Publications 2012

@book{swarts_structural_2012,
	address = {Center for Desert Archaeology},
	series = {Anthropological {Papers}},
	title = {Structural {Wood} {Choice} and {Cultural} {Meaning} at {Honey} {Bee} {Village}. {Life} in the valley of gold, archaeological investigations at {Honey} {Bee} {Village}, a prehistoric {Hohokam} ballcourt village in the {Canada} del {Oro} {Valley} of southern {Arizona}: introduction, chronology, material culture investigations and research results.},
	shorttitle = {Life in the {Valley} of {Gold}},
	abstract = {Honey Bee Village was a sizeable prehistoric Hohokam village complete with a plaza, mounds, and ballcourt located in the Cañada del Oro Valley north of Tucson, Arizona. In 2006 and 2007, nearly three-quarters of the village was intensively excavated under contract with Pima County and Vistoso Partners. The core of the site is a 13-acre preserve that was tested in the 1980s. Outside the core area, the full plan of the village was revealed, resulting in the identification of 2,004 cultural features. Occupation ranged from late in the Tortolita phase to the early Tanque Verde phase, roughly A.D. 650-1200. Overall, 947 cultural features were fully or partially excavated, including 183 pit structures, possible structures, and adobe rooms, 207 human burial features, 11 animal burials, 24 trash mounds or concentrations, and 522 extramural features. Particularly interesting remains uncovered include a golden eagle burial and a Late Rincon phase plaza and plaza cemetery. The wide excavation coverage permitted an unusually complete view of a Hohokam village and of surface-subsurface comparisons.

The archaeological features and artifacts recovered are documented in this two-volume report. A large set of radiocarbon and archaeomagnetic dates is discussed. Household economic specialization and architectural practices are addressed. Cremation mortuary practices are reconstructed, and Hohokam perspectives on death and the dead are considered. The history and shifting settlement structure of the village are considered in relation to its nearby sister village, Sleeping Snake. Of special interest is the discovery that logs obtained from the Santa Catalina Mountains were used in house construction.},
	language = {en-US},
	urldate = {2024-03-22},
	publisher = {Archaeology Southwest},
	author = {Swarts, Kelly},
	month = jun,
	year = {2012},
	note = {Edited by Henry D. Wallace},
}

Honey Bee Village was a sizeable prehistoric Hohokam village complete with a plaza, mounds, and ballcourt located in the Cañada del Oro Valley north of Tucson, Arizona. In 2006 and 2007, nearly three-quarters of the village was intensively excavated under contract with Pima County and Vistoso Partners. The core of the site is a 13-acre preserve that was tested in the 1980s. Outside the core area, the full plan of the village was revealed, resulting in the identification of 2,004 cultural features. Occupation ranged from late in the Tortolita phase to the early Tanque Verde phase, roughly A.D. 650-1200. Overall, 947 cultural features were fully or partially excavated, including 183 pit structures, possible structures, and adobe rooms, 207 human burial features, 11 animal burials, 24 trash mounds or concentrations, and 522 extramural features. Particularly interesting remains uncovered include a golden eagle burial and a Late Rincon phase plaza and plaza cemetery. The wide excavation coverage permitted an unusually complete view of a Hohokam village and of surface-subsurface comparisons. The archaeological features and artifacts recovered are documented in this two-volume report. A large set of radiocarbon and archaeomagnetic dates is discussed. Household economic specialization and architectural practices are addressed. Cremation mortuary practices are reconstructed, and Hohokam perspectives on death and the dead are considered. The history and shifting settlement structure of the village are considered in relation to its nearby sister village, Sleeping Snake. Of special interest is the discovery that logs obtained from the Santa Catalina Mountains were used in house construction.

@article{nookaraju_role_2012,
	title = {Role of {Ca2}+-mediated signaling in potato tuberization: {An} overview},
	volume = {53},
	url = {https://ejournal.sinica.edu.tw/bbas/content/2012/2/Bot532-01/Bot532-01.html},
	abstract = {Potato tuberization represents the morphogenetic transition of underground shoot to tuber in­volving several biochemical and molecular changes under complex environmental, nutritional and endogenous regulation. Among the nutritional factors, the role of calcium in potato tuberization is documented in several earlier studies. Calcium is a major essential nutrient required for normal growth and development of plants. As a second messenger it plays a role in a number of fundamental cellular processes like cytoplasmic streaming, thigmotropism, gravitropism, cell division, cell differentiation, photomorphogenesis, plant defense and various stress responses. Calcium in the cytosol regulates the activity of Ca2+-sensor proteins and these proteins will subsequently activate and/or modify the activity of target proteins in biological pathways. Also, cytosolic cal­cium regulates oxidative burst via calcium dependent protein kinases (CDPKs) and induces many intracellular signaling pathways. Studies suggest that Ca2+ and Ca2+-sensor protein calmodulin (CaM) have a role as signal molecules for tuber induction in potato. Also, a potato Ca2+-dependent protein kinase, StCDPK1, is reported to be transiently expressed in tuberizing stolons suggesting its possible involvement in potato tuberization by transcriptional activation of some of the tuberizing genes. Though Ca2+ and Ca2+-regulated proteins influence many developmental processes in plants, the exact molecular and biochemical mechanism of Ca2+-mediated signal pathways controlling potato tuberization is still not clear. This review sheds some light on the possible molecular mechanisms involved in the Ca2+-mediated signaling in potato tuberization.},
	urldate = {2023-11-14},
	journal = {Botanical Studies},
	author = {Nookaraju, Akula and Pandey, Shashank and Upadhyaya, Chandrama and Heung, Jeon Jae and Kim, Hyun S and Chun, Se Chul and Kim, Doo Hwan and Park, Se Won},
	year = {2012},
	keywords = {⛔ No DOI found},
	pages = {177--189},
}

Potato tuberization represents the morphogenetic transition of underground shoot to tuber in­volving several biochemical and molecular changes under complex environmental, nutritional and endogenous regulation. Among the nutritional factors, the role of calcium in potato tuberization is documented in several earlier studies. Calcium is a major essential nutrient required for normal growth and development of plants. As a second messenger it plays a role in a number of fundamental cellular processes like cytoplasmic streaming, thigmotropism, gravitropism, cell division, cell differentiation, photomorphogenesis, plant defense and various stress responses. Calcium in the cytosol regulates the activity of Ca2+-sensor proteins and these proteins will subsequently activate and/or modify the activity of target proteins in biological pathways. Also, cytosolic cal­cium regulates oxidative burst via calcium dependent protein kinases (CDPKs) and induces many intracellular signaling pathways. Studies suggest that Ca2+ and Ca2+-sensor protein calmodulin (CaM) have a role as signal molecules for tuber induction in potato. Also, a potato Ca2+-dependent protein kinase, StCDPK1, is reported to be transiently expressed in tuberizing stolons suggesting its possible involvement in potato tuberization by transcriptional activation of some of the tuberizing genes. Though Ca2+ and Ca2+-regulated proteins influence many developmental processes in plants, the exact molecular and biochemical mechanism of Ca2+-mediated signal pathways controlling potato tuberization is still not clear. This review sheds some light on the possible molecular mechanisms involved in the Ca2+-mediated signaling in potato tuberization.

@article{gururani_plant_2012,
	title = {Plant disease resistance genes: {Current} status and future directions},
	volume = {78},
	issn = {0885-5765},
	shorttitle = {Plant disease resistance genes},
	url = {https://www.sciencedirect.com/science/article/pii/S0885576512000033},
	doi = {10.1016/j.pmpp.2012.01.002},
	abstract = {Plant diseases can drastically abate the crop yields as the degree of disease outbreak is getting severe around the world. Therefore, plant disease management has always been one of the main objectives of any crop improvement program. Plant disease resistance (R) genes have the ability to detect a pathogen attack and facilitate a counter attack against the pathogen. Numerous plant R-genes have been used with varying degree of success in crop improvement programs in the past and many of them are being continuously exploited. With the onset of recent genomic, bioinformatics and molecular biology techniques, it is quite possible to tame the R-genes for efficiently controlling the plant diseases caused by pathogens. This review summarizes the recent applications and future potential of R-genes in crop disease management.},
	urldate = {2023-11-14},
	journal = {Physiological and Molecular Plant Pathology},
	author = {Gururani, Mayank Anand and Venkatesh, Jelli and Upadhyaya, Chandrama Prakash and Nookaraju, Akula and Pandey, Shashank Kumar and Park, Se Won},
	month = apr,
	year = {2012},
	keywords = {Disease management, Plant diseases, Plant pathogens, Resistance genes},
	pages = {51--65},
}

Plant diseases can drastically abate the crop yields as the degree of disease outbreak is getting severe around the world. Therefore, plant disease management has always been one of the main objectives of any crop improvement program. Plant disease resistance (R) genes have the ability to detect a pathogen attack and facilitate a counter attack against the pathogen. Numerous plant R-genes have been used with varying degree of success in crop improvement programs in the past and many of them are being continuously exploited. With the onset of recent genomic, bioinformatics and molecular biology techniques, it is quite possible to tame the R-genes for efficiently controlling the plant diseases caused by pathogens. This review summarizes the recent applications and future potential of R-genes in crop disease management.

@article{gao_demography_2012,
	title = {Demography and speciation history of the homoploid hybrid pine {Pinus} densata on the {Tibetan} {Plateau}},
	volume = {21},
	issn = {1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2012.05712.x},
	doi = {10.1111/j.1365-294X.2012.05712.x},
	abstract = {Pinus densata is an ecologically successful homoploid hybrid that inhabits vast areas of heterogeneous terrain on the south-eastern Tibetan Plateau as a result of multiple waves of colonization. Its region of origin, route of colonization onto the plateau and the directions of introgression with its parental species have previously been defined, but little is known about the isolation and divergence history of its populations. In this study, we surveyed nucleotide polymorphism over eight nuclear loci in 19 representative populations of P. densata and its parental species. Using this information and coalescence simulations, we assessed the historical changes in its population size, gene flow and divergence in time and space. The results indicate a late Miocene origin for P. densata associated with the recent uplift of south-eastern Tibet. The subsequent differentiation between geographical regions of this species began in the late Pliocene and was induced by regional topographical changes and Pleistocene glaciations. The ancestral P. densata population had a large effective population size but the central and western populations were established by limited founders, suggesting that there were severe bottlenecks during the westward migration out of the ancestral hybrid zone. After separating from their ancestral populations, population expansion occurred in all geographical regions especially in the western range. Gene flow in P. densata was restricted to geographically neighbouring populations, resulting in significant differentiation between regional groups. The new information on the divergence and demographic history of P. densata reported herein enhances our understanding of its speciation process on the Tibetan Plateau.},
	language = {en},
	number = {19},
	urldate = {2023-04-27},
	journal = {Molecular Ecology},
	author = {Gao, Jie and Wang, Baosheng and Mao, Jian-Feng and Ingvarsson, Pär and Zeng, Qing-Yin and Wang, Xiao-Ru},
	year = {2012},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-294X.2012.05712.x},
	keywords = {coalescent simulation, effective population size, gene flow, hybrid speciation, isolation history, nucleotide diversity},
	pages = {4811--4827},
}

Pinus densata is an ecologically successful homoploid hybrid that inhabits vast areas of heterogeneous terrain on the south-eastern Tibetan Plateau as a result of multiple waves of colonization. Its region of origin, route of colonization onto the plateau and the directions of introgression with its parental species have previously been defined, but little is known about the isolation and divergence history of its populations. In this study, we surveyed nucleotide polymorphism over eight nuclear loci in 19 representative populations of P. densata and its parental species. Using this information and coalescence simulations, we assessed the historical changes in its population size, gene flow and divergence in time and space. The results indicate a late Miocene origin for P. densata associated with the recent uplift of south-eastern Tibet. The subsequent differentiation between geographical regions of this species began in the late Pliocene and was induced by regional topographical changes and Pleistocene glaciations. The ancestral P. densata population had a large effective population size but the central and western populations were established by limited founders, suggesting that there were severe bottlenecks during the westward migration out of the ancestral hybrid zone. After separating from their ancestral populations, population expansion occurred in all geographical regions especially in the western range. Gene flow in P. densata was restricted to geographically neighbouring populations, resulting in significant differentiation between regional groups. The new information on the divergence and demographic history of P. densata reported herein enhances our understanding of its speciation process on the Tibetan Plateau.

@article{gendron_brassinosteroids_2012,
	title = {Brassinosteroids regulate organ boundary formation in the shoot apical meristem of {Arabidopsis}},
	volume = {109},
	url = {https://www.pnas.org/doi/full/10.1073/pnas.1210799110},
	doi = {10.1073/pnas.1210799110},
	abstract = {Spatiotemporal control of the formation of organ primordia and organ boundaries from the stem cell niche in the shoot apical meristem (SAM) determines the patterning and architecture of plants, but the underlying signaling mechanisms remain poorly understood. Here we show that brassinosteroids (BRs) play a key role in organ boundary formation by repressing organ boundary identity genes. BR-hypersensitive mutants display organ-fusion phenotypes, whereas BR-insensitive mutants show enhanced organ boundaries. The BR-activated transcription factor BZR1 directly represses the CUP-SHAPED COTYLEDON (CUC) family of organ boundary identity genes. In WT plants, BZR1 accumulates at high levels in the nuclei of central meristem and organ primordia but at a low level in organ boundary cells to allow CUC gene expression. Activation of BR signaling represses CUC gene expression and causes organ fusion phenotypes. This study uncovers a role for BR in the spatiotemporal control of organ boundary formation and morphogenesis in the SAM.},
	number = {51},
	urldate = {2022-11-30},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Gendron, Joshua M. and Liu, Jiang-Shu and Fan, Min and Bai, Ming-Yi and Wenkel, Stephan and Springer, Patricia S. and Barton, M. Kathryn and Wang, Zhi-Yong},
	month = dec,
	year = {2012},
	pages = {21152--21157},
}

Spatiotemporal control of the formation of organ primordia and organ boundaries from the stem cell niche in the shoot apical meristem (SAM) determines the patterning and architecture of plants, but the underlying signaling mechanisms remain poorly understood. Here we show that brassinosteroids (BRs) play a key role in organ boundary formation by repressing organ boundary identity genes. BR-hypersensitive mutants display organ-fusion phenotypes, whereas BR-insensitive mutants show enhanced organ boundaries. The BR-activated transcription factor BZR1 directly represses the CUP-SHAPED COTYLEDON (CUC) family of organ boundary identity genes. In WT plants, BZR1 accumulates at high levels in the nuclei of central meristem and organ primordia but at a low level in organ boundary cells to allow CUC gene expression. Activation of BR signaling represses CUC gene expression and causes organ fusion phenotypes. This study uncovers a role for BR in the spatiotemporal control of organ boundary formation and morphogenesis in the SAM.

@article{bou-torrent_athb4_2012,
	title = {{ATHB4} and {HAT3}, two class {II} {HD}-{ZIP} transcription factors, control leaf development in {Arabidopsis}},
	volume = {7},
	issn = {null},
	url = {https://doi.org/10.4161/psb.21824},
	doi = {10.4161/psb.21824},
	abstract = {In response to plant proximity or canopy shade, plants can react by altering elongation growth and development. Several members of the class II homeodomain-leucine zipper (HD-ZIPII) transcription factor family have been shown to play an instrumental role in the responses to shade. HD-ZIP members of the class III (HD-ZIPIII), by contrast, are involved in basic patterning processes. We recently showed that REVOLUTA (REV), a member of the HD-ZIPIII family, directly and positively regulates the expression of several genes involved in shade-induced growth, such as those encoding HD-ZIPII factors HAT2, HAT3, ATHB2/HAT4 and ATHB4, and of the components of the auxin biosynthesis pathway YUCCA5 and TAA1. Furthermore, we could demonstrate a novel role for HD-ZIPIII in shade-induced promotion of growth. Here we show that besides responding to shade, ATHB4 and HAT3 have a critical role in establishing the dorso-ventral axis in cotyledons and developing leaves. Loss-of-function mutations in these two HD-ZIPII genes (athb4 hat3) results in severely abaxialized, entirely radialized leaves. Conversely, overexpression of HAT3 results in adaxialized leaf development. Taken together, our findings unravel a so far unappreciated role for an HD-ZIPII/HD-ZIPIII module required for dorso-ventral patterning of leaves. The finding that HD-ZIPII/HD-ZIPIII also function in shade avoidance suggests that this module is at the nexus of patterning and growth promotion.},
	number = {11},
	urldate = {2022-11-30},
	journal = {Plant Signaling \& Behavior},
	author = {Bou-Torrent, Jordi and Salla-Martret, Mercè and Brandt, Ronny and Musielak, Thomas and Palauqui, Jean-Christophe and Martínez-García, Jaime F. and Wenkel, Stephan},
	month = nov,
	year = {2012},
	keywords = {Arabidopsis thaliana, HD-ZIPII, HD-ZIPIII, auxin, leaf development, shade avoidance},
	pages = {1382--1387},
}

In response to plant proximity or canopy shade, plants can react by altering elongation growth and development. Several members of the class II homeodomain-leucine zipper (HD-ZIPII) transcription factor family have been shown to play an instrumental role in the responses to shade. HD-ZIP members of the class III (HD-ZIPIII), by contrast, are involved in basic patterning processes. We recently showed that REVOLUTA (REV), a member of the HD-ZIPIII family, directly and positively regulates the expression of several genes involved in shade-induced growth, such as those encoding HD-ZIPII factors HAT2, HAT3, ATHB2/HAT4 and ATHB4, and of the components of the auxin biosynthesis pathway YUCCA5 and TAA1. Furthermore, we could demonstrate a novel role for HD-ZIPIII in shade-induced promotion of growth. Here we show that besides responding to shade, ATHB4 and HAT3 have a critical role in establishing the dorso-ventral axis in cotyledons and developing leaves. Loss-of-function mutations in these two HD-ZIPII genes (athb4 hat3) results in severely abaxialized, entirely radialized leaves. Conversely, overexpression of HAT3 results in adaxialized leaf development. Taken together, our findings unravel a so far unappreciated role for an HD-ZIPII/HD-ZIPIII module required for dorso-ventral patterning of leaves. The finding that HD-ZIPII/HD-ZIPIII also function in shade avoidance suggests that this module is at the nexus of patterning and growth promotion.

@article{brandt_genome-wide_2012,
	title = {Genome-wide binding-site analysis of {REVOLUTA} reveals a link between leaf patterning and light-mediated growth responses},
	volume = {72},
	issn = {1365-313X},
	doi = {10/f3srjk},
	abstract = {Unlike the situation in animals, the final morphology of the plant body is highly modulated by the environment. During Arabidopsis development, intrinsic factors provide the framework for basic patterning processes. CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) transcription factors are involved in embryo, shoot and root patterning. During vegetative growth HD-ZIPIII proteins control several polarity set-up processes such as in leaves and the vascular system. We have identified several direct target genes of the HD-ZIPIII transcription factor REVOLUTA (REV) using a chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) approach. This analysis revealed that REV acts upstream of auxin biosynthesis and affects directly the expression of several class II HD-ZIP transcription factors that have been shown to act in the shade-avoidance response pathway. We show that, as well as involvement in basic patterning, HD-ZIPIII transcription factors have a critical role in the control of the elongation growth that is induced when plants experience shade. Leaf polarity is established by the opposed actions of HD-ZIPIII and KANADI transcription factors. Finally, our study reveals that the module that consists of HD-ZIPIII/KANADI transcription factors controls shade growth antagonistically and that this antagonism is manifested in the opposed regulation of shared target genes.},
	language = {eng},
	number = {1},
	journal = {The Plant Journal: For Cell and Molecular Biology},
	author = {Brandt, Ronny and Salla-Martret, Mercè and Bou-Torrent, Jordi and Musielak, Thomas and Stahl, Mark and Lanz, Christa and Ott, Felix and Schmid, Markus and Greb, Thomas and Schwarz, Martina and Choi, Sang-Bong and Barton, M. Kathryn and Reinhart, Brenda J. and Liu, Tie and Quint, Marcel and Palauqui, Jean-Christophe and Martínez-García, Jaime F. and Wenkel, Stephan},
	month = oct,
	year = {2012},
	keywords = {Adaptation, Physiological, Arabidopsis, Arabidopsis Proteins, Arabidopsis thaliana, Binding Sites, Body Patterning, Chromatin Immunoprecipitation, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Genome, Plant, HD-ZIPII, HD-ZIPIII, Homeodomain Proteins, Hypocotyl, In Situ Hybridization, Indoleacetic Acids, Light, Mutation, Phylogeny, Plant Leaves, Sequence Analysis, DNA, Signal Transduction, Transcription Factors, auxin, leaf development, shade avoidance},
	pages = {31--42},
}

Unlike the situation in animals, the final morphology of the plant body is highly modulated by the environment. During Arabidopsis development, intrinsic factors provide the framework for basic patterning processes. CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) transcription factors are involved in embryo, shoot and root patterning. During vegetative growth HD-ZIPIII proteins control several polarity set-up processes such as in leaves and the vascular system. We have identified several direct target genes of the HD-ZIPIII transcription factor REVOLUTA (REV) using a chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) approach. This analysis revealed that REV acts upstream of auxin biosynthesis and affects directly the expression of several class II HD-ZIP transcription factors that have been shown to act in the shade-avoidance response pathway. We show that, as well as involvement in basic patterning, HD-ZIPIII transcription factors have a critical role in the control of the elongation growth that is induced when plants experience shade. Leaf polarity is established by the opposed actions of HD-ZIPIII and KANADI transcription factors. Finally, our study reveals that the module that consists of HD-ZIPIII/KANADI transcription factors controls shade growth antagonistically and that this antagonism is manifested in the opposed regulation of shared target genes.

@article{graeff_regulation_2012,
	title = {Regulation of protein function by interfering protein species},
	volume = {3},
	issn = {1868-503X},
	url = {https://www.degruyter.com/document/doi/10.1515/bmc.2011.053/html?lang=en},
	doi = {10.1515/bmc.2011.053},
	abstract = {Most proteins do not function alone but act in protein complexes. For several transcriptional regulators, it is known that they have to homo- or heterodimerize prior to DNA binding. These protein interactions occur through defined protein-protein-interaction (PPI) domains. More than two decades ago, inhibitor of DNA binding (ID), a small protein containing a single helix-loop-helix (HLH) motif was identified. ID is able to interact with the larger DNA-binding basic helix-loop-helix (bHLH) transcription factors, but due to the lack of the basic domain required for DNA binding, ID traps bHLH proteins in non-functional complexes. Work in plants has, in the recent years, identified more small proteins acting in analogy to ID. A hallmark of these small negative acting proteins is the presence of a protein-interaction domain and the absence of other functional domains required for transcriptional activation or DNA binding. Because these proteins are often very small and function in analogy to microRNAs (meaning in a dominant-negative manner), we propose to refer to these protein species as ‘microProteins’ (miPs). miPs can be encoded in the genome as individual transcription units but can also be produced by alternative splicing. Other negatively acting proteins, consisting of more than one domain, have also been identified, and we propose to call these proteins ‘interfering proteins’ (iPs). The aim of this review is to state more precisely how to discriminate miPs from iPs. Therefore, we will highlight recent findings on both protein species and describe their mode of action. Furthermore, miPs have the ability to regulate proteins of diverse functions, emphasizing their value as biotechnological tools.},
	language = {en},
	number = {1},
	urldate = {2022-11-30},
	journal = {BioMolecular Concepts},
	author = {Graeff, Moritz and Wenkel, Stephan},
	month = feb,
	year = {2012},
	keywords = {homotypic interaction, interfering protein, microProtein, protein-protein interaction, transcription factor inactivation},
	pages = {71--78},
}

Most proteins do not function alone but act in protein complexes. For several transcriptional regulators, it is known that they have to homo- or heterodimerize prior to DNA binding. These protein interactions occur through defined protein-protein-interaction (PPI) domains. More than two decades ago, inhibitor of DNA binding (ID), a small protein containing a single helix-loop-helix (HLH) motif was identified. ID is able to interact with the larger DNA-binding basic helix-loop-helix (bHLH) transcription factors, but due to the lack of the basic domain required for DNA binding, ID traps bHLH proteins in non-functional complexes. Work in plants has, in the recent years, identified more small proteins acting in analogy to ID. A hallmark of these small negative acting proteins is the presence of a protein-interaction domain and the absence of other functional domains required for transcriptional activation or DNA binding. Because these proteins are often very small and function in analogy to microRNAs (meaning in a dominant-negative manner), we propose to refer to these protein species as ‘microProteins’ (miPs). miPs can be encoded in the genome as individual transcription units but can also be produced by alternative splicing. Other negatively acting proteins, consisting of more than one domain, have also been identified, and we propose to call these proteins ‘interfering proteins’ (iPs). The aim of this review is to state more precisely how to discriminate miPs from iPs. Therefore, we will highlight recent findings on both protein species and describe their mode of action. Furthermore, miPs have the ability to regulate proteins of diverse functions, emphasizing their value as biotechnological tools.

@article{plackett_analysis_2012,
	title = {Analysis of the {Developmental} {Roles} of the {Arabidopsis} {Gibberellin} 20-{Oxidases} {Demonstrates} {That} {GA20ox1} , -2 , and -3 {Are} the {Dominant} {Paralogs}},
	volume = {24},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/24/3/941-960/6097253},
	doi = {10/f238b4},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Plackett, Andrew R.G. and Powers, Stephen J. and Fernandez-Garcia, Nieves and Urbanova, Terezie and Takebayashi, Yumiko and Seo, Mitsunori and Jikumaru, Yusuke and Benlloch, Reyes and Nilsson, Ove and Ruiz-Rivero, Omar and Phillips, Andrew L. and Wilson, Zoe A. and Thomas, Stephen G. and Hedden, Peter},
	month = mar,
	year = {2012},
	pages = {941--960},
}

@article{rapatskiy_detection_2012,
	title = {Detection of the {Water}-{Binding} {Sites} of the {Oxygen}-{Evolving} {Complex} of {Photosystem} {II} {Using} {W}-{Band} 17 {O} {Electron}–{Electron} {Double} {Resonance}-{Detected} {NMR} {Spectroscopy}},
	volume = {134},
	issn = {0002-7863, 1520-5126},
	url = {https://pubs.acs.org/doi/10.1021/ja3053267},
	doi = {10/f2z5c6},
	language = {en},
	number = {40},
	urldate = {2021-06-08},
	journal = {Journal of the American Chemical Society},
	author = {Rapatskiy, Leonid and Cox, Nicholas and Savitsky, Anton and Ames, William M. and Sander, Julia and Nowaczyk, Marc. M. and Rögner, Matthias and Boussac, Alain and Neese, Frank and Messinger, Johannes and Lubitz, Wolfgang},
	month = oct,
	year = {2012},
	pages = {16619--16634},
}

@article{shaikhali_cryptochrome1-dependent_2012,
	title = {The {CRYPTOCHROME1}-{Dependent} {Response} to {Excess} {Light} {Is} {Mediated} through the {Transcriptional} {Activators} {ZINC} {FINGER} {PROTEIN} {EXPRESSED} {IN} {INFLORESCENCE} {MERISTEM} {LIKE1} and {ZML2} in {Arabidopsis}},
	volume = {24},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/24/7/3009-3025/6100855},
	doi = {10/f23c7q},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Shaikhali, Jehad and de Dios Barajas-Lopéz, Juan and Ötvös, Krisztina and Kremnev, Dmitry and Garcia, Ana Sánchez and Srivastava, Vaibhav and Wingsle, Gunnar and Bakó, Laszlo and Strand, Åsa},
	month = jul,
	year = {2012},
	pages = {3009--3025},
}

@article{suorsa_proton_2012,
	title = {{PROTON} {GRADIENT} {REGULATION5} {Is} {Essential} for {Proper} {Acclimation} of {Arabidopsis} {Photosystem} {I} to {Naturally} and {Artificially} {Fluctuating} {Light} {Conditions}},
	volume = {24},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/24/7/2934-2948/6100862},
	doi = {10/f242kc},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Suorsa, Marjaana and Järvi, Sari and Grieco, Michele and Nurmi, Markus and Pietrzykowska, Malgorzata and Rantala, Marjaana and Kangasjärvi, Saijaliisa and Paakkarinen, Virpi and Tikkanen, Mikko and Jansson, Stefan and Aro, Eva-Mari},
	month = jul,
	year = {2012},
	pages = {2934--2948},
}

@incollection{sane_thermoluminescence_2012,
	address = {Dordrecht},
	series = {Advances in {Photosynthesis} and {Respiration}},
	title = {Thermoluminescence},
	isbn = {978-94-007-1579-0},
	url = {https://doi.org/10.1007/978-94-007-1579-0_19},
	abstract = {SummaryThermoluminescence (TL) of photosynthetic membranes was discovered by William Arnold and Helen Sherwood in 1957. In the last half century, several studies have elucidated the mechanism of TL emission, which showed that the recombination of different charge pairs generated and trapped during pre-illumination are responsible for the observed light emission. Since most of the TL bands originate within Photosystem II (PS II), the technique of TL has become a useful complementary tool to chlorophyll a fluorescence to probe subtle changes in PS II photochemistry. The technique is simple and non-invasive; it has been successfully used to study leaf, cells, thylakoids and even reaction center preparations. The TL technique provides quick information about the redox potential changes of the bound primary quinone (QA) and the secondary quinone (QB) acceptors of PS II; TL has been extensively used to study the effects of photoinhibition, mutations, stresses and myriad responses of the photosynthetic apparatus during acclimation and adaptation. This chapter reviews crucial evidence for the identification of charge pairs responsible for the generation of different TL bands; the relationship of these bands to the components of delayed light emission; responses to excitation pressure arising out of environmental factors; methodology, and instrumentation. A model based on the detailed analysis of the redox shifts of the PS II electron acceptors QA and QB, explaining the possibility of non-radiative dissipation of excess light energy within the reaction center of PS II (reaction center quenching) and its physiological significance in photo-protection of the photosynthetic membranes has been suggested. Developments in the analysis of biophysical parameters and the non-adherence of photosynthetic TL to the analysis by the 1945 theory of J.T. Randall and M.H.F. Wilkins have been briefly reviewed.},
	language = {en},
	urldate = {2021-06-08},
	booktitle = {Photosynthesis: {Plastid} {Biology}, {Energy} {Conversion} and {Carbon} {Assimilation}},
	publisher = {Springer Netherlands},
	author = {Sane, Prafullachandra Vishnu and Ivanov, Alexander G. and Öquist, Gunnar and Hüner, Norman P. A.},
	editor = {Eaton-Rye, Julian J. and Tripathy, Baishnab C. and Sharkey, Thomas D.},
	year = {2012},
	keywords = {Charge Pair, Cyclic Electron Flow, Ethylene Glycol Tetraacetic Acid, Glow Curve, Glow Peak},
	pages = {445--474},
}

SummaryThermoluminescence (TL) of photosynthetic membranes was discovered by William Arnold and Helen Sherwood in 1957. In the last half century, several studies have elucidated the mechanism of TL emission, which showed that the recombination of different charge pairs generated and trapped during pre-illumination are responsible for the observed light emission. Since most of the TL bands originate within Photosystem II (PS II), the technique of TL has become a useful complementary tool to chlorophyll a fluorescence to probe subtle changes in PS II photochemistry. The technique is simple and non-invasive; it has been successfully used to study leaf, cells, thylakoids and even reaction center preparations. The TL technique provides quick information about the redox potential changes of the bound primary quinone (QA) and the secondary quinone (QB) acceptors of PS II; TL has been extensively used to study the effects of photoinhibition, mutations, stresses and myriad responses of the photosynthetic apparatus during acclimation and adaptation. This chapter reviews crucial evidence for the identification of charge pairs responsible for the generation of different TL bands; the relationship of these bands to the components of delayed light emission; responses to excitation pressure arising out of environmental factors; methodology, and instrumentation. A model based on the detailed analysis of the redox shifts of the PS II electron acceptors QA and QB, explaining the possibility of non-radiative dissipation of excess light energy within the reaction center of PS II (reaction center quenching) and its physiological significance in photo-protection of the photosynthetic membranes has been suggested. Developments in the analysis of biophysical parameters and the non-adherence of photosynthetic TL to the analysis by the 1945 theory of J.T. Randall and M.H.F. Wilkins have been briefly reviewed.

@article{yu_gibberellin_2012,
	title = {Gibberellin {Regulates} the {Arabidopsis} {Floral} {Transition} through {miR156}-{Targeted} {SQUAMOSA} {PROMOTER} {BINDING}–{LIKE} {Transcription} {Factors}[{W}]},
	volume = {24},
	issn = {1040-4651},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3462634/},
	doi = {10.1105/tpc.112.101014},
	abstract = {This article examines the crosstalk between gibberellin responses, which result in degradation of DELLAs, and the microRNA-regulated SQUAMOSA PROMOTER BINDING LIKE (SPL) transcription factors, which activate miR172 and MADS box transcription factors. The authors find that DELLA binds to SPLs and interfere with SPL transcriptional activation of miR172 and MADS box genes, thereby delaying flowering., Gibberellin (), a diterpene hormone, plays diverse roles in plant growth and development, including seed germination, stem elongation, and flowering time. Although it is known that  accelerates flowering through degradation of transcription repressors, DELLAs, the underlying mechanism is poorly understood. We show here that DELLA directly binds to microRNA156 (miR156)-targeted SQUAMOSA PROMOTER BINDING–LIKE (SPL) transcription factors, which promote flowering by activating miR172 and MADS box genes. The interaction between DELLA and SPL interferes with SPL transcriptional activity and consequently delays floral transition through inactivating miR172 in leaves and MADS box genes at shoot apex under long-day conditions or through repressing MADS box genes at the shoot apex under short-day conditions. Our results elucidate the molecular mechanism by which  controls flowering and provide the missing link between DELLA and MADS box genes.},
	number = {8},
	urldate = {2021-10-22},
	journal = {The Plant Cell},
	author = {Yu, Sha and Galvão, Vinicius C. and Zhang, Yan-Chun and Horrer, Daniel and Zhang, Tian-Qi and Hao, Yan-Hong and Feng, Yu-Qi and Wang, Shui and Schmid, Markus and Wang, Jia-Wei},
	month = aug,
	year = {2012},
	pmid = {22942378},
	pmcid = {PMC3462634},
	pages = {3320--3332},
}

This article examines the crosstalk between gibberellin responses, which result in degradation of DELLAs, and the microRNA-regulated SQUAMOSA PROMOTER BINDING LIKE (SPL) transcription factors, which activate miR172 and MADS box transcription factors. The authors find that DELLA binds to SPLs and interfere with SPL transcriptional activation of miR172 and MADS box genes, thereby delaying flowering., Gibberellin (), a diterpene hormone, plays diverse roles in plant growth and development, including seed germination, stem elongation, and flowering time. Although it is known that accelerates flowering through degradation of transcription repressors, DELLAs, the underlying mechanism is poorly understood. We show here that DELLA directly binds to microRNA156 (miR156)-targeted SQUAMOSA PROMOTER BINDING–LIKE (SPL) transcription factors, which promote flowering by activating miR172 and MADS box genes. The interaction between DELLA and SPL interferes with SPL transcriptional activity and consequently delays floral transition through inactivating miR172 in leaves and MADS box genes at shoot apex under long-day conditions or through repressing MADS box genes at the shoot apex under short-day conditions. Our results elucidate the molecular mechanism by which controls flowering and provide the missing link between DELLA and MADS box genes.

@article{kindgren_plastid_2012,
	title = {The plastid redox insensitive 2 mutant of {Arabidopsis} is impaired in {PEP} activity and high light-dependent plastid redox signalling to the nucleus},
	volume = {70},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2011.04865.x},
	doi = {10/fzx2j5},
	abstract = {The photosynthetic apparatus is composed of proteins encoded by genes from both the nuclear and the chloroplastic genomes. The activities of the nuclear and chloroplast genomes must therefore be closely coordinated through intracellular signalling. The plastids produce multiple retrograde signals at different times of their development, and in response to changes in the environment. These signals regulate the expression of nuclear-encoded photosynthesis genes to match the current status of the plastids. Using forward genetics we identified PLASTID REDOX INSENSITIVE 2 (PRIN2), a chloroplast component involved in redox-mediated retrograde signalling. The allelic mutants prin2-1 and prin2-2 demonstrated a misregulation of photosynthesis-associated nuclear gene expression in response to excess light, and an inhibition of photosynthetic electron transport. As a consequence of the misregulation of LHCB1.1 and LHCB2.4, the prin2 mutants displayed a high irradiance-sensitive phenotype with significant photoinactivation of photosystem II, indicated by a reduced variable to maximal fluorescence ratio (Fv/Fm). PRIN2 is localized to the nucleoids, and plastid transcriptome analyses demonstrated that PRIN2 is required for full expression of genes transcribed by the plastid-encoded RNA polymerase (PEP). Similarly to the prin2 mutants, the ys1 mutant with impaired PEP activity also demonstrated a misregulation of LHCB1.1 and LHCB2.4 expression in response to excess light, suggesting a direct role for PEP activity in redox-mediated retrograde signalling. Taken together, our results indicate that PRIN2 is part of the PEP machinery, and that the PEP complex responds to photosynthetic electron transport and generates a retrograde signal, enabling the plant to synchronize the expression of photosynthetic genes from both the nuclear and plastidic genomes.},
	language = {en},
	number = {2},
	urldate = {2021-09-02},
	journal = {The Plant Journal},
	author = {Kindgren, Peter and Kremnev, Dmitry and Blanco, Nicolás E. and López, Juan de Dios Barajas and Fernández, Aurora Piñas and Tellgren-Roth, Christian and Small, Ian and Strand, Åsa},
	year = {2012},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2011.04865.x},
	keywords = {LHCB, PEP, chloroplast, photosynthesis, redox, signalling},
	pages = {279--291},
}

The photosynthetic apparatus is composed of proteins encoded by genes from both the nuclear and the chloroplastic genomes. The activities of the nuclear and chloroplast genomes must therefore be closely coordinated through intracellular signalling. The plastids produce multiple retrograde signals at different times of their development, and in response to changes in the environment. These signals regulate the expression of nuclear-encoded photosynthesis genes to match the current status of the plastids. Using forward genetics we identified PLASTID REDOX INSENSITIVE 2 (PRIN2), a chloroplast component involved in redox-mediated retrograde signalling. The allelic mutants prin2-1 and prin2-2 demonstrated a misregulation of photosynthesis-associated nuclear gene expression in response to excess light, and an inhibition of photosynthetic electron transport. As a consequence of the misregulation of LHCB1.1 and LHCB2.4, the prin2 mutants displayed a high irradiance-sensitive phenotype with significant photoinactivation of photosystem II, indicated by a reduced variable to maximal fluorescence ratio (Fv/Fm). PRIN2 is localized to the nucleoids, and plastid transcriptome analyses demonstrated that PRIN2 is required for full expression of genes transcribed by the plastid-encoded RNA polymerase (PEP). Similarly to the prin2 mutants, the ys1 mutant with impaired PEP activity also demonstrated a misregulation of LHCB1.1 and LHCB2.4 expression in response to excess light, suggesting a direct role for PEP activity in redox-mediated retrograde signalling. Taken together, our results indicate that PRIN2 is part of the PEP machinery, and that the PEP complex responds to photosynthetic electron transport and generates a retrograde signal, enabling the plant to synchronize the expression of photosynthetic genes from both the nuclear and plastidic genomes.

@article{kindgren_interplay_2012,
	title = {Interplay between {HEAT} {SHOCK} {PROTEIN} 90 and {HY5} {Controls} {PhANG} {Expression} in {Response} to the {GUN5} {Plastid} {Signal}},
	volume = {5},
	issn = {1674-2052},
	url = {https://www.sciencedirect.com/science/article/pii/S1674205214602057},
	doi = {10/fxpbcj},
	abstract = {The presence of genes encoding organellar proteins in different cellular compartments necessitates a tight coordination of expression by the different genomes of the eukaryotic cell. This coordination of gene expression is achieved by organelle-to-nucleus or retrograde communication. Stress-induced perturbations of the tetrapyrrole pathway trigger large changes in nuclear gene expression in plants. Recently, we identified HSP90 proteins as ligands of the putative plastid signal Mg-ProtoIX. In order to investigate whether the interaction between HSP90 and Mg-ProtoIX is biologically relevant, we produced transgenic lines with reduced levels of cytosolic HSP90 in wild-type and gun5 backgrounds. Our work reveals that HSP90 proteins respond to the tetrapyrrole-mediated plastid signal to control expression of photosynthesis-associated nuclear genes (PhANG) during the response to oxidative stress. We also show that the hy5 mutant is insensitive to tetrapyrrole accumulation and that Mg-ProtoIX, cytosolic HSP90, and HY5 are all part of the same signaling pathway. These findings suggest that a regulatory complex controlling gene expression that includes HSP90 proteins and a transcription factor that is modified by tetrapyrroles in response to changes in the environment is evolutionarily conserved between yeast and plants.},
	language = {en},
	number = {4},
	urldate = {2021-09-02},
	journal = {Molecular Plant},
	author = {Kindgren, Peter and Norén, Louise and Barajas López, Juan de Dios and Shaikhali, Jehad and Strand, Åsa},
	month = jul,
	year = {2012},
	keywords = {abiotic/environmental stress, cell signaling, organelle biogenesis/function},
	pages = {901--913},
}

The presence of genes encoding organellar proteins in different cellular compartments necessitates a tight coordination of expression by the different genomes of the eukaryotic cell. This coordination of gene expression is achieved by organelle-to-nucleus or retrograde communication. Stress-induced perturbations of the tetrapyrrole pathway trigger large changes in nuclear gene expression in plants. Recently, we identified HSP90 proteins as ligands of the putative plastid signal Mg-ProtoIX. In order to investigate whether the interaction between HSP90 and Mg-ProtoIX is biologically relevant, we produced transgenic lines with reduced levels of cytosolic HSP90 in wild-type and gun5 backgrounds. Our work reveals that HSP90 proteins respond to the tetrapyrrole-mediated plastid signal to control expression of photosynthesis-associated nuclear genes (PhANG) during the response to oxidative stress. We also show that the hy5 mutant is insensitive to tetrapyrrole accumulation and that Mg-ProtoIX, cytosolic HSP90, and HY5 are all part of the same signaling pathway. These findings suggest that a regulatory complex controlling gene expression that includes HSP90 proteins and a transcription factor that is modified by tetrapyrroles in response to changes in the environment is evolutionarily conserved between yeast and plants.

@article{takata_simple_2012,
	title = {A simple and efficient transient transformation for hybrid aspen ({Populus} tremula × {P}. tremuloides)},
	volume = {8},
	issn = {1746-4811},
	url = {http://plantmethods.biomedcentral.com/articles/10.1186/1746-4811-8-30},
	doi = {10/f236z7},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Methods},
	author = {Takata, Naoki and Eriksson, Maria E.},
	year = {2012},
	pages = {30},
}

@article{rigal_aintegumenta_2012,
	title = {The {AINTEGUMENTA} {LIKE1} homeotic transcription factor {PtAIL1} controls the formation of adventitious root primordia in poplar},
	volume = {160},
	issn = {1532-2548},
	doi = {10/f2ztb6},
	abstract = {Adventitious rooting is an essential but sometimes rate-limiting step in the clonal multiplication of elite tree germplasm, because the ability to form roots declines rapidly with age in mature adult plant tissues. In spite of the importance of adventitious rooting, the mechanism behind this developmental process remains poorly understood. We have described the transcriptional profiles that are associated with the developmental stages of adventitious root formation in the model tree poplar (Populus trichocarpa). Transcriptome analyses indicate a highly specific temporal induction of the AINTEGUMENTA LIKE1 (PtAIL1) transcription factor of the AP2 family during adventitious root formation. Transgenic poplar samples that overexpressed PtAIL1 were able to grow an increased number of adventitious roots, whereas RNA interference mediated the down-expression of PtAIL1 expression, which led to a delay in adventitious root formation. Microarray analysis showed that the expression of 15 genes, including the transcription factors AGAMOUS-Like6 and MYB36, was overexpressed in the stem tissues that generated root primordia in PtAIL1-overexpressing plants, whereas their expression was reduced in the RNA interference lines. These results demonstrate that PtAIL1 is a positive regulator of poplar rooting that acts early in the development of adventitious roots.},
	language = {eng},
	number = {4},
	journal = {Plant Physiology},
	author = {Rigal, Adeline and Yordanov, Yordan S. and Perrone, Irene and Karlberg, Anna and Tisserant, Emilie and Bellini, Catherine and Busov, Victor B. and Martin, Francis and Kohler, Annegret and Bhalerao, Rishikesh P. and Legué, Valérie},
	month = dec,
	year = {2012},
	pmid = {23077242},
	pmcid = {PMC3510126},
	keywords = {Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Genes, Homeobox, Plant Proteins, Plant Roots, Plants, Genetically Modified, Populus, RNA Interference, RNA, Messenger, Transcription Factors, Transcriptome},
	pages = {1996--2006},
}

Adventitious rooting is an essential but sometimes rate-limiting step in the clonal multiplication of elite tree germplasm, because the ability to form roots declines rapidly with age in mature adult plant tissues. In spite of the importance of adventitious rooting, the mechanism behind this developmental process remains poorly understood. We have described the transcriptional profiles that are associated with the developmental stages of adventitious root formation in the model tree poplar (Populus trichocarpa). Transcriptome analyses indicate a highly specific temporal induction of the AINTEGUMENTA LIKE1 (PtAIL1) transcription factor of the AP2 family during adventitious root formation. Transgenic poplar samples that overexpressed PtAIL1 were able to grow an increased number of adventitious roots, whereas RNA interference mediated the down-expression of PtAIL1 expression, which led to a delay in adventitious root formation. Microarray analysis showed that the expression of 15 genes, including the transcription factors AGAMOUS-Like6 and MYB36, was overexpressed in the stem tissues that generated root primordia in PtAIL1-overexpressing plants, whereas their expression was reduced in the RNA interference lines. These results demonstrate that PtAIL1 is a positive regulator of poplar rooting that acts early in the development of adventitious roots.

@article{cruz-ramirez_bistable_2012,
	title = {A {Bistable} {Circuit} {Involving} {SCARECROW}-{RETINOBLASTOMA} {Integrates} {Cues} to {Inform} {Asymmetric} {Stem} {Cell} {Division}},
	volume = {150},
	issn = {00928674},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S009286741200880X},
	doi = {10/f3n3f8},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Cell},
	author = {Cruz-Ramírez, Alfredo and Díaz-Triviño, Sara and Blilou, Ikram and Grieneisen, Verônica A. and Sozzani, Rosangela and Zamioudis, Christos and Miskolczi, Pál and Nieuwland, Jeroen and Benjamins, René and Dhonukshe, Pankaj and Caballero-Pérez, Juan and Horvath, Beatrix and Long, Yuchen and Mähönen, Ari Pekka and Zhang, Hongtao and Xu, Jian and Murray, James A.H. and Benfey, Philip N. and Bakó, Laszlo and Marée, Athanasius F.M. and Scheres, Ben},
	month = aug,
	year = {2012},
	pages = {1002--1015},
}

@article{magyar_arabidopsis_2012,
	title = {Arabidopsis {E2FA} stimulates proliferation and endocycle separately through {RBR}-bound and {RBR}-free complexes},
	volume = {31},
	issn = {0261-4189},
	url = {https://www.embopress.org/doi/full/10.1038/emboj.2012.13},
	doi = {10/f24b6f},
	abstract = {Post-embryonic growth in plants depends on the continuous supply of undifferentiated cells within meristems. Proliferating cells maintain their competence for division by active repression of differentiation and the associated endocycle entry. We show by upregulation and downregulation of E2FA that it is required for maintaining proliferation, as well as for endocycle entry. While E2FB?RBR1 (retinoblastoma-related protein 1) complexes are reduced after sucrose addition or at elevated CYCD3;1 levels, E2FA maintains a stable complex with RBR1 in proliferating cells. Chromatin immunoprecipitation shows that RBR1 binds in the proximity of E2F promoter elements in CCS52A1 and CSS52A2 genes, central regulators for the switch from proliferation to endocycles. Overexpression of a truncated E2FA mutant (E2FA?RB) lacking the RBR1-binding domain interferes with RBR1 recruitment to promoters through E2FA, leading to decreased meristem size in roots, premature cell expansion and hyperactivated endocycle in leaves. E2F target genes, including CCS52A1 and CCS52A2, are upregulated in E2FA?RB and e2fa knockout lines. These data suggest that E2FA in complex with RBR1 forms a repressor complex in proliferating cells to inhibit premature differentiation and endocycle entry. Thus, E2FA regulates organ growth via two distinct, sequentially operating pathways.},
	number = {6},
	urldate = {2021-06-21},
	journal = {The EMBO Journal},
	author = {Magyar, Zoltán and Horváth, Beatrix and Khan, Safina and Mohammed, Binish and Henriques, Rossana and De Veylder, Lieven and Bakó, László and Scheres, Ben and Bögre, László},
	month = mar,
	year = {2012},
	note = {Publisher: John Wiley \& Sons, Ltd},
	keywords = {Arabidopsis, E2F, cell proliferation, endocycle, retinoblastoma},
	pages = {1480--1493},
}

Post-embryonic growth in plants depends on the continuous supply of undifferentiated cells within meristems. Proliferating cells maintain their competence for division by active repression of differentiation and the associated endocycle entry. We show by upregulation and downregulation of E2FA that it is required for maintaining proliferation, as well as for endocycle entry. While E2FB?RBR1 (retinoblastoma-related protein 1) complexes are reduced after sucrose addition or at elevated CYCD3;1 levels, E2FA maintains a stable complex with RBR1 in proliferating cells. Chromatin immunoprecipitation shows that RBR1 binds in the proximity of E2F promoter elements in CCS52A1 and CSS52A2 genes, central regulators for the switch from proliferation to endocycles. Overexpression of a truncated E2FA mutant (E2FA?RB) lacking the RBR1-binding domain interferes with RBR1 recruitment to promoters through E2FA, leading to decreased meristem size in roots, premature cell expansion and hyperactivated endocycle in leaves. E2F target genes, including CCS52A1 and CCS52A2, are upregulated in E2FA?RB and e2fa knockout lines. These data suggest that E2FA in complex with RBR1 forms a repressor complex in proliferating cells to inhibit premature differentiation and endocycle entry. Thus, E2FA regulates organ growth via two distinct, sequentially operating pathways.

@article{albrectsen_diversity_2012,
	title = {The diversity and identification of eulophid parasitic wasps ({Hymenoptera}: {Chalcidoidea}: {Eulophidae}) on {Phyllocnistis} labyrinthella ({Lepidoptera}: {Gracillariidae}) from {Västerbotten}, {Sweden}},
	volume = {133},
	shorttitle = {The diversity and identification of eulophid parasitic wasps ({Hymenoptera}},
	abstract = {The diversity and identification of eulophid parasitic wasps (Hymenoptera: Chalcidoidea: Eulophidae) on Phyllocnistis labyrinthella (Lepi-doptera: Gracillariidae) from Västerbotten, Sweden. [Diversitet och identifiering av fin-glanssteklar (Hymenoptera: Chalcidoidea: Eulophidae) på aspsaftmal (Phyllocnistis labyrinthella) (Lepidoptera: Gracillariidae) i Västerbotten, Sverige.] – Entomologisk Tidskrift 133(3): 111-118. Uppsala, Sweden 2012. ISSN 0013-886x. Caterpillars of the mining micro-moth Phyllocnistis labyrinthella feed on leaves of as-pen (Populus tremula) and are often parasitized by eulophid wasps. The parasitoids are a potential important cause of death for the miners. During 2009-2011 we collected mined leaves from an experimental stand of aspen trees in Västerbotten. Adults emerged from 17-35 percent of the mines and of these every second to third specimen appeared as wasps. These wasps represented seven species of eulophid parasitoids of which three were new to Västerbotten: Chrysocharis nitetis (Walker), Cirrospilus diallus (Walker) och Cirrospilus pictus (Nees). We include an identification key that may be used to identify these eulophid species. 

http://www.sef.nu/download/entomologisk\_tidskrift/et\_2012/ET2012\%20111-118.pdf},
	author = {Albrectsen, Benedicte and Hansson, Christer},
	month = jan,
	year = {2012},
}

The diversity and identification of eulophid parasitic wasps (Hymenoptera: Chalcidoidea: Eulophidae) on Phyllocnistis labyrinthella (Lepi-doptera: Gracillariidae) from Västerbotten, Sweden. [Diversitet och identifiering av fin-glanssteklar (Hymenoptera: Chalcidoidea: Eulophidae) på aspsaftmal (Phyllocnistis labyrinthella) (Lepidoptera: Gracillariidae) i Västerbotten, Sverige.] – Entomologisk Tidskrift 133(3): 111-118. Uppsala, Sweden 2012. ISSN 0013-886x. Caterpillars of the mining micro-moth Phyllocnistis labyrinthella feed on leaves of as-pen (Populus tremula) and are often parasitized by eulophid wasps. The parasitoids are a potential important cause of death for the miners. During 2009-2011 we collected mined leaves from an experimental stand of aspen trees in Västerbotten. Adults emerged from 17-35 percent of the mines and of these every second to third specimen appeared as wasps. These wasps represented seven species of eulophid parasitoids of which three were new to Västerbotten: Chrysocharis nitetis (Walker), Cirrospilus diallus (Walker) och Cirrospilus pictus (Nees). We include an identification key that may be used to identify these eulophid species. http://www.sef.nu/download/entomologisk_tidskrift/et_2012/ET2012%20111-118.pdf

@article{viswanath_global_2012,
	title = {Global regulatory burden for field testing of genetically modified trees},
	volume = {8},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-011-0445-8},
	doi = {10/dsk6sw},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Viswanath, Venkatesh and Albrectsen, Benedicte R. and Strauss, Steven H.},
	month = apr,
	year = {2012},
	pages = {221--226},
}

@article{jones_subterranean_2012,
	title = {Subterranean space exploration: the development of root system architecture},
	volume = {15},
	issn = {13695266},
	shorttitle = {Subterranean space exploration},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526611001646},
	doi = {10/frcjbh},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Current Opinion in Plant Biology},
	author = {Jones, Brian and Ljung, Karin},
	month = feb,
	year = {2012},
	pages = {97--102},
}

@article{marino_matrix_2012,
	title = {Matrix metalloproteinases in plants: a brief overview},
	volume = {145},
	issn = {00319317},
	shorttitle = {Matrix metalloproteinases in plants},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2011.01544.x},
	doi = {10/b9vtgc},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Marino, Giada and Funk, Christiane},
	month = may,
	year = {2012},
	pages = {196--202},
}

@article{grebe_patterning_2012,
	title = {The patterning of epidermal hairs in {Arabidopsis}—updated},
	volume = {15},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526611001713},
	doi = {10/cf6z9c},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Current Opinion in Plant Biology},
	author = {Grebe, Markus},
	month = feb,
	year = {2012},
	pages = {31--37},
}

@article{mellerowicz_tensional_2012,
	title = {Tensional stress generation in gelatinous fibres: a review and possible mechanism based on cell-wall structure and composition},
	volume = {63},
	issn = {0022-0957, 1460-2431},
	shorttitle = {Tensional stress generation in gelatinous fibres},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/err339},
	doi = {10/cn6bx8},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Mellerowicz, E. J. and Gorshkova, T. A.},
	month = jan,
	year = {2012},
	pages = {551--565},
}

@article{gapare_genetic_2012,
	title = {Genetic parameters and provenance variation of {Pinus} radiata {D}. {Don}. ‘{Eldridge} collection’ in {Australia} 1: growth and form traits},
	volume = {8},
	issn = {1614-2942, 1614-2950},
	shorttitle = {Genetic parameters and provenance variation of {Pinus} radiata {D}. {Don}. ‘{Eldridge} collection’ in {Australia} 1},
	url = {http://link.springer.com/10.1007/s11295-011-0449-4},
	doi = {10/c4rg94},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Gapare, Washington J. and Ivković, Miloš and Dutkowski, Gregory W. and Spencer, David J. and Buxton, Peter and Wu, Harry X.},
	month = apr,
	year = {2012},
	pages = {391--407},
}

@article{sillanpaa_simultaneous_2012,
	title = {Simultaneous estimation of multiple quantitative trait loci and growth curve parameters through hierarchical {Bayesian} modeling},
	volume = {108},
	issn = {0018-067X, 1365-2540},
	url = {http://www.nature.com/articles/hdy201156},
	doi = {10/dtwmdk},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Heredity},
	author = {Sillanpää, M J and Pikkuhookana, P and Abrahamsson, S and Knürr, T and Fries, A and Lerceteau, E and Waldmann, P and García-Gil, M R},
	month = feb,
	year = {2012},
	pages = {134--146},
}

@article{shi_photosystem_2012,
	title = {Photosystem {II}, a growing complex: {Updates} on newly discovered components and low molecular mass proteins},
	volume = {1817},
	issn = {00052728},
	shorttitle = {Photosystem {II}, a growing complex},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272811001988},
	doi = {10/bhjzwv},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Shi, Lan-Xin and Hall, Michael and Funk, Christiane and Schröder, Wolfgang P.},
	month = jan,
	year = {2012},
	pages = {13--25},
}

@article{shiryaeva_pair-wise_2012,
	title = {Pair-wise multicomparison and {OPLS} analyses of cold-acclimation phases in {Siberian} spruce},
	volume = {8},
	issn = {1573-3882, 1573-3890},
	url = {http://link.springer.com/10.1007/s11306-011-0304-5},
	doi = {10/bjrk4n},
	language = {en},
	number = {S1},
	urldate = {2021-06-08},
	journal = {Metabolomics},
	author = {Shiryaeva, Liudmila and Antti, Henrik and Schröder, Wolfgang P. and Strimbeck, Richard and Shiriaev, Anton S.},
	month = jun,
	year = {2012},
	pages = {123--130},
}

@article{kudahettige_characterization_2012,
	title = {Characterization of {Bioethanol} {Production} from {Hexoses} and {Xylose} by the {White} {Rot} {Fungus} {Trametes} versicolor},
	volume = {5},
	issn = {1939-1234, 1939-1242},
	url = {http://link.springer.com/10.1007/s12155-011-9119-5},
	doi = {10/dbhx8z},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {BioEnergy Research},
	author = {Kudahettige, Rasika L. and Holmgren, Marie and Imerzeel, Peter and Sellstedt, Anita},
	month = jun,
	year = {2012},
	pages = {277--285},
}

@article{chatchai_hydrogen_2012,
	title = {Hydrogen yield from a hydrogenase in {Frankia} {R43} at different levels of the carbon source propionate},
	volume = {95},
	issn = {03014797},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0301479711000065},
	doi = {10/b8mrnc},
	language = {en},
	urldate = {2021-06-08},
	journal = {Journal of Environmental Management},
	author = {Chatchai, Kosawang and Rasika Lasanthi, Kudahettige and Lars, Resman and Anita, Sellstedt},
	month = mar,
	year = {2012},
	pages = {S365--S368},
}

@article{galvao_synteny-based_2012,
	title = {Synteny-based mapping-by-sequencing enabled by targeted enrichment},
	volume = {71},
	issn = {1365-313X},
	doi = {10/gkgdms},
	abstract = {Mapping-by-sequencing, as implemented in SHOREmap ('SHOREmapping'), is greatly accelerating the identification of causal mutations. The original SHOREmap approach based on resequencing of bulked segregants required a highly accurate and complete reference sequence. However, current whole-genome or transcriptome assemblies from next-generation sequencing data of non-model organisms do not produce chromosome-length scaffolds. We have therefore developed a method that exploits synteny with a related genome for genetic mapping. We first demonstrate how mapping-by-sequencing can be performed using a reduced number of markers, and how the associated decrease in the number of markers can be compensated for by enrichment of marker sequences. As proof of concept, we apply this method to Arabidopsis thaliana gene models ordered by synteny with the genome sequence of the distant relative Brassica rapa, whose genome has several large-scale rearrangements relative to A. thaliana. Our approach provides an alternative method for high-resolution genetic mapping in species that lack finished genome reference sequences or for which only RNA-seq assemblies are available. Finally, for improved identification of causal mutations by fine-mapping, we introduce a new likelihood ratio test statistic, transforming local allele frequency estimations into a confidence interval similar to conventional mapping intervals.},
	language = {eng},
	number = {3},
	journal = {The Plant Journal: For Cell and Molecular Biology},
	author = {Galvão, Vinicius C. and Nordström, Karl J. V. and Lanz, Christa and Sulz, Patric and Mathieu, Johannes and Posé, David and Schmid, Markus and Weigel, Detlef and Schneeberger, Korbinian},
	month = aug,
	year = {2012},
	pmid = {22409706},
	keywords = {Arabidopsis, Arabidopsis Proteins, Brassica rapa, Chromosome Mapping, DNA Mutational Analysis, DNA, Plant, Flowers, Gene Frequency, Gene Library, Genetic Linkage, Genome, Plant, High-Throughput Nucleotide Sequencing, MADS Domain Proteins, Mutation, Sequence Analysis, DNA, Synteny, Transcriptome},
	pages = {517--526},
}

Mapping-by-sequencing, as implemented in SHOREmap ('SHOREmapping'), is greatly accelerating the identification of causal mutations. The original SHOREmap approach based on resequencing of bulked segregants required a highly accurate and complete reference sequence. However, current whole-genome or transcriptome assemblies from next-generation sequencing data of non-model organisms do not produce chromosome-length scaffolds. We have therefore developed a method that exploits synteny with a related genome for genetic mapping. We first demonstrate how mapping-by-sequencing can be performed using a reduced number of markers, and how the associated decrease in the number of markers can be compensated for by enrichment of marker sequences. As proof of concept, we apply this method to Arabidopsis thaliana gene models ordered by synteny with the genome sequence of the distant relative Brassica rapa, whose genome has several large-scale rearrangements relative to A. thaliana. Our approach provides an alternative method for high-resolution genetic mapping in species that lack finished genome reference sequences or for which only RNA-seq assemblies are available. Finally, for improved identification of causal mutations by fine-mapping, we introduce a new likelihood ratio test statistic, transforming local allele frequency estimations into a confidence interval similar to conventional mapping intervals.

@article{xue_paramutation-like_2012,
	title = {Paramutation-{Like} {Interaction} of {T}-{DNA} {Loci} in {Arabidopsis}},
	volume = {7},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0051651},
	doi = {10/f22djh},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Xue, Weiya and Ruprecht, Colin and Street, Nathaniel and Hematy, Kian and Chang, Christine and Frommer, Wolf B. and Persson, Staffan and Niittylä, Totte},
	editor = {Schiefelbein, John},
	month = dec,
	year = {2012},
	pages = {e51651},
}

@article{buren_use_2012,
	title = {Use of the {Foot}-and-{Mouth} {Disease} {Virus} {2A} {Peptide} {Co}-{Expression} {System} to {Study} {Intracellular} {Protein} {Trafficking} in {Arabidopsis}},
	volume = {7},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0051973},
	doi = {10/f224q9},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Burén, Stefan and Ortega-Villasante, Cristina and Ötvös, Krisztina and Samuelsson, Göran and Bakó, László and Villarejo, Arsenio},
	editor = {Caplan, Steve},
	month = dec,
	year = {2012},
	pages = {e51973},
}

@article{caseys_effects_2012,
	title = {Effects of interspecific recombination on functional traits in trees revealed by metabolomics and genotyping-by-resequencing},
	volume = {5},
	issn = {1755-0874, 1755-1668},
	url = {http://www.tandfonline.com/doi/abs/10.1080/17550874.2012.748850},
	doi = {10/f24bc2},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Ecology \& Diversity},
	author = {Caseys, Celine and Glauser, Gaetan and Stölting, Kai N. and Christe, Camille and Albrectsen, Benedicte R. and Lexer, Christian},
	month = dec,
	year = {2012},
	pages = {457--471},
}

@article{baster_scftir1afb-auxin_2012,
	title = {{SCFTIR1}/{AFB}-auxin signalling regulates {PIN} vacuolar trafficking and auxin fluxes during root gravitropism},
	volume = {32},
	issn = {0261-4189, 1460-2075},
	url = {http://emboj.embopress.org/cgi/doi/10.1038/emboj.2012.310},
	doi = {10/f3m3cc},
	number = {2},
	urldate = {2021-06-08},
	journal = {The EMBO Journal},
	author = {Baster, Paweł and Robert, Stéphanie and Kleine-Vehn, Jürgen and Vanneste, Steffen and Kania, Urszula and Grunewald, Wim and De Rybel, Bert and Beeckman, Tom and Friml, Jiří},
	month = dec,
	year = {2012},
	pages = {260--274},
}

@article{blanco-rivero_phosphorylation_2012,
	title = {Phosphorylation {Controls} the {Localization} and {Activation} of the {Lumenal} {Carbonic} {Anhydrase} in {Chlamydomonas} reinhardtii},
	volume = {7},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0049063},
	doi = {10/f3m4g8},
	language = {en},
	number = {11},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Blanco-Rivero, Amaya and Shutova, Tatiana and Román, María José and Villarejo, Arsenio and Martinez, Flor},
	editor = {Subramanyam, Rajagopal},
	month = nov,
	year = {2012},
	pages = {e49063},
}

@article{chow_quantifying_2012,
	title = {Quantifying and monitoring functional photosystem {II} and the stoichiometry of the two photosystems in leaf segments: approaches and approximations},
	volume = {113},
	issn = {0166-8595, 1573-5079},
	shorttitle = {Quantifying and monitoring functional photosystem {II} and the stoichiometry of the two photosystems in leaf segments},
	url = {http://link.springer.com/10.1007/s11120-012-9740-y},
	doi = {10/f24pmz},
	language = {en},
	number = {1-3},
	urldate = {2021-06-08},
	journal = {Photosynthesis Research},
	author = {Chow, Wah Soon and Fan, Da-Yong and Oguchi, Riichi and Jia, Husen and Losciale, Pasquale and Park, Youn-Il and He, Jie and Öquist, Gunnar and Shen, Yun-Gang and Anderson, Jan M.},
	month = sep,
	year = {2012},
	pages = {63--74},
}

@article{nakamura_planar_2012,
	title = {Planar polarity, tissue polarity and planar morphogenesis in plants},
	volume = {15},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526612001033},
	doi = {10/f24dsf},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Current Opinion in Plant Biology},
	author = {Nakamura, Moritaka and Kiefer, Christian S and Grebe, Markus},
	month = dec,
	year = {2012},
	pages = {593--600},
}

@article{tsai_constitutive_2012,
	title = {Constitutive expression of a fungal glucuronoyl esterase in {Arabidopsis} reveals altered cell wall composition and structure: {Transgenic} expression of {PcGCE} in {Arabidopsis}},
	volume = {10},
	issn = {14677644},
	shorttitle = {Constitutive expression of a fungal glucuronoyl esterase in {Arabidopsis} reveals altered cell wall composition and structure},
	url = {http://doi.wiley.com/10.1111/j.1467-7652.2012.00735.x},
	doi = {10/f2zwvt},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {Plant Biotechnology Journal},
	author = {Tsai, Alex Y.-L. and Canam, Thomas and Gorzsás, András and Mellerowicz, Ewa J. and Campbell, Malcolm M. and Master, Emma R.},
	month = dec,
	year = {2012},
	pages = {1077--1087},
}

@article{svedstrom_hierarchical_2012,
	title = {Hierarchical structure of juvenile hybrid aspen xylem revealed using {X}-ray scattering and microtomography},
	volume = {26},
	issn = {0931-1890, 1432-2285},
	url = {http://link.springer.com/10.1007/s00468-012-0748-x},
	doi = {10/f229zh},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Trees},
	author = {Svedström, Kirsi and Lucenius, Jessica and Van den Bulcke, Jan and Van Loo, Denis and Immerzeel, Peter and Suuronen, Jussi-Petteri and Brabant, Loes and Van Acker, Joris and Saranpää, Pekka and Fagerstedt, Kurt and Mellerowicz, Ewa and Serimaa, Ritva},
	month = dec,
	year = {2012},
	pages = {1793--1804},
}

@article{bielach_spatiotemporal_2012,
	title = {Spatiotemporal {Regulation} of {Lateral} {Root} {Organogenesis} in \textit{{Arabidopsis}} by {Cytokinin}},
	volume = {24},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/24/10/3967-3981/6101532},
	doi = {10/f4ffx8},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Bielach, Agnieszka and Podlešáková, Kateřina and Marhavý, Peter and Duclercq, Jérôme and Cuesta, Candela and Müller, Bruno and Grunewald, Wim and Tarkowski, Petr and Benková, Eva},
	month = oct,
	year = {2012},
	pages = {3967--3981},
}

@article{chen_phylogeography_2012,
	title = {Phylogeography of {Quercus} variabilis {Based} on {Chloroplast} {DNA} {Sequence} in {East} {Asia}: {Multiple} {Glacial} {Refugia} and {Mainland}-{Migrated} {Island} {Populations}},
	volume = {7},
	issn = {1932-6203},
	shorttitle = {Phylogeography of {Quercus} variabilis {Based} on {Chloroplast} {DNA} {Sequence} in {East} {Asia}},
	url = {https://dx.plos.org/10.1371/journal.pone.0047268},
	doi = {10/f23cz3},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Chen, Dongmei and Zhang, Xianxian and Kang, Hongzhang and Sun, Xiao and Yin, Shan and Du, Hongmei and Yamanaka, Norikazu and Gapare, Washington and Wu, Harry X. and Liu, Chunjiang},
	editor = {Shaw, Peter},
	month = oct,
	year = {2012},
	pages = {e47268},
}

@article{gorshkova_plant_2012,
	title = {Plant {Fiber} {Formation}: {State} of the {Art}, {Recent} and {Expected} {Progress}, and {Open} {Questions}},
	volume = {31},
	issn = {0735-2689, 1549-7836},
	shorttitle = {Plant {Fiber} {Formation}},
	url = {http://www.tandfonline.com/doi/abs/10.1080/07352689.2011.616096},
	doi = {10/f2z5m4},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Critical Reviews in Plant Sciences},
	author = {Gorshkova, Tatyana and Brutch, Nina and Chabbert, Brigitte and Deyholos, Michael and Hayashi, Takahisa and Lev-Yadun, Simcha and Mellerowicz, Ewa J. and Morvan, Claudine and Neutelings, Godfrey and Pilate, Gilles},
	month = may,
	year = {2012},
	pages = {201--228},
}

@article{li_linking_2012,
	title = {Linking photoreceptor excitation to changes in plant architecture},
	volume = {26},
	issn = {0890-9369},
	url = {http://genesdev.cshlp.org/cgi/doi/10.1101/gad.187849.112},
	doi = {10/f2zrkq},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Genes \& Development},
	author = {Li, L. and Ljung, K. and Breton, G. and Schmitz, R. J. and Pruneda-Paz, J. and Cowing-Zitron, C. and Cole, B. J. and Ivans, L. J. and Pedmale, U. V. and Jung, H.-S. and Ecker, J. R. and Kay, S. A. and Chory, J.},
	month = apr,
	year = {2012},
	pages = {785--790},
}

@article{lilley_endogenous_2012,
	title = {An {Endogenous} {Carbon}-{Sensing} {Pathway} {Triggers} {Increased} {Auxin} {Flux} and {Hypocotyl} {Elongation}},
	volume = {160},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/160/4/2261/6109644},
	doi = {10/f22bb5},
	abstract = {Abstract
            The local environment has a substantial impact on early seedling development. Applying excess carbon in the form of sucrose is known to alter both the timing and duration of seedling growth. Here, we show that sucrose changes growth patterns by increasing auxin levels and rootward auxin transport in Arabidopsis (Arabidopsis thaliana). Sucrose likely interacts with an endogenous carbon-sensing pathway via the PHYTOCHROME-INTERACTING FACTOR (PIF) family of transcription factors, as plants grown in elevated carbon dioxide showed the same PIF-dependent growth promotion. Overexpression of PIF5 was sufficient to suppress photosynthetic rate, enhance response to elevated carbon dioxide, and prolong seedling survival in nitrogen-limiting conditions. Thus, PIF transcription factors integrate growth with metabolic demands and thereby facilitate functional equilibrium during photomorphogenesis.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Lilley, Jodi L. Stewart and Gee, Christopher W. and Sairanen, Ilkka and Ljung, Karin and Nemhauser, Jennifer L.},
	month = dec,
	year = {2012},
	pages = {2261--2270},
}

Abstract The local environment has a substantial impact on early seedling development. Applying excess carbon in the form of sucrose is known to alter both the timing and duration of seedling growth. Here, we show that sucrose changes growth patterns by increasing auxin levels and rootward auxin transport in Arabidopsis (Arabidopsis thaliana). Sucrose likely interacts with an endogenous carbon-sensing pathway via the PHYTOCHROME-INTERACTING FACTOR (PIF) family of transcription factors, as plants grown in elevated carbon dioxide showed the same PIF-dependent growth promotion. Overexpression of PIF5 was sufficient to suppress photosynthetic rate, enhance response to elevated carbon dioxide, and prolong seedling survival in nitrogen-limiting conditions. Thus, PIF transcription factors integrate growth with metabolic demands and thereby facilitate functional equilibrium during photomorphogenesis.

@article{keech_genetic_2012,
	title = {The {Genetic} {Dissection} of a {Short}-{Term} {Response} to {Low} {CO2} {Supports} the {Possibility} for {Peroxide}-{Mediated} {Decarboxylation} of {Photorespiratory} {Intermediates} in the {Peroxisome}},
	volume = {5},
	issn = {16742052},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1674205214601647},
	doi = {10/gkgdr5},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Molecular Plant},
	author = {Keech, Olivier and Zhou, Wenxu and Fenske, Ricarda and Colas-des-Francs-Small, Catherine and Bussell, John D. and Badger, Murray R. and Smith, Steven M.},
	month = nov,
	year = {2012},
	pages = {1413--1416},
}

@article{ivanov_implications_2012,
	title = {Implications of alternative electron sinks in increased resistance of {PSII} and {PSI} photochemistry to high light stress in cold-acclimated {Arabidopsis} thaliana},
	volume = {113},
	issn = {0166-8595, 1573-5079},
	url = {http://link.springer.com/10.1007/s11120-012-9769-y},
	doi = {10/f23h5g},
	language = {en},
	number = {1-3},
	urldate = {2021-06-08},
	journal = {Photosynthesis Research},
	author = {Ivanov, A. G. and Rosso, D. and Savitch, L. V. and Stachula, P. and Rosembert, M. and Oquist, G. and Hurry, V. and Hüner, N. P. A.},
	month = sep,
	year = {2012},
	pages = {191--206},
}

@article{cheregi_search_2012,
	title = {The search for new chlorophyll-binding proteins in the cyanobacterium {Synechocystis} sp. {PCC} 6803},
	volume = {162},
	issn = {01681656},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0168165612003550},
	doi = {10/f23dpr},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Journal of Biotechnology},
	author = {Cheregi, Otilia and Vermaas, Wim and Funk, Christiane},
	month = nov,
	year = {2012},
	pages = {124--133},
}

@article{fuentes_fruit_2012,
	title = {Fruit {Growth} in \textit{{Arabidopsis}} {Occurs} via {DELLA}-{Dependent} and {DELLA}-{Independent} {Gibberellin} {Responses}},
	volume = {24},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/24/10/3982-3996/6101547},
	doi = {10/f22dj7},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Fuentes, Sara and Ljung, Karin and Sorefan, Karim and Alvey, Elizabeth and Harberd, Nicholas P. and Østergaard, Lars},
	month = oct,
	year = {2012},
	pages = {3982--3996},
}

@article{klintenas_analysis_2012,
	title = {Analysis of conifer \textit{{FLOWERING} {LOCUS} {T}} / \textit{{TERMINAL} {FLOWER1}} ‐like genes provides evidence for dramatic biochemical evolution in the angiosperm {\textless}span style="font-variant:small-caps;"{\textgreater} \textit{{FT}} {\textless}/span{\textgreater} lineage},
	volume = {196},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Analysis of conifer \textit{{FLOWERING} {LOCUS} {T}} / \textit{{TERMINAL} {FLOWER1}} ‐like genes provides evidence for dramatic biochemical evolution in the angiosperm {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2012.04332.x},
	doi = {10/f23gx2},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Klintenäs, Maria and Pin, Pierre A. and Benlloch, Reyes and Ingvarsson, Pär K. and Nilsson, Ove},
	month = dec,
	year = {2012},
	pages = {1260--1273},
}

@article{roberts_degradation_2012,
	title = {Degradation of {PsbO} by the {Deg} {Protease} {HhoA} {Is} {Thioredoxin} {Dependent}},
	volume = {7},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0045713},
	doi = {10/f25qns},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Roberts, Irma N. and Lam, Xuan Tam and Miranda, Helder and Kieselbach, Thomas and Funk, Christiane},
	editor = {Börnke, Frederik},
	month = sep,
	year = {2012},
	pages = {e45713},
}

@article{surowiec_mass_2012,
	title = {Mass spectrometric identification of new minor indigoids in shellfish purple dye from {Hexaplex} trunculus},
	volume = {94},
	issn = {01437208},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0143720812000320},
	doi = {10/f2zz55},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Dyes and Pigments},
	author = {Surowiec, Izabella and Nowik, Witold and Moritz, Thomas},
	month = aug,
	year = {2012},
	pages = {363--369},
}

@article{sahlin_improved_2012,
	title = {Improved gap size estimation for scaffolding algorithms},
	volume = {28},
	issn = {1460-2059, 1367-4803},
	url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bts441},
	doi = {10/f2zsch},
	language = {en},
	number = {17},
	urldate = {2021-06-08},
	journal = {Bioinformatics},
	author = {Sahlin, Kristoffer and Street, Nathaniel and Lundeberg, Joakim and Arvestad, Lars},
	month = sep,
	year = {2012},
	pages = {2215--2222},
}

@article{zang_effects_2012,
	title = {Effects of oestrogen and testosterone therapy on serum metabolites in postmenopausal women},
	volume = {77},
	issn = {03000664},
	url = {http://doi.wiley.com/10.1111/j.1365-2265.2012.04374.x},
	doi = {10/f2znjv},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Clinical Endocrinology},
	author = {Zang, Hong and Moritz, Thomas and Norstedt, Gunnar and Hirschberg, Angelica L. and Tollet-Egnell, Petra},
	month = aug,
	year = {2012},
	pages = {288--295},
}

@article{gutierrez_auxin_2012,
	title = {Auxin {Controls} {Arabidopsis} {Adventitious} {Root} {Initiation} by {Regulating} {Jasmonic} {Acid} {Homeostasis}},
	volume = {24},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.112.099119},
	doi = {10/f22j9d},
	abstract = {Vegetative shoot-based propagation of plants, including mass propagation of elite genotypes, is dependent on the development of shoot-borne roots, which are also called adventitious roots. Multiple endogenous and environmental factors control the complex process of adventitious rooting. In the past few years, we have shown that the auxin response factors ARF6 and ARF8, targets of the microRNA miR167, are positive regulators of adventitious rooting, whereas ARF17, a target of miR160, is a negative regulator. We showed that these genes have overlapping expression profiles during adventitious rooting and that they regulate each other's expression at the transcriptional and posttranscriptional levels by modulating the homeostasis of miR160 and miR167. We demonstrate here that this complex network of transcription factors regulates the expression of three auxin-inducible Gretchen Hagen3 (GH3) genes, GH3.3, GH3.5, and GH3.6, encoding acyl-acid-amido synthetases. We show that these three GH3 genes are required for fine-tuning adventitious root initiation in the Arabidopsis thaliana hypocotyl, and we demonstrate that they act by modulating jasmonic acid homeostasis. We propose a model in which adventitious rooting is an adaptive developmental response involving crosstalk between the auxin and jasmonate regulatory pathways.},
	number = {6},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Gutierrez, Laurent and Mongelard, Gaëlle and Floková, Kristýna and Păcurar, Daniel I. and Novák, Ondřej and Staswick, Paul and Kowalczyk, Mariusz and Păcurar, Monica and Demailly, Hervé and Geiss, Gaia and Bellini, Catherine},
	month = jun,
	year = {2012},
	pages = {2515--2527},
}

Vegetative shoot-based propagation of plants, including mass propagation of elite genotypes, is dependent on the development of shoot-borne roots, which are also called adventitious roots. Multiple endogenous and environmental factors control the complex process of adventitious rooting. In the past few years, we have shown that the auxin response factors ARF6 and ARF8, targets of the microRNA miR167, are positive regulators of adventitious rooting, whereas ARF17, a target of miR160, is a negative regulator. We showed that these genes have overlapping expression profiles during adventitious rooting and that they regulate each other's expression at the transcriptional and posttranscriptional levels by modulating the homeostasis of miR160 and miR167. We demonstrate here that this complex network of transcription factors regulates the expression of three auxin-inducible Gretchen Hagen3 (GH3) genes, GH3.3, GH3.5, and GH3.6, encoding acyl-acid-amido synthetases. We show that these three GH3 genes are required for fine-tuning adventitious root initiation in the Arabidopsis thaliana hypocotyl, and we demonstrate that they act by modulating jasmonic acid homeostasis. We propose a model in which adventitious rooting is an adaptive developmental response involving crosstalk between the auxin and jasmonate regulatory pathways.

@article{bielach_genetic_2012,
	title = {Genetic approach towards the identification of auxin–cytokinin crosstalk components involved in root development},
	volume = {367},
	url = {https://royalsocietypublishing.org/doi/10.1098/rstb.2011.0233},
	doi = {10/f32frv},
	abstract = {Phytohormones are important plant growth regulators that control many developmental processes, such as cell division, cell differentiation, organogenesis and morphogenesis. They regulate a multitude of apparently unrelated physiological processes, often with overlapping roles, and they mutually modulate their effects. These features imply important synergistic and antagonistic interactions between the various plant hormones. Auxin and cytokinin are central hormones involved in the regulation of plant growth and development, including processes determining root architecture, such as root pole establishment during early embryogenesis, root meristem maintenance and lateral root organogenesis. Thus, to control root development both pathways put special demands on the mechanisms that balance their activities and mediate their interactions. Here, we summarize recent knowledge on the role of auxin and cytokinin in the regulation of root architecture with special focus on lateral root organogenesis, discuss the latest findings on the molecular mechanisms of their interactions, and present forward genetic screen as a tool to identify novel molecular components of the auxin and cytokinin crosstalk.},
	number = {1595},
	urldate = {2021-06-08},
	journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
	author = {Bielach, Agnieszka and Duclercq, Jérôme and Marhavý, Peter and Benková, Eva},
	month = jun,
	year = {2012},
	note = {Publisher: Royal Society},
	pages = {1469--1478},
}

Phytohormones are important plant growth regulators that control many developmental processes, such as cell division, cell differentiation, organogenesis and morphogenesis. They regulate a multitude of apparently unrelated physiological processes, often with overlapping roles, and they mutually modulate their effects. These features imply important synergistic and antagonistic interactions between the various plant hormones. Auxin and cytokinin are central hormones involved in the regulation of plant growth and development, including processes determining root architecture, such as root pole establishment during early embryogenesis, root meristem maintenance and lateral root organogenesis. Thus, to control root development both pathways put special demands on the mechanisms that balance their activities and mediate their interactions. Here, we summarize recent knowledge on the role of auxin and cytokinin in the regulation of root architecture with special focus on lateral root organogenesis, discuss the latest findings on the molecular mechanisms of their interactions, and present forward genetic screen as a tool to identify novel molecular components of the auxin and cytokinin crosstalk.

@article{li_identification_2012,
	title = {Identification of putative candidate genes for juvenile wood density in {Pinus} radiata},
	volume = {32},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tps060},
	doi = {10/f24jz3},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Tree Physiology},
	author = {Li, X. and Wu, H. X. and Southerton, S. G.},
	month = aug,
	year = {2012},
	pages = {1046--1057},
}

@article{madsen_metabolic_2012,
	title = {Metabolic {Responses} to {Change} in {Disease} {Activity} during {Tumor} {Necrosis} {Factor} {Inhibition} in {Patients} with {Rheumatoid} {Arthritis}},
	volume = {11},
	issn = {1535-3893, 1535-3907},
	url = {https://pubs.acs.org/doi/10.1021/pr300296v},
	doi = {10/f24g7h},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Journal of Proteome Research},
	author = {Madsen, Rasmus and Rantapää-Dahlqvist, Solbritt and Lundstedt, Torbjörn and Moritz, Thomas and Trygg, Johan},
	month = jul,
	year = {2012},
	pages = {3796--3804},
}

@article{novak_tissue-specific_2012,
	title = {Tissue-specific profiling of the \textit{{Arabidopsis} thaliana} auxin metabolome: \textit{{Auxin} metabolite profiling in} {Arabidopsis}},
	volume = {72},
	issn = {09607412},
	shorttitle = {Tissue-specific profiling of the \textit{{Arabidopsis} thaliana} auxin metabolome},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2012.05085.x},
	doi = {10/f23drs},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Novák, Ondřej and Hényková, Eva and Sairanen, Ilkka and Kowalczyk, Mariusz and Pospíšil, Tomáš and Ljung, Karin},
	month = nov,
	year = {2012},
	pages = {523--536},
}

@article{shaikhali_redox-mediated_2012,
	title = {Redox-mediated {Mechanisms} {Regulate} {DNA} {Binding} {Activity} of the {G}-group of {Basic} {Region} {Leucine} {Zipper} ({bZIP}) {Transcription} {Factors} in {Arabidopsis}},
	volume = {287},
	issn = {00219258},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925820477762},
	doi = {10/f22pjj},
	language = {en},
	number = {33},
	urldate = {2021-06-08},
	journal = {Journal of Biological Chemistry},
	author = {Shaikhali, Jehad and Norén, Louise and de Dios Barajas-López, Juan and Srivastava, Vaibhav and König, Janine and Sauer, Uwe H. and Wingsle, Gunnar and Dietz, Karl-Josef and Strand, Åsa},
	month = aug,
	year = {2012},
	pages = {27510--27525},
}

@article{pin_multifaceted_2012,
	title = {The multifaceted roles of {FLOWERING} {LOCUS} {T} in plant development: {FT}, a multifunctional protein},
	volume = {35},
	issn = {01407791},
	shorttitle = {The multifaceted roles of {FLOWERING} {LOCUS} {T} in plant development},
	url = {http://doi.wiley.com/10.1111/j.1365-3040.2012.02558.x},
	doi = {10/f23ndf},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {Plant, Cell \& Environment},
	author = {Pin, P. A. and Nilsson, O.},
	month = oct,
	year = {2012},
	pages = {1742--1755},
}

@article{tuskan_obscure_2012,
	title = {The obscure events contributing to the evolution of an incipient sex chromosome in {Populus}: a retrospective working hypothesis},
	volume = {8},
	issn = {1614-2950},
	shorttitle = {The obscure events contributing to the evolution of an incipient sex chromosome in {Populus}},
	url = {https://doi.org/10.1007/s11295-012-0495-6},
	doi = {10/f24dvz},
	abstract = {Genetic determination of gender is a fundamental developmental and evolutionary process in plants. Although it appears that dioecy in Populus is genetically controlled, the precise gender-determining systems remain unclear. The recently released second draft assembly and annotated gene set of the Populus genome provided an opportunity to revisit this topic. We hypothesized that over evolutionary time, selective pressure has reformed the genome structure and gene composition in the peritelomeric region of the chromosome XIX, which has resulted in a distinctive genome structure and cluster of genes contributing to gender determination in Populus trichocarpa. Multiple lines of evidence support this working hypothesis. First, the peritelomeric region of the chromosome XIX contains significantly fewer single nucleotide polymorphisms than the rest of Populus genome and has a distinct evolutionary history. Second, the peritelomeric end of chromosome XIX contains the largest cluster of the nucleotide-binding site–leucine-rich repeat (NBS–LRR) class of disease resistance genes in the entire Populus genome. Third, there is a high occurrence of small microRNAs on chromosome XIX, which is coincident to the region containing the putative gender-determining locus and the major cluster of NBS–LRR genes. Further, by analyzing the metabolomic profiles of floral bud in male and female Populus trees using a gas chromatography-mass spectrometry, we found that there are gender-specific accumulations of phenolic glycosides. Taken together, these findings led to the hypothesis that resistance to and regulation of a floral pathogen and gender determination coevolved, and that these events triggered the emergence of a nascent sex chromosome. Further studies of chromosome XIX will provide new insights into the genetic control of gender determination in Populus.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Tuskan, Gerald A. and DiFazio, Steve and Faivre-Rampant, Patricia and Gaudet, Muriel and Harfouche, Antoine and Jorge, Véronique and Labbé, Jessy L. and Ranjan, Priya and Sabatti, Maurizio and Slavov, Gancho and Street, Nathaniel and Tschaplinski, Timothy J. and Yin, Tongming},
	month = jun,
	year = {2012},
	pages = {559--571},
}

Genetic determination of gender is a fundamental developmental and evolutionary process in plants. Although it appears that dioecy in Populus is genetically controlled, the precise gender-determining systems remain unclear. The recently released second draft assembly and annotated gene set of the Populus genome provided an opportunity to revisit this topic. We hypothesized that over evolutionary time, selective pressure has reformed the genome structure and gene composition in the peritelomeric region of the chromosome XIX, which has resulted in a distinctive genome structure and cluster of genes contributing to gender determination in Populus trichocarpa. Multiple lines of evidence support this working hypothesis. First, the peritelomeric region of the chromosome XIX contains significantly fewer single nucleotide polymorphisms than the rest of Populus genome and has a distinct evolutionary history. Second, the peritelomeric end of chromosome XIX contains the largest cluster of the nucleotide-binding site–leucine-rich repeat (NBS–LRR) class of disease resistance genes in the entire Populus genome. Third, there is a high occurrence of small microRNAs on chromosome XIX, which is coincident to the region containing the putative gender-determining locus and the major cluster of NBS–LRR genes. Further, by analyzing the metabolomic profiles of floral bud in male and female Populus trees using a gas chromatography-mass spectrometry, we found that there are gender-specific accumulations of phenolic glycosides. Taken together, these findings led to the hypothesis that resistance to and regulation of a floral pathogen and gender determination coevolved, and that these events triggered the emergence of a nascent sex chromosome. Further studies of chromosome XIX will provide new insights into the genetic control of gender determination in Populus.

@article{cooke_dynamic_2012,
	title = {The dynamic nature of bud dormancy in trees: environmental control and molecular mechanisms: {Bud} dormancy in trees},
	volume = {35},
	issn = {01407791},
	shorttitle = {The dynamic nature of bud dormancy in trees},
	url = {http://doi.wiley.com/10.1111/j.1365-3040.2012.02552.x},
	doi = {10/f22v73},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {Plant, Cell \& Environment},
	author = {Cooke, Janice E. K. and Eriksson, Maria E. and Junttila, Olavi},
	month = oct,
	year = {2012},
	pages = {1707--1728},
}

@article{chibani_atypical_2012,
	title = {Atypical {Thioredoxins} in {Poplar}: {The} {Glutathione}-{Dependent} {Thioredoxin}-{Like} 2.1 {Supports} the {Activity} of {Target} {Enzymes} {Possessing} a {Single} {Redox} {Active} {Cysteine}},
	volume = {159},
	issn = {1532-2548},
	shorttitle = {Atypical {Thioredoxins} in {Poplar}},
	url = {https://academic.oup.com/plphys/article/159/2/592/6109157},
	doi = {10/f3ptz3},
	abstract = {Abstract
            Plant thioredoxins (Trxs) constitute a complex family of thiol oxidoreductases generally sharing a WCGPC active site sequence. Some recently identified plant Trxs (Clot, Trx-like1 and -2, Trx-lilium1, -2, and -3) display atypical active site sequences with altered residues between the two conserved cysteines. The transcript expression patterns, subcellular localizations, and biochemical properties of some representative poplar (Populus spp.) isoforms were investigated. Measurements of transcript levels for the 10 members in poplar organs indicate that most genes are constitutively expressed. Using transient expression of green fluorescent protein fusions, Clot and Trx-like1 were found to be mainly cytosolic, whereas Trx-like2.1 was located in plastids. All soluble recombinant proteins, except Clot, exhibited insulin reductase activity, although with variable efficiencies. Whereas Trx-like2.1 and Trx-lilium2.2 were efficiently regenerated both by NADPH-Trx reductase and glutathione, none of the proteins were reduced by the ferredoxin-Trx reductase. Only Trx-like2.1 supports the activity of plastidial thiol peroxidases and methionine sulfoxide reductases employing a single cysteine residue for catalysis and using a glutathione recycling system. The second active site cysteine of Trx-like2.1 is dispensable for this reaction, indicating that the protein possesses a glutaredoxin-like activity. Interestingly, the Trx-like2.1 active site replacement, from WCRKC to WCGPC, suppresses its capacity to use glutathione as a reductant but is sufficient to allow the regeneration of target proteins employing two cysteines for catalysis, indicating that the nature of the residues composing the active site sequence is crucial for substrate selectivity/recognition. This study provides another example of the cross talk existing between the glutathione/glutaredoxin and Trx-dependent pathways.},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Chibani, Kamel and Tarrago, Lionel and Gualberto, José Manuel and Wingsle, Gunnar and Rey, Pascal and Jacquot, Jean-Pierre and Rouhier, Nicolas},
	month = jun,
	year = {2012},
	pages = {592--605},
}

Abstract Plant thioredoxins (Trxs) constitute a complex family of thiol oxidoreductases generally sharing a WCGPC active site sequence. Some recently identified plant Trxs (Clot, Trx-like1 and -2, Trx-lilium1, -2, and -3) display atypical active site sequences with altered residues between the two conserved cysteines. The transcript expression patterns, subcellular localizations, and biochemical properties of some representative poplar (Populus spp.) isoforms were investigated. Measurements of transcript levels for the 10 members in poplar organs indicate that most genes are constitutively expressed. Using transient expression of green fluorescent protein fusions, Clot and Trx-like1 were found to be mainly cytosolic, whereas Trx-like2.1 was located in plastids. All soluble recombinant proteins, except Clot, exhibited insulin reductase activity, although with variable efficiencies. Whereas Trx-like2.1 and Trx-lilium2.2 were efficiently regenerated both by NADPH-Trx reductase and glutathione, none of the proteins were reduced by the ferredoxin-Trx reductase. Only Trx-like2.1 supports the activity of plastidial thiol peroxidases and methionine sulfoxide reductases employing a single cysteine residue for catalysis and using a glutathione recycling system. The second active site cysteine of Trx-like2.1 is dispensable for this reaction, indicating that the protein possesses a glutaredoxin-like activity. Interestingly, the Trx-like2.1 active site replacement, from WCRKC to WCGPC, suppresses its capacity to use glutathione as a reductant but is sufficient to allow the regeneration of target proteins employing two cysteines for catalysis, indicating that the nature of the residues composing the active site sequence is crucial for substrate selectivity/recognition. This study provides another example of the cross talk existing between the glutathione/glutaredoxin and Trx-dependent pathways.

@article{chen_abp1_2012,
	title = {{ABP1} and {ROP6} {GTPase} {Signaling} {Regulate} {Clathrin}-{Mediated} {Endocytosis} in {Arabidopsis} {Roots}},
	volume = {22},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982212005738},
	doi = {10/f35br9},
	language = {en},
	number = {14},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Chen, Xu and Naramoto, Satoshi and Robert, Stéphanie and Tejos, Ricardo and Löfke, Christian and Lin, Deshu and Yang, Zhenbiao and Friml, Jiří},
	month = jul,
	year = {2012},
	pages = {1326--1332},
}

@article{pin_role_2012,
	title = {The {Role} of a {Pseudo}-{Response} {Regulator} {Gene} in {Life} {Cycle} {Adaptation} and {Domestication} of {Beet}},
	volume = {22},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982212003946},
	doi = {10/f233wd},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Pin, Pierre A. and Zhang, Wenying and Vogt, Sebastian H. and Dally, Nadine and Büttner, Bianca and Schulze-Buxloh, Gretel and Jelly, Noémie S. and Chia, Tansy Y.P. and Mutasa-Göttgens, Effie S. and Dohm, Juliane C. and Himmelbauer, Heinz and Weisshaar, Bernd and Kraus, Josef and Gielen, Jan J.L. and Lommel, Murielle and Weyens, Guy and Wahl, Bettina and Schechert, Axel and Nilsson, Ove and Jung, Christian and Kraft, Thomas and Müller, Andreas E.},
	month = jun,
	year = {2012},
	pages = {1095--1101},
}

@article{fries_genetic_2012,
	title = {Genetic parameters, genetic gain and correlated responses in growth, fibre dimensions and wood density in a {Scots} pine breeding population},
	volume = {69},
	issn = {1286-4560, 1297-966X},
	url = {http://link.springer.com/10.1007/s13595-012-0202-7},
	doi = {10/f2zq2g},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Annals of Forest Science},
	author = {Fries, Anders},
	month = oct,
	year = {2012},
	pages = {783--794},
}

@article{gapare_genetic_2012,
	title = {Genetic parameters and provenance variation of {Pinus} radiata {D}. {Don}. ‘{Eldridge} collection’ in {Australia} 2: wood properties},
	volume = {8},
	issn = {1614-2942, 1614-2950},
	shorttitle = {Genetic parameters and provenance variation of {Pinus} radiata {D}. {Don}. ‘{Eldridge} collection’ in {Australia} 2},
	url = {http://link.springer.com/10.1007/s11295-012-0475-x},
	doi = {10/f3p3cs},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Gapare, Washington J. and Ivković, Miloš and Dillon, Shannon K. and Chen, Fiona and Evans, Robert and Wu, Harry X.},
	month = aug,
	year = {2012},
	pages = {895--910},
}

@article{robinson_genetic_2012,
	title = {Genetic {Variation} in {Functional} {Traits} {Influences} {Arthropod} {Community} {Composition} in {Aspen} ({Populus} tremula {L}.)},
	volume = {7},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0037679},
	doi = {10/f24ksj},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Robinson, Kathryn M. and Ingvarsson, Pär K. and Jansson, Stefan and Albrectsen, Benedicte R.},
	editor = {Kliebenstein, Daniel J.},
	month = may,
	year = {2012},
	pages = {e37679},
}

@article{gerber_multivariate_2012,
	title = {Multivariate curve resolution provides a high-throughput data processing pipeline for pyrolysis-gas chromatography/mass spectrometry},
	volume = {95},
	issn = {01652370},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0165237012000137},
	doi = {10/fxs9zf},
	language = {en},
	urldate = {2021-06-08},
	journal = {Journal of Analytical and Applied Pyrolysis},
	author = {Gerber, Lorenz and Eliasson, Mattias and Trygg, Johan and Moritz, Thomas and Sundberg, Björn},
	month = may,
	year = {2012},
	pages = {95--100},
}

@article{inselsbacher_belowground_2012,
	title = {The below‐ground perspective of forest plants: soil provides mainly organic nitrogen for plants and mycorrhizal fungi},
	volume = {195},
	issn = {0028-646X, 1469-8137},
	shorttitle = {The below‐ground perspective of forest plants},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2012.04169.x},
	doi = {10/f23c63},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Inselsbacher, Erich and Näsholm, Torgny},
	month = jul,
	year = {2012},
	pages = {329--334},
}

@article{hornitschek_phytochrome_2012,
	title = {Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling: {PIF4} and {PIF5} control auxin signaling},
	volume = {71},
	issn = {09607412},
	shorttitle = {Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2012.05033.x},
	doi = {10/f233dh},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Hornitschek, Patricia and Kohnen, Markus V. and Lorrain, Séverine and Rougemont, Jacques and Ljung, Karin and López-Vidriero, Irene and Franco-Zorrilla, José M. and Solano, Roberto and Trevisan, Martine and Pradervand, Sylvain and Xenarios, Ioannis and Fankhauser, Christian},
	month = sep,
	year = {2012},
	pages = {699--711},
}

@article{roberts_senescence-associated_2012,
	title = {Senescence-associated proteases in plants},
	volume = {145},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2012.01574.x},
	doi = {10/fxs9pf},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Roberts, Irma N. and Caputo, Carla and Criado, María Victoria and Funk, Christiane},
	month = may,
	year = {2012},
	pages = {130--139},
}

@article{wagner_ftsh_2012,
	title = {{FtsH} proteases located in the plant chloroplast},
	volume = {145},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2011.01548.x},
	doi = {10/d467t4},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Wagner, Raik and Aigner, Harald and Funk, Christiane},
	month = may,
	year = {2012},
	pages = {203--214},
}

@article{ismail_comparative_2012,
	title = {Comparative {Nucleotide} {Diversity} {Across} {North} {American} and {European} {Populus} {Species}},
	volume = {74},
	issn = {0022-2844, 1432-1432},
	url = {http://link.springer.com/10.1007/s00239-012-9504-5},
	doi = {10/f23j7s},
	language = {en},
	number = {5-6},
	urldate = {2021-06-08},
	journal = {Journal of Molecular Evolution},
	author = {Ismail, Mohamed and Soolanayakanahally, Raju Y. and Ingvarsson, Pär K. and Guy, Robert D. and Jansson, Stefan and Silim, Salim N. and El-Kassaby, Yousry A.},
	month = jun,
	year = {2012},
	pages = {257--272},
}

@article{hummel_dynamic_2012,
	title = {Dynamic protein composition of {Arabidopsis} thaliana cytosolic ribosomes in response to sucrose feeding as revealed by label free {MSE} proteomics},
	volume = {12},
	issn = {16159853},
	url = {http://doi.wiley.com/10.1002/pmic.201100413},
	doi = {10/f23s9x},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {PROTEOMICS},
	author = {Hummel, Maureen and Cordewener, Jan H. G. and de Groot, Joost C. M. and Smeekens, Sjef and America, Antoine H. P. and Hanson, Johannes},
	month = apr,
	year = {2012},
	pages = {1024--1038},
}

@article{strengbom_physical_2012,
	title = {Physical disturbance determines effects from nitrogen addition on ground vegetation in boreal coniferous forests},
	volume = {23},
	issn = {11009233},
	url = {http://doi.wiley.com/10.1111/j.1654-1103.2011.01359.x},
	doi = {10/b523g8},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Journal of Vegetation Science},
	author = {Strengbom, Joachim and Nordin, Annika},
	editor = {Chiarucci, Alessandro},
	month = apr,
	year = {2012},
	pages = {361--371},
}

@article{madsen_altered_2012,
	title = {Altered {Metabolic} {Signature} in {Pre}-{Diabetic} {NOD} {Mice}},
	volume = {7},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0035445},
	doi = {10/f23mgb},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Madsen, Rasmus and Banday, Viqar Showkat and Moritz, Thomas and Trygg, Johan and Lejon, Kristina},
	editor = {Maedler, Kathrin},
	month = apr,
	year = {2012},
	pages = {e35445},
}

@article{decker_substrate_2012,
	title = {Substrate kinetics and substrate effects on the quaternary structure of barley {UDP}-glucose pyrophosphorylase},
	volume = {79},
	issn = {00319422},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0031942212001471},
	doi = {10/f2z82t},
	language = {en},
	urldate = {2021-06-08},
	journal = {Phytochemistry},
	author = {Decker, Daniel and Meng, Meng and Gornicka, Agnieszka and Hofer, Anders and Wilczynska, Malgorzata and Kleczkowski, Leszek A.},
	month = jul,
	year = {2012},
	pages = {39--45},
}

@article{chorell_physical_2012,
	title = {Physical fitness level is reflected by alterations in the human plasma metabolome},
	volume = {8},
	issn = {1742-206X, 1742-2051},
	url = {http://xlink.rsc.org/?DOI=c2mb05428k},
	doi = {10/fxnw3m},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Molecular BioSystems},
	author = {Chorell, Elin and Svensson, Michael B. and Moritz, Thomas and Antti, Henrik},
	year = {2012},
	pages = {1187},
}

@article{pesquet_plant_2012,
	title = {Plant proteases – from detection to function},
	volume = {145},
	copyright = {Copyright © Physiologia Plantarum 2012},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1399-3054.2012.01614.x},
	doi = {10/f2zzbt},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Pesquet, Edouard},
	year = {2012},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1399-3054.2012.01614.x},
	pages = {1--4},
}

@article{dinh_floral_2012,
	title = {The floral homeotic protein {APETALA2} recognizes and acts through an {AT}-rich sequence element},
	volume = {139},
	issn = {1477-9129},
	doi = {10/f3xzq8},
	abstract = {Cell fate specification in development requires transcription factors for proper regulation of gene expression. In Arabidopsis, transcription factors encoded by four classes of homeotic genes, A, B, C and E, act in a combinatorial manner to control proper floral organ identity. The A-class gene APETALA2 (AP2) promotes sepal and petal identities in whorls 1 and 2 and restricts the expression of the C-class gene AGAMOUS (AG) from whorls 1 and 2. However, it is unknown how AP2 performs these functions. Unlike the other highly characterized floral homeotic proteins containing MADS domains, AP2 has two DNA-binding domains referred to as the AP2 domains and its DNA recognition sequence is still unknown. Here, we show that the second AP2 domain in AP2 binds a non-canonical AT-rich target sequence, and, using a GUS reporter system, we demonstrate that the presence of this sequence in the AG second intron is important for the restriction of AG expression in vivo. Furthermore, we show that AP2 binds the AG second intron and directly regulates AG expression through this sequence element. Computational analysis reveals that the binding site is highly conserved in the second intron of AG orthologs throughout Brassicaceae. By uncovering a biologically relevant AT-rich target sequence, this work shows that AP2 domains have wide-ranging target specificities and provides a missing link in the mechanisms that underlie flower development. It also sets the foundation for understanding the basis of the broad biological functions of AP2 in Arabidopsis, as well as the divergent biological functions of AP2 orthologs in dicotyledonous plants.},
	language = {eng},
	number = {11},
	journal = {Development (Cambridge, England)},
	author = {Dinh, Thanh Theresa and Girke, Thomas and Liu, Xigang and Yant, Levi and Schmid, Markus and Chen, Xuemei},
	month = jun,
	year = {2012},
	pmid = {22513376},
	pmcid = {PMC3347690},
	keywords = {AGAMOUS Protein, Arabidopsis, Arabidopsis, Arabidopsis Proteins, Base Sequence, Cell Differentiation, Chromatin Immunoprecipitation, Computational Biology, Electrophoretic Mobility Shift Assay, Flowers, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Homeodomain Proteins, Molecular Sequence Data, Nuclear Proteins, Sequence Analysis, DNA, Species Specificity},
	pages = {1978--1986},
}

Cell fate specification in development requires transcription factors for proper regulation of gene expression. In Arabidopsis, transcription factors encoded by four classes of homeotic genes, A, B, C and E, act in a combinatorial manner to control proper floral organ identity. The A-class gene APETALA2 (AP2) promotes sepal and petal identities in whorls 1 and 2 and restricts the expression of the C-class gene AGAMOUS (AG) from whorls 1 and 2. However, it is unknown how AP2 performs these functions. Unlike the other highly characterized floral homeotic proteins containing MADS domains, AP2 has two DNA-binding domains referred to as the AP2 domains and its DNA recognition sequence is still unknown. Here, we show that the second AP2 domain in AP2 binds a non-canonical AT-rich target sequence, and, using a GUS reporter system, we demonstrate that the presence of this sequence in the AG second intron is important for the restriction of AG expression in vivo. Furthermore, we show that AP2 binds the AG second intron and directly regulates AG expression through this sequence element. Computational analysis reveals that the binding site is highly conserved in the second intron of AG orthologs throughout Brassicaceae. By uncovering a biologically relevant AT-rich target sequence, this work shows that AP2 domains have wide-ranging target specificities and provides a missing link in the mechanisms that underlie flower development. It also sets the foundation for understanding the basis of the broad biological functions of AP2 in Arabidopsis, as well as the divergent biological functions of AP2 orthologs in dicotyledonous plants.

@article{pose_end_2012,
	title = {The end of innocence: flowering networks explode in complexity},
	volume = {15},
	issn = {1879-0356},
	shorttitle = {The end of innocence},
	doi = {10/fphkmr},
	abstract = {Substantial recent advances in genome-scale transcription factor target mapping have provided a fresh view of the gene networks governing developmental transitions. In particular, our understanding of the fine-scale spatial and temporal dynamics underlying the floral transition at the shoot apex has seen great advances in the past two years. Single transcription factors are regularly observed to act in complex manners, directly promoting the expression of particular targets while directly repressing the expression of others, based at least partly on defined heterodimerization patterns. For single regulators this behavior reaches into distinct physiological processes, providing compelling evidence that particular transcription factors act to directly integrate diverse processes to orchestrate complex developmental transitions.},
	language = {eng},
	number = {1},
	journal = {Current Opinion in Plant Biology},
	author = {Posé, David and Yant, Levi and Schmid, Markus},
	month = feb,
	year = {2012},
	pmid = {21974961},
	keywords = {Flowers, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Gene Regulatory Networks, Genes, Plant, Plant Shoots},
	pages = {45--50},
}

Substantial recent advances in genome-scale transcription factor target mapping have provided a fresh view of the gene networks governing developmental transitions. In particular, our understanding of the fine-scale spatial and temporal dynamics underlying the floral transition at the shoot apex has seen great advances in the past two years. Single transcription factors are regularly observed to act in complex manners, directly promoting the expression of particular targets while directly repressing the expression of others, based at least partly on defined heterodimerization patterns. For single regulators this behavior reaches into distinct physiological processes, providing compelling evidence that particular transcription factors act to directly integrate diverse processes to orchestrate complex developmental transitions.

@article{immink_characterization_2012,
	title = {Characterization of {SOC1}'s central role in flowering by the identification of its upstream and downstream regulators},
	volume = {160},
	issn = {1532-2548},
	doi = {10/f36vk3},
	abstract = {The transition from vegetative to reproductive development is one of the most important phase changes in the plant life cycle. This step is controlled by various environmental signals that are integrated at the molecular level by so-called floral integrators. One such floral integrator in Arabidopsis (Arabidopsis thaliana) is the MADS domain transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). Despite extensive genetic studies, little is known about the transcriptional control of SOC1, and we are just starting to explore the network of genes under the direct control of SOC1 transcription factor complexes. Here, we show that several MADS domain proteins, including SOC1 heterodimers, are able to bind SOC1 regulatory sequences. Genome-wide target gene analysis by ChIP-seq confirmed the binding of SOC1 to its own locus and shows that it also binds to a plethora of flowering-time regulatory and floral homeotic genes. In turn, the encoded floral homeotic MADS domain proteins appear to bind SOC1 regulatory sequences. Subsequent in planta analyses revealed SOC1 repression by several floral homeotic MADS domain proteins, and we show that, mechanistically, this depends on the presence of the SOC1 protein. Together, our data show that SOC1 constitutes a major hub in the regulatory networks underlying floral timing and flower development and that these networks are composed of many positive and negative autoregulatory and feedback loops. The latter seems to be crucial for the generation of a robust flower-inducing signal, followed shortly after by repression of the SOC1 floral integrator.},
	language = {eng},
	number = {1},
	journal = {Plant Physiology},
	author = {Immink, Richard G. H. and Posé, David and Ferrario, Silvia and Ott, Felix and Kaufmann, Kerstin and Valentim, Felipe Leal and de Folter, Stefan and van der Wal, Froukje and van Dijk, Aalt D. J. and Schmid, Markus and Angenent, Gerco C.},
	month = sep,
	year = {2012},
	pmid = {22791302},
	pmcid = {PMC3440217},
	keywords = {Arabidopsis, Arabidopsis Proteins, Feedback, Physiological, Flowers, Gene Expression Regulation, Plant, Genes, Plant, Genes, Reporter, Genetic Complementation Test, Genetic Loci, Green Fluorescent Proteins, Immunoprecipitation, MADS Domain Proteins, Promoter Regions, Genetic, Protein Binding, Regulatory Sequences, Nucleic Acid, Signal Transduction, Time Factors, Transcription, Genetic, Two-Hybrid System Techniques},
	pages = {433--449},
}

The transition from vegetative to reproductive development is one of the most important phase changes in the plant life cycle. This step is controlled by various environmental signals that are integrated at the molecular level by so-called floral integrators. One such floral integrator in Arabidopsis (Arabidopsis thaliana) is the MADS domain transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). Despite extensive genetic studies, little is known about the transcriptional control of SOC1, and we are just starting to explore the network of genes under the direct control of SOC1 transcription factor complexes. Here, we show that several MADS domain proteins, including SOC1 heterodimers, are able to bind SOC1 regulatory sequences. Genome-wide target gene analysis by ChIP-seq confirmed the binding of SOC1 to its own locus and shows that it also binds to a plethora of flowering-time regulatory and floral homeotic genes. In turn, the encoded floral homeotic MADS domain proteins appear to bind SOC1 regulatory sequences. Subsequent in planta analyses revealed SOC1 repression by several floral homeotic MADS domain proteins, and we show that, mechanistically, this depends on the presence of the SOC1 protein. Together, our data show that SOC1 constitutes a major hub in the regulatory networks underlying floral timing and flower development and that these networks are composed of many positive and negative autoregulatory and feedback loops. The latter seems to be crucial for the generation of a robust flower-inducing signal, followed shortly after by repression of the SOC1 floral integrator.

@article{band_root_2012,
	title = {Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism},
	volume = {109},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/109/12/4668},
	doi = {10/f2392k},
	abstract = {Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAA-based reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 90° gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 40° to the horizontal. We hypothesize roots use a “tipping point” mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Band, Leah R. and Wells, Darren M. and Larrieu, Antoine and Sun, Jianyong and Middleton, Alistair M. and French, Andrew P. and Brunoud, Géraldine and Sato, Ethel Mendocilla and Wilson, Michael H. and Péret, Benjamin and Oliva, Marina and Swarup, Ranjan and Sairanen, Ilkka and Parry, Geraint and Ljung, Karin and Beeckman, Tom and Garibaldi, Jonathan M. and Estelle, Mark and Owen, Markus R. and Vissenberg, Kris and Hodgman, T. Charlie and Pridmore, Tony P. and King, John R. and Vernoux, Teva and Bennett, Malcolm J.},
	month = mar,
	year = {2012},
	pmid = {22393022},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {environmental sensing, systems biology},
	pages = {4668--4673},
}

Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAA-based reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 90° gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 40° to the horizontal. We hypothesize roots use a “tipping point” mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.

@article{staldal_arabidopsis_2012,
	title = {The {Arabidopsis} thaliana transcriptional activator {STYLISH1} regulates genes affecting stamen development, cell expansion and timing of flowering},
	volume = {78},
	issn = {0167-4412, 1573-5028},
	url = {http://link.springer.com/10.1007/s11103-012-9888-z},
	doi = {10/f24hk4},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Plant Molecular Biology},
	author = {Ståldal, Veronika and Cierlik, Izabela and Chen, Song and Landberg, Katarina and Baylis, Tammy and Myrenås, Mattias and Sundström, Jens F. and Eklund, D. Magnus and Ljung, Karin and Sundberg, Eva},
	month = apr,
	year = {2012},
	pages = {545--559},
}

@article{jankanpaa_metabolic_2012,
	title = {Metabolic profiling reveals metabolic shifts in {Arabidopsis} plants grown under different light conditions: {Metabolic} profiling under different light regime},
	volume = {35},
	issn = {01407791},
	shorttitle = {Metabolic profiling reveals metabolic shifts in {Arabidopsis} plants grown under different light conditions},
	url = {http://doi.wiley.com/10.1111/j.1365-3040.2012.02519.x},
	doi = {10/f2z77r},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {Plant, Cell \& Environment},
	author = {Jänkänpää, Hanna Johansson and Mishra, Yogesh and Schröder, Wolfgang P. and Jansson, Stefan},
	month = oct,
	year = {2012},
	pages = {1824--1836},
}

@article{pesquet_plant_2012,
	title = {Plant proteases - from detection to function},
	volume = {145},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2012.01614.x},
	doi = {10/f2zzbt},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Pesquet, Edouard},
	month = may,
	year = {2012},
	pages = {1--4},
}

@article{ivanov_restricted_2012,
	title = {Restricted capacity for {PSI}-dependent cyclic electron flow in Δ{petE} mutant compromises the ability for acclimation to iron stress in {Synechococcus} sp. {PCC} 7942 cells},
	volume = {1817},
	issn = {00052728},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272812000898},
	doi = {10/f246hp},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Ivanov, A.G. and Sane, P.V. and Simidjiev, I. and Park, Y.-I. and Huner, N.P.A. and Öquist, G.},
	month = aug,
	year = {2012},
	pages = {1277--1284},
}

@article{galvao_spatial_2012,
	title = {Spatial control of flowering by {DELLA} proteins in {Arabidopsis} thaliana},
	volume = {139},
	issn = {1477-9129},
	doi = {10/f4cgh5},
	abstract = {The transition from vegetative to reproductive development is a central event in the plant life cycle. To time the induction of flowering correctly, plants integrate environmental and endogenous signals such as photoperiod, temperature and hormonal status. The hormone gibberellic acid (GA) has long been known to regulate flowering. However, the spatial contribution of GA signaling in flowering time control is poorly understood. Here we have analyzed the effect of tissue-specific misexpression of wild-type and GA-insensitive (dellaΔ17) DELLA proteins on the floral transition in Arabidopsis thaliana. We demonstrate that under long days, GA affects the floral transition by promoting the expression of flowering time integrator genes such as FLOWERING LOCUS T (FT) and TWIN SISTER OF FT (TSF) in leaves independently of CONSTANS (CO) and GIGANTEA (GI). In addition, GA signaling promotes flowering independently of photoperiod through the regulation of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes in both the leaves and at the shoot meristem. Our data suggest that GA regulates flowering by controlling the spatial expression of floral regulatory genes throughout the plant in a day-length-specific manner.},
	language = {eng},
	number = {21},
	journal = {Development (Cambridge, England)},
	author = {Galvão, Vinicius C. and Horrer, Daniel and Küttner, Frank and Schmid, Markus},
	month = nov,
	year = {2012},
	pmid = {22992955},
	keywords = {Arabidopsis, Arabidopsis Proteins, Flowers, Gene Expression Regulation, Plant, Gibberellins},
	pages = {4072--4082},
}

The transition from vegetative to reproductive development is a central event in the plant life cycle. To time the induction of flowering correctly, plants integrate environmental and endogenous signals such as photoperiod, temperature and hormonal status. The hormone gibberellic acid (GA) has long been known to regulate flowering. However, the spatial contribution of GA signaling in flowering time control is poorly understood. Here we have analyzed the effect of tissue-specific misexpression of wild-type and GA-insensitive (dellaΔ17) DELLA proteins on the floral transition in Arabidopsis thaliana. We demonstrate that under long days, GA affects the floral transition by promoting the expression of flowering time integrator genes such as FLOWERING LOCUS T (FT) and TWIN SISTER OF FT (TSF) in leaves independently of CONSTANS (CO) and GIGANTEA (GI). In addition, GA signaling promotes flowering independently of photoperiod through the regulation of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes in both the leaves and at the shoot meristem. Our data suggest that GA regulates flowering by controlling the spatial expression of floral regulatory genes throughout the plant in a day-length-specific manner.

@article{keel_allocation_2012,
	title = {Allocation of carbon to fine root compounds and their residence times in a boreal forest depend on root size class and season},
	volume = {194},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2012.04120.x},
	doi = {10/f24b8q},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Keel, Sonja G. and Campbell, Catherine D. and Högberg, Mona N. and Richter, Andreas and Wild, Birgit and Zhou, Xuhui and Hurry, Vaughan and Linder, Sune and Näsholm, Torgny and Högberg, Peter},
	month = jun,
	year = {2012},
	pages = {972--981},
}

@article{bernhardsson_geographical_2012,
	title = {Geographical structure and adaptive population differentiation in herbivore defence genes in {European} aspen ( \textit{{Populus} tremula} {L}., {Salicaceae}): {POPULATION} {STRUCTURE} {IN} \textit{{POPULUS}} {DEFENCE} {GENES}},
	volume = {21},
	issn = {09621083},
	shorttitle = {Geographical structure and adaptive population differentiation in herbivore defence genes in {European} aspen ( \textit{{Populus} tremula} {L}., {Salicaceae})},
	url = {http://doi.wiley.com/10.1111/j.1365-294X.2012.05524.x},
	doi = {10/f23st3},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {Molecular Ecology},
	author = {Bernhardsson, Carolina and Ingvarsson, Pär K.},
	month = may,
	year = {2012},
	pages = {2197--2207},
}

@article{wuolikainen_als_2012,
	title = {{ALS} patients with mutations in the {SOD1} gene have an unique metabolomic profile in the cerebrospinal fluid compared with {ALS} patients without mutations},
	volume = {105},
	issn = {10967192},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1096719211006184},
	doi = {10/ffcrdm},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Molecular Genetics and Metabolism},
	author = {Wuolikainen, Anna and Andersen, Peter M. and Moritz, Thomas and Marklund, Stefan L. and Antti, Henrik},
	month = mar,
	year = {2012},
	pages = {472--478},
}

@article{selles_hydroperoxide_2012,
	title = {Hydroperoxide and peroxynitrite reductase activity of poplar thioredoxin-dependent glutathione peroxidase 5: kinetics, catalytic mechanism and oxidative inactivation},
	volume = {442},
	issn = {0264-6021, 1470-8728},
	shorttitle = {Hydroperoxide and peroxynitrite reductase activity of poplar thioredoxin-dependent glutathione peroxidase 5},
	url = {https://portlandpress.com/biochemj/article/442/2/369/45982/Hydroperoxide-and-peroxynitrite-reductase-activity},
	doi = {10/bqg8zt},
	abstract = {Gpxs (glutathione peroxidases) constitute a family of peroxidases, including selenocysteine- or cysteine-containing isoforms (SeCys-Gpx or Cys-Gpx), which are regenerated by glutathione or Trxs (thioredoxins) respectively. In the present paper we show new data concerning the substrates of poplar Gpx5 and the residues involved in its catalytic mechanism. The present study establishes the capacity of this Cys-Gpx to reduce peroxynitrite with a catalytic efficiency of 106 M−1·s−1. In PtGpx5 (poplar Gpx5; Pt is Populus trichocarpa), Glu79, which replaces the glutamine residue usually found in the Gpx catalytic tetrad, is likely to be involved in substrate selectivity. Although the redox midpoint potential of the Cys44–Cys92 disulfide bond and the pKa of Cys44 are not modified in the E79Q variant, it exhibited significantly improved kinetic parameters (Kperoxide and kcat) with tert-butyl hydroperoxide. The characterization of the monomeric Y151R variant demonstrated that PtGpx5 is not an obligate homodimer. Also, we show that the conserved Phe90 is important for Trx recognition and that Trx-mediated recycling of PtGpx5 occurs via the formation of a transient disulfide bond between the Trx catalytic cysteine residue and the Gpx5 resolving cysteine residue. Finally, we demonstrate that the conformational changes observed during the transition from the reduced to the oxidized form of PtGpx5 are primarily determined by the oxidation of the peroxidatic cysteine into sulfenic acid. Also, MS analysis of in-vitro-oxidized PtGpx5 demonstrated that the peroxidatic cysteine residue can be over-oxidized into sulfinic or sulfonic acids. This suggests that some isoforms could have dual functions potentially acting as hydrogen-peroxide- and peroxynitrite-scavenging systems and/or as mediators of peroxide signalling as proposed for 2-Cys peroxiredoxins.},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Biochemical Journal},
	author = {Selles, Benjamin and Hugo, Martin and Trujillo, Madia and Srivastava, Vaibhav and Wingsle, Gunnar and Jacquot, Jean-Pierre and Radi, Rafael and Rouhier, Nicolas},
	month = mar,
	year = {2012},
	pages = {369--380},
}

Gpxs (glutathione peroxidases) constitute a family of peroxidases, including selenocysteine- or cysteine-containing isoforms (SeCys-Gpx or Cys-Gpx), which are regenerated by glutathione or Trxs (thioredoxins) respectively. In the present paper we show new data concerning the substrates of poplar Gpx5 and the residues involved in its catalytic mechanism. The present study establishes the capacity of this Cys-Gpx to reduce peroxynitrite with a catalytic efficiency of 106 M−1·s−1. In PtGpx5 (poplar Gpx5; Pt is Populus trichocarpa), Glu79, which replaces the glutamine residue usually found in the Gpx catalytic tetrad, is likely to be involved in substrate selectivity. Although the redox midpoint potential of the Cys44–Cys92 disulfide bond and the pKa of Cys44 are not modified in the E79Q variant, it exhibited significantly improved kinetic parameters (Kperoxide and kcat) with tert-butyl hydroperoxide. The characterization of the monomeric Y151R variant demonstrated that PtGpx5 is not an obligate homodimer. Also, we show that the conserved Phe90 is important for Trx recognition and that Trx-mediated recycling of PtGpx5 occurs via the formation of a transient disulfide bond between the Trx catalytic cysteine residue and the Gpx5 resolving cysteine residue. Finally, we demonstrate that the conformational changes observed during the transition from the reduced to the oxidized form of PtGpx5 are primarily determined by the oxidation of the peroxidatic cysteine into sulfenic acid. Also, MS analysis of in-vitro-oxidized PtGpx5 demonstrated that the peroxidatic cysteine residue can be over-oxidized into sulfinic or sulfonic acids. This suggests that some isoforms could have dual functions potentially acting as hydrogen-peroxide- and peroxynitrite-scavenging systems and/or as mediators of peroxide signalling as proposed for 2-Cys peroxiredoxins.

@article{abrahamsson_inheritance_2012,
	title = {Inheritance of height growth and autumn cold hardiness based on two generations of full-sib and half-sib families of \textit{{Pinus} sylvestris}},
	volume = {27},
	issn = {0282-7581, 1651-1891},
	url = {http://www.tandfonline.com/doi/abs/10.1080/02827581.2012.663403},
	doi = {10/f25q9r},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Scandinavian Journal of Forest Research},
	author = {Abrahamsson, Sara and Nilsson, Jan-Erik and Wu, Harry and García Gil, MarÍa Rosario and Andersson, Bengt},
	month = jul,
	year = {2012},
	pages = {405--413},
}

@article{castelain_non-dna-binding_2012,
	title = {The non-{DNA}-binding {bHLH} transcription factor {PRE3}/{bHLH135}/{ATBS1}/{TMO7} is involved in the regulation of light signaling pathway in {Arabidopsis}},
	volume = {145},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2012.01600.x},
	doi = {10/f2z8jx},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Castelain, Mathieu and Le Hir, Rozenn and Bellini, Catherine},
	month = jul,
	year = {2012},
	pages = {450--460},
}

@article{torimaru_effects_2012,
	title = {Effects of male fecundity, interindividual distance and anisotropic pollen dispersal on mating success in a {Scots} pine ({Pinus} sylvestris) seed orchard},
	volume = {108},
	issn = {0018-067X, 1365-2540},
	url = {http://www.nature.com/articles/hdy201176},
	doi = {10/d5fhfb},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Heredity},
	author = {Torimaru, T and Wennström, U and Lindgren, D and Wang, X-R},
	month = mar,
	year = {2012},
	pages = {312--321},
}

@article{businge_metabolite_2012,
	title = {Metabolite profiling reveals clear metabolic changes during somatic embryo development of {Norway} spruce ({Picea} abies)},
	volume = {32},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpr142},
	doi = {10/f24n88},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Tree Physiology},
	author = {Businge, E. and Brackmann, K. and Moritz, T. and Egertsdotter, U.},
	month = feb,
	year = {2012},
	pages = {232--244},
}

@article{danielsson_development_2012,
	title = {Development of a gas chromatography/mass spectrometry based metabolomics protocol by means of statistical experimental design},
	volume = {8},
	issn = {1573-3882, 1573-3890},
	url = {http://link.springer.com/10.1007/s11306-011-0283-6},
	doi = {10/cbcwmc},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Metabolomics},
	author = {Danielsson, Anders P. H. and Moritz, Thomas and Mulder, Hindrik and Spégel, Peter},
	month = feb,
	year = {2012},
	pages = {50--63},
}

@article{bollhoner_xylem_2012,
	title = {Xylem cell death: emerging understanding of regulation and function},
	volume = {63},
	issn = {0022-0957, 1460-2431},
	shorttitle = {Xylem cell death},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/err438},
	doi = {10/fx99k4},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Bollhoner, B. and Prestele, J. and Tuominen, H.},
	month = feb,
	year = {2012},
	pages = {1081--1094},
}

@article{mishra_arabidopsis_2012,
	title = {Arabidopsis plants grown in the field and climate chambers significantly differ in leaf morphology and photosystem components},
	volume = {12},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-12-6},
	doi = {10/fx7f9h},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Mishra, Yogesh and Johansson Jänkänpää, Hanna and Kiss, Anett Z and Funk, Christiane and Schröder, Wolfgang P and Jansson, Stefan},
	year = {2012},
	pages = {6},
}

@article{pacurar_collection_2012,
	title = {A collection of {INDEL} markers for map-based cloning in seven {Arabidopsis} accessions},
	volume = {63},
	issn = {1460-2431, 0022-0957},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/err422},
	doi = {10/fxrh28},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Păcurar, Daniel Ioan and Păcurar, Monica Lăcrămioara and Street, Nathaniel and Bussell, John Desmond and Pop, Tiberia Ioana and Gutierrez, Laurent and Bellini, Catherine},
	month = apr,
	year = {2012},
	pages = {2491--2501},
}

@article{roach_fructokinase_2012,
	title = {Fructokinase is required for carbon partitioning to cellulose in aspen wood: {Fructokinase} in aspen wood formation},
	volume = {70},
	issn = {09607412},
	shorttitle = {Fructokinase is required for carbon partitioning to cellulose in aspen wood},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2012.04929.x},
	doi = {10/fzm62x},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Roach, Melissa and Gerber, Lorenz and Sandquist, David and Gorzsás, András and Hedenström, Mattias and Kumar, Manoj and Steinhauser, Marie Caroline and Feil, Regina and Daniel, Geoffrey and Stitt, Mark and Sundberg, Björn and Niittylä, Totte},
	month = jun,
	year = {2012},
	pages = {967--977},
}

@article{lara-chavez_comparison_2012,
	title = {Comparison of gene expression markers during zygotic and somatic embryogenesis in pine},
	volume = {48},
	issn = {1054-5476, 1475-2689},
	url = {http://link.springer.com/10.1007/s11627-012-9440-5},
	doi = {10/f328xq},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {In Vitro Cellular \& Developmental Biology - Plant},
	author = {Lara-Chavez, Alejandra and Egertsdotter, Ulrika and Flinn, Barry S.},
	month = jun,
	year = {2012},
	pages = {341--354},
}

@article{brouwer_impact_2012,
	title = {The impact of light intensity on shade-induced leaf senescence: {Light}-dependent induction of leaf senescence},
	volume = {35},
	issn = {01407791},
	shorttitle = {The impact of light intensity on shade-induced leaf senescence},
	url = {http://doi.wiley.com/10.1111/j.1365-3040.2011.02474.x},
	doi = {10/dthghs},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Plant, Cell \& Environment},
	author = {Brouwer, Bastiaan and Ziolkowska, Agnieszka and Bagard, Matthieu and Keech, Olivier and Gardeström, Per},
	month = jun,
	year = {2012},
	pages = {1084--1098},
}

@incollection{dunwell_how_2012,
	address = {Totowa, NJ},
	title = {How to {Grow} {Transgenic} {Arabidopsis} in the {Field}},
	volume = {847},
	isbn = {978-1-61779-557-2 978-1-61779-558-9},
	url = {http://link.springer.com/10.1007/978-1-61779-558-9_37},
	urldate = {2021-06-08},
	booktitle = {Transgenic {Plants}},
	publisher = {Humana Press},
	author = {Jänkänpää, Hanna Johansson and Jansson, Stefan},
	editor = {Dunwell, Jim M. and Wetten, Andy C.},
	year = {2012},
	doi = {10.1007/978-1-61779-558-9_37},
	note = {Series Title: Methods in Molecular Biology},
	pages = {483--494},
}

@article{kaewthai_group_2012,
	title = {Group {III}-{A} \textit{{XTH}} {Genes} of {Arabidopsis} {Encode} {Predominant} {Xyloglucan} {Endohydrolases} {That} {Are} {Dispensable} for {Normal} {Growth}},
	volume = {161},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/161/1/440/6110726},
	doi = {10/f24f58},
	abstract = {Abstract
            The molecular basis of primary wall extension endures as one of the central enigmas in plant cell morphogenesis. Classical cell wall models suggest that xyloglucan endo-transglycosylase activity is the primary catalyst (together with expansins) of controlled cell wall loosening through the transient cleavage and religation of xyloglucan-cellulose cross links. The genome of Arabidopsis (Arabidopsis thaliana) contains 33 phylogenetically diverse XYLOGLUCAN ENDO-TRANSGLYCOSYLASE/HYDROLASE (XTH) gene products, two of which were predicted to be predominant xyloglucan endohydrolases due to clustering into group III-A. Enzyme kinetic analysis of recombinant AtXTH31 confirmed this prediction and indicated that this enzyme had similar catalytic properties to the nasturtium (Tropaeolum majus) xyloglucanase1 responsible for storage xyloglucan hydrolysis during germination. Global analysis of Genevestigator data indicated that AtXTH31 and the paralogous AtXTH32 were abundantly expressed in expanding tissues. Microscopy analysis, utilizing the resorufin β-glycoside of the xyloglucan oligosaccharide XXXG as an in situ probe, indicated significant xyloglucan endohydrolase activity in specific regions of both roots and hypocotyls, in good correlation with transcriptomic data. Moreover, this hydrolytic activity was essentially completely eliminated in AtXTH31/AtXTH32 double knockout lines. However, single and double knockout lines, as well as individual overexpressing lines, of AtXTH31 and AtXTH32 did not demonstrate significant growth or developmental phenotypes. These results suggest that although xyloglucan polysaccharide hydrolysis occurs in parallel with primary wall expansion, morphological effects are subtle or may be compensated by other mechanisms. We hypothesize that there is likely to be an interplay between these xyloglucan endohydrolases and recently discovered apoplastic exo-glycosidases in the hydrolytic modification of matrix xyloglucans.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Kaewthai, Nomchit and Gendre, Delphine and Eklöf, Jens M. and Ibatullin, Farid M. and Ezcurra, Ines and Bhalerao, Rishikesh P. and Brumer, Harry},
	month = dec,
	year = {2012},
	pages = {440--454},
}

Abstract The molecular basis of primary wall extension endures as one of the central enigmas in plant cell morphogenesis. Classical cell wall models suggest that xyloglucan endo-transglycosylase activity is the primary catalyst (together with expansins) of controlled cell wall loosening through the transient cleavage and religation of xyloglucan-cellulose cross links. The genome of Arabidopsis (Arabidopsis thaliana) contains 33 phylogenetically diverse XYLOGLUCAN ENDO-TRANSGLYCOSYLASE/HYDROLASE (XTH) gene products, two of which were predicted to be predominant xyloglucan endohydrolases due to clustering into group III-A. Enzyme kinetic analysis of recombinant AtXTH31 confirmed this prediction and indicated that this enzyme had similar catalytic properties to the nasturtium (Tropaeolum majus) xyloglucanase1 responsible for storage xyloglucan hydrolysis during germination. Global analysis of Genevestigator data indicated that AtXTH31 and the paralogous AtXTH32 were abundantly expressed in expanding tissues. Microscopy analysis, utilizing the resorufin β-glycoside of the xyloglucan oligosaccharide XXXG as an in situ probe, indicated significant xyloglucan endohydrolase activity in specific regions of both roots and hypocotyls, in good correlation with transcriptomic data. Moreover, this hydrolytic activity was essentially completely eliminated in AtXTH31/AtXTH32 double knockout lines. However, single and double knockout lines, as well as individual overexpressing lines, of AtXTH31 and AtXTH32 did not demonstrate significant growth or developmental phenotypes. These results suggest that although xyloglucan polysaccharide hydrolysis occurs in parallel with primary wall expansion, morphological effects are subtle or may be compensated by other mechanisms. We hypothesize that there is likely to be an interplay between these xyloglucan endohydrolases and recently discovered apoplastic exo-glycosidases in the hydrolytic modification of matrix xyloglucans.

@article{marhavy_auxin_2012,
	title = {Auxin reflux between the endodermis and pericycle promotes lateral root initiation},
	volume = {32},
	issn = {0261-4189, 1460-2075},
	url = {http://emboj.embopress.org/cgi/doi/10.1038/emboj.2012.303},
	doi = {10/gkgdj3},
	number = {1},
	urldate = {2021-06-08},
	journal = {The EMBO Journal},
	author = {Marhavý, Peter and Vanstraelen, Marleen and De Rybel, Bert and Zhaojun, Ding and Bennett, Malcolm J and Beeckman, Tom and Benková, Eva},
	month = nov,
	year = {2012},
	pages = {149--158},
}