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22 results on '"Department of Plant Biology [Carnegie] (DPB)"'

1. Light-independent regulation of algal photoprotection by CO2 availability

Author: M. Águila Ruiz-Sola, Serena Flori, Yizhong Yuan, Gaelle Villain, Emanuel Sanz-Luque, Petra Redekop, Ryutaro Tokutsu, Anika Küken, Angeliki Tsichla, Georgios Kepesidis, Guillaume Allorent, Marius Arend, Fabrizio Iacono, Giovanni Finazzi, Michael Hippler, Zoran Nikoloski, Jun Minagawa, Arthur R. Grossman, Dimitris Petroutsos, Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Light Photosynthesis & Metabolism (Photosynthesis), Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science, Universidad de Córdoba = University of Córdoba [Córdoba], National Institute for Basic Biology [Okazaki] (NIBB), Graduate University for Advanced Studies [Hayama] (SOKENDAI), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, University of Potsdam = Universität Potsdam, The Human Frontiers Science Program through the funding of the project RGP0046/2018, Prestige Marie-Curie co-financing grant PRESTIGE-2017-1-0028, The International Max Planck Research School 'Primary Metabolism and Plant Growth' at the Max Planck Institute of Molecular Plant Physiology, The program ‘Plan Propio UCO’ from University of Cordoba, The Carnegie Institution for Science and the Department of Energy, DE-SC0019417, The Marie Curie Initial Training Network Accliphot FP7-PEPOPLE-2012-ITN, The Japan Society for the Promotion of Science, JSPS, for the grants-in-Aid for Scientific Research, KAKENHI, 21H04778 and 21H05040, The German Research Foundation DFG HI 739/9.2, ANR-18-CE20-0006,MetaboLIGHT,Regulation de la photosynthèse par la Lumière et le métabolisme chez les algues(2018), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-15-IDEX-0002,UGA,IDEX UGA(2015), and European Project: 751039,UNREDE
Subjects: MESH: Chlamydomonas reinhardtii, Multidisciplinary, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Photosystem II Protein Complex, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], General Physics and Astronomy, MESH: Proteins, General Chemistry, MESH: Carbon Dioxide, General Biochemistry, Genetics and Molecular Biology, MESH: Photosynthesis
Abstract: Photosynthetic algae have evolved mechanisms to cope with suboptimal light and CO2 conditions. When light energy exceeds CO2 fixation capacity, Chlamydomonas reinhardtii activates photoprotection, mediated by LHCSR1/3 and PSBS, and the CO2 Concentrating Mechanism (CCM). How light and CO2 signals converge to regulate these processes remains unclear. Here, we show that excess light activates photoprotection- and CCM-related genes by altering intracellular CO2 concentrations and that depletion of CO2 drives these responses, even in total darkness. High CO2 levels, derived from respiration or impaired photosynthetic fixation, repress LHCSR3/CCM genes while stabilizing the LHCSR1 protein. Finally, we show that the CCM regulator CIA5 also regulates photoprotection, controlling LHCSR3 and PSBS transcript accumulation while inhibiting LHCSR1 protein accumulation. This work has allowed us to dissect the effect of CO2 and light on CCM and photoprotection, demonstrating that light often indirectly affects these processes by impacting intracellular CO2 levels.
Published: 2023

2. Transcriptome analyses reveal the synergistic effects of feeding and eyestalk ablation on ovarian maturation in black tiger shrimp

Author: Kanchana Sittikankaew, Chutima Sonthirod, Umaporn Uawisetwathana, Duangjai Sangsrakru, Jutatip Khudet, Thippawan Yoocha, Intawat Nookaew, Wirulda Pootakham, Wanilada Rungrassamee, Nitsara Karoonuthaisiri, Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science [Washington], Systems Biology, and Chalmers University of Technology [Göteborg]
Subjects: 0301 basic medicine, Eyestalk ablation, [SDV]Life Sciences [q-bio], Science, lcsh:Medicine, Ovary, Broodstock, Article, Penaeus monodon, Gene regulatory networks, Transcriptome, 03 medical and health sciences, medicine, Transcriptomics, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Regulation of gene expression, Multidisciplinary, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, lcsh:R, 04 agricultural and veterinary sciences, biology.organism_classification, Oocyte, Cell biology, Gene expression profiling, 030104 developmental biology, medicine.anatomical_structure, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Medicine, lcsh:Q
Abstract: Unilateral eyestalk ablation in the female black tiger shrimp Penaeus monodon is commonly employed to induce ovarian maturation. However, the importance of complementing this practice with the provision of live feed supplement (such as polychaetes) has not been emphasized in previous studies. Indeed, it has been less emphasized that female broodstock must be fed with live feeds such as polychaetes for this practice to be effective. While the effects of eyestalk ablation have been thoroughly studied in various aspects, the synergistic effects of feeding with live feeds and the ablation have never been elucidated at a transcriptome-wide level. With recent advances in the next-generation sequencing platforms, it is now possible to investigate the effects of eyestalk ablation and live feeds at the transcriptomic levels. This study employed both short-read Illumina RNA sequencing and long-read Pacific Biosciences (PacBio) isoform sequencing (Iso-seq) to generate the first high-quality ovarian reference transcriptome in P. monodon. This novel assembly allowed us to dissect the effects of feeds and eyestalk ablation and reveal their synergistic effects at the transcriptomic level through the regulation of important genes involved in fatty acid regulation, energy production, and hormone-mediated oocyte maturation pathways. The synergistic effects between the polychaete feeding and the eyestalk ablation in the process of ovarian maturation in black tiger shrimp suggest that without having proper nutrients from the polychaetes, female broodstock might not be ready to develop its ovary. However, even with proper nutrients, the eyestalk ablation is still necessary to perhaps manipulate the female endocrine of the black tiger shrimp. These findings shed the light on molecular mechanisms and key molecular pathways that lead to successful ovarian maturation.
Published: 2020

3. Transcriptional regulation of photoprotection in dark-to-light transition - more than just a matter of excess light energy

Author: Emanuel Sanz-Luque, Gaelle Villain, Dimitris Petroutsos, Arthur R. Grossman, Petra Redekop, Yizhong Yuan, Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science, Stanford University, ANR-18-CE20-0006,MetaboLIGHT,Regulation de la photosynthèse par la Lumière et le métabolisme chez les algues(2018), European Project: 751039,UNREDE, European Project: Ecole doctorale DS4H,DS4H, and Carnegie Institution for Science [Washington]
Subjects: 0106 biological sciences, LHCSR, Photosynthesis, 01 natural sciences, 03 medical and health sciences, PHOT, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Enhancer, Transcription factor, 030304 developmental biology, 0303 health sciences, Quenching (fluorescence), Chemistry, UVB light, light harvesting family, Chlamydomonas, UVR8, PSBS, Electron transport chain, blue light, Light quality, Light intensity, photoprotection, CIA5, Photoprotection, Biophysics, non-photochemical quenching, 010606 plant biology & botany
Abstract: In nature, photosynthetic organisms are exposed to different light spectra and intensities depending on the time of day and atmospheric and environmental conditions. When photosynthetic cells absorb excess light, they induce non-photochemical quenching to avoid photo-damage and trigger expression of ‘photoprotective’ genes. In this work, we used the green alga Chlamydomonas reinhardtii to assess the impact of light intensity, light quality, wavelength, photosynthetic electron transport and CO2 on induction of the ‘photoprotective’ genes (LHCSR1, LHCSR3 and PSBS) during dark-to-light transitions. Induction (mRNA accumulation) occurred at very low light intensity, was independently modulated by blue and UV-B radiation through specific photoreceptors, and only LHCSR3 was strongly controlled by CO2 levels through a putative enhancer function of CIA5, a transcription factor that controls genes of the carbon concentrating mechanism. We propose a model that integrates inputs of independent signaling pathways and how they may help the cells anticipate diel conditions and survive in a dynamic light environment.
Published: 2021

4. Interdependent Iron and Phosphorus Availability Controls Photosynthesis Through Retrograde Signaling

Author: Nadia Bouain, Hatem Rouached, Cho H, Yanniv Dorone, Zaigham Shahzad, Clowez S, Hye-In Nam, Seung Y. Rhee, Kangmei Zhao, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science [Washington], Department of Cell and Developmental Biology [Norwich], and John Innes Centre [Norwich]-Institute of Department of cell and Developmental Biology
Subjects: 2. Zero hunger, 0106 biological sciences, 0303 health sciences, Chlorosis, Chemistry, [SDV]Life Sciences [q-bio], Mutant, Photosynthesis, 01 natural sciences, Cell biology, 03 medical and health sciences, chemistry.chemical_compound, Downregulation and upregulation, Chlorophyll, Retrograde signaling, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Iron deficiency (plant disorder), Transcription factor, 030304 developmental biology, 010606 plant biology & botany
Abstract: Iron deficiency hampers photosynthesis and is associated with chlorosis. We recently showed that iron deficiency-induced chlorosis depends on phosphorus availability. How plants integrate these cues to control chlorophyll accumulation is unknown. Here, we show that iron limitation downregulates photosynthesis genes in a phosphorus-dependent manner. Using transcriptomics and genome-wide association analysis, we identify two genes, a chloroplastic ascorbate transporter (PHT4;4) and a nuclear transcription factor (bZIP58), which prevent the downregulation of photosynthesis genes leading to the stay-green phenotype under iron-phosphorus deficiency. Joint limitation of these nutrients induces ascorbate accumulation by activating expression of an ascorbate biosynthesis gene, VTC4, which requires bZIP58. Exogenous ascorbate prevents iron deficiency-induced chlorosis in vtc4 mutants, but not in bzip58 or pht4;4. Our study demonstrates chloroplastic ascorbate transport is essential for preventing the downregulation of photosynthesis genes under iron-phosphorus combined deficiency. These findings uncover a molecular pathway coordinating chloroplast-nucleus communication to adapt photosynthesis to nutrient availability.
Published: 2021

5. Soil exchange rates of COS and CO18O differ with the diversity of microbial communities and their carbonic anhydrase enzymes

Author: Meredith, Laura K., Ogée, Jérôme, Boye, Kristin, Singer, Esther, Wingate, Lisa, von Sperber, Christian, Sengupta, Aditi, Whelan, Mary, Pang, Erin, Keiluweit, Marco, Brüggemann, Nicolas, Berry, Joe A., Welander, Paula V., Department of Earth System Science, University of California Irvine (UCI), School of Natural Resources and the Environment, University of Arizona, Interactions Sol Plante Atmosphère (UMR ISPA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), SLAC National Accelerator Laboratory (SLAC), Stanford University, United States Department of Energy, Rheinische Friedrich-Wilhelms-Universität Bonn, McGill University = Université McGill [Montréal, Canada], biosphere 2, Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science [Washington], Stockbridge School of Agriculture, University of Massachusetts System (UMASS), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, National Science Foundation Atmospheric and Geospace Sciences Postdoctoral Fellowship 1331214, US Department of Energy (DOE) Joint Genome Institute (JGI) Community Science Program 2033, European Research Council (ERC) under the European Union's Seventh Framework Programme (FP7/2007-2013), ANR-13-BS06- 0005-01, DOE Office of Science, Office of Biological and Environmental Research through the SLAC National Accelerator Laboratory scientific focus area DE-AC02-76SF00515, DOE JGI a Office of Science User Facility DE-AC02-05CH11231, Swiss National Science Foundation Early Postdoc Mobility Fellowship, European Project: 338264,EC:FP7:ERC,ERC-2013-StG,SOLCA(2014), Biosphere 2 [University of Arizona], and Carnegie Institution for Science
Subjects: Technology, Bacteria, [SDV]Life Sciences [q-bio], Microbiota, Fungi, Sulfur Oxides, Biological Sciences, Carbon Dioxide, Oxygen Isotopes, Microbiology, Article, Soil, ddc:570, [SDE]Environmental Sciences, Photosynthesis, Environmental Sciences, Soil Microbiology, Carbonic Anhydrases
Abstract: International audience; Differentiating the contributions of photosynthesis and respiration to the global carbon cycle is critical for improving predictive climate models. Carbonic anhydrase (CA) activity in leaves is responsible for the largest biosphere-atmosphere trace gas fluxes of carbonyl sulfide (COS) and the oxygen-18 isotopologue of carbon dioxide (CO18O) that both reflect gross photosynthetic rates. However, CA activity also occurs in soils and will be a source of uncertainty in the use of COS and CO18O as carbon cycle tracers until process-based constraints are improved. In this study, we measured COS and CO18O exchange rates and estimated the corresponding CA activity in soils from a range of biomes and land use types. Soil CA activity was not uniform for COS and CO2, and patterns of divergence were related to microbial community composition and CA gene expression patterns. In some cases, the same microbial taxa and CA classes catalyzed both COS and CO2 reactions in soil, but in other cases the specificity towards the two substrates differed markedly. CA activity for COS was related to fungal taxa and β-D-CA expression, whereas CA activity for CO2 was related to algal and bacterial taxa and α-CA expression. This study integrates gas exchange measurements, enzyme activity models, and characterization of soil taxonomic and genetic diversity to build connections between CA activity and the soil microbiome. Importantly, our results identify kinetic parameters to represent soil CA activity during application of COS and CO18O as carbon cycle tracers.
Published: 2018

6. Systems genomics approaches provide new insights into Arabidopsis thaliana root growth regulation under combinatorial mineral nutrient limitation

Author: Bouain, Nadia, Korte, Arthur, Satbhai, Santosh B., Nam, Hye-In, Rhee, Seung Y., Busch, Wolfgang, Rouached, Hatem, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Evolutionary Genomics Center for Computational and Theoretical Biology (CCTB), Gregor Mendel Institute, Plant Molecular and Cellular Biology Laboratory, Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science [Washington], Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), and Carnegie Institution for Science
Subjects: Arabidopsis, Gene Expression, Plant Science, QH426-470, Plant Roots, fer, iron, Gene Expression Regulation, Plant, Medicine and Health Sciences, phosphorus, Plant Growth and Development, Minerals, Systems Biology, Nutritional Deficiencies, Eukaryota, Genomics, Iron Deficiencies, deficiency, Plants, Zinc, Root Growth, Experimental Organism Systems, Micronutrient Deficiencies, disponibilité d'éléments nutritifs, genome wide association study (GWAS), Genome, Plant, Research Article, Brassica, carence en zinc, Research and Analysis Methods, Model Organisms, Plant and Algal Models, Genome-Wide Association Studies, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene Regulation, Nutrition, carence, arabidopsis thaliana, Organisms, Biology and Life Sciences, Computational Biology, Correction, Human Genetics, Nutrients, Genome Analysis, phosphore, croissance racinaire, Seedlings, Iron Deficiency, Animal Studies, Developmental Biology, Genome-Wide Association Study
Abstract: The molecular mechanisms by which plants modulate their root growth rate (RGR) in response to nutrient deficiency are largely unknown. Using Arabidopsis thaliana accessions, we analyzed RGR variation under combinatorial mineral nutrient deficiencies involving phosphorus (P), iron (Fe), and zinc (Zn). While -P stimulated early RGR of most accessions, -Fe or -Zn reduced it. The combination of either -P-Fe or -P-Zn led to suppression of the growth inhibition exerted by -Fe or -Zn alone. Surprisingly, root growth responses of the reference accession Columbia (Col-0) were not representative of the species under -P nor -Zn. Using a systems approach that combines GWAS, network-based candidate identification, and reverse genetic screen, we identified new genes that regulate root growth in -P-Fe: VIM1, FH6, and VDAC3. Our findings provide a framework to systematically identifying favorable allelic variations to improve root growth, and to better understand how plants sense and respond to multiple environmental cues., Author summary Plants thrive in highly heterogenous soils. How they compute a multitude of contrasting stimuli and mount an adaptive response without a centralized information processing unit is an intriguing question. For instance, below ground, roots can sense and respond to the single or multiple nutrient stresses, and adjust its growth rate accordingly. Nevertheless, the genetic architecture of root growth responses under single and combined stress remains poorly understood. To fill this gap in our understanding about such crucial phenomenon for plant survival, we explored the natural variation of root growth rate (RGR) in Arabidopsis grown under single and combined nutritional stress, including deficiencies of iron (-Fe), zinc (-Zn), phosphate and iron (-P-Fe) and phosphate and zinc (-P-Zn). Our GWAS revealed distinct genetic architectures underlying root growth responses to single or combined nutrient stresses. By integrating GWAS and coexpression networks, we identified and validated genes controlling the variation of root growth to combined nutrient-deficiency, namely VARIANT IN METHYLATION 1, FORMIN-LIKE-PROTEIN-6 and VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 3. Our findings provide a framework to accelerate future research aiming at better understanding how plants sense and respond to multiple environmental inputs, and promise to help designing new agronomical and biotechnological strategies to improve root growth.
Published: 2019

7. Magnetic fields in the infrared dark cloud G34.43+0.24

Author: Archana Soam, Tie Liu, B-G Andersson, Chang Won Lee, Junhao Liu, Mika Juvela, Pak Shing Li, Paul F. Goldsmith, Qizhou Zhang, Patrick M. Koch, Kee-Tae Kim, Keping Qiu, Neal J. Evans II, Doug Johnstone, Mark Thompson, Derek Ward-Thompson, James Di Francesco, Ya-Wen Tang, Julien Montillaud, Gwanjeong Kim, Steve Mairs, Patricio Sanhueza, Shinyoung Kim, David Berry, Michael S. Gordon, Ken’ichi Tatematsu, Sheng-Yuan Liu, Kate Pattle, David Eden, Peregrine M. McGehee, Ke Wang, I. Ristorcelli, Sarah F. Graves, Dana Alina, Kevin M. Lacaille, Ludovic Montier, Geumsook Park, Woojin Kwon, Eun Jung Chung, Veli-Matti Pelkonen, Elisabetta R. Micelotta, Mika Saajasto, Gary Fuller, Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science [Washington], Div Life Sci, Lab Proteome Anal & Mol Physiol, Gyeongsang Natl Univ, University of Helsinki, Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), Harvard-Smithsonian Center for Astrophysics (CfA), Smithsonian Institution-Harvard University [Cambridge], Korea Astronomy and Space Science Institute (KASI), Okayama University, Fluids Laboratory for Aeronautical and Industrial Research, Department of Mechanical Engineering (FLAIR), Fluids Laboratory for Aeronautical and Industrial Research, National Research Council of Canada (NRC), Univers, Transport, Interfaces, Nanostructures, Atmosphère et environnement, Molécules (UMR 6213) (UTINAM), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Moss Landing Marine Laboratories, Marine Chemical Research Institute - State Key Laboratory of Marine Paint, China Haohua Chemical Group Co., Centre d'étude spatiale des rayonnements (CESR), Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Institut de recherche en astrophysique et planétologie (IRAP), Institut national des sciences de l'Univers (INSU - CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Helsinki], Falculty of Science [Helsinki], University of Helsinki-University of Helsinki, King‘s College London, Department of Physics, and Particle Physics and Astrophysics
Subjects: POLARIZATION, 010504 meteorology & atmospheric sciences, Field (physics), FOS: Physical sciences, Field strength, F500, Astrophysics, 01 natural sciences, 114 Physical sciences, STAR-FORMATION, Protein filament, 0103 physical sciences, Perpendicular, SCUBA-2, Infrared dark cloud, 010303 astronomy & astrophysics, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Physics, PRECURSORS, Velocity dispersion, Astronomy and Astrophysics, 115 Astronomy, Space science, Astrophysics - Astrophysics of Galaxies, Magnetic field, Space and Planetary Science, Astrophysics of Galaxies (astro-ph.GA), ISM: magnetic fields, Magnetohydrodynamics, MOLECULAR OUTFLOWS, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph]
Abstract: We present the B-fields mapped in IRDC G34.43+0.24 using 850\,$\mu$m polarized dust emission observed with the POL-2 instrument at JCMT. We examine the magnetic field geometries and strengths in the northern, central, and southern regions of the filament. The overall field geometry is ordered and aligned closely perpendicular to the filament's main axis, particularly in regions containing the central clumps MM1 and MM2, whereas MM3 in the north has field orientations aligned with its major axis. The overall field orientations are uniform at large (POL-2 at 14$\arcsec$ and SHARP at 10$\arcsec$) to small scales (TADPOL at 2.5$\arcsec$ and SMA at 1.5$\arcsec$) in the MM1 and MM2 regions. SHARP/CSO observations in MM3 at 350\,$\mu$m from Tang et al. show a similar trend as seen in our POL-2 observations. TADPOL observations demonstrate a well-defined field geometry in MM1/MM2 consistent with MHD simulations of accreting filaments. We obtained a plane-of-sky magnetic field strength of 470$\pm$190\,$\mu$G, 100$\pm$40\,$\mu$G, and 60$\pm$34\,$\mu$G in the central, northern and southern regions of G34, respectively, using the updated Davis-Chandrasekhar-Fermi relation. The estimated value of field strength, combined with column density and velocity dispersion values available in the literature, suggests G34 to be marginally critical with criticality parameter $\rm \lambda$ values 0.8$\pm$0.4, 1.1$\pm$0.8, and 0.9$\pm$0.5 in the central, northern, and southern regions, respectively. The turbulent motions in G34 are sub-Alfv\'{e}nic with Alfv\'{e}nic Mach numbers of 0.34$\pm$0.13, 0.53$\pm$0.30, and 0.49$\pm$0.26 in the three regions. The observed aligned B-fields in G34.43+0.24 are consistent with theoretical models suggesting that B-fields play an important role in guiding the contraction of the cloud driven by gravity., Comment: 16 pages, 10 figures, Accepted for publication in ApJ
Published: 2019
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8. Systems approaches provide new insights into Arabidopsis thaliana root growth under mineral nutrient limitation

Author: Hatem Rouached, Wolfgang Busch, Nadia Bouain, Arthur Korte, Seung Y. Rhee, Santosh B. Satbhai, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Equipe Hormones, Nutriments et Développement (HoNuDe) (HONUDE), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Evolutionary Genomics Center for Computational and Theoretical Biology (CCTB), Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), Austrian Academy of Sciences, Vienna Biocenter, Gregor Mendel Institute, Integrative Biology Laboratory, Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, Department of Plant Biology [Carnegie Institution], Carnegie Institution for Science [Washington], Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Department of Plant Biology [Carnegie] (DPB)
Subjects: 0106 biological sciences, Candidate gene, Micronutrient deficiency, regulatory gene, 01 natural sciences, fer, 03 medical and health sciences, chemistry.chemical_compound, iron, Arabidopsis, Botany, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Allele, phosphorus, Gene, 030304 developmental biology, gène régulateur, 2. Zero hunger, 0303 health sciences, carence, biology, arabidopsis thaliana, zinc, deficiency, Cell cycle, biology.organism_classification, phosphore, croissance racinaire, chemistry, Growth inhibition, 010606 plant biology & botany
Abstract: The molecular genetic mechanisms by which plants modulate their root growth rate (RGR) in response to nutrient deficiency are largely unknown. Using a panel of Arabidopsis thaliana natural accessions, we provide a comprehensive combinatorial analysis of RGR variation under macro- and micronutrient deficiency, namely phosphorus (P), iron (Fe), and zinc (Zn), which affect root growth in opposite directions. We found that while -P stimulates early RGR of most accessions, -Fe or -Zn reduces it. The combination of either -P-Fe or -P-Zn leads to suppression of the growth inhibition exerted by -Fe or -Zn alone. Surprisingly, Arabidopsis reference accession Columbia (Col-0) is not representative of the species under -P and -Zn. Using a genome wide association study, we identify candidate genes that control RGR under the assayed nutrient deficiency conditions. By using a network biology driven search using these candidate genes, we further identify a functional module enriched in regulation of cell cycle, DNA replication and chromatin modification that possibly underlies the suppression of root growth reduction in -P-Fe conditions. Collectively, our findings provide a framework for understanding the regulation of RGR under nutrient deficiency, and open new routes for the identification of both large effect genes and favorable allelic variations to improve root growth.
Published: 2018

9. The Properties of Planck Galactic Cold Clumps in the L1495 Dark Cloud

Author: Sheng-Li Qin, Yuefang Wu, Chang Won Lee, Maria Cunningham, Jonathan Rawlings, Archana Soam, Mengyao Tang, Kee-Tae Kim, Ken'ichi Tatematsu, Mark G. Rawlings, L. Viktor Tóth, Tie Liu, David Eden, Harriet Parsons, Patrick M. Koch, Jinghua Yuan, Ke Wang, J. Montillaud, Derek Ward-Thompson, Chuan Peng Zhang, James Di Francesco, Patricio Sanhueza, Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science [Washington], Univers, Transport, Interfaces, Nanostructures, Atmosphère et environnement, Molécules (UMR 6213) (UTINAM), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), and Swinburne University of Technology (Hawthorn campus)
Subjects: Continuum (design consultancy), FOS: Physical sciences, Astrophysics, F500, 01 natural sciences, Virial theorem, symbols.namesake, Thermal velocity, 0103 physical sciences, Planck, 010303 astronomy & astrophysics, QC, ComputingMilieux_MISCELLANEOUS, QB, Physics, Molecular line, 010308 nuclear & particles physics, Star formation, Molecular cloud, F510, Astronomy and Astrophysics, Astrophysics - Astrophysics of Galaxies, Magnetic field, Space and Planetary Science, Astrophysics of Galaxies (astro-ph.GA), symbols, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph]
Abstract: Planck Galactic Cold Clumps (PGCCs) possibly represent the early stages of star formation. To understand better the properties of PGCCs, we studied 16 PGCCs in the L1495 cloud with molecular lines and continuum data from Herschel, JCMT/SCUBA-2 and the PMO 13.7 m telescope. Thirty dense cores were identified in 16 PGCCs from 2-D Gaussian fitting. The dense cores have dust temperatures of $T_{\rm d}$ = 11-14 K, and H$_{2}$ column densities of $N_{\rm H_{2}}$ = 0.36-2.5$\times10^{22}$ cm$^{-2}$. We found that not all PGCCs contain prestellar objects. In general, the dense cores in PGCCs are usually at their earliest evolutionary stages. All the dense cores have non-thermal velocity dispersions larger than the thermal velocity dispersions from molecular line data, suggesting that the dense cores may be turbulence-dominated. We have calculated the virial parameter $\alpha$ and found that 14 of the dense cores have $\alpha$ $$ 2. This suggests that some of the dense cores are not bound in the absence of external pressure and magnetic fields. The column density profiles of dense cores were fitted. The sizes of the flat regions and core radii decrease with the evolution of dense cores. CO depletion was found to occur in all the dense cores, but is more significant in prestellar core candidates than in protostellar or starless cores. The protostellar cores inside the PGCCs are still at a very early evolutionary stage, sharing similar physical and chemical properties with the prestellar core candidates.
Published: 2018

10. Dust spectrum and polarisation at 850 μm in the massive IRDC G035.39-00.33

Author: Juvela, Mika, Guillet, V., Liu, Tie, Ristorcelli, Isabelle, Pelkonen, Veli-Matti, Alina, Dana, Bronfman, Leonardo, Eden, David J., Kim, Kee Tae, Koch, Patrick M., Kwon, Woojin, Lee, Chang Won, Malinen, Johanna, Micelotta, Elisabetta, Montillaud, Julien, Rawlings, Mark G., Sanhueza, Patricio, Soam, Archana, Traficante, Alessio, Ysard, Nathalie, Zhang, Chuan-Peng, Eden, David, Koch, Patrick, Rawlings, Mark, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Institut d'astrophysique spatiale (IAS), Université Paris-Sud - Paris 11 (UP11)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), Laboratoire Univers et Particules de Montpellier (LUPM), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science, Centre d'étude spatiale des rayonnements (CESR), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Department of Physics [Helsinki], Falculty of Science [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Liverpool John Moores University (LJMU), Academia Sinica, Div Life Sci, Lab Proteome Anal & Mol Physiol, Gyeongsang Natl Univ, University of Cologne, Univers, Transport, Interfaces, Nanostructures, Atmosphère et environnement, Molécules (UMR 6213) (UTINAM), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), University of Hawai'i [Hilo], NASA Ames Research Center Cooperative for Research in Earth Science in Technology (ARC-CREST), NASA Ames Research Center (ARC), Chinese Academy of Sciences [Beijing] (CAS), University of Helsinki, Université Paris-Sud - Paris 11 (UP11)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Carnegie Institution for Science [Washington], Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, University of Helsinki-University of Helsinki, Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS), and Department of Physics
Subjects: GRAIN ALIGNMENT, Opacity, RADIATIVE TORQUES, SCUBA-2 OBSERVATIONS, INFRARED OBSERVATIONS, Extinction (astronomy), FOS: Physical sciences, Context (language use), Astrophysics, MOLECULAR CLOUD, POLARIMETRY, ISM: clouds, 01 natural sciences, Molecular physics, Protein filament, DARK CLOUD, 0103 physical sciences, Radiative transfer, TAURUS, GOULD BELT SURVEY, 010303 astronomy & astrophysics, QC, ComputingMilieux_MISCELLANEOUS, QB, infrared: ISM, Physics, Spectral index, stars: formation, stars: protostars, extinction, 010308 nuclear & particles physics, Molecular cloud, MAGNETIC-FIELD, Astronomy and Astrophysics, 115 Astronomy, Space science, Astrophysics - Astrophysics of Galaxies, Magnetic field, 13. Climate action, Space and Planetary Science, Astrophysics of Galaxies (astro-ph.GA), submillimeter: ISM, dust, extinction, dust, [SDU.ASTR.GA]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Galactic Astrophysics [astro-ph.GA], [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph]
Abstract: The dust sub-millimetre polarisation of star-forming clouds carries information on dust and the role of magnetic fields in cloud evolution. With observations of a dense filamentary cloud G035.39-00.33, we aim to characterise the dust emission properties and the variations of the polarisation fraction. JCMT SCUBA-2/POL-2 data at 850um are combined with Planck 850um (353GHz) data to map polarisation fractions. With previous SCUBA-2 observations (450um and 850um) and Herschel data, the column densities are determined via modified blackbody fits and via radiative transfer modelling. Models are constructed to examine how the polarisation angles and fractions depend on potential magnetic field geometries and grain alignment. POL-2 data show clear changes in the magnetic field orientation. The filament has a peak column density of N(H2)~7 10^22 cm-2, a minimum dust temperature of T~12 K, and a mass of some 4300Msun for the area N(H2)> 5 10^21 cm-2. The estimated average value of the dust opacity spectral index is beta ~ 1.9. The ratio of sub-millimetre and J band optical depths is tau(250 um)/tau(J) ~ 2.5 10^-3, more than four times the typical values for diffuse medium. The polarisation fraction decreases as a function of column density to p ~ 1% in the central filament. Because of noise, the observed decrease of p(N) is significant only at N(H2)>2 10^22 cm-2. The observations suggest that the grain alignment is not constant. Although the data can be explained with a complete loss of alignment at densities above ~ 10^4 cm-3 or using the predictions of radiative torques alignment, the uncertainty of the field geometry and the spatial filtering of the SCUBA-2 data prevent strong conclusions. G035.39-00.33 shows strong signs of dust evolution and the low polarisation fraction is suggestive of a loss of polarised emission from its densest parts., accepted for publication in Astronomy and Astrophysics
Published: 2018

11. Interactions of the Infrared bubble N4 with the surroundings

Author: Gloria Mabel Dubner, Sergio Molinari, Yuefang Wu, Jin-Zeng Li, Hong-Li Liu, M. E. Ortega, Si Ju Zhang, Sergio Ariel Paron, Ya Fang Huang, Maohai Huang, Jinghua Yuan, Tie Liu, Annie Zavagno, Manash R. Samal, Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science, Instituto de Astronomía y Física del Espacio [Buenos Aires] (IAFE), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad de Buenos Aires [Buenos Aires] (UBA), Laboratoire d'Astrophysique de Marseille (LAM), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), Carnegie Institution for Science [Washington], and Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Centre National d'Études Spatiales [Toulouse] (CNES)
Subjects: H II region, Hydrogen, Infrared, Ciencias Físicas, Bubble, chemistry.chemical_element, FOS: Physical sciences, Astrophysics, 01 natural sciences, 0103 physical sciences, 010303 astronomy & astrophysics, Cosmic dust, Physics, formation [stars], 010308 nuclear & particles physics, Star formation, Astronomy and Astrophysics, Astrophysics - Astrophysics of Galaxies, bubbles [ISM], Astronomía, Wavelength, Stars, chemistry, 13. Climate action, Space and Planetary Science, Astrophysics of Galaxies (astro-ph.GA), HII regions [ISM], [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], CIENCIAS NATURALES Y EXACTAS
Abstract: The physical mechanisms that induce the transformation of a certain mass of gas in new stars are far from being well understood. Infrared bubbles associated with HII regions have been considered to be good samples of investigating triggered star formation. In this paper we report on the investigation of the dust properties of the infrared bubble N4 around the HII region G11.898+0.747, analyzing its interaction with its surroundings and star formation histories therein, with the aim of determining the possibility of star formation triggered by the expansion of the bubble. Using Herschel PACS and SPIRE images with a wide wavelength coverage, we reveal the dust properties over the entire bubble. Meanwhile, we are able to identify six dust clumps surrounding the bubble, with a mean size of 0.50 pc, temperature of about 22 K, mean column density of 1.7 $\times10^{22}$ cm$^{-2}$, mean volume density of about 4.4 $\times10^{4}$ cm$^{-3}$, and a mean mass of 320 $M_{\odot}$. In addition, from PAH emission seen at 8 $\mu$m, free-free emission detected at 20 cm and a probability density function in special regions, we could identify clear signatures of the influence of the HII region on the surroundings. There are hints of star formation, though further investigation is required to demonstrate that N4 is the triggering source., Comment: Accepted by ApJ (16 pages, 11 figures, 9 tables)
Published: 2016

12. Coupled Biological and Abiotic Mechanisms Driving Carbonyl Sulfide Production in Soils

Author: Meredith, Laura, Youngerman, Connor, Boye, Kristin, Whelan, Mary, Ogée, Jérôme, Sauze, Joana, Wingate, Lisa, School of Natural Resources and the Environment, University of Arizona, Department of Earth System Science, University of California Irvine (UCI), SLAC National Accelerator Laboratory (SLAC), Stanford University, Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science [Washington], Interactions Sol Plante Atmosphère (UMR ISPA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), French Agence Nationale de la Recherche ANR-13-BS06-0005-01, National Science Foundation Atmospheric and Geospace Sciences Postdoctoral Fellowship 1331214, DOE Office of Science, Office of Biological and Environmental Research through the SLAC National Accelerator Laboratory scientific focus area DE-AC02-76SF00515, European Project: 338264,EC:FP7:ERC,ERC-2013-StG,SOLCA(2014), and Carnegie Institution for Science
Subjects: 0301 basic medicine, 010504 meteorology & atmospheric sciences, Soil production function, [SDV]Life Sciences [q-bio], 030106 microbiology, Soil Science, complex mixtures, 01 natural sciences, soil, Carbon cycle, 03 medical and health sciences, chemistry.chemical_compound, sulfur cycle, Soil pH, carbon cycle, Ecosystem, COS, 0105 earth and related environmental sciences, Earth-Surface Processes, Carbonyl sulfide, 2. Zero hunger, Abiotic component, carbonyl sulfide, OCS, Sulfur cycle, 15. Life on land, gas flux, chemistry, 13. Climate action, Environmental chemistry, [SDE]Environmental Sciences, Soil water, Environmental science
Abstract: International audience; Understanding soil production of the trace gas carbonyl sulfide (OCS) is key to its use as a tracer of ecosystem function. Underlying its application is the observation that vascular plants consume atmospheric OCS via their stomatal pores in proportion with CO2 photosynthesis and that soil fluxes of OCS are negligible in comparison. Recent soil-centered studies demonstrate that soils can produce OCS and contribute as much as a quarter of the atmospheric terrestrial flux. Despite the potential widespread importance of soil OCS emissions, insufficient data exist to predict variations in OCS production across ecosystems, and the chemical and biological drivers of OCS production are virtually unknown. In this study, we address this knowledge gap by investigating variables controlling OCS soil production including soil physical and chemical properties, microbial community composition, and sulfur speciation in two independent surveys. We found that soil OCS production was nearly ubiquitous across the 58 sites, increased exponentially with temperature, and was insensitive to visible light conditioning. Soil pH, N, and C/N were predictors of OCS soil production rates in both soil surveys. Patterns in soil S speciation and predicted microbial S-cycling pathways both pointed to S-containing amino acids such as cysteine and methionine and their derivatives as potential precursors for OCS production. Elevated sulfate levels were associated with OCS production in some soils. This study provides new mechanistic insight into OCS production in soils and presents strategies to represent soil OCS fluxes that facilitate the use of OCS as a tracer for leaf-level processes related to carbon and water cycling.
Published: 2018

13. microProtein Prediction Program (miP3)

Author: Enrico Magnani, Michael Banf, Niek de Klein, Seung Y. Rhee, Department of Plant Biology [Carnegie Institution], Carnegie Institution for Science [Washington], Department of Genetics, University Medical Center Groningen [Groningen] (UMCG), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Techniekbeurs of the Hogeschool Arnhem Nijmegen National Science Foundation MCB-1052348 IOS-1026003 MCB-0820823 Department of Energy BER65472 Association for Independent Plant Research Institutes (AIPI), and Department of Plant Biology [Carnegie] (DPB)
Subjects: InterPro, Article Subject, lcsh:QH426-470, Computer science, DATABASE, [SDV]Life Sciences [q-bio], Pharmaceutical Science, Computational biology, computer.software_genre, INTERPRO, Biochemistry, Genome, Software, Genetics, Transcriptional regulation, Molecular Biology, Transcription factor, Gene, computer.programming_language, business.industry, fungi, HOMEODOMAIN, Python (programming language), GENE, lcsh:Genetics, ComputingMethodologies_PATTERNRECOGNITION, Data mining, business, computer, Research Article
Abstract: An emerging concept in transcriptional regulation is that a class of truncated transcription factors (TFs), called microProteins (miPs), engages in protein-protein interactions with TF complexes and provides feedback controls. A handful of miP examples have been described in the literature but the extent of their prevalence is unclear. Here we present an algorithm that predicts miPs and their target TFs from a sequenced genome. The algorithm is called miP prediction program (miP3), which is implemented in Python. The software will help shed light on the prevalence, biological roles, and evolution of miPs. Moreover, miP3 can be used to predict other types of miP-like proteins that may have evolved from other functional classes such as kinases and receptors. The program is freely available and can be applied to any sequenced genome.
Published: 2015

14. CESA TRAFFICKING INHIBITOR Inhibits Cellulose Deposition and Interferes with the Trafficking of Cellulose Synthase Complexes and Their Associated Proteins KORRIGAN1 and POM2/CELLULOSE SYNTHASE INTERACTIVE PROTEIN1

Author: Thomas Wilkop, Jose M. Alonso, Samantha Vernhettes, Bart C. Weimer, Natasha Worden, Glenn R. Hicks, John M. Labavitch, Richard Jeannotte, Victor Esteva Esteve, Staffan Persson, Georgia Drakakaki, Rahul Lathe, David W. Ehrhardt, Dept Plant Sci, University of California [Davis] (UC Davis), University of California-University of California, Dept Vet Med, Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Dept Vet Med, Davis, Department of Botany and Plant Sciences [Riverside], University of California [Riverside] (UCR), Dept Plant & Microbial Biol, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Ctr Excellence Plant Cell Walls, University of Melbourne, Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science [Washington], Dept Plant Sc, and Department of Plant Biology [Carnegie Institution]
Subjects: ATP synthase, Physiology, anisotropic cell expansion, [SDV]Life Sciences [q-bio], plasma-membrane, Plant Science, Arabidopsis-Thaliana, Biology, biology.organism_classification, golgi-apparatus, Transport protein, Cell biology, chemistry.chemical_compound, corticol microtubules, chemistry, Membrane protein, Biochemistry, Cytoplasm, Arabidopsis, Cell cortex, Genetics, biology.protein, Syntaxin, Cellulose
Abstract: Cellulose synthase complexes (CSCs) at the plasma membrane (PM) are aligned with cortical microtubules (MTs) and direct the biosynthesis of cellulose. The mechanism of the interaction between CSCs and MTs, and the cellular determinants that control the delivery of CSCs at the PM, are not yet well understood. We identified a unique small molecule, CESA TRAFFICKING INHIBITOR (CESTRIN), which reduces cellulose content and alters the anisotropic growth of Arabidopsis (Arabidopsis thaliana) hypocotyls. We monitored the distribution and mobility of fluorescently labeled cellulose synthases (CESAs) in live Arabidopsis cells under chemical exposure to characterize their subcellular effects. CESTRIN reduces the velocity of PM CSCs and causes their accumulation in the cell cortex. The CSC-associated proteins KORRIGAN1 (KOR1) and POM2/CELLULOSE SYNTHASE INTERACTIVE PROTEIN1 (CSI1) were differentially affected by CESTRIN treatment, indicating different forms of association with the PM CSCs. KOR1 accumulated in bodies similar to CESA; however, POM2/CSI1 dissociated into the cytoplasm. In addition, MT stability was altered without direct inhibition of MT polymerization, suggesting a feedback mechanism caused by cellulose interference. The selectivity of CESTRIN was assessed using a variety of subcellular markers for which no morphological effect was observed. The association of CESAs with vesicles decorated by the trans-Golgi network-localized protein SYNTAXIN OF PLANTS61 (SYP61) was increased under CESTRIN treatment, implicating SYP61 compartments in CESA trafficking. The properties of CESTRIN compared with known CESA inhibitors afford unique avenues to study and understand the mechanism under which PM-associated CSCs are maintained and interact with MTs and to dissect their trafficking routes in etiolated hypocotyls.
Published: 2015

15. Compact genome of the Antarctic midge is likely an adaptation to an extreme environment

Author: Nicholas M. Teets, Richard E. Lee, J. Spencer Johnston, Carlos Bustamante, Joanna L. Kelley, Justin T. Peyton, Muh-Ching Yee, Anna-Sophie Fiston-Lavier, David L. Denlinger, Department of Genetics [Stanford], Stanford Medicine, Stanford University-Stanford University, School of Biological Sciences, Washington State University (WSU), Ohio State University [Columbus] (OSU), Stanford University, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, University of Florida [Gainesville] (UF), Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science [Washington], Texas A&M University [College Station], Miami University [Ohio] (MU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), and Carnegie Institution for Science
Subjects: Transposable element, Physiological, Acclimatization, Genome, Insect, Antarctic Regions, General Physics and Astronomy, Genes, Insect, Environment, Genome, Article, Chironomidae, General Biochemistry, Genetics and Molecular Biology, Genetics, Animals, Extremophile, Extreme environment, Adaptation, Gene, Belgica antarctica, Multidisciplinary, biology, Ecology, Human Genome, fungi, DNA, General Chemistry, biology.organism_classification, Adaptation, Physiological, Introns, Cold Temperature, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Genes, 13. Climate action, Evolutionary biology, Multigene Family, Midge, Insect, Biotechnology
Abstract: The midge, Belgica antarctica, is the only insect endemic to Antarctica, and thus it offers a powerful model for probing responses to extreme temperatures, freeze tolerance, dehydration, osmotic stress, ultraviolet radiation and other forms of environmental stress. Here we present the first genome assembly of an extremophile, the first dipteran in the family Chironomidae, and the first Antarctic eukaryote to be sequenced. At 99 megabases, B. antarctica has the smallest insect genome sequenced thus far. Although it has a similar number of genes as other Diptera, the midge genome has very low repeat density and a reduction in intron length. Environmental extremes appear to constrain genome architecture, not gene content. The few transposable elements present are mainly ancient, inactive retroelements. An abundance of genes associated with development, regulation of metabolism and responses to external stimuli may reflect adaptations for surviving in this harsh environment., The Antarctic midge, Belgica antarctica, is the only insect endemic to Antarctica. Here, the authors sequence the B. antarctica genome, the smallest insect genome yet reported, and suggest that genes involved in development, metabolism and stimuli response may have had a role in how this insect adapted to survive in such a harsh environment.
Published: 2014

16. A Comprehensive Analysis of MicroProteins Reveals Their Potentially Widespread Mechanism of Transcriptional Regulation

Author: Kimberly Pham, Niek de Klein, Seung Y. Rhee, Elisa Fiume, Jung-Gun Kim, Enrico Magnani, Mary Beth Mudgett, Hye-In Nam, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Plant Biology [Carnegie Institution], Carnegie Institution for Science [Washington], Department of Biology, Stanford University [Stanford], Carnegie Inst Sci, Dept Plant Biol, Stanford, CA 94305 USA, Université Paris Diderot - Paris 7 (UPD7), Carnegie Institution for Science, Life Sciences Research Foundation (Howard Hughes Medical Institute Fellowship), National Science Foundation [0929413], National Institutes of Health [2R01 GM068886-06A1], Department of Plant Biology [Carnegie] (DPB), and Stanford University
Subjects: Time Factors, Transcription, Genetic, Physiology, Evolution, [SDV]Life Sciences [q-bio], Arabidopsis, Plant Science, Computational biology, Flowers, Bioinformatics, Evolution, Molecular, Genetic, Gene Expression Regulation, Plant, Transcription (biology), Genetics, Transcriptional regulation, Animals, Transcription factor, Gene, Phylogeny, Disease Resistance, Plant Diseases, Regulation of gene expression, biology, Arabidopsis Proteins, Molecular, food and beverages, Plant, Biotic stress, biology.organism_classification, Gene Expression Regulation, Homeobox, Transcription, Transcription Factors
Abstract: Truncated transcription factor-like proteins called microProteins (miPs) can modulate transcription factor activities, thereby increasing transcriptional regulatory complexity. To understand their prevalence, evolution, and function, we predicted over 400 genes that encode putative miPs from Arabidopsis (Arabidopsis thaliana) using a bioinformatics pipeline and validated two novel miPs involved in flowering time and response to abiotic and biotic stress. We provide an evolutionary perspective for a class of miPs targeting homeodomain transcription factors in plants and metazoans. We identify domain loss as one mechanism of miP evolution and suggest the possible roles of miPs on the evolution of their target transcription factors. Overall, we reveal a prominent layer of transcriptional regulation by miPs, show pervasiveness of such proteins both within and across genomes, and provide a framework for studying their function and evolution.
Published: 2014

17. Amino acid transporter inventory of the Selaginella genome

Author: Wolf B. Frommer, Sylvie Lalonde, Dominique Loqué, Daniel Wipf, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Joint BioEnergy Institute, Department of Plant Biology [Carnegie] (DPB), and Carnegie Institution for Science [Washington]
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Plant Science, Biology, lcsh:Plant culture, 01 natural sciences, Genome, 03 medical and health sciences, amino-acid, transporter, selaginella, Selaginella, amino acide, Protein biosynthesis, Hormone metabolism, lcsh:SB1-1110, Amino acid transporter, Gene, Original Research, 030304 developmental biology, Genetics, chemistry.chemical_classification, 0303 health sciences, biology.organism_classification, Amino acid, chemistry, [SDE]Environmental Sciences, amino acid, Function (biology), 010606 plant biology & botany
Abstract: International audience; Amino acids play fundamental roles in a multitude of functions including protein synthesis, hormone metabolism, nerve transmission, cell growth, production of metabolic energy, nucleobase synthesis, nitrogen metabolism, and urea biosynthesis. Selaginella as a member of the lycophytes is part of an ancient lineage of vascular plants that had arisen 400 million years ago. In angiosperms, which have attracted most of the attention for nutrient transport so far, we have been able to identify many of the key transporters for nitrogen. Their role is not always fully clear, thus an analysis of Selaginella as a representative of an ancient vascular plant may help shed light on the evolution and function of these diverse transporters. Here we annotated and analyzed the genes encoding putative transporters involved in cellular uptake of amino acids present in the Selaginella genome
Published: 2012

18. Paramutation-like interaction of T-DNA loci in Arabidopsis

Author: Totte Niittylä, Colin Ruprecht, Christine Chang, Kian Hématy, Weiya Xue, Wolf B. Frommer, Staffan Persson, Nathaniel R. Street, Dept Forest Genet & Plant Physiol, Umea Plant Sci Ctr, Swedish University of Agricultural Sciences (SLU), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Dept Plant Physiol, Umea Plant Sci Ctr, Umeå University, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Plant Biology [Carnegie Institution], Carnegie Institution for Science [Washington], Swedish research agency FORMAS, Human Frontier Science Program and Bio4Energy, Swedish Programme for renewable energy, Umea Plant Science Center (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), and Department of Plant Biology [Carnegie] (DPB)
Subjects: 0106 biological sciences, EPIGENETIC INHERITANCE, [SDV]Life Sciences [q-bio], Mutant, Arabidopsis, Plant Science, Plant Genetics, 01 natural sciences, Epigenesis, Genetic, RNA-POLYMERASE, Cell Wall, Gene Expression Regulation, Plant, R1 LOCUS, ZEA-MAYS, DNA Modification Methylases, Genetics, Regulation of gene expression, 0303 health sciences, Multidisciplinary, Nuclear Proteins, ORIENTED CELL EXPANSION, Phenotype, Multigene Family, DNA methylation, DEFENSE RESPONSES, Codon, Terminator, Medicine, Epigenetics, Research Article, DNA, Bacterial, Arabidopsis Thaliana, Plant Cell Biology, Science, Biology, Genes, Plant, Paramutation, 03 medical and health sciences, ANCHORED PROTEIN, Model Organisms, Plant and Algal Models, Gene Silencing, RNA, Messenger, Allele, Genetik, Cellulose, Gene, Transgenic Plants, Alleles, Crosses, Genetic, 030304 developmental biology, METHYLATION PATTERNS, CYTOSINE METHYLATION, MAIZE, oriented cell expansion, methylation patterns, epigenetic inheritance, cytosine methylation, defense responses, anchored protein, rna-polymerase, r1 locus, zea-mays, maize, Arabidopsis Proteins, Genetic Complementation Test, biology.organism_classification, Mutation, Plant Biotechnology, Plant Cell Wall, 010606 plant biology & botany
Abstract: In paramutation, epigenetic information is transferred from one allele to another to create a gene expression state which is stably inherited over generations. Typically, paramutation describes a phenomenon where one allele of a gene down-regulates the expression of another allele. Paramutation has been described in several eukaryotes and is best understood in plants. Here we describe an unexpected paramutation-like trans SALK T-DNA interaction in Arabidopsis. Unlike most of the previously described paramutations, which led to gene silencing, the trans SALK T-DNA interaction caused an increase in the transcript levels of the endogenous gene (COBRA) where the T-DNA was inserted. This increased COBRA expression state was stably inherited for several generations and led to the partial suppression of the cobra phenotype. DNA methylation was implicated in this trans SALK T-DNA interaction since mutation of the DNA methyltransferase 1 in the suppressed cobra caused a reversal of the suppression. In addition, null mutants of the DNA demethylase ROS1 caused a similar COBRA transcript increase in the cobra SALK T-DNA mutant as the trans T-DNA interaction. Our results provide a new example of a paramutation-like trans T-DNA interaction in Arabidopsis, and establish a convenient hypocotyl elongation assay to study this phenomenon. The results also alert to the possibility of unexpected endogenous transcript increase when two T-DNAs are combined in the same genetic background. Citation: Xue W, Ruprecht C, Street N, Hematy K, Chang C, et al. (2012) Paramutation-Like Interaction of T-DNA Loci in Arabidopsis. PLoS ONE 7(12): e51651. doi:10.1371/journal.pone.0051651
Published: 2012

19. Genome-wide binding-site analysis of REVOLUTA reveals a link between leaf patterning and light-mediated growth responses

Author: Brandt, Ronny, Salla-Martret, Merce, Bou-Torrent, Jordi, Musielak, Thomas, Stahl, Mark, Lanz, Christa, Ott, Felix, Schmid, Markus, Greb, Thomas, Schwarz, Martina, Choi, Sang-Bong, Barton, M. Kathryn, Reinhart, Brenda J., Liu, Tie, Quint, Marcel, Palauqui, Jean-Christophe, Martinez-Garcia, Jaime F., Wenkel, Stephan, National Science Foundation (US), Generalitat de Catalunya, Ministerio de Ciencia e Innovación (España), German Research Foundation, Robert Bosch Foundation, Federal Ministry of Food and Agriculture (Germany), European Commission, Zentrum für Molekularbiologie der Pflanzen (ZMBP), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Department of Molecular Biology [Tübingen], Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Sch Biotechnol & Environm Engn, Myongji Univ, Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science [Washington], Dept Mol Signal Proc, D-06120 Halle, Leibniz Institute of Plant Biochemistry (IPB), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Carnegie Institution for Science, National Science Foundation (NSF) [0929413], Generalitat de Catalunya (Xarba) [2009-SGR697], MICINN - FEDER funds [BIO2005-00154, CSD2007-00036, BIO2008-00169], Deutsche Forschungsgemeinschaft (DFG) [WE4281/6-1], European Union [256502], Ministry for Agriculture (Bundesanstalt fur Landwirtschaft und Ernahrung) [CHN 13-22/12-13], Eberhard Karls Universität Tübingen, Department of Plant Biology [Carnegie Institution], Zentrum für Molekularbiologie der Pflanzen ( ZMBP ), Dept Mol Biol, Gregor Mendel Institute of Molecular Plant Biology ( GMI ), Austrian Academy of Sciences ( OeAW ), Leibniz Institute of Plant Biochemistry, Institut Jean-Pierre Bourgin ( IJPB ), and Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Arabidopsis thaliana, PLANT DEVELOPMENT, fungi, HD-ZIPIII, SHADE-AVOIDANCE RESPONSES, ARABIDOPSIS, GENE, HD-ZIPII, CELL FATE, TRANSCRIPTION, auxin, AUXIN BIOSYNTHESIS, REGULATOR, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, shade avoidance, ZIP, leaf development, POLARITY
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., The Barton lab receives funding from the Carnegie Institution for Science and the National Science Foundation (NSF2010, grant #0929413). Research in the JFM-G laboratory is supported by grants from the Generalitat de Catalunya (Xarba, 2009-SGR697) and MICINN – FEDER funds (BIO2005-00154, CSD2007-00036, BIO2008-00169). Research in the SW laboratory is made possible by funding from the Deutsche Forschungsgemeinschaft (DFG, WE4281/6-1), the European Union (FP7 No. 256502), the Robert Bosch Foundation and the Ministry for Agriculture (Bundesanstalt für Landwirtschaft und Ernährung; CHN13-22/12-13) to SW.
Published: 2012

20. A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation

Author: Kashchandra G. Raghothama, Audrey Creff, Luis Herrerra-Estrella, Patrick Doumas, Juliette Jouhet, Laurent Nussaume, Maryse A. Block, Philippe Nacry, Ajay N. Jain, Richard Bligny, Shauna Somerville, Norbert Rolland, Philippe Ortet, Marie-Christine Thibaud, Julie Misson, Biologie cellulaire et moléculaire des plantes et des bactéries (BCMPB), Université de la Méditerranée - Aix-Marseille 2-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Department of Horticulture and Landscape Architecture, Purdue University [West Lafayette], Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecophysiologie Moléculaire des Plantes (LEMP), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Plant Biology [Carnegie Institution], Carnegie Institution for Science [Washington], Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Departamento de Ingenieria Genetica de Plantas, (DIGP), Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de la Méditerranée - Aix-Marseille 2, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Biology [Carnegie] (DPB), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Protéines de Protection des Végétaux (PPV), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Carnegie Institution for Science, Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Plant Environmental Physiology and Stress Signaling (PEPSS)
Subjects: 0106 biological sciences, Transcription, Genetic, biosynthèse, 01 natural sciences, Genome, stress, Gene Expression Regulation, Plant, Arabidopsis, monogalactosylglycérol, Gene expression, Transcriptional regulation, Oligonucleotide Array Sequence Analysis, 2. Zero hunger, Regulation of gene expression, 0303 health sciences, Multidisciplinary, biology, Biological Sciences, Phenotype, plante expérimentale, carence en phosphate, acid, DNA microarray, microarray, Genome, Plant, expression des gènes, roots, TECHNIQUE D'ANALYSE, Computational biology, transporters, Genes, Plant, Phosphates, stress nutritionnel, 03 medical and health sciences, expression, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, lipide, phosphate, 030304 developmental biology, Arabidopsis Proteins, Microarray analysis techniques, génome, starvation, Reproducibility of Results, biology.organism_classification, Molecular biology, arabidopsis, microarray analysis, digalactosylglycérol, biosynthesis, phosphorus deficiency, metabolism, 010606 plant biology & botany
Abstract: Phosphorus, one of the essential elements for plants, is often a limiting nutrient because of its low availability and mobility in soils. Significant changes in plant morphology and biochemical processes are associated with phosphate (Pi) deficiency. However, the molecular bases of these responses to Pi deficiency are not thoroughly elucidated. Therefore, a comprehensive survey of global gene expression in response to Pi deprivation was done by using Arabidopsis thaliana whole genome Affymetrix gene chip (ATH1) to quantify the spatio-temporal variations in transcript abundance of 22,810 genes. The analysis revealed a coordinated induction and suppression of 612 and 254 Pi-responsive genes, respectively. The functional classification of some of these genes indicated their involvement in various metabolic pathways, ion transport, signal transduction, transcriptional regulation, and other processes related to growth and development. This study is a detailed analysis of Pi starvation-induced changes in gene expression of the entire genome of Arabidopsis correlated with biochemical processes. The results not only enhance our knowledge about molecular processes associated with Pi deficiency, but also facilitate the identification of key molecular determinants for improving Pi use by crop species.
Published: 2005

21. Fifteen compelling open questions in plant cell biology

Author: Ram Dixit, Maria J. Harrison, Gohta Goshima, Adrienne H. K. Roeder, David W. Ehrhardt, Christine Faulkner, Jeff J. Doyle, Jeremy E. Coate, Marisa S. Otegui, Arezki Boudaoud, Keiko Sugimoto, Yan Zhang, Liam Dolan, Charlotte Kirchhelle, Carlos D. Messina, Heather M Meyer, Olivier Hamant, Charles T. Anderson, Cornell University [New York], University of Wisconsin-Madison, Washington University in Saint Louis (WUSTL), Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, UK, Sugashima Marine Biological Laboratory, Nagoya University, Marine Biological Laboratory, Woods Hole, Massachusetts, USA, Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science, Laboratoire d'hydrodynamique (LadHyX), and École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Cell type, AcademicSubjects/SCI01280, Somatic cell, [SDV]Life Sciences [q-bio], Reviews, Plant Science, Plasmodesma, Vacuole, Biology, 01 natural sciences, 03 medical and health sciences, Organelle, Cortical microtubule cytoskeleton, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, AcademicSubjects/SCI01270, AcademicSubjects/SCI02288, AcademicSubjects/SCI02287, fungi, AcademicSubjects/SCI02286, food and beverages, Cell Biology, Cell biology, Focus on Cell Biology, Retrograde signaling, 010606 plant biology & botany, Cell division site
Abstract: As scientists, we are at least as excited about the open questions—the things we do not know—as the discoveries. Here, we asked 15 experts to describe the most compelling open questions in plant cell biology. These are their questions: How are organelle identity, domains, and boundaries maintained under the continuous flux of vesicle trafficking and membrane remodeling? Is the plant cortical microtubule cytoskeleton a mechanosensory apparatus? How are the cellular pathways of cell wall synthesis, assembly, modification, and integrity sensing linked in plants? Why do plasmodesmata open and close? Is there retrograde signaling from vacuoles to the nucleus? How do root cells accommodate fungal endosymbionts? What is the role of cell edges in plant morphogenesis? How is the cell division site determined? What are the emergent effects of polyploidy on the biology of the cell, and how are any such “rules” conditioned by cell type? Can mechanical forces trigger new cell fates in plants? How does a single differentiated somatic cell reprogram and gain pluripotency? How does polarity develop de-novo in isolated plant cells? What is the spectrum of cellular functions for membraneless organelles and intrinsically disordered proteins? How do plants deal with internal noise? How does order emerge in cells and propagate to organs and organisms from complex dynamical processes? We hope you find the discussions of these questions thought provoking and inspiring., We asked 15 experts to address what they consider to be the most compelling open questions in plant cell biology and these are their questions.
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22. Submillimeter continuum variability in planck galactic cold clumps

Author: Kee-Tae Kim, Minho Choi, Chuan Peng Zhang, Miju Kang, Jonathan Rawlings, Steve Mairs, Archana Soam, Tie Liu, Sung-ju Kang, J. Montillaud, David Eden, Hyunju Yoo, Patrick M. Koch, Chang Won Lee, Jeong-Eun Lee, Doug Johnstone, Dimitris Stamatellos, Gary A. Fuller, Patricio Sanhueza, Woojin Kwon, Gwanjeong Kim, Geumsook Park, Mika Juvela, Department of Physics, Korea Astronomy and Space Science Institute (KASI), Okayama University, Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science [Washington], University of Helsinki, Univers, Transport, Interfaces, Nanostructures, Atmosphère et environnement, Molécules (UMR 6213) (UTINAM), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), King‘s College London, Div Life Sci, Lab Proteome Anal & Mol Physiol, and Gyeongsang Natl Univ
Subjects: Astrophysics::High Energy Astrophysical Phenomena, FOS: Physical sciences, Astrophysics, Astrophysics::Cosmology and Extragalactic Astrophysics, Surveys, general [Submillimeter], 01 natural sciences, symbols.namesake, Accretion rate, surveys, 0103 physical sciences, Protostar, Astrophysics::Solar and Stellar Astrophysics, SCUBA-2, RATES, Planck, ACCRETION, OUTBURST, COLLAPSE, 010303 astronomy & astrophysics, formation [Stars], James Clerk Maxwell Telescope, ComputingMilieux_MISCELLANEOUS, Astrophysics::Galaxy Astrophysics, QC, QB, Physics, stars: formation, Continuum (measurement), STAR, 010308 nuclear & particles physics, Star formation, ATLASGAL, ISM [Submillimeter], Astrophysics::Instrumentation and Methods for Astrophysics, Astronomy and Astrophysics, Observable, submillimeter: general, 115 Astronomy, Space science, Astrophysics - Astrophysics of Galaxies, EVOLUTION, Wavelength, 13. Climate action, Space and Planetary Science, Astrophysics of Galaxies (astro-ph.GA), symbols, submillimeter: ISM, COMPLETE SAMPLE, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph]
Abstract: In the early stages of star formation, a protostar is deeply embedded in an optically thick envelope such that it is not directly observable. Variations in the protostellar accretion rate, however, will cause luminosity changes that are reprocessed by the surrounding envelope and are observable at submillimeter wavelengths. We searched for submillimeter flux variability toward 12 Planck Galactic Cold Clumps detected by the James Clerk Maxwell Telescope (JCMT)-SCUBA-2 Continuum Observations of Pre-protostellar Evolution (SCOPE) survey. These observations were conducted at 850 um using the JCMT/SCUBA-2. Each field was observed three times over about 14 months between 2016 April and 2017 June. We applied a relative flux calibration and achieved a calibration uncertainty of ~ 3.6% on average. We identified 136 clumps across 12 fields and detected four sources with flux variations of ~ 30%. For three of these sources, the variations appear to be primarily due to large-scale contamination, leaving one plausible candidate. The flux change of the candidate may be associated with low- or intermediate-mass star formation assuming a distance of 1.5 kpc, although we cannot completely rule out the possibility that it is a random deviation. Further studies with dedicated monitoring would provide a better understanding of the detailed relationship between submillimeter flux and accretion rate variabilities while enhancing the search for variability in star-forming clumps farther away than the Gould Belt., 14 pages, 7 figures, 3 tables; accepted for publication in ApJS, LaTeX; minor corrections (typos, acronyms, etc.), update of authors' information

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22 results on '"Department of Plant Biology [Carnegie] (DPB)"'

1. Light-independent regulation of algal photoprotection by CO2 availability

2. Transcriptome analyses reveal the synergistic effects of feeding and eyestalk ablation on ovarian maturation in black tiger shrimp

3. Transcriptional regulation of photoprotection in dark-to-light transition - more than just a matter of excess light energy

4. Interdependent Iron and Phosphorus Availability Controls Photosynthesis Through Retrograde Signaling

5. Soil exchange rates of COS and CO18O differ with the diversity of microbial communities and their carbonic anhydrase enzymes

6. Systems genomics approaches provide new insights into Arabidopsis thaliana root growth regulation under combinatorial mineral nutrient limitation

7. Magnetic fields in the infrared dark cloud G34.43+0.24

8. Systems approaches provide new insights into Arabidopsis thaliana root growth under mineral nutrient limitation

9. The Properties of Planck Galactic Cold Clumps in the L1495 Dark Cloud

10. Dust spectrum and polarisation at 850 μm in the massive IRDC G035.39-00.33

11. Interactions of the Infrared bubble N4 with the surroundings

12. Coupled Biological and Abiotic Mechanisms Driving Carbonyl Sulfide Production in Soils

13. microProtein Prediction Program (miP3)

14. CESA TRAFFICKING INHIBITOR Inhibits Cellulose Deposition and Interferes with the Trafficking of Cellulose Synthase Complexes and Their Associated Proteins KORRIGAN1 and POM2/CELLULOSE SYNTHASE INTERACTIVE PROTEIN1

15. Compact genome of the Antarctic midge is likely an adaptation to an extreme environment

16. A Comprehensive Analysis of MicroProteins Reveals Their Potentially Widespread Mechanism of Transcriptional Regulation

17. Amino acid transporter inventory of the Selaginella genome

18. Paramutation-like interaction of T-DNA loci in Arabidopsis

19. Genome-wide binding-site analysis of REVOLUTA reveals a link between leaf patterning and light-mediated growth responses

20. A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation

21. Fifteen compelling open questions in plant cell biology

22. Submillimeter continuum variability in planck galactic cold clumps

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22 results on '"Department of Plant Biology [Carnegie] (DPB)"'

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