex {II} during high-light acclimation and senescence},
	volume = {102},
	copyright = {Copyright © 2005, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/102/38/13699},
	doi = {10.1073/pnas.0503472102},
	abstract = {Degradation of the most abundant membrane protein on earth, the light-harvesting complex of Photosystem II (LHC II), is highly regulated under various environmental conditions, e.g., light stress, to prevent photochemical damage to the reaction center. We identified the LHC II degrading protease in Arabidopsis thaliana as a Zn2+-dependent metalloprotease, activated by the removal of unknown extrinsic factors, similar to the proteolytic activity directed against Lhcb3 in barley. By using a reversed genetic approach, the chloroplast-targeted protease FtsH6 was identified as being responsible for the degradation. T-DNA KO A. thaliana mutants, lacking ftsH6, were unable to degrade either Lhcb3 during dark-induced senescence or Lhcb1 and Lhcb3 during highlight acclimation. The A. thaliana ftsH6 gene has a clear orthologue in the genome of Populus trichocarpa. It is likely that FtsH6 is a general LHC II protease and that FtsH6-dependent LHC II proteolysis is a feature of all higher plants.},
	language = {en},
	number = {38},
	urldate = {2021-06-11},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Żelisko, Agnieszka and García-Lorenzo, Maribel and Jackowski, Grzegorz and Jansson, Stefan and Funk, Christiane},
	month = sep,
	year = {2005},
	pmid = {16157880},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {membrane protein, photosynthesis, protease},
	pages = {13699--13704},
}

Degradation of the most abundant membrane protein on earth, the light-harvesting complex of Photosystem II (LHC II), is highly regulated under various environmental conditions, e.g., light stress, to prevent photochemical damage to the reaction center. We identified the LHC II degrading protease in Arabidopsis thaliana as a Zn2+-dependent metalloprotease, activated by the removal of unknown extrinsic factors, similar to the proteolytic activity directed against Lhcb3 in barley. By using a reversed genetic approach, the chloroplast-targeted protease FtsH6 was identified as being responsible for the degradation. T-DNA KO A. thaliana mutants, lacking ftsH6, were unable to degrade either Lhcb3 during dark-induced senescence or Lhcb1 and Lhcb3 during highlight acclimation. The A. thaliana ftsH6 gene has a clear orthologue in the genome of Populus trichocarpa. It is likely that FtsH6 is a general LHC II protease and that FtsH6-dependent LHC II proteolysis is a feature of all higher plants.

@article{kepinski_arabidopsis_2005,
	title = {The {Arabidopsis} {F}-box protein {TIR1} is an auxin receptor},
	volume = {435},
	copyright = {2005 Macmillan Magazines Ltd.},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/nature03542},
	doi = {10.1038/nature03542},
	abstract = {Despite 100 years of evidence showing a pivotal role for indole-3-acetic acid (IAA or auxin) in plant development, the mechanism of auxin perception has remained elusive. Central to auxin response are changes in gene expression, brought about by auxin-induced interaction between the Aux/IAA transcriptional repressor proteins and the ubiquitin–ligase complex SCFTIR1, thus targeting for them proteolysis. Regulated SCF-mediated protein degradation is a widely occurring signal transduction mechanism. Target specificity is conferred by the F-box protein subunit of the SCF (TIR1 in the case of Aux/IAAs) and there are multiple F-box protein genes in all eukaryotic genomes examined so far. Although SCF–target interaction is usually regulated by signal-induced modification of the target, we have previously shown that auxin signalling involves the modification of SCFTIR1. Here we show that this modification involves the direct binding of auxin to TIR1 and thus that TIR1 is an auxin receptor mediating transcriptional responses to auxin.},
	language = {en},
	number = {7041},
	urldate = {2021-06-11},
	journal = {Nature},
	author = {Kepinski, Stefan and Leyser, Ottoline},
	month = may,
	year = {2005},
	note = {Number: 7041
Publisher: Nature Publishing Group},
	pages = {446--451},
}

Despite 100 years of evidence showing a pivotal role for indole-3-acetic acid (IAA or auxin) in plant development, the mechanism of auxin perception has remained elusive. Central to auxin response are changes in gene expression, brought about by auxin-induced interaction between the Aux/IAA transcriptional repressor proteins and the ubiquitin–ligase complex SCFTIR1, thus targeting for them proteolysis. Regulated SCF-mediated protein degradation is a widely occurring signal transduction mechanism. Target specificity is conferred by the F-box protein subunit of the SCF (TIR1 in the case of Aux/IAAs) and there are multiple F-box protein genes in all eukaryotic genomes examined so far. Although SCF–target interaction is usually regulated by signal-induced modification of the target, we have previously shown that auxin signalling involves the modification of SCFTIR1. Here we show that this modification involves the direct binding of auxin to TIR1 and thus that TIR1 is an auxin receptor mediating transcriptional responses to auxin.

@article{lindon_summary_2005,
	title = {Summary recommendations for standardization and reporting of metabolic analyses},
	volume = {23},
	copyright = {2005 Nature Publishing Group},
	issn = {1546-1696},
	url = {https://www.nature.com/articles/nbt0705-833},
	doi = {10.1038/nbt0705-833},
	abstract = {The Standard Metabolic Reporting Structures (SMRS) working group outlines its vision for an open,community-driven specification for the standardization and reporting of metabolic studies.},
	language = {en},
	number = {7},
	urldate = {2021-06-11},
	journal = {Nature Biotechnology},
	author = {Lindon, John C and Nicholson, Jeremy K and Holmes, Elaine and Keun, Hector C and Craig, Andrew and Pearce, Jake T M and Bruce, Stephen J and Hardy, Nigel and Sansone, Susanna-Assunta and Antti, Henrik and Jonsson, Par and Daykin, Clare and Navarange, Mahendra and Beger, Richard D and Verheij, Elwin R and Amberg, Alexander and Baunsgaard, Dorrit and Cantor, Glenn H and Lehman-McKeeman, Lois and Earll, Mark and Wold, Svante and Johansson, Erik and Haselden, John N and Kramer, Kerstin and Thomas, Craig and Lindberg, Johann and Schuppe-Koistinen, Ina and Wilson, Ian D and Reily, Michael D and Robertson, Donald G and Senn, Hans and Krotzky, Arno and Kochhar, Sunil and Powell, Jonathan and van der Ouderaa, Frans and Plumb, Robert and Schaefer, Hartmut and Spraul, Manfred and {The Standard Metabolic Reporting Structures working group}},
	month = jul,
	year = {2005},
	note = {Number: 7
Publisher: Nature Publishing Group},
	pages = {833--838},
}

The Standard Metabolic Reporting Structures (SMRS) working group outlines its vision for an open,community-driven specification for the standardization and reporting of metabolic studies.

@article{persson_diversity_2005,
	title = {Diversity of the protein disulfide isomerase family: {Identification} of breast tumor induced {Hag2} and {Hag3} as novel members of the protein family},
	volume = {36},
	issn = {1055-7903},
	shorttitle = {Diversity of the protein disulfide isomerase family},
	url = {https://www.sciencedirect.com/science/article/pii/S1055790305001132},
	doi = {10.1016/j.ympev.2005.04.002},
	language = {en},
	number = {3},
	urldate = {2021-06-11},
	journal = {Molecular Phylogenetics and Evolution},
	author = {Persson, Staffan and Rosenquist, Magnus and Knoblach, Barbara and Khosravi-Far, Roya and Sommarin, Marianne and Michalak, Marek},
	month = sep,
	year = {2005},
	pages = {734--740},
}

@article{ingvarsson_molecular_2005,
	title = {Molecular {Population} {Genetics} of {Herbivore}-induced {Protease} {Inhibitor} {Genes} in {European} {Aspen} ({Populus} tremula {L}., {Salicaceae})},
	volume = {22},
	issn = {0737-4038},
	url = {https://doi.org/10.1093/molbev/msi171},
	doi = {10.1093/molbev/msi171},
	abstract = {Plants defend themselves against the attack of natural enemies by using an array of both constitutively expressed and induced defenses. Long-lived woody perennials are overrepresented among plant species that show strong induced defense responses, whereas annual plants and crop species are underrepresented. However, most studies of plant defense genes have been performed on annual or short-lived perennial weeds or crop species. Here I use molecular population genetic methods to survey six wound-inducible protease inhibitors (PIs) in a long-lived woody, perennial plant species, the European aspen (Populus tremula), to evaluate the likelihood of either recurrent selective sweeps or balancing selection maintaining amino acid polymorphisms in these genes. The results show that none of the six PI genes have reduced diversities at synonymous sites, as would be expected in the presence of recurrent selective sweeps. However, several genes show some evidence of nonneutral evolution such as enhanced linkage disequilibrium and a large number of high-frequency–derived mutations. A group of at least four Kunitz trypsin inhibitor genes appear to have experienced elevated levels of nonsynonymous substitutions, indicating allelic turnover on an evolutionary timescale. One gene, TI1, has enhanced levels of intraspecific polymorphism at nonsynonymous sites and also has an unusual haplotype structure characterized by two divergent haplotypes occurring at roughly equal frequencies in the sample. One haplotype has very low levels of intraallelic nucleotide diversity, whereas the other haplotype has levels of diversity comparable to other genes in P. tremula. Patterns of sequence diversity at TI1 do not fit a simple model of either balancing selection or recurrent selective sweeps. This suggests that selection at TI1 is more complex, possibly involving allelic cycling.},
	number = {9},
	urldate = {2021-06-11},
	journal = {Molecular Biology and Evolution},
	author = {Ingvarsson, Pär K.},
	month = sep,
	year = {2005},
	pages = {1802--1812},
}

Plants defend themselves against the attack of natural enemies by using an array of both constitutively expressed and induced defenses. Long-lived woody perennials are overrepresented among plant species that show strong induced defense responses, whereas annual plants and crop species are underrepresented. However, most studies of plant defense genes have been performed on annual or short-lived perennial weeds or crop species. Here I use molecular population genetic methods to survey six wound-inducible protease inhibitors (PIs) in a long-lived woody, perennial plant species, the European aspen (Populus tremula), to evaluate the likelihood of either recurrent selective sweeps or balancing selection maintaining amino acid polymorphisms in these genes. The results show that none of the six PI genes have reduced diversities at synonymous sites, as would be expected in the presence of recurrent selective sweeps. However, several genes show some evidence of nonneutral evolution such as enhanced linkage disequilibrium and a large number of high-frequency–derived mutations. A group of at least four Kunitz trypsin inhibitor genes appear to have experienced elevated levels of nonsynonymous substitutions, indicating allelic turnover on an evolutionary timescale. One gene, TI1, has enhanced levels of intraspecific polymorphism at nonsynonymous sites and also has an unusual haplotype structure characterized by two divergent haplotypes occurring at roughly equal frequencies in the sample. One haplotype has very low levels of intraallelic nucleotide diversity, whereas the other haplotype has levels of diversity comparable to other genes in P. tremula. Patterns of sequence diversity at TI1 do not fit a simple model of either balancing selection or recurrent selective sweeps. This suggests that selection at TI1 is more complex, possibly involving allelic cycling.

@article{wedin_generic_2005,
	title = {Generic delimitations in the family {Stictidaceae} ({Ostropales}, {Ascomycota}): the {Stictis}–{Conotrema} problem},
	volume = {37},
	issn = {1096-1135, 0024-2829},
	shorttitle = {Generic delimitations in the family {Stictidaceae} ({Ostropales}, {Ascomycota})},
	url = {https://www.cambridge.org/core/journals/lichenologist/article/generic-delimitations-in-the-family-stictidaceae-ostropales-ascomycota-the-stictisconotrema-problem/D573F5D4A2519AA373CE10B2D7C1C6EE#},
	doi = {10.1017/S0024282904014653},
	abstract = {The family Stictidaceae (Ostropales, Ascomycota) contains both lichenized and non-lichenized fungi. Here, we test if Conotrema (lichenized) and Stictis (non-lichenized) as currently delimited are distinct monophyletic genera, by parsimony and parsimony jackknifing analyses of combined nuclear rDNA (ITS and partial LSU rDNA) and mitochondrial SSU rDNA sequence data matrices. The study includes four species of Stictis, three species of Conotrema, and representatives of the related Schizoxylon (lichenized), Odontotrema, Carestiella (at least sometimes associated with algae), Cryptodiscus and Thelotrema (lichenized). In all analyses, the Conotrema species were nested within Stictis with high support. Thus, we conclude that Conotrema are only lichenized representatives of Stictis. The type species of the two generic names, C. urceolatum and S. radiata, are sister taxa in our analyses. Furthermore, the analysis gave no support for the present infrageneric classification of Stictis. Carestiella socia (the type of Carestiella) and the two representatives of Schizoxylon studied were also nested within Stictis s. lat. The Odontotremataceae is the sister group to the Stictidaceae, and Cryptodiscus foveolaris groups with Thelotrema rather than with the Stictidaceae. We conclude that lichenization in the Stictidaceae does not characterize natural groups, and that Conotrema should be considered a synonym to Stictis, as predicted by anatomical characteristics. The new combinations Stictis urceolatum and Stictis populorum are made.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {The Lichenologist},
	author = {Wedin, Mats and Döring, Heidi and Könberg, Kristina and Gilenstam, Gunnar},
	month = jan,
	year = {2005},
	note = {Publisher: Cambridge University Press},
	keywords = {Carestiella, Conotrema, Schizoxylon, Stictidaceae, evolution, lichenization, phylogeny, saprotrophy},
	pages = {67--75},
}

The family Stictidaceae (Ostropales, Ascomycota) contains both lichenized and non-lichenized fungi. Here, we test if Conotrema (lichenized) and Stictis (non-lichenized) as currently delimited are distinct monophyletic genera, by parsimony and parsimony jackknifing analyses of combined nuclear rDNA (ITS and partial LSU rDNA) and mitochondrial SSU rDNA sequence data matrices. The study includes four species of Stictis, three species of Conotrema, and representatives of the related Schizoxylon (lichenized), Odontotrema, Carestiella (at least sometimes associated with algae), Cryptodiscus and Thelotrema (lichenized). In all analyses, the Conotrema species were nested within Stictis with high support. Thus, we conclude that Conotrema are only lichenized representatives of Stictis. The type species of the two generic names, C. urceolatum and S. radiata, are sister taxa in our analyses. Furthermore, the analysis gave no support for the present infrageneric classification of Stictis. Carestiella socia (the type of Carestiella) and the two representatives of Schizoxylon studied were also nested within Stictis s. lat. The Odontotremataceae is the sister group to the Stictidaceae, and Cryptodiscus foveolaris groups with Thelotrema rather than with the Stictidaceae. We conclude that lichenization in the Stictidaceae does not characterize natural groups, and that Conotrema should be considered a synonym to Stictis, as predicted by anatomical characteristics. The new combinations Stictis urceolatum and Stictis populorum are made.

@article{ciereszko_interactive_2005,
	title = {Interactive effects of phosphate deficiency, sucrose and light/dark conditions on gene expression of {UDP}-glucose pyrophosphory lase in {Arabidopsis}},
	volume = {162},
	issn = {0176-1617},
	doi = {10.1016/j.jplph.2004.08.003},
	abstract = {The effects of inorganic phosphate (Pi) status, light/dark and sucrose on expression of UDP-glucose pyrophosphorylase (UGPase) gene (Ugp), which is involved in sucrose/ polysaccharides metabolism, were investigated using Arabidopsis wild-type (wt) plants and mutants impaired in Pi and carbohydrate status. Generally, P-deficiency resulted in increased Ugp expression and enhanced UGPase activity and protein content, as found for wt plants grown on P-deficient and complete nutrient solution, as well as for pho1 (P-deficient) mutants. Ugp was highly expressed in darkened leaves of pho1, but not wt plants; daily tight exposure enhanced Ugp expression both in wt and pho mutants. The pho1 and pho2 (Pi-accumulating) mutations had Little or no effect on leaf contents of glucose and fructose, regardless of light/dark conditions, whereas pho1 plants had much higher Levels of sucrose and starch in the dark than pho2 and wt plants. The Ugp was up-regutated when leaves were fed with sucrose in wt plants, but the expression in pho2 background was much less sensitive to sucrose supply than in wt and pho1 plants. Expression of Ugp in pgm1 and sex1 mutants (impaired in starch/sugar content) was not dependent on starch content, and not tightly correlated with soluble sugar status. Okadaic acid (OKA) effectively blocked the P-starvation and sucrose -dependent expression of Ugp in excised leaves, whereas staurosporine (STA) had only a small effect on both processes (especially in -P leaves), suggesting that P-starvation and sucrose effects on Ugp are transmitted by pathways that may share similar components with respect to their (in)sensitivity to OKA and STA. The results of this study suggest that Ugp expression is modulated by an interaction of signals derived from P-deficiency status, sucrose content and dark/ light conditions, and that light/ sucrose and P-deficiency may have additive effects on Ugp expression. (c) 2004 Elsevier GmbH. All rights reserved.},
	language = {English},
	number = {3},
	journal = {Journal of Plant Physiology},
	author = {Ciereszko, I. and Johansson, H. and Kleczkowski, L. A.},
	month = mar,
	year = {2005},
	note = {Place: Jena
Publisher: Elsevier Gmbh, Urban \& Fischer Verlag
WOS:000228215900012},
	keywords = {accumulation, bean-plants, gene regulation, metabolism, okadaic acid, pho mutants, phosphate deficiency, phosphorus, photosynthesis, pi and sucrose   signaling, protein, roots, starch mutants, sucrose metabolism, thaliana},
	pages = {343--353},
}

The effects of inorganic phosphate (Pi) status, light/dark and sucrose on expression of UDP-glucose pyrophosphorylase (UGPase) gene (Ugp), which is involved in sucrose/ polysaccharides metabolism, were investigated using Arabidopsis wild-type (wt) plants and mutants impaired in Pi and carbohydrate status. Generally, P-deficiency resulted in increased Ugp expression and enhanced UGPase activity and protein content, as found for wt plants grown on P-deficient and complete nutrient solution, as well as for pho1 (P-deficient) mutants. Ugp was highly expressed in darkened leaves of pho1, but not wt plants; daily tight exposure enhanced Ugp expression both in wt and pho mutants. The pho1 and pho2 (Pi-accumulating) mutations had Little or no effect on leaf contents of glucose and fructose, regardless of light/dark conditions, whereas pho1 plants had much higher Levels of sucrose and starch in the dark than pho2 and wt plants. The Ugp was up-regutated when leaves were fed with sucrose in wt plants, but the expression in pho2 background was much less sensitive to sucrose supply than in wt and pho1 plants. Expression of Ugp in pgm1 and sex1 mutants (impaired in starch/sugar content) was not dependent on starch content, and not tightly correlated with soluble sugar status. Okadaic acid (OKA) effectively blocked the P-starvation and sucrose -dependent expression of Ugp in excised leaves, whereas staurosporine (STA) had only a small effect on both processes (especially in -P leaves), suggesting that P-starvation and sucrose effects on Ugp are transmitted by pathways that may share similar components with respect to their (in)sensitivity to OKA and STA. The results of this study suggest that Ugp expression is modulated by an interaction of signals derived from P-deficiency status, sucrose content and dark/ light conditions, and that light/ sucrose and P-deficiency may have additive effects on Ugp expression. (c) 2004 Elsevier GmbH. All rights reserved.

@article{gentili_physiological_2005,
	title = {Physiological and molecular diversity of feather moss associative {N}-2-fixing cyanobacteria},
	volume = {56},
	issn = {0022-0957},
	doi = {10.1093/jxb/eri309},
	abstract = {Cyanobacteria colonizing the feather moss Pleurozium schreberi were isolated from moss samples collected in northern Sweden and subjected to physiological and molecular characterization. Morphological studies of isolated and moss-associated cyanobacteria were carried out by light microscopy. Molecular tools were used for cyanobacteria identification, and a reconstitution experiment of the association between non-associative mosses and cyanobacteria was conducted. The influence of temperature on N-2 fixation in the different cyanobacterial isolates and the influence of light and temperature on N-2-fixation rates in the moss were studied using the acetylene reduction assay. Two different cyanobacteria were effectively isolated from P. schreberi: Nostoc sp. and Calothrix sp. A third genus, Stigonema sp. was identified by microscopy, but could not be isolated. The Nostoc sp. was found to fix N-2 at lower temperatures than Calothrix sp. Nostoc sp. and Stigonema sp. were the predominant cyanobacteria colonizing the moss. The attempt to reconstitute the association between the moss and cyanobacteria was successful. The two isolated genera of cyanobacteria in feather moss samples collected in northern Sweden differ in their temperature optima, which may have important ecological implications.},
	language = {English},
	number = {422},
	journal = {Journal of Experimental Botany},
	author = {Gentili, F. and Nilsson, M. C. and Zackrisson, O. and DeLuca, T. H. and Sellstedt, A.},
	month = dec,
	year = {2005},
	note = {Place: Oxford
Publisher: Oxford Univ Press
WOS:000233491300011},
	keywords = {Calothrix, N-2   fixation Nostoc, Stigonema, abiotic factors, acetylene reduction assay (ARA), antarctica, biological nitrogen-fixation, boreal forests, communities, cyanobacteria, devon-island, ecosystems, lowland, moss, svalbard, vegetation},
	pages = {3121--3127},
}

Cyanobacteria colonizing the feather moss Pleurozium schreberi were isolated from moss samples collected in northern Sweden and subjected to physiological and molecular characterization. Morphological studies of isolated and moss-associated cyanobacteria were carried out by light microscopy. Molecular tools were used for cyanobacteria identification, and a reconstitution experiment of the association between non-associative mosses and cyanobacteria was conducted. The influence of temperature on N-2 fixation in the different cyanobacterial isolates and the influence of light and temperature on N-2-fixation rates in the moss were studied using the acetylene reduction assay. Two different cyanobacteria were effectively isolated from P. schreberi: Nostoc sp. and Calothrix sp. A third genus, Stigonema sp. was identified by microscopy, but could not be isolated. The Nostoc sp. was found to fix N-2 at lower temperatures than Calothrix sp. Nostoc sp. and Stigonema sp. were the predominant cyanobacteria colonizing the moss. The attempt to reconstitute the association between the moss and cyanobacteria was successful. The two isolated genera of cyanobacteria in feather moss samples collected in northern Sweden differ in their temperature optima, which may have important ecological implications.

@article{witzell_polyamine_2005,
	title = {Polyamine {Profiles} {Of} {Healthy} and {Parasite}-{Infected} {Vaccinium} {Myrtillus} {Plants} {Under} {Nitrogen} {Enrichment}},
	volume = {31},
	issn = {1573-1561},
	url = {https://doi.org/10.1007/s10886-005-2041-6},
	doi = {10.1007/s10886-005-2041-6},
	abstract = {Addition of nitrogen (N) to the field layer of boreal forests has been shown to increase the occurrence of the parasitic fungus Valdensia heterodoxa on Vaccinium myrtillus plants. We investigated whether N addition to soil alters the levels of polyamines in V. myrtillus shoots, and discuss here whether such changes could promote the spread of the parasitic fungus on V. myrtillus. Using HPLC, we analyzed the concentrations of free and conjugated polyamines in healthy and naturally V. heterodoxa-infected V. myrtillus plants, which had received a moderate or high dose of N fertilizer, or no additional N. Fertilization with N increased the concentrations of free diamines (putrescine and diaminopropane), but had no significant effect on conjugated amines. Thus, N-induced changes in the constitutive levels of soluble conjugated amines do not seem to explain the increased parasite susceptibility of V. myrtillus under N enrichment. Generally, the concentrations of free diamines and insoluble conjugated putrescine were higher in diseased than in healthy shoots, suggesting parasite-induced accumulation of diamines. Free spermine seemed to accumulate in unfertilized, diseased plants, but in fertilized plants this induction was dampened, suggesting that N-induced alterations in spermine metabolism may promote the spread of parasites on V. myrtillus under N-enrichment.},
	language = {en},
	number = {3},
	urldate = {2021-06-11},
	journal = {Journal of Chemical Ecology},
	author = {Witzell, Johanna and Kuusela, Tiina and Sarjala, Tytti},
	month = mar,
	year = {2005},
	pages = {561--575},
}

Addition of nitrogen (N) to the field layer of boreal forests has been shown to increase the occurrence of the parasitic fungus Valdensia heterodoxa on Vaccinium myrtillus plants. We investigated whether N addition to soil alters the levels of polyamines in V. myrtillus shoots, and discuss here whether such changes could promote the spread of the parasitic fungus on V. myrtillus. Using HPLC, we analyzed the concentrations of free and conjugated polyamines in healthy and naturally V. heterodoxa-infected V. myrtillus plants, which had received a moderate or high dose of N fertilizer, or no additional N. Fertilization with N increased the concentrations of free diamines (putrescine and diaminopropane), but had no significant effect on conjugated amines. Thus, N-induced changes in the constitutive levels of soluble conjugated amines do not seem to explain the increased parasite susceptibility of V. myrtillus under N enrichment. Generally, the concentrations of free diamines and insoluble conjugated putrescine were higher in diseased than in healthy shoots, suggesting parasite-induced accumulation of diamines. Free spermine seemed to accumulate in unfertilized, diseased plants, but in fertilized plants this induction was dampened, suggesting that N-induced alterations in spermine metabolism may promote the spread of parasites on V. myrtillus under N-enrichment.

@article{karlsson_hydrogen_2005,
	title = {Hydrogen peroxide and expression of {hipI}-superoxide dismutase are associated with the development of secondary cell walls in {Zinnia} elegans},
	volume = {56},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/eri207},
	doi = {10.1093/jxb/eri207},
	abstract = {A special form of a CuZn-superoxide dismutase with a high isoelectric point (hipI-SOD; EC 1.15.1.1) and hydrogen peroxide (H2O2) production were studied during the secondary cell wall formation of the inducible tracheary element cell-culture system of Zinnia elegans L. Confocal microscopy after labelling with 2′,7′-dichlorofluorescin diacetate showed H2O2 to be located largely in the secondary cell walls in developing tracheary elements. Fluorescence-activated cell sorting analysis showed there were lower levels of H2O2 in the population containing tracheary elements when H2O2 scavengers such as ascorbate, catalase, and reduced glutathione were applied to the cell culture. Inhibitors of NADPH oxidase and SOD also reduced the amount of H2O2 in the tracheary elements. Furthermore, addition of these compounds to cell cultures at the time of tracheary element initiation reduced the amount of lignin and the development of the secondary cell walls. Analysis of UV excitation under a confocal laser scanning microscope confirmed these results. The expression of hipI-SOD increased as the number of tracheary elements in the cell culture increased and developed. Additionally, immunolocalization of a hipI-SOD isoform during the tracheary element differentiation showed a developmental build-up of the protein in the Golgi apparatus and the secondary cell wall. These findings suggest a novel hipI-SOD could be involved in the regulation of H2O2 required for the development of the secondary cell walls of tracheary elements.},
	number = {418},
	urldate = {2021-06-11},
	journal = {Journal of Experimental Botany},
	author = {Karlsson, Marlene and Melzer, Michael and Prokhorenko, Isabella and Johansson, Thorsten and Wingsle, Gunnar},
	month = aug,
	year = {2005},
	pages = {2085--2093},
}

A special form of a CuZn-superoxide dismutase with a high isoelectric point (hipI-SOD; EC 1.15.1.1) and hydrogen peroxide (H2O2) production were studied during the secondary cell wall formation of the inducible tracheary element cell-culture system of Zinnia elegans L. Confocal microscopy after labelling with 2′,7′-dichlorofluorescin diacetate showed H2O2 to be located largely in the secondary cell walls in developing tracheary elements. Fluorescence-activated cell sorting analysis showed there were lower levels of H2O2 in the population containing tracheary elements when H2O2 scavengers such as ascorbate, catalase, and reduced glutathione were applied to the cell culture. Inhibitors of NADPH oxidase and SOD also reduced the amount of H2O2 in the tracheary elements. Furthermore, addition of these compounds to cell cultures at the time of tracheary element initiation reduced the amount of lignin and the development of the secondary cell walls. Analysis of UV excitation under a confocal laser scanning microscope confirmed these results. The expression of hipI-SOD increased as the number of tracheary elements in the cell culture increased and developed. Additionally, immunolocalization of a hipI-SOD isoform during the tracheary element differentiation showed a developmental build-up of the protein in the Golgi apparatus and the secondary cell wall. These findings suggest a novel hipI-SOD could be involved in the regulation of H2O2 required for the development of the secondary cell walls of tracheary elements.

@article{hoglund_both_2005,
	title = {Both hypersensitive and non-hypersensitive responses are associated with resistance in {Salix} viminalis against the gall midge {Dasineura} marginemtorquens},
	volume = {56},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/eri318},
	doi = {10.1093/jxb/eri318},
	abstract = {Hypersensitivity responses (HR) play a major role in plant resistance to pathogens. It is often claimed that HR is also important in plant resistance to insects, although there is little unambiguous documentation. Large genotypic variation in resistance against the gall midge Dasineura marginemtorquens is found in Salix viminalis. Variation in larval performance and induced responses within a full-sib S. viminalis family is reported here; 36 sibling plants were completely resistant (larvae died within 48 h after egg hatch, no gall induction), 11 plants were totally susceptible, 25 plants were variable (living and dead larvae present on the same plant). Resistance was associated with HR, but to different degrees; 21 totally resistant genotypes showed typical HR symptoms (many distinct necrotic spots) whereas the remaining 15 genotypes showed no, or very few, such symptoms. Hydrogen peroxide, used as a marker for HR, was induced in genotypes expressing HR symptoms but not in resistant genotypes without symptoms, or in susceptible genotypes. These data suggest that production of hydrogen peroxide, and accompanying cell death, cannot explain larval mortality in the symptomless reaction. Another, as yet unknown, mechanism of resistance may be present. If so, then it is possible that this unknown mechanism also contributes to resistance in plants displaying HR. The apparent complexity observed in this interaction, with both visible and invisible plant responses associated with resistance against an adapted insect species, may have implications for the study of resistance factors in other plant–insect interactions.},
	number = {422},
	urldate = {2021-06-11},
	journal = {Journal of Experimental Botany},
	author = {Höglund, Solveig and Larsson, Stig and Wingsle, Gunnar},
	month = dec,
	year = {2005},
	pages = {3215--3222},
}

Hypersensitivity responses (HR) play a major role in plant resistance to pathogens. It is often claimed that HR is also important in plant resistance to insects, although there is little unambiguous documentation. Large genotypic variation in resistance against the gall midge Dasineura marginemtorquens is found in Salix viminalis. Variation in larval performance and induced responses within a full-sib S. viminalis family is reported here; 36 sibling plants were completely resistant (larvae died within 48 h after egg hatch, no gall induction), 11 plants were totally susceptible, 25 plants were variable (living and dead larvae present on the same plant). Resistance was associated with HR, but to different degrees; 21 totally resistant genotypes showed typical HR symptoms (many distinct necrotic spots) whereas the remaining 15 genotypes showed no, or very few, such symptoms. Hydrogen peroxide, used as a marker for HR, was induced in genotypes expressing HR symptoms but not in resistant genotypes without symptoms, or in susceptible genotypes. These data suggest that production of hydrogen peroxide, and accompanying cell death, cannot explain larval mortality in the symptomless reaction. Another, as yet unknown, mechanism of resistance may be present. If so, then it is possible that this unknown mechanism also contributes to resistance in plants displaying HR. The apparent complexity observed in this interaction, with both visible and invisible plant responses associated with resistance against an adapted insect species, may have implications for the study of resistance factors in other plant–insect interactions.

@article{storf_pigment_2005,
	title = {Pigment {Binding}, {Fluorescence} {Properties}, and {Oligomerization} {Behavior} of {Lhca5}, a {Novel} {Light}-harvesting {Protein}*},
	volume = {280},
	issn = {0021-9258},
	url = {https://www.sciencedirect.com/science/article/pii/S0021925819630103},
	doi = {10.1074/jbc.M411248200},
	abstract = {A new potential light-harvesting protein, named Lhca5, was recently detected in higher plants. Because of the low amount of Lhca5 in thylakoid membranes, the isolation of a native Lhca5 pigment-protein complex has not been achieved to date. Therefore, we used in vitro reconstitution to analyze whether Lhca5 binds pigments and is actually an additional light-harvesting protein. By this approach we could demonstrate that Lhca5 binds pigments in a unique stoichiometry. Analyses of pigment requirements for light-harvesting complex formation by Lhca5 revealed that chlorophyll b is the only indispensable pigment. Fluorescence measurements showed that ligated chlorophylls and carotenoids are arranged in a way that allows directed energy transfer within the light-harvesting complex. Reconstitutions of Lhca5 together with other Lhca proteins resulted in the formation of heterodimers with Lhca1. This result demonstrates that Lhca5 is indeed a protein belonging to the light-harvesting antenna of photosystem I. The properties of Lhca5 are compared with those of previously characterized Lhca proteins, and the consequences of an additional Lhca protein for the composition of the light-harvesting antenna of photosystem I are discussed in view of the recently published photosystem I structure of the pea.},
	language = {en},
	number = {7},
	urldate = {2021-06-11},
	journal = {Journal of Biological Chemistry},
	author = {Storf, Stefanie and Jansson, Stefan and Schmid, Volkmar H. R.},
	month = feb,
	year = {2005},
	pages = {5163--5168},
}

A new potential light-harvesting protein, named Lhca5, was recently detected in higher plants. Because of the low amount of Lhca5 in thylakoid membranes, the isolation of a native Lhca5 pigment-protein complex has not been achieved to date. Therefore, we used in vitro reconstitution to analyze whether Lhca5 binds pigments and is actually an additional light-harvesting protein. By this approach we could demonstrate that Lhca5 binds pigments in a unique stoichiometry. Analyses of pigment requirements for light-harvesting complex formation by Lhca5 revealed that chlorophyll b is the only indispensable pigment. Fluorescence measurements showed that ligated chlorophylls and carotenoids are arranged in a way that allows directed energy transfer within the light-harvesting complex. Reconstitutions of Lhca5 together with other Lhca proteins resulted in the formation of heterodimers with Lhca1. This result demonstrates that Lhca5 is indeed a protein belonging to the light-harvesting antenna of photosystem I. The properties of Lhca5 are compared with those of previously characterized Lhca proteins, and the consequences of an additional Lhca protein for the composition of the light-harvesting antenna of photosystem I are discussed in view of the recently published photosystem I structure of the pea.

@article{morosinotto_association_2005,
	title = {The {Association} of the {Antenna} {System} to {Photosystem} {I} in {Higher} {Plants}: {COOPERATIVE} {INTERACTIONS} {STABILIZE} {THE} {SUPRAMOLECULAR} {COMPLEX} {AND} {ENHANCE} {RED}-{SHIFTED} {SPECTRAL} {FORMS}*},
	volume = {280},
	issn = {0021-9258},
	shorttitle = {The {Association} of the {Antenna} {System} to {Photosystem} {I} in {Higher} {Plants}},
	url = {https://www.sciencedirect.com/science/article/pii/S0021925820793798},
	doi = {10.1074/jbc.M502935200},
	abstract = {We report on the association of the antenna system to the reaction center in Photosystem I. Biochemical analysis of mutants depleted in antenna polypeptides showed that the binding of the antenna moiety is strongly cooperative. The minimal building block for the antenna system was shown to be a dimer. Specific protein-protein interactions play an important role in antenna association, and the gap pigments, bound at the interface between core and antenna, are proposed to mediate these interactions Gap pigments have been characterized by comparing the spectra of the Photosystem I to those of the isolated antenna and core components. CD spectroscopy showed that they are involved in pigment-pigment interactions, supporting their relevance in energy transfer from antenna to the reaction center. Moreover, gap pigments contribute to the red-shifted emission forms of Photosystem I antenna. When compared with Photosystem II, the association of peripheral antenna complexes in PSI appears to be more stable, but far less flexible and functional implications are discussed.},
	language = {en},
	number = {35},
	urldate = {2021-06-11},
	journal = {Journal of Biological Chemistry},
	author = {Morosinotto, Tomas and Ballottari, Matteo and Klimmek, Frank and Jansson, Stefan and Bassi, Roberto},
	month = sep,
	year = {2005},
	pages = {31050--31058},
}

We report on the association of the antenna system to the reaction center in Photosystem I. Biochemical analysis of mutants depleted in antenna polypeptides showed that the binding of the antenna moiety is strongly cooperative. The minimal building block for the antenna system was shown to be a dimer. Specific protein-protein interactions play an important role in antenna association, and the gap pigments, bound at the interface between core and antenna, are proposed to mediate these interactions Gap pigments have been characterized by comparing the spectra of the Photosystem I to those of the isolated antenna and core components. CD spectroscopy showed that they are involved in pigment-pigment interactions, supporting their relevance in energy transfer from antenna to the reaction center. Moreover, gap pigments contribute to the red-shifted emission forms of Photosystem I antenna. When compared with Photosystem II, the association of peripheral antenna complexes in PSI appears to be more stable, but far less flexible and functional implications are discussed.

@article{moreau_genomic_2005,
	title = {A genomic approach to investigate developmental cell death in woody tissues of {Populus} trees},
	volume = {6},
	issn = {1474-760X},
	doi = {10.1186/gb-2005-6-4-r34},
	abstract = {Background: Poplar ( Populus sp.) has emerged as the main model system for molecular and genetic studies of forest trees. A Populus expressed sequence tag ( EST) database (POPULUSDB) was previously created from 19 cDNA libraries each originating from different Populus tree tissues, and opened to the public in September 2004. We used this dataset for in silico transcript profiling of a particular process in the woody tissues of the Populus stem: the programmed death of xylem fibers. Results: One EST library in POPULUSDB originates from woody tissues of the Populus stem where xylem fibers undergo cell death. Analysis of EST abundances and library distribution within the POPULUSDB revealed a large number of previously uncharacterized transcripts that were unique in this library and possibly related to the death of xylem fibers. The in silico analysis was complemented by a microarray analysis utilizing a novel Populus cDNA array with a unigene set of 25,000 sequences. Conclusions: In silico analysis, combined with the microarray analysis, revealed the usefulness of non-normalized EST libraries in elucidating transcriptional regulation of previously uncharacterized physiological processes. The data suggested the involvement of two novel extracellular serine proteases, nodulin-like proteins and an Arabidopsis thaliana OPEN STOMATA 1 (AtOST1) homolog in signaling fiber-cell death, as well as mechanisms responsible for hormonal control, nutrient remobilization, regulation of vacuolar integrity and autolysis of the dying fibers.},
	language = {English},
	number = {4},
	journal = {Genome Biology},
	author = {Moreau, C. and Aksenov, N. and Lorenzo, M. G. and Segerman, B. and Funk, C. and Nilsson, P. and Jansson, S. and Tuominen, H.},
	year = {2005},
	note = {Place: London
Publisher: Bmc
WOS:000228436000011},
	keywords = {arabidopsis, arabinogalactan proteins, expression, poplar, secondary   growth, senescence, serine proteases, tracheary element differentiation, transcriptome, xylogenesis},
	pages = {R34},
}

Background: Poplar ( Populus sp.) has emerged as the main model system for molecular and genetic studies of forest trees. A Populus expressed sequence tag ( EST) database (POPULUSDB) was previously created from 19 cDNA libraries each originating from different Populus tree tissues, and opened to the public in September 2004. We used this dataset for in silico transcript profiling of a particular process in the woody tissues of the Populus stem: the programmed death of xylem fibers. Results: One EST library in POPULUSDB originates from woody tissues of the Populus stem where xylem fibers undergo cell death. Analysis of EST abundances and library distribution within the POPULUSDB revealed a large number of previously uncharacterized transcripts that were unique in this library and possibly related to the death of xylem fibers. The in silico analysis was complemented by a microarray analysis utilizing a novel Populus cDNA array with a unigene set of 25,000 sequences. Conclusions: In silico analysis, combined with the microarray analysis, revealed the usefulness of non-normalized EST libraries in elucidating transcriptional regulation of previously uncharacterized physiological processes. The data suggested the involvement of two novel extracellular serine proteases, nodulin-like proteins and an Arabidopsis thaliana OPEN STOMATA 1 (AtOST1) homolog in signaling fiber-cell death, as well as mechanisms responsible for hormonal control, nutrient remobilization, regulation of vacuolar integrity and autolysis of the dying fibers.

@article{ingvarsson_nucleotide_2005,
	title = {Nucleotide polymorphism and linkage disequilbrium within and among natural populations of {European} {Aspen} ({Populus} tremula {L}., {Salicaceae})},
	volume = {169},
	issn = {0016-6731},
	doi = {10.1534/genetics.104.034959},
	abstract = {Populus is an important model organism in forest biology, but levels of nucleotide polymorphisms and linkage disequilibrium have never been investigated in natural populations. Here I present a study on levels of nucleotide polymorphism, haplotype structure, and population subdivision in five nuclear genes in the European aspen Populus tremula. Results show substantial levels of genetic variation. Levels of silent site polymorphisms, pi(s), averaged 0.016 across the five genes. Linkage disequilibrium was generally low, extending only a few hundred base pairs, suggesting that rates of recombination are high in this obligate outcrossing species. Significant genetic differentiation was found at all five genes, with an average estimate of F-ST = 0.116. Levels of polymorphism in P. tremula are 2- to 10-fold higher than those in other woody, long-lived perennial plants, such as Pinus and Cryptomeria. The high levels of nucleotide polymorphism and low linkage disequilibrium suggest that it may be possible to map functional variation to very fine scales in P. tremula using association-mapping approaches.},
	language = {English},
	number = {2},
	journal = {Genetics},
	author = {Ingvarsson, P. K.},
	month = feb,
	year = {2005},
	note = {Place: Bethesda
Publisher: Genetics Society America
WOS:000227697200037},
	keywords = {disequilibrium, dna   variation, genetic diversity, haplotype structure, locus, nuclear, patterns, recombination, sequence diversity, subdivision},
	pages = {945--953},
}

Populus is an important model organism in forest biology, but levels of nucleotide polymorphisms and linkage disequilibrium have never been investigated in natural populations. Here I present a study on levels of nucleotide polymorphism, haplotype structure, and population subdivision in five nuclear genes in the European aspen Populus tremula. Results show substantial levels of genetic variation. Levels of silent site polymorphisms, pi(s), averaged 0.016 across the five genes. Linkage disequilibrium was generally low, extending only a few hundred base pairs, suggesting that rates of recombination are high in this obligate outcrossing species. Significant genetic differentiation was found at all five genes, with an average estimate of F-ST = 0.116. Levels of polymorphism in P. tremula are 2- to 10-fold higher than those in other woody, long-lived perennial plants, such as Pinus and Cryptomeria. The high levels of nucleotide polymorphism and low linkage disequilibrium suggest that it may be possible to map functional variation to very fine scales in P. tremula using association-mapping approaches.

@article{galindo_induction_2005,
	title = {On the induction of cold acclimation in carrots ({Daucus} carota {L}.) and its influence on storage performance},
	volume = {38},
	issn = {0963-9969},
	doi = {10.1016/j.foodres.2004.07.004},
	abstract = {We investigated the role of cold acclimation in carrot plants with respect to its influence on the storage performance of the harvested taproots. The induction of cold acclimation was followed in plants cultivated in a growth chamber under strict climate control and in taproots harvested from two separate field cultivations where the plants had been exposed to the natural variations in climate. Under controlled growth conditions, levels of antifreeze protein (AFP) mRNA were used as a marker for cold acclimation in carrot taproot tissue. Expression of this gene was induced by cold in discs excised from harvested taproots and this induction was clearly affected by the growth temperature of the plants from which the taproots were taken. These in vitro data were consistent with those from field-grown plants. In the cell wall of taproots harvested in year 2000, where the intact plants had frequently been exposed to temperatures below 6degreesC, a 36 kDa AFP accumulated to higher levels during storage than in the taproots harvested from plants grown in year 2001, where cultivation temperatures had rarely dropped below 6degreesC. The taproots from 2001 exhibited poor storage performance as shown by an earlier increase in relative electrolyte leakage and decrease in dry matter compared to taproots harvested in 2000. The capacity of the AFP to accumulate during storage was consistent with a high storage performance. (C) 2004 Elsevier Ltd. All rights reserved.},
	language = {English},
	number = {1},
	journal = {Food Research International},
	author = {Galindo, F. G. and Elias, L. and Gekas, V. and Herppich, W. B. and Smallwood, M. and Sommarin, M. and Worrall, D. and Sjoholm, I.},
	year = {2005},
	note = {Place: Amsterdam
Publisher: Elsevier Science Bv
WOS:000226445900004},
	keywords = {antifreeze protein, carrots, cold acclimation, electrolyte leakage, freezing tolerance, genes, latitudes, leaves, mechanisms, storage performance, temperatures, wheat},
	pages = {29--36},
}

We investigated the role of cold acclimation in carrot plants with respect to its influence on the storage performance of the harvested taproots. The induction of cold acclimation was followed in plants cultivated in a growth chamber under strict climate control and in taproots harvested from two separate field cultivations where the plants had been exposed to the natural variations in climate. Under controlled growth conditions, levels of antifreeze protein (AFP) mRNA were used as a marker for cold acclimation in carrot taproot tissue. Expression of this gene was induced by cold in discs excised from harvested taproots and this induction was clearly affected by the growth temperature of the plants from which the taproots were taken. These in vitro data were consistent with those from field-grown plants. In the cell wall of taproots harvested in year 2000, where the intact plants had frequently been exposed to temperatures below 6degreesC, a 36 kDa AFP accumulated to higher levels during storage than in the taproots harvested from plants grown in year 2001, where cultivation temperatures had rarely dropped below 6degreesC. The taproots from 2001 exhibited poor storage performance as shown by an earlier increase in relative electrolyte leakage and decrease in dry matter compared to taproots harvested in 2000. The capacity of the AFP to accumulate during storage was consistent with a high storage performance. (C) 2004 Elsevier Ltd. All rights reserved.

@article{ihalainen_excitation_2005,
	title = {Excitation energy trapping in photosystem {I} complexes depleted in {Lhca1} and {Lhca4}},
	volume = {579},
	copyright = {FEBS Letters 579 (2005) 1873-3468 © 2015 Federation of European Biochemical Societies},
	issn = {1873-3468},
	url = {https://febs.onlinelibrary.wiley.com/doi/abs/10.1016/j.febslet.2005.06.091},
	doi = {10.1016/j.febslet.2005.06.091},
	abstract = {We report a time-resolved fluorescence spectroscopy characterization of photosystem I (PSI) particles prepared from Arabidopsis lines with knock-out mutations against the peripheral antenna proteins of Lhca1 or Lhca4. The first mutant retains Lhca2 and Lhca3 while the second retains one other light-harvesting protein of photosystem I (Lhca) protein, probably Lhca5. The results indicate that Lhca2/3 and Lhca1/4 each provides about equally effective energy transfer routes to the PSI core complex, and that Lhca5 provides a less effective energy transfer route. We suggest that the specific location of each Lhca protein within the PSI–LHCI supercomplex is more important than the presence of so-called red chlorophylls in the Lhca proteins.},
	language = {en},
	number = {21},
	urldate = {2021-06-11},
	journal = {FEBS Letters},
	author = {Ihalainen, Janne A. and Klimmek, Frank and Ganeteg, Ulrika and Stokkum, Ivo H. M. van and Grondelle, Rienk van and Jansson, Stefan and Dekker, Jan P.},
	year = {2005},
	note = {\_eprint: https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/j.febslet.2005.06.091},
	keywords = {DAS, Excitation energy trapping, LHCI, Lhca, Light-harvesting, PSI, Photosynthesis, WT, decay-associated spectra, light-harvesting complex I, light-harvesting protein of photosystem I, photosystem I, wild type},
	pages = {4787--4791},
}

We report a time-resolved fluorescence spectroscopy characterization of photosystem I (PSI) particles prepared from Arabidopsis lines with knock-out mutations against the peripheral antenna proteins of Lhca1 or Lhca4. The first mutant retains Lhca2 and Lhca3 while the second retains one other light-harvesting protein of photosystem I (Lhca) protein, probably Lhca5. The results indicate that Lhca2/3 and Lhca1/4 each provides about equally effective energy transfer routes to the PSI core complex, and that Lhca5 provides a less effective energy transfer route. We suggest that the specific location of each Lhca protein within the PSI–LHCI supercomplex is more important than the presence of so-called red chlorophylls in the Lhca proteins.

@article{bilir_fertility_2005,
	title = {Fertility variation in six populations of {Brutian} pine ({Pinus} brutia {Ten}.) over altitudinal ranges},
	volume = {141},
	issn = {0014-2336},
	doi = {10.1007/s10681-005-6803-6},
	abstract = {Fertility (number of strobili) was investigated in six natural populations over three ranges of altitudes (215-960 m) in Brutian pine (Pinus brutia Ten.) for two consecutive years. The fertility and fertility variation varied among populations and years. The average of strobilus production varied between 173 and 269 in female, and between 533 and 1,060 in male, respectively. The fertility variation did not seem closely related to the altitude, and it was not consistently dependent on the richness of strobilus production. Positive significant correlations were found between female and male strobilus production for all populations and years. Coefficient of variation in strobilus production among individual trees varied between 0.638 and 0.838 for female; and between 0.603 and 0.809 for male when flowering assessments were combined. The clone fertility variations among trees were slightly different among all six stands (sibling coefficient ranged from 1.354 to 1.525) and it is unlikely that trees in typical stands vary extremely in reproductive success.},
	language = {English},
	number = {1-2},
	journal = {Euphytica},
	author = {Bilir, N. and Kang, K. S. and Lindgren, D.},
	year = {2005},
	note = {Place: Dordrecht
Publisher: Springer
WOS:000228957300018},
	keywords = {Pinus brutia, altitude, cone production, fertility variation, genetic diversity, natural population, number, picea-abies, radiata, seed orchard, sibling   coefficient, spruce, sylvestris},
	pages = {163--168},
}

Fertility (number of strobili) was investigated in six natural populations over three ranges of altitudes (215-960 m) in Brutian pine (Pinus brutia Ten.) for two consecutive years. The fertility and fertility variation varied among populations and years. The average of strobilus production varied between 173 and 269 in female, and between 533 and 1,060 in male, respectively. The fertility variation did not seem closely related to the altitude, and it was not consistently dependent on the richness of strobilus production. Positive significant correlations were found between female and male strobilus production for all populations and years. Coefficient of variation in strobilus production among individual trees varied between 0.638 and 0.838 for female; and between 0.603 and 0.809 for male when flowering assessments were combined. The clone fertility variations among trees were slightly different among all six stands (sibling coefficient ranged from 1.354 to 1.525) and it is unlikely that trees in typical stands vary extremely in reproductive success.

@article{norberg_blade_2005,
	title = {The {BLADE} {ON} {PETIOLE} genes act redundantly to control the growth and development of lateral organs},
	volume = {132},
	issn = {0950-1991},
	url = {https://doi.org/10.1242/dev.01815},
	doi = {10.1242/dev.01815},
	abstract = {Developmental processes in multicellular organisms involve an intricate balance between mechanisms that promote cell division activity and growth, and others that promote cell differentiation. Leaf development in Arabidopsis thaliana is controlled by genes like BLADE ON PETIOLE1(BOP1), which prevent the development of ectopic meristematic activity that leads to the formation of new organs, and JAGGED(JAG), which control the proximodistal development of the leaf by regulating cell-division activity. We have isolated and characterized the BOP1 gene together with a functionally redundant close homolog that we name BOP2. The BOP genes are members of a gene family containing ankyrin repeats and a BTB/POZ domain, suggesting a role in protein-protein interaction. We show that the BOP genes are expressed in the proximal parts of plant lateral organs where they repress the transcription not only of class 1 knox genes but also of JAG. We also show that the BOP genes are acting together with the flower meristem identity gene LEAFY in the suppression of bract formation. These findings show that the BOP genes are important regulators of the growth and development of lateral organs.},
	number = {9},
	urldate = {2021-06-11},
	journal = {Development},
	author = {Norberg, Mikael and Holmlund, Mattias and Nilsson, Ove},
	month = may,
	year = {2005},
	pages = {2203--2213},
}

Developmental processes in multicellular organisms involve an intricate balance between mechanisms that promote cell division activity and growth, and others that promote cell differentiation. Leaf development in Arabidopsis thaliana is controlled by genes like BLADE ON PETIOLE1(BOP1), which prevent the development of ectopic meristematic activity that leads to the formation of new organs, and JAGGED(JAG), which control the proximodistal development of the leaf by regulating cell-division activity. We have isolated and characterized the BOP1 gene together with a functionally redundant close homolog that we name BOP2. The BOP genes are members of a gene family containing ankyrin repeats and a BTB/POZ domain, suggesting a role in protein-protein interaction. We show that the BOP genes are expressed in the proximal parts of plant lateral organs where they repress the transcription not only of class 1 knox genes but also of JAG. We also show that the BOP genes are acting together with the flower meristem identity gene LEAFY in the suppression of bract formation. These findings show that the BOP genes are important regulators of the growth and development of lateral organs.

@article{yanai_arabidopsis_2005,
	title = {Arabidopsis {KNOXI} {Proteins} {Activate} {Cytokinin} {Biosynthesis}},
	volume = {15},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982205008444},
	doi = {10.1016/j.cub.2005.07.060},
	abstract = {Plant architecture is shaped through the continuous formation of organs by meristems [1]. Class I KNOTTED1-like homeobox (KNOXI) genes are expressed in the shoot apical meristem (SAM) and are required for SAM maintenance [2, 3, 4, 5, 6]. KNOXI proteins and cytokinin, a plant hormone intimately associated with the regulation of cell division [7, 8], share overlapping roles, such as meristem maintenance and repression of senescence [2, 9, 10, 11], but their mechanistic and hierarchical relationship have yet to be defined. Here, we show that activation of three different KNOXI proteins using an inducible system resulted in a rapid increase in mRNA levels of the cytokinin biosynthesis gene isopentenyl transferase 7 (AtIPT7) and in the activation of ARR5, a cytokinin response factor. We further demonstrate a rapid and dramatic increase in cytokinin levels following activation of the KNOXI protein SHOOT MERISTEMLESS (STM). Application of exogenous cytokinin or expression of a cytokinin biosynthesis gene through the STM promoter partially rescued the stm mutant. We conclude that activation of cytokinin biosynthesis mediates KNOXI function in meristem maintenance. KNOXI proteins emerge as central regulators of hormone levels in plant meristems.},
	language = {en},
	number = {17},
	urldate = {2021-06-11},
	journal = {Current Biology},
	author = {Yanai, Osnat and Shani, Eilon and Dolezal, Karel and Tarkowski, Petr and Sablowski, Robert and Sandberg, Goran and Samach, Alon and Ori, Naomi},
	month = sep,
	year = {2005},
	pages = {1566--1571},
}

Plant architecture is shaped through the continuous formation of organs by meristems [1]. Class I KNOTTED1-like homeobox (KNOXI) genes are expressed in the shoot apical meristem (SAM) and are required for SAM maintenance [2, 3, 4, 5, 6]. KNOXI proteins and cytokinin, a plant hormone intimately associated with the regulation of cell division [7, 8], share overlapping roles, such as meristem maintenance and repression of senescence [2, 9, 10, 11], but their mechanistic and hierarchical relationship have yet to be defined. Here, we show that activation of three different KNOXI proteins using an inducible system resulted in a rapid increase in mRNA levels of the cytokinin biosynthesis gene isopentenyl transferase 7 (AtIPT7) and in the activation of ARR5, a cytokinin response factor. We further demonstrate a rapid and dramatic increase in cytokinin levels following activation of the KNOXI protein SHOOT MERISTEMLESS (STM). Application of exogenous cytokinin or expression of a cytokinin biosynthesis gene through the STM promoter partially rescued the stm mutant. We conclude that activation of cytokinin biosynthesis mediates KNOXI function in meristem maintenance. KNOXI proteins emerge as central regulators of hormone levels in plant meristems.

@article{carlsbecker_phloem_2005,
	series = {Cell signalling and gene regulation},
	title = {Phloem and xylem specification: pieces of the puzzle emerge},
	volume = {8},
	issn = {1369-5266},
	shorttitle = {Phloem and xylem specification},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526605000919},
	doi = {10.1016/j.pbi.2005.07.001},
	abstract = {The plant vascular system is composed of two tissue types, xylem and phloem, which originate from the vascular meristem, the procambium. Recently, several regulatory mechanisms that control the specification of these two tissue types have been uncovered. These include the asymmetric patterning of xylem and phloem in the vascular bundle by the class III HD-ZIP and KANADI genes, the tissue-type-specific control of vascular cell proliferation by brassinosteroids and class III HD-ZIP genes, the regulation of vascular tissue identity by the MYB-like transcription factor APL, and inductive signalling during xylem differentiation by xylogen. These findings define an emerging developmental framework for the control of vascular tissue specification.},
	language = {en},
	number = {5},
	urldate = {2021-06-11},
	journal = {Current Opinion in Plant Biology},
	author = {Carlsbecker, Annelie and Helariutta, Ykä},
	month = oct,
	year = {2005},
	pages = {512--517},
}

The plant vascular system is composed of two tissue types, xylem and phloem, which originate from the vascular meristem, the procambium. Recently, several regulatory mechanisms that control the specification of these two tissue types have been uncovered. These include the asymmetric patterning of xylem and phloem in the vascular bundle by the class III HD-ZIP and KANADI genes, the tissue-type-specific control of vascular cell proliferation by brassinosteroids and class III HD-ZIP genes, the regulation of vascular tissue identity by the MYB-like transcription factor APL, and inductive signalling during xylem differentiation by xylogen. These findings define an emerging developmental framework for the control of vascular tissue specification.

@article{leul_biodiversity_2005,
	title = {Biodiversity of {Hydrogenases} in {Frankia}},
	volume = {50},
	issn = {1432-0991},
	url = {https://doi.org/10.1007/s00284-004-4323-6},
	doi = {10.1007/s00284-004-4323-6},
	abstract = {Eighteen Frankia strains originally isolated from nine different host plants were used to study the biodiversity of hydrogenase in Frankia. In the physiological analysis, the activities of uptake hydrogenase and bidirectional hydrogenase were performed by monitoring the oxidation of hydrogen after supplying the cells with 1\% hydrogen and the evolution of hydrogen using methyl viologen as an electron donor, respectively. These analyses were supported with a study of the immunological relationship between Frankia hydrogenase and other different known hydrogenases from other microorganisms. Uptake hydrogenase activity was recorded from all the Frankia strains investigated. A methyl-viologen-mediated hydrogen evolution was recorded from only four Frankia strains irrespective of the source of Frankia. From the immunological and physiological studies, we here report that there are at least three types of hydrogenases in Frankia: Ni-Fe uptake hydrogenase, hydrogen-evolving hydrogenase, and [Fe]-hydrogenase. An immunogold localization study, by cryosection technique, of the effect of nickel on the intercellular distribution of hydrogenase proteins in Frankia indicated that nickel affects the transfer of hydrogenase proteins into the membrane.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {Current Microbiology},
	author = {Leul, Melakeselam and Mohapatra, Anasuya and Sellstedt, Anita},
	month = jan,
	year = {2005},
	pages = {17--23},
}

Eighteen Frankia strains originally isolated from nine different host plants were used to study the biodiversity of hydrogenase in Frankia. In the physiological analysis, the activities of uptake hydrogenase and bidirectional hydrogenase were performed by monitoring the oxidation of hydrogen after supplying the cells with 1% hydrogen and the evolution of hydrogen using methyl viologen as an electron donor, respectively. These analyses were supported with a study of the immunological relationship between Frankia hydrogenase and other different known hydrogenases from other microorganisms. Uptake hydrogenase activity was recorded from all the Frankia strains investigated. A methyl-viologen-mediated hydrogen evolution was recorded from only four Frankia strains irrespective of the source of Frankia. From the immunological and physiological studies, we here report that there are at least three types of hydrogenases in Frankia: Ni-Fe uptake hydrogenase, hydrogen-evolving hydrogenase, and [Fe]-hydrogenase. An immunogold localization study, by cryosection technique, of the effect of nickel on the intercellular distribution of hydrogenase proteins in Frankia indicated that nickel affects the transfer of hydrogenase proteins into the membrane.

@article{kepinski_plant_2005,
	title = {Plant {Development}: {Auxin} in {Loops}},
	volume = {15},
	issn = {0960-9822},
	shorttitle = {Plant {Development}},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982205002745},
	doi = {10.1016/j.cub.2005.03.012},
	abstract = {Concentration gradients of the hormone auxin are associated with various patterning events in plants. Recent work has refined our picture of the complex and dynamic system of auxin transport underlying the formation of these gradients.},
	language = {en},
	number = {6},
	urldate = {2021-06-11},
	journal = {Current Biology},
	author = {Kepinski, Stefan and Leyser, Ottoline},
	month = mar,
	year = {2005},
	pages = {R208--R210},
}

Concentration gradients of the hormone auxin are associated with various patterning events in plants. Recent work has refined our picture of the complex and dynamic system of auxin transport underlying the formation of these gradients.

@article{wirta_assembly_2005,
	title = {Assembly of a gene sequence tag microarray by reversible biotin-streptavidin capture for transcript analysis of {Arabidopsis} thaliana},
	volume = {5},
	issn = {1472-6750},
	url = {https://doi.org/10.1186/1472-6750-5-5},
	doi = {10.1186/1472-6750-5-5},
	abstract = {Transcriptional profiling using microarrays has developed into a key molecular tool for the elucidation of gene function and gene regulation. Microarray platforms based on either oligonucleotides or purified amplification products have been utilised in parallel to produce large amounts of data. Irrespective of platform examined, the availability of genome sequence or a large number of representative expressed sequence tags (ESTs) is, however, a pre-requisite for the design and selection of specific and high-quality microarray probes. This is of great importance for organisms, such as Arabidopsis thaliana, with a high number of duplicated genes, as cross-hybridisation signals between evolutionary related genes cannot be distinguished from true signals unless the probes are carefully designed to be specific.},
	number = {1},
	urldate = {2021-06-11},
	journal = {BMC Biotechnology},
	author = {Wirta, Valtteri and Holmberg, Anders and Lukacs, Morten and Nilsson, Peter and Hilson, Pierre and Uhlén, Mathias and Bhalerao, Rishikesh P. and Lundeberg, Joakim},
	month = feb,
	year = {2005},
	keywords = {Additional Data File, Auxin Regulation, Auxin Transporter, Multiple Reuse, Photo Multiplier Tube},
	pages = {5},
}

Transcriptional profiling using microarrays has developed into a key molecular tool for the elucidation of gene function and gene regulation. Microarray platforms based on either oligonucleotides or purified amplification products have been utilised in parallel to produce large amounts of data. Irrespective of platform examined, the availability of genome sequence or a large number of representative expressed sequence tags (ESTs) is, however, a pre-requisite for the design and selection of specific and high-quality microarray probes. This is of great importance for organisms, such as Arabidopsis thaliana, with a high number of duplicated genes, as cross-hybridisation signals between evolutionary related genes cannot be distinguished from true signals unless the probes are carefully designed to be specific.

@article{bylesjo_masqot_2005,
	title = {{MASQOT}: a method for {cDNA} microarray spot quality control},
	volume = {6},
	issn = {1471-2105},
	shorttitle = {{MASQOT}},
	url = {https://doi.org/10.1186/1471-2105-6-250},
	doi = {10.1186/1471-2105-6-250},
	abstract = {cDNA microarray technology has emerged as a major player in the parallel detection of biomolecules, but still suffers from fundamental technical problems. Identifying and removing unreliable data is crucial to prevent the risk of receiving illusive analysis results. Visual assessment of spot quality is still a common procedure, despite the time-consuming work of manually inspecting spots in the range of hundreds of thousands or more.},
	number = {1},
	urldate = {2021-06-11},
	journal = {BMC Bioinformatics},
	author = {Bylesjö, Max and Eriksson, Daniel and Sjödin, Andreas and Sjöström, Michael and Jansson, Stefan and Antti, Henrik and Trygg, Johan},
	month = oct,
	year = {2005},
	keywords = {Classification Training, Foreground Region, Microarray Slide, Partial Little Square, Spot Quality},
	pages = {250},
}

cDNA microarray technology has emerged as a major player in the parallel detection of biomolecules, but still suffers from fundamental technical problems. Identifying and removing unreliable data is crucial to prevent the risk of receiving illusive analysis results. Visual assessment of spot quality is still a common procedure, despite the time-consuming work of manually inspecting spots in the range of hundreds of thousands or more.

@article{zelent_optical_2005,
	title = {Optical {Spectra} of {Lactoperoxidase} as a {Function} of {Solvent}},
	volume = {44},
	issn = {0006-2960},
	url = {https://doi.org/10.1021/bi0513655},
	doi = {10.1021/bi0513655},
	abstract = {The iron of lactoperoxidase is predominantly high-spin at ambient temperature. Optical spectra of lactoperoxidase indicate that the iron changes from high-spin to low-spin in the temperature range from room temperature to 20 K. The transformation is independent of whether the enzyme is in glycerol/water or solid sugar glass. Addition of the inhibitor benzohydroxamic acid increases the amount of the low-spin form, and again the transformation is independent of whether the protein is in an aqueous solution or a nearly anhydrous sugar. In contrast to lactoperoxidase, horseradish peroxidase remains high-spin over the temperature excursion in both solvents and with addition of benzohydroxamic acid. We conclude that details of the heme pocket of lactoperoxidase allow ligation changes with temperature that are dependent upon the apoprotein but independent of solvent fluctuations. At low pH, lactoperoxidase shows a solvent-dependent transition; the high-spin form is predominant in anhydrous sugar glass, but in the presence of water, the low-spin form is also present in abundance. The active site of lactoperoxidase is not as tightly constrained at low pH as at neutrality, though the enzyme is active over a wide pH range.},
	number = {48},
	urldate = {2021-06-11},
	journal = {Biochemistry},
	author = {Zelent, B. and Yano, T. and Ohlsson, P.-I. and Smith, M. L. and Paul, J. and Vanderkooi, J. M.},
	month = dec,
	year = {2005},
	note = {Publisher: American Chemical Society},
	pages = {15953--15959},
}

The iron of lactoperoxidase is predominantly high-spin at ambient temperature. Optical spectra of lactoperoxidase indicate that the iron changes from high-spin to low-spin in the temperature range from room temperature to 20 K. The transformation is independent of whether the enzyme is in glycerol/water or solid sugar glass. Addition of the inhibitor benzohydroxamic acid increases the amount of the low-spin form, and again the transformation is independent of whether the protein is in an aqueous solution or a nearly anhydrous sugar. In contrast to lactoperoxidase, horseradish peroxidase remains high-spin over the temperature excursion in both solvents and with addition of benzohydroxamic acid. We conclude that details of the heme pocket of lactoperoxidase allow ligation changes with temperature that are dependent upon the apoprotein but independent of solvent fluctuations. At low pH, lactoperoxidase shows a solvent-dependent transition; the high-spin form is predominant in anhydrous sugar glass, but in the presence of water, the low-spin form is also present in abundance. The active site of lactoperoxidase is not as tightly constrained at low pH as at neutrality, though the enzyme is active over a wide pH range.

@article{shutova_structural_2005,
	title = {Structural {Dynamics} of the {Manganese}-{Stabilizing} {ProteinEffect} of {pH}, {Calcium}, and {Manganese}},
	volume = {44},
	issn = {0006-2960},
	url = {https://doi.org/10.1021/bi0512750},
	doi = {10.1021/bi0512750},
	abstract = {The photosystem-II-associated 33-kDa extrinsic manganese-stabilizing protein is found in all oxygen-evolving organisms. In this paper, we show that this protein undergoes pH-induced conformational changes in the physiological pH range. At a neutral pH of 7.2, the hydrophobic amino acid residues that are most likely located inside the β barrel are “closed” and the protein binds neither Mn2+ nor Ca2+ ions. When the protein is transferred to a solution with a slightly acidic pH of 5.7, hydrophobic amino acid residues become exposed to the surrounding medium, enabling them to bind the fluorescent probe 8,1-ANS. At this pH-induced open state, Mn2+ and Ca2+ bind to the manganese-stabilizing protein. The pH values used in this study, 7.2 and 5.7, are typical of the pH found in the thylakoid lumen in the dark and light, respectively. A model is presented in which the manganese-stabilizing protein undergoes a pH-dependent conformational change that in turn influences its capacity to bind calcium and manganese. In this model, the proton-dependent conformational changes of the tertiary structure of the manganese-stabilizing protein are of functional relevance for the regulation of substrate (water) delivery to and product (proton) release from the water-oxidizing complex by forming a proton-sensing proton-transport pathway.},
	number = {46},
	urldate = {2021-06-11},
	journal = {Biochemistry},
	author = {Shutova, Tatiana and Nikitina, Julia and Deikus, Gintaras and Andersson, Bertil and Klimov, Vyacheslav and Samuelsson, Göran},
	month = nov,
	year = {2005},
	note = {Publisher: American Chemical Society},
	pages = {15182--15192},
}

The photosystem-II-associated 33-kDa extrinsic manganese-stabilizing protein is found in all oxygen-evolving organisms. In this paper, we show that this protein undergoes pH-induced conformational changes in the physiological pH range. At a neutral pH of 7.2, the hydrophobic amino acid residues that are most likely located inside the β barrel are “closed” and the protein binds neither Mn2+ nor Ca2+ ions. When the protein is transferred to a solution with a slightly acidic pH of 5.7, hydrophobic amino acid residues become exposed to the surrounding medium, enabling them to bind the fluorescent probe 8,1-ANS. At this pH-induced open state, Mn2+ and Ca2+ bind to the manganese-stabilizing protein. The pH values used in this study, 7.2 and 5.7, are typical of the pH found in the thylakoid lumen in the dark and light, respectively. A model is presented in which the manganese-stabilizing protein undergoes a pH-dependent conformational change that in turn influences its capacity to bind calcium and manganese. In this model, the proton-dependent conformational changes of the tertiary structure of the manganese-stabilizing protein are of functional relevance for the regulation of substrate (water) delivery to and product (proton) release from the water-oxidizing complex by forming a proton-sensing proton-transport pathway.

@article{leul_molecular_2005,
	title = {Molecular characterization of uptake hydrogenase in {Frankia}},
	volume = {33},
	issn = {0300-5127},
	url = {https://doi.org/10.1042/BST0330064},
	doi = {10.1042/BST0330064},
	abstract = {A molecular characterization of uptake hydrogenase in Frankia was performed by using two-dimensional gel electrophoresis, matrix-assisted laser-desorption ionization–time-of-flight mass spectrometry, PCR amplification and Southern blotting. A polypeptide of approx. 60 kDa was recognized in Frankia UGL011102, AVCI1 and KB5 on the two-dimensional gel by blotting with Ralstonia eutropha (Hox G) antibody. Further analysis by MS resulted in a peptide ‘fingerprint’, which was similar to the membrane-bound hydrogenase 2 large subunit (HYD2) in Escherichia coli. In addition, a 127 bp PCR fragment could also be amplified from Frankia AVCI1, which gave a 76\% similarity with the large subunit of hydrogenase in, e.g., Azotobacter chrococcum, Bradyrhizobium japonicum and Rhizobium leguminosarum. Although immunological similarity between the small subunit of Frankia hydrogenase and that of other organisms has not yet been found, a PCR product of 500 bp could be amplified from the local source of Frankia, the analysis of which gave 69 and 67\% identity with the small subunit of hydrogenases in B. japonicum and R. leguminosarum respectively. A Southern-blot analysis further indicated evidence for the presence of the small hydrogenase subunit in other Frankia strains, i.e. KB5, AvcI1 and CcI3.},
	number = {1},
	urldate = {2021-06-11},
	journal = {Biochemical Society Transactions},
	author = {Leul, M. and Mattsson, U. and Sellstedt, A.},
	month = feb,
	year = {2005},
	pages = {64--66},
}

A molecular characterization of uptake hydrogenase in Frankia was performed by using two-dimensional gel electrophoresis, matrix-assisted laser-desorption ionization–time-of-flight mass spectrometry, PCR amplification and Southern blotting. A polypeptide of approx. 60 kDa was recognized in Frankia UGL011102, AVCI1 and KB5 on the two-dimensional gel by blotting with Ralstonia eutropha (Hox G) antibody. Further analysis by MS resulted in a peptide ‘fingerprint’, which was similar to the membrane-bound hydrogenase 2 large subunit (HYD2) in Escherichia coli. In addition, a 127 bp PCR fragment could also be amplified from Frankia AVCI1, which gave a 76% similarity with the large subunit of hydrogenase in, e.g., Azotobacter chrococcum, Bradyrhizobium japonicum and Rhizobium leguminosarum. Although immunological similarity between the small subunit of Frankia hydrogenase and that of other organisms has not yet been found, a PCR product of 500 bp could be amplified from the local source of Frankia, the analysis of which gave 69 and 67% identity with the small subunit of hydrogenases in B. japonicum and R. leguminosarum respectively. A Southern-blot analysis further indicated evidence for the presence of the small hydrogenase subunit in other Frankia strains, i.e. KB5, AvcI1 and CcI3.

@article{barker-astrom_chlorosis_2005,
	title = {Chlorosis during nitrogen starvation is altered by carbon dioxide and temperature status and is mediated by the {ClpP1} protease in {Synechococcus} elongatus},
	volume = {183},
	issn = {1432-072X},
	url = {https://doi.org/10.1007/s00203-004-0741-x},
	doi = {10.1007/s00203-004-0741-x},
	abstract = {The interactive effects of inorganic carbon status, temperature and light on chlorosis induced by nitrogen deficiency, and the roles of Clp proteases in this process were investigated. In wild-type cultures grown in high or ambient CO2, following transfer to media lacking combined nitrogen, phycocyanin per cell dropped primarily through dilution of the pigment through cell division, and also suffered variable degrees of net degradation. When grown at high CO2 (5\%), chlorophyll (Chl) suffered net degradation to a greater extent than phycocyanin. In marked contrast, growth at ambient CO2 resulted in Chl per cell dropping through dilution. Conditions that drove net Chl degradation in the wild-type resulted in little or no net Chl degradation in a clpPI inactivation mutant, with Chl content dropping largely through growth dilution in the mutant. The chlorotic response of a clpPII inactivation strain was nearly the same as that of wild-type, although phycocyanin degradation may have been slightly accelerated in the former.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {Archives of Microbiology},
	author = {Barker-Åström, Kara and Schelin, Jenny and Gustafsson, Petter and Clarke, Adrian K. and Campbell, Douglas A.},
	month = jan,
	year = {2005},
	pages = {66--69},
}

The interactive effects of inorganic carbon status, temperature and light on chlorosis induced by nitrogen deficiency, and the roles of Clp proteases in this process were investigated. In wild-type cultures grown in high or ambient CO2, following transfer to media lacking combined nitrogen, phycocyanin per cell dropped primarily through dilution of the pigment through cell division, and also suffered variable degrees of net degradation. When grown at high CO2 (5%), chlorophyll (Chl) suffered net degradation to a greater extent than phycocyanin. In marked contrast, growth at ambient CO2 resulted in Chl per cell dropping through dilution. Conditions that drove net Chl degradation in the wild-type resulted in little or no net Chl degradation in a clpPI inactivation mutant, with Chl content dropping largely through growth dilution in the mutant. The chlorotic response of a clpPII inactivation strain was nearly the same as that of wild-type, although phycocyanin degradation may have been slightly accelerated in the former.

@article{rouhier_identification_2005,
	title = {Identification of {Plant} {Glutaredoxin} {Targets}},
	volume = {7},
	issn = {1523-0864},
	url = {https://www.liebertpub.com/doi/10.1089/ars.2005.7.919},
	doi = {10.1089/ars.2005.7.919},
	abstract = {Glutaredoxins (Grxs) are small ubiquitous proteins of the thioredoxin (Trx) family, which catalyze dithiol–disulfide exchange reactions or reduce protein-mixed glutathione disulfides. In plants, several Trx-interacting proteins have been isolated from different compartments, whereas very few Grx-interacting proteins are known. We describe here the determination of Grx target proteins using a mutated poplar Grx, various tissular and subcellular plant extracts, and liquid chromatography coupled to tandem mass spectrometry detection. We have identified 94 putative targets, involved in many processes, including oxidative stress response [peroxiredoxins (Prxs), ascorbate peroxidase, catalase], nitrogen, sulfur, and carbon metabolisms (methionine synthase, alanine aminotransferase, phosphoglycerate kinase), translation (elongation factors E and Tu), or protein folding (heat shock protein 70). Some of these proteins were previously found to interact with Trx or to be glutathiolated in other organisms, but others could be more specific partners of Grx. To substantiate further these data, Grx was shown to support catalysis of the stroma β-type carbonic anhydrase and Prx IIF of Arabidopsis thaliana, but not of poplar 2-Cys Prx. Overall, these data suggest that the interaction could occur randomly either with exposed cysteinyl disulfide bonds formed within or between target proteins or with mixed disulfides between a protein thiol and glutathione.Antioxid. Redox Signal. 7, 919–929.},
	number = {7-8},
	urldate = {2021-06-11},
	journal = {Antioxidants \& Redox Signaling},
	author = {Rouhier, Nicolas and Villarejo, Arsenio and Srivastava, Manoj and Gelhaye, Eric and Keech, Olivier and Droux, Michel and Finkemeier, Iris and Samuelsson, Göran and Dietz, Karl Josef and Jacquot, Jean-Pierre and Wingsle, Gunnar},
	month = jul,
	year = {2005},
	note = {Publisher: Mary Ann Liebert, Inc., publishers},
	pages = {919--929},
}

Glutaredoxins (Grxs) are small ubiquitous proteins of the thioredoxin (Trx) family, which catalyze dithiol–disulfide exchange reactions or reduce protein-mixed glutathione disulfides. In plants, several Trx-interacting proteins have been isolated from different compartments, whereas very few Grx-interacting proteins are known. We describe here the determination of Grx target proteins using a mutated poplar Grx, various tissular and subcellular plant extracts, and liquid chromatography coupled to tandem mass spectrometry detection. We have identified 94 putative targets, involved in many processes, including oxidative stress response [peroxiredoxins (Prxs), ascorbate peroxidase, catalase], nitrogen, sulfur, and carbon metabolisms (methionine synthase, alanine aminotransferase, phosphoglycerate kinase), translation (elongation factors E and Tu), or protein folding (heat shock protein 70). Some of these proteins were previously found to interact with Trx or to be glutathiolated in other organisms, but others could be more specific partners of Grx. To substantiate further these data, Grx was shown to support catalysis of the stroma β-type carbonic anhydrase and Prx IIF of Arabidopsis thaliana, but not of poplar 2-Cys Prx. Overall, these data suggest that the interaction could occur randomly either with exposed cysteinyl disulfide bonds formed within or between target proteins or with mixed disulfides between a protein thiol and glutathione.Antioxid. Redox Signal. 7, 919–929.

@article{jonsson_high-throughput_2005,
	title = {High-{Throughput} {Data} {Analysis} for {Detecting} and {Identifying} {Differences} between {Samples} in {GC}/{MS}-{Based} {Metabolomic} {Analyses}},
	volume = {77},
	issn = {0003-2700},
	url = {https://doi.org/10.1021/ac050601e},
	doi = {10.1021/ac050601e},
	abstract = {In metabolomics, the objective is to identify differences in metabolite profiles between samples. A widely used tool in metabolomics investigations is gas chromatography−mass spectrometry (GC/MS). More than 400 compounds can be detected in a single analysis, if overlapping GC/MS peaks are deconvoluted. However, the deconvolution process is time-consuming and difficult to automate, and additional processing is needed in order to compare samples. Therefore, there is a need to improve and automate the data processing strategy for data generated in GC/MS-based metabolomics; if not, the processing step will be a major bottleneck for high-throughput analyses. Here we describe a new semiautomated strategy using a hierarchical multivariate curve resolution approach that processes all samples simultaneously. The presented strategy generates (after appropriate treatment, e.g., multivariate analysis) tables of all the detected metabolites that differ in relative concentrations between samples. The processing of 70 samples took similar time to that of the GC/TOFMS analyses of the samples. The strategy has been validated using two different sets of samples:  a complex mixture of standard compounds and Arabidopsis samples.},
	number = {17},
	urldate = {2021-06-11},
	journal = {Analytical Chemistry},
	author = {Jonsson, Pär and Johansson, Annika I. and Gullberg, Jonas and Trygg, Johan and A, Jiye and Grung, Bjørn and Marklund, Stefan and Sjöström, Michael and Antti, Henrik and Moritz, Thomas},
	month = sep,
	year = {2005},
	note = {Publisher: American Chemical Society},
	pages = {5635--5642},
}

In metabolomics, the objective is to identify differences in metabolite profiles between samples. A widely used tool in metabolomics investigations is gas chromatography−mass spectrometry (GC/MS). More than 400 compounds can be detected in a single analysis, if overlapping GC/MS peaks are deconvoluted. However, the deconvolution process is time-consuming and difficult to automate, and additional processing is needed in order to compare samples. Therefore, there is a need to improve and automate the data processing strategy for data generated in GC/MS-based metabolomics; if not, the processing step will be a major bottleneck for high-throughput analyses. Here we describe a new semiautomated strategy using a hierarchical multivariate curve resolution approach that processes all samples simultaneously. The presented strategy generates (after appropriate treatment, e.g., multivariate analysis) tables of all the detected metabolites that differ in relative concentrations between samples. The processing of 70 samples took similar time to that of the GC/TOFMS analyses of the samples. The strategy has been validated using two different sets of samples:  a complex mixture of standard compounds and Arabidopsis samples.

@article{a_extraction_2005,
	title = {Extraction and {GC}/{MS} {Analysis} of the {Human} {Blood} {Plasma} {Metabolome}},
	volume = {77},
	issn = {0003-2700},
	url = {https://doi.org/10.1021/ac051211v},
	doi = {10.1021/ac051211v},
	abstract = {Analysis of the entire set of low molecular weight compounds (LMC), the metabolome, could provide deeper insights into mechanisms of disease and novel markers for diagnosis. In the investigation, we developed an extraction and derivatization protocol, using experimental design theory (design of experiment), for analyzing the human blood plasma metabolome by GC/MS. The protocol was optimized by evaluating the data for more than 500 resolved peaks using multivariate statistical tools including principal component analysis and partial least-squares projections to latent structures (PLS). The performance of five organic solvents (methanol, ethanol, acetonitrile, acetone, chloroform), singly and in combination, was investigated to optimize the LMC extraction. PLS analysis demonstrated that methanol extraction was particularly efficient and highly reproducible. The extraction and derivatization conditions were also optimized. Quantitative data for 32 endogenous compounds showed good precision and linearity. In addition, the determined amounts of eight selected compounds agreed well with analyses by independent methods in accredited laboratories, and most of the compounds could be detected at absolute levels of ∼0.1 pmol injected, corresponding to plasma concentrations between 0.1 and 1 μM. The results suggest that the method could be usefully integrated into metabolomic studies for various purposes, e.g., for identifying biological markers related to diseases.},
	number = {24},
	urldate = {2021-06-11},
	journal = {Analytical Chemistry},
	author = {A, Jiye and Trygg, Johan and Gullberg, Jonas and Johansson, Annika I. and Jonsson, Pär and Antti, Henrik and Marklund, Stefan L. and Moritz, Thomas},
	month = dec,
	year = {2005},
	note = {Publisher: American Chemical Society},
	pages = {8086--8094},
}

Analysis of the entire set of low molecular weight compounds (LMC), the metabolome, could provide deeper insights into mechanisms of disease and novel markers for diagnosis. In the investigation, we developed an extraction and derivatization protocol, using experimental design theory (design of experiment), for analyzing the human blood plasma metabolome by GC/MS. The protocol was optimized by evaluating the data for more than 500 resolved peaks using multivariate statistical tools including principal component analysis and partial least-squares projections to latent structures (PLS). The performance of five organic solvents (methanol, ethanol, acetonitrile, acetone, chloroform), singly and in combination, was investigated to optimize the LMC extraction. PLS analysis demonstrated that methanol extraction was particularly efficient and highly reproducible. The extraction and derivatization conditions were also optimized. Quantitative data for 32 endogenous compounds showed good precision and linearity. In addition, the determined amounts of eight selected compounds agreed well with analyses by independent methods in accredited laboratories, and most of the compounds could be detected at absolute levels of ∼0.1 pmol injected, corresponding to plasma concentrations between 0.1 and 1 μM. The results suggest that the method could be usefully integrated into metabolomic studies for various purposes, e.g., for identifying biological markers related to diseases.

@article{cloarec_evaluation_2005,
	title = {Evaluation of the {Orthogonal} {Projection} on {Latent} {Structure} {Model} {Limitations} {Caused} by {Chemical} {Shift} {Variability} and {Improved} {Visualization} of {Biomarker} {Changes} in {1H} {NMR} {Spectroscopic} {Metabonomic} {Studies}},
	volume = {77},
	issn = {0003-2700},
	url = {https://doi.org/10.1021/ac048803i},
	doi = {10.1021/ac048803i},
	abstract = {In general, applications of metabonomics using biofluid NMR spectroscopic analysis for probing abnormal biochemical profiles in disease or due to toxicity have all relied on the use of chemometric techniques for sample classification. However, the well-known variability of some chemical shifts in 1H NMR spectra of biofluids due to environmental differences such as pH variation, when coupled with the large number of variables in such spectra, has led to the situation where it is necessary to reduce the size of the spectra or to attempt to align the shifting peaks, to get more robust and interpretable chemometric models. Here, a new approach that avoids this problem is demonstrated and shows that, moreover, inclusion of variable peak position data can be beneficial and can lead to useful biochemical information. The interpretation of chemometric models using combined back-scaled loading plots and variable weights demonstrates that this peak position variation can be handled successfully and also often provides additional information on the physicochemical variations in metabonomic data sets.},
	number = {2},
	urldate = {2021-06-11},
	journal = {Analytical Chemistry},
	author = {Cloarec, Olivier and Dumas, Marc E. and Trygg, Johan and Craig, Andrew and Barton, Richard H. and Lindon, John C. and Nicholson, Jeremy K. and Holmes, Elaine},
	month = jan,
	year = {2005},
	note = {Publisher: American Chemical Society},
	pages = {517--526},
}

In general, applications of metabonomics using biofluid NMR spectroscopic analysis for probing abnormal biochemical profiles in disease or due to toxicity have all relied on the use of chemometric techniques for sample classification. However, the well-known variability of some chemical shifts in 1H NMR spectra of biofluids due to environmental differences such as pH variation, when coupled with the large number of variables in such spectra, has led to the situation where it is necessary to reduce the size of the spectra or to attempt to align the shifting peaks, to get more robust and interpretable chemometric models. Here, a new approach that avoids this problem is demonstrated and shows that, moreover, inclusion of variable peak position data can be beneficial and can lead to useful biochemical information. The interpretation of chemometric models using combined back-scaled loading plots and variable weights demonstrates that this peak position variation can be handled successfully and also often provides additional information on the physicochemical variations in metabonomic data sets.

@article{jonsson_extraction_2005,
	title = {Extraction, interpretation and validation of information for comparing samples in metabolic {LC}/{MS} data sets},
	volume = {130},
	issn = {1364-5528},
	url = {https://pubs.rsc.org/en/content/articlelanding/2005/an/b501890k},
	doi = {10.1039/B501890K},
	abstract = {LC/MS is an analytical technique that, due to its high sensitivity, has become increasingly popular for the generation of metabolic signatures in biological samples and for the building of metabolic data bases. However, to be able to create robust and interpretable (transparent) multivariate models for the comparison of many samples, the data must fulfil certain specific criteria: (i) that each sample is characterized by the same number of variables, (ii) that each of these variables is represented across all observations, and (iii) that a variable in one sample has the same biological meaning or represents the same metabolite in all other samples. In addition, the obtained models must have the ability to make predictions of, e.g. related and independent samples characterized accordingly to the model samples. This method involves the construction of a representative data set, including automatic peak detection, alignment, setting of retention time windows, summing in the chromatographic dimension and data compression by means of alternating regression, where the relevant metabolic variation is retained for further modelling using multivariate analysis. This approach has the advantage of allowing the comparison of large numbers of samples based on their LC/MS metabolic profiles, but also of creating a means for the interpretation of the investigated biological system. This includes finding relevant systematic patterns among samples, identifying influential variables, verifying the findings in the raw data, and finally using the models for predictions. The presented strategy was here applied to a population study using urine samples from two cohorts, Shanxi (People’s Republic of China) and Honolulu (USA). The results showed that the evaluation of the extracted information data using partial least square discriminant analysis (PLS-DA) provided a robust, predictive and transparent model for the metabolic differences between the two populations. The presented findings suggest that this is a general approach for data handling, analysis, and evaluation of large metabolic LC/MS data sets.},
	language = {en},
	number = {5},
	urldate = {2021-06-11},
	journal = {Analyst},
	author = {Jonsson, Pär and Bruce, Stephen J. and Moritz, Thomas and Trygg, Johan and Sjöström, Michael and Plumb, Robert and Granger, Jennifer and Maibaum, Elaine and Nicholson, Jeremy K. and Holmes, Elaine and Antti, Henrik},
	month = apr,
	year = {2005},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {701--707},
}

LC/MS is an analytical technique that, due to its high sensitivity, has become increasingly popular for the generation of metabolic signatures in biological samples and for the building of metabolic data bases. However, to be able to create robust and interpretable (transparent) multivariate models for the comparison of many samples, the data must fulfil certain specific criteria: (i) that each sample is characterized by the same number of variables, (ii) that each of these variables is represented across all observations, and (iii) that a variable in one sample has the same biological meaning or represents the same metabolite in all other samples. In addition, the obtained models must have the ability to make predictions of, e.g. related and independent samples characterized accordingly to the model samples. This method involves the construction of a representative data set, including automatic peak detection, alignment, setting of retention time windows, summing in the chromatographic dimension and data compression by means of alternating regression, where the relevant metabolic variation is retained for further modelling using multivariate analysis. This approach has the advantage of allowing the comparison of large numbers of samples based on their LC/MS metabolic profiles, but also of creating a means for the interpretation of the investigated biological system. This includes finding relevant systematic patterns among samples, identifying influential variables, verifying the findings in the raw data, and finally using the models for predictions. The presented strategy was here applied to a population study using urine samples from two cohorts, Shanxi (People’s Republic of China) and Honolulu (USA). The results showed that the evaluation of the extracted information data using partial least square discriminant analysis (PLS-DA) provided a robust, predictive and transparent model for the metabolic differences between the two populations. The presented findings suggest that this is a general approach for data handling, analysis, and evaluation of large metabolic LC/MS data sets.

@article{nordin_nitrogen_2005,
	title = {Nitrogen deposition and the biodiversity of boreal forests: {Implications} for the nitrogen critical load},
	volume = {34},
	issn = {0044-7447},
	shorttitle = {Nitrogen deposition and the biodiversity of boreal forests},
	doi = {10.1639/0044-7447(2005)034[0020:NDATBO]2.0.CO;2},
	abstract = {The critical load concept is used to establish the deposition levels which ecosystems can tolerate without significant harmful effects. Here we summarize work within the Swedish research program Abatement Strategies for Transboundary Air Pollution (ASTA) assessing the critical load of N for boreal forests. Results from both field experiments in an area with low background N deposition in northern Sweden, and from a large-scale monitoring study, show that important vegetational changes start to take place when adding low N doses and that recovery of the vegetation after ceasing N input is a very slow process. The data presented indicate that changes in key ecosystem components occur even at a lower rate of N input than the present recommended empirical critical load for boreal forest understorey vegetation of 10-15 kg N ha(-1) yr(-1). Based on the data presented, we suggest that the critical load should be lowered to 6 kg N ha(-1) yr(-1).},
	language = {English},
	number = {1},
	journal = {Ambio},
	author = {Nordin, A. and Strengbom, J. and Witzell, J. and Nasholm, T. and Ericson, L.},
	month = feb,
	year = {2005},
	note = {Place: Dordrecht
Publisher: Springer
WOS:000226782600003},
	keywords = {accumulation, acidification, bryophytes, diversity, ecosystem, fertilization, growth, plants, sphagnum, vegetation},
	pages = {20--24},
}

The critical load concept is used to establish the deposition levels which ecosystems can tolerate without significant harmful effects. Here we summarize work within the Swedish research program Abatement Strategies for Transboundary Air Pollution (ASTA) assessing the critical load of N for boreal forests. Results from both field experiments in an area with low background N deposition in northern Sweden, and from a large-scale monitoring study, show that important vegetational changes start to take place when adding low N doses and that recovery of the vegetation after ceasing N input is a very slow process. The data presented indicate that changes in key ecosystem components occur even at a lower rate of N input than the present recommended empirical critical load for boreal forest understorey vegetation of 10-15 kg N ha(-1) yr(-1). Based on the data presented, we suggest that the critical load should be lowered to 6 kg N ha(-1) yr(-1).

@article{stahl_measuring_2005,
	title = {Measuring nitrogen fixation by {Sesbania} sesban planted fallows using {15N} tracer technique in {Kenya}},
	volume = {65},
	issn = {1572-9680},
	url = {https://doi.org/10.1007/s10457-004-6072-8},
	doi = {10.1007/s10457-004-6072-8},
	abstract = {A field experiment was performed in eastern Kenya to estimate N2 fixation by Sesbania sesban over an 18-month period using the 15N dilution method. The influence of three reference species, Senna spectabilis, Eucalyptus saligna and Grevillea robusta, on the estimates of N2 fixation was also assessed. Percentage Ndfa (nitrogen derived from the atmosphere) was calculated based on foliar atom excess (FAE), above-ground atom excess (AAE) or whole tree atom excess (WAE) data. The differences in atom\% 15N excess values between species and plant parts are presented and discussed. We recommend the use of several reference species for estimating \%Ndfa and that the different results obtained should be carefully considered in relation to the issues being addressed. In this study, Senna was the most suitable of the three reference species because its N uptake pattern and phenology were very similar to those of Sesbania. When well established, the amount of N fixed by Sesbania accounts for more than 80\% of its total N content, according to FAE-based estimates. We estimated the Ndfa by Sesbania after 18 months to between 500 and 600 kg ha−1 , depending on whether FAE, AAE or WAE data were used and on the choice of reference species. The substantial accumulation of N in planted Sesbania highlighted its potential to increase the sustainability of crop production on N-limited soils. We consider the 15N dilution method to be appropriate for quantifying N2 fixation in improved fallows in studies, similar to this one, of young trees with high N2-fixing ability.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {Agroforestry Systems},
	author = {Ståhl, Lena and Högberg, Peter and Sellstedt, Anita and Buresh, Roland J.},
	month = oct,
	year = {2005},
	pages = {67--79},
}

A field experiment was performed in eastern Kenya to estimate N2 fixation by Sesbania sesban over an 18-month period using the 15N dilution method. The influence of three reference species, Senna spectabilis, Eucalyptus saligna and Grevillea robusta, on the estimates of N2 fixation was also assessed. Percentage Ndfa (nitrogen derived from the atmosphere) was calculated based on foliar atom excess (FAE), above-ground atom excess (AAE) or whole tree atom excess (WAE) data. The differences in atom% 15N excess values between species and plant parts are presented and discussed. We recommend the use of several reference species for estimating %Ndfa and that the different results obtained should be carefully considered in relation to the issues being addressed. In this study, Senna was the most suitable of the three reference species because its N uptake pattern and phenology were very similar to those of Sesbania. When well established, the amount of N fixed by Sesbania accounts for more than 80% of its total N content, according to FAE-based estimates. We estimated the Ndfa by Sesbania after 18 months to between 500 and 600 kg ha−1 , depending on whether FAE, AAE or WAE data were used and on the choice of reference species. The substantial accumulation of N in planted Sesbania highlighted its potential to increase the sustainability of crop production on N-limited soils. We consider the 15N dilution method to be appropriate for quantifying N2 fixation in improved fallows in studies, similar to this one, of young trees with high N2-fixing ability.

@article{ciereszko_expression_2005,
	title = {Expression of several genes involved in sucrose/starch metabolism as affected by different strategies to induce phosphate deficiency in {Arabidopsis}},
	volume = {27},
	issn = {0137-5881},
	doi = {10.1007/s11738-005-0018-2},
	abstract = {The effects of inorganic phosphate (Pi) deficiency on expression of genes encoding ADP-glucose pyrophosphorylase small and large subunits (ApS and ApL1, ApL2, ApL3 genes), UDP-glucose pyrophosphorylase (Ugp gene), sucrose synthase (Sus]), Soluble and insoluble acid invertases (Invand Invcw) and hexokinase (Hxk1 gene), all involved in carbohydrate metabolism, were investigated in Arabidopsis thaliana (L.) Heynh. We used soil-grown pho mutants affected in Pi status, as well as wild-type (wt) plants grown under Pi deficiency conditions in liquid medium, and leaves of wt plants fed with D-mannose. Generally, ApS, ApL1, Ugp and Inv genes were upregulated, although to a varied degree, under conditions of Pi-stress. The applied conditions had differential effects on expression of other genes Studied. For instance, Susl was downregulated in phol (Pi-deficient) mutant, but was unaffected in wt plants grown in liquid medium under P-deficiency. Mannose had distinct coil contration-dependent effects on expression of genes under Study, possibly reflecting a dual role of mannose as a sink for Pi and as glucose analog. Feeding- Pi (at up to 200 mM) to the detached leaves of wt plants strongly affected the expression of ApL1, ApL2, Sus1 and Inv genes, possibly due to an osmotic effect exerted by Pi. The data Suggest that ADP-glucose and UDP-glucose pyrophosphorylases (ent, 0 zymes indirectly involved in Pi recycling) as well as invertases (sucrose hydrolysis) are transcriptionally regulated by Pi-deficiency, which may play a role in homeostatic mechanisms that acclimate the plant to the Pi-stress conditions.},
	language = {English},
	number = {2},
	journal = {Acta Physiologiae Plantarum},
	author = {Ciereszko, I. and Kleczkowski, L. A.},
	year = {2005},
	note = {Place: Heidelberg
Publisher: Springer Heidelberg
WOS:000229991800002},
	keywords = {Arabidopsis, acclimation, adp-glucose pyrophosphorylase, bean roots, carbohydrate metabolism regulation, gene expression, light, phaseolus-vulgaris l., pho   mutants, phosphate starvation, photosynthesis, small-subunit, sugars, thaliana, transduction},
	pages = {147--155},
}

The effects of inorganic phosphate (Pi) deficiency on expression of genes encoding ADP-glucose pyrophosphorylase small and large subunits (ApS and ApL1, ApL2, ApL3 genes), UDP-glucose pyrophosphorylase (Ugp gene), sucrose synthase (Sus]), Soluble and insoluble acid invertases (Invand Invcw) and hexokinase (Hxk1 gene), all involved in carbohydrate metabolism, were investigated in Arabidopsis thaliana (L.) Heynh. We used soil-grown pho mutants affected in Pi status, as well as wild-type (wt) plants grown under Pi deficiency conditions in liquid medium, and leaves of wt plants fed with D-mannose. Generally, ApS, ApL1, Ugp and Inv genes were upregulated, although to a varied degree, under conditions of Pi-stress. The applied conditions had differential effects on expression of other genes Studied. For instance, Susl was downregulated in phol (Pi-deficient) mutant, but was unaffected in wt plants grown in liquid medium under P-deficiency. Mannose had distinct coil contration-dependent effects on expression of genes under Study, possibly reflecting a dual role of mannose as a sink for Pi and as glucose analog. Feeding- Pi (at up to 200 mM) to the detached leaves of wt plants strongly affected the expression of ApL1, ApL2, Sus1 and Inv genes, possibly due to an osmotic effect exerted by Pi. The data Suggest that ADP-glucose and UDP-glucose pyrophosphorylases (ent, 0 zymes indirectly involved in Pi recycling) as well as invertases (sucrose hydrolysis) are transcriptionally regulated by Pi-deficiency, which may play a role in homeostatic mechanisms that acclimate the plant to the Pi-stress conditions.