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13 results on '"School of Biological Sciences [Auckland, New Zealand]"'

1. Telomeres, pace of life and extinction in warm climates. Lizards from warm and declining populations are born with extremely short telomeres

Author

Dupoué, Andréaz, Blaimont, Pauline, Angelier, Frédéric, Ribout, Cecile, Rozen‐rechels, David, Richards, Murielle, Miles, Donald, de Villemereuil, Pierre, Rutschmann, Alexis, Badiane, Arnaud, Aubret, Fabien, Lourdais, Olivier, Meylan, Sandrine, Cote, Julilen, Clobert, Jean, Le Galliard, Jean‐françois, Unité de Physiologie Fonctionnelle des Organismes Marins, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Department of Ecology and Evolutionary Biology [Santa Cruz], University of California [Santa Cruz] (UCSC), University of California-University of California, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Station d’Ecologie Théorique et Expérimentale de Moulis, Centre National de la Recherche Scientifique (CNRS), Department of Biological Sciences [Ohio, USA], Ohio University, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), School of Biological Sciences [Auckland, New Zealand], University of Auckland [Auckland], and Laboratoire Évolution et Diversité Biologique, UMR 5174, CNRS, Université Toulouse III - Paul Sabatier

Subjects
[SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2022

2. Tracking of marine predators to protect Southern Ocean ecosystems

Author

Marthán N Bester, Birgitte I. McDonald, Karine Delord, Ben Raymond, Jaimie Cleeland, Steven L. Chown, Jean-Benoît Charrassin, Daniel P. Costa, Norman Ratcliffe, Michael E. Goebel, Henri Weimerskirch, Bruno Danis, Rachael Alderman, Simon D. Goldsworthy, Akiko Kato, Keith W. Nicholls, Peter G. Ryan, Nick Gales, Luciano Dalla Rosa, Andrew D. Lowther, Pierre A. Pistorius, Rochelle Constantine, P J Nico de Bruyn, Christian Lydersen, Mike Double, Jefferson T. Hinke, Stuart Corney, Arnaud Tarroux, Kieran Lawton, Yan Ropert-Coudert, Colin Southwell, Kerstin Jerosch, Silvia Olmastroni, Richard A. Phillips, Dominik A Nachtsheim, David R. Thompson, Robert J. M. Crawford, Ian D. Jonsen, Kimberly T. Goetz, Mary-Anne Lea, José C. Xavier, Sébastien Descamps, Charles-André Bost, Michael A. Fedak, Grant Ballard, Robert Harcourt, Mônica M. C. Muelbert, Klemens Pütz, Christophe Guinet, Simon Wotherspoon, Kit M. Kovacs, Iain J. Staniland, Leigh G. Torres, Luis A. Hückstädt, Phil O'b. Lyver, Ari S. Friedlaender, Arnoldus Schytte Blix, Azwianewi B. Makhado, Mercedes Santos, Roger Kirkwood, Peter L. Boveng, John L. Bengtson, Erling S. Nordøy, Barbara Wienecke, Mark A. Hindell, Ryan R. Reisinger, Wayne Z. Trivelpiece, Joachim Plötz, Knowles Kerry, Ben Arthur, Akinori Takahashi, Virginia Andrews-Goff, Horst Bornemann, M. E. I. Marquez, Clive R. McMahon, Gerald L. Kooyman, Anton Van de Putte, Ewan D. Wakefield, Lars Boehme, Philip N. Trathan, Louise Emmerson, Antarctic Wildlife Research Unit, University of Tasmania [Hobart, Australia] (UTAS), Processus et interactions de fine échelle océanique (PROTEO), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), CESAB-FRB [France], Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Ecology and Evolutionary Biology (University of California Santa Cruz), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC)-University of California (UC), Department of Ecology and Evolutionary Biology [Santa Cruz], Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), School of Biological Sciences [Victoria, Australia] (Monash University), Monash University [Victoria, Australia], Marine Biology Laboratory, Université libre de Bruxelles (ULB), Institute for Marine and Antarctic Studies [Hobart] (IMAS), National Institute of Water and Atmospheric Research [Wellington] (NIWA), Marine Mammal Institute, Oregon State University (OSU), BEDIC, OD Nature [Brussels, Belgium], Royal Belgian Institute for Natural Sciences [Belgium], Department of Primary Industries [Australia], Department of Primary Industries, Parks, Water and Environment, Australian Antarctic Division (AAD), Australian Government, Department of the Environment and Energy, PRBO Conservation Science, Department of Zoology and Entomology [Pretoria], University of Pretoria [South Africa], The Arctic University of Norway [Tromsø, Norway] (UiT), Scottish Oceans Institute, University of St Andrews [Scotland], School of Biological Sciences [Auckland, New Zealand], University of Auckland [Auckland], Antarctic Climate and Ecosystems Cooperative Research Centre (ACE-CRC), Department of Environment, Agriculture and Fisheries [South Africa] (Oceans and Coasts), Laboratório de Ecologia e Conservação da Megafauna Marinha [Rio Grande, Brazil], Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), Norvegian Polar Research Institute (NPRI), Norwegian Polar Institute, Institute of Marine Sciences, Long Marine Laboratory, South Australian Research and Development Institute [Australia], Department of Biological Sciences [North Ryde], Macquarie University, Antarctic Ecosystem Research Division, National Oceanic and Atmospheric Administration (NOAA)-National Marine Fisheries Service, Scholander Hall, Scripps Institution of Oceanography [CA, USA], Scripps Institution of Oceanography (SIO - UC San Diego), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC)-University of California [San Diego] (UC San Diego), FRAM Centre, Norwegian Polar Institute, Fram Centre, Manaaki Whenua – Landcare Research [Lincoln], Instituto Antartico Argentino, Moss Landing Marine Laboratories [CA, USA] (San José State University), San Jose State University [San Jose] (SJSU), University of Sydney Institute of Marine Science (USIMS), The University of Sydney, Universidade Federal do Rio Grande, British Antarctic Survey (BAS), Natural Environment Research Council (NERC), University of Tromsø (UiT), Dipartimento di Scienze Ambientali 'G. Sarfatti', Università degli Studi di Siena = University of Siena (UNISI), National Research Foundation Centre of Excellence at the Percy FitzPatrick Institute, Antarctic Research Trust, British Antarctic Survey NERC [UK], DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology [South Africa], Nelson Mandela University [Port Elizabeth], Instituto Antártico Argentino, National Insitute of Polar Research, National Institute of Polar Research [Tokyo] (NiPR), Southwest Fisheries Science Center (SWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Institute of Biodiversity, Animal Health and Comparative Medicine, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Natural Environment Research Council - British Antarctic Survey [Cambridge, UK], Department of Biological Sciences, Macquarie University (Australia), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of California [Santa Cruz] (UCSC), University of California-University of California, Institute for Marine and Antarctic Studies [Horbat] (IMAS), The Arctic University of Norway (UiT), Universidade Federal do Rio Grande do Sul (UFRGS), Scripps Institution of Oceanography, San Jose State University [San José] (SJSU), and Nelson Mandela University

Subjects
0106 biological sciences, Conservation of Natural Resources, Aquatic Organisms, Food Chain, bird, 010504 meteorology & atmospheric sciences, General Science & Technology, Oceans and Seas, Climate Change, Fishing, Population Dynamics, Animal Identification Systems, Climate change, Antarctic Regions, climate chang, mammal, 01 natural sciences, Predation, long-term change, Birds, bird, climate chang, econtinental shelf, exploitation, long-term change, mammal, predator tracking, Animals, Ecosystem, Ice Cover, 14. Life underwater, econtinental shelf, Life Below Water, Exploitation of natural resources, 0105 earth and related environmental sciences, Mammals, geography, Multidisciplinary, geography.geographical_feature_category, Continental shelf, predator tracking, 010604 marine biology & hydrobiology, Fishes, Biodiversity, Fishery, Climate Action, 13. Climate action, Predatory Behavior, Ecological significance, [SDE]Environmental Sciences, Environmental science, exploitation, Sciences exactes et naturelles
Abstract

International audience; Southern Ocean ecosystems are under pressure from resource exploitation and climate change1,2. Mitigation requires the identification and protection of Areas of Ecological Significance (AESs), which have so far not been determined at the ocean-basin scale. Here, using assemblage-level tracking of marine predators, we identify AESs for this globally important region and assess current threats and protection levels. Integration of more than 4,000 tracks from 17 bird and mammal species reveals AESs around sub-Antarctic islands in the Atlantic and Indian Oceans and over the Antarctic continental shelf. Fishing pressure is disproportionately concentrated inside AESs, and climate change over the next century is predicted to impose pressure on these areas, particularly around the Antarctic continent. At present, 7.1% of the ocean south of 40°S is under formal protection, including 29% of the total AESs. The establishment and regular revision of networks of protection that encompass AESs are needed to provide long-term mitigation of growing pressures on Southern Ocean ecosystems.

Published
2020
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3. Killer whale genomes reveal a complex history of recurrent admixture and vicariance

Author

Paul R. Wade, Cory J. D. Matthews, Steven H. Ferguson, Ana Amaral, Nicholas J. Davison, Michael D. Martin, Wayne Hoggard, Marie Louis, Sara Tavares, Andrew Brownlow, Andrew D. Foote, Jay Barlow, Phillip A. Morin, Ruth Esteban, Luciano Dalla Rosa, Paul Tixier, Willy Dabin, Tim Gerrodette, M. Thomas P. Gilbert, Robin W. Baird, Jochen B. W. Wolf, Laurent Excoffier, Tim Collins, John A. Totterdell, Lisa T. Ballance, C. S. Baker, Kelly M. Robertson, Renaud de Stephanis, M. Bradley Hanson, Rochelle Constantine, John W. Durban, Mikkel-Holger S. Sinding, George Pacheco, Christophe Guinet, Filipa I. P. Samarra, Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, NTNU University Museum [Trondheim], Norwegian University of Science and Technology [Trondheim] (NTNU), Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Scottish Oceans Institute, University of St Andrews [Scotland], Marine Mammal and Turtle Division (MMTD), Southwest Fisheries Science Center (SWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), American Museum of Natural History (AMNH), Cascadia Research [Washington, USA], Department of Fisheries and Wildlife, Marine Mammal Institute [Oregon, USA], Oregon State University (OSU), Wildlife Conservation Society (WCS), School of Biological Sciences [Auckland, New Zealand], University of Auckland [Auckland], Observatoire PELAGIS UMS 3462 (PELAGIS), LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratório de Ecologia e Conservação da Megafauna Marinha [Rio Grande, Brazil], Universidade Federal do Rio Grande do Sul (UFRGS), Animal Health and Veterinary Laboratories Agency, CIRCE (Conservation, Information and Research on Cetaceans), Fisheries & Oceans Canada [Canada], Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), National Oceanic and Atmospheric Administration (NOAA), National Marine Fisheries Service [Mississippi, USA], Southeast Fisheries Science Center [USA], Repositório da Universidade de Lisboa, Norwegian University of Science and Technology (NTNU)-Norwegian University of Science and Technology (NTNU), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), and Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, 0301 basic medicine, Gene Flow, Population, Antarctic Regions, Genomics, 010603 evolutionary biology, 01 natural sciences, DNA, Mitochondrial, 03 medical and health sciences, Genetic drift, Phylogenetics, biology.animal, Genetics, Vicariance, genomics, Animals, 14. Life underwater, secondary contact, education, Ecology, Evolution, Behavior and Systematics, Alleles, Phylogeny, Cell Nucleus, education.field_of_study, Principal Component Analysis, Genome, biology, Base Sequence, Geography, Models, Genetic, Whale, drift, Genetic Drift, Genetic Variation, population structure, Markov Chains, 030104 developmental biology, Sympatric speciation, Evolutionary biology, [SDE]Environmental Sciences, Biological dispersal, admixture, Whale, Killer
Abstract

Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.

Published
2019
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4. The retrospective analysis of Antarctic tracking data project

Author

Luciano Dalla Rosa, Henri Weimerskirch, Kerstin Jerosch, Sébastien Descamps, Marthán N Bester, Klemens Pütz, Charles-André Bost, Phil O'b. Lyver, Christophe Guinet, Akiko Kato, Horst Bornemann, John L. Bengtson, Jaimie Cleeland, Mary-Anne Lea, Silvia Olmastroni, Rochelle Constantine, Richard A. Phillips, Jean-Benoît Charrassin, Peter G. Ryan, Simon D. Goldsworthy, Roger Kirkwood, Louise Emmerson, Wayne Z. Trivelpiece, Christian Lydersen, Ben Raymond, Mark A. Hindell, Dominik A Nachtsheim, Jefferson T. Hinke, Nick Gales, Arnaud Tarroux, Simon Wotherspoon, Robert J. M. Crawford, Mônica M. C. Muelbert, Pierre A. Pistorius, Kimberly T. Goetz, Andrew D. Lowther, David R. Thompson, Virginia Andrews-Goff, Ian D. Jonsen, M. E. I. Marquez, Clive R. McMahon, Karine Delord, Mike Double, Gerald L. Kooyman, Kit M. Kovacs, José C. Xavier, Anton Van de Putte, Colin Southwell, Ewan D. Wakefield, Erling S. Nordøy, Barbara Wienecke, Mercedes Santos, Birgitte I. McDonald, Daniel P. Costa, Lars Boehme, Norman Ratcliffe, Ryan R. Reisinger, Arnoldus Schytte Blix, Michael A. Fedak, Peter L. Boveng, Rachael Alderman, Robert Harcourt, Iain J. Staniland, Leigh G. Torres, Ari S. Friedlaender, Yan Ropert-Coudert, Azwianewi B. Makhado, M. Goebel, Kieran Lawton, Philip N. Trathan, P J Nico de Bruyn, Luis A. Hückstädt, Keith W. Nicholls, Grant Ballard, Bruno Danis, Joachim Plötz, Knowles Kerry, David G. Ainley, Ben Arthur, Akinori Takahashi, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), BEDIC, OD Nature [Brussels, Belgium], Royal Belgian Institute for Natural Sciences [Belgium], Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Processus et interactions de fine échelle océanique (PROTEO), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Department of Ecology and Evolutionary Biology [Santa Cruz], University of California [Santa Cruz] (UCSC), University of California-University of California, Laboratoire de Biologie Marine, Université libre de Bruxelles (ULB), Department of Biological Sciences [Sydney, Australia] (Macquarie University), Macquarie University, Institute for Marine and Antarctic Studies [Horbat] (IMAS), University of Tasmania [Hobart, Australia] (UTAS), National Institute of Water and Atmospheric Research [Wellington] (NIWA), Hatfield Marine Science Center [Newport, USA], British Antarctic Survey (BAS), Natural Environment Research Council (NERC), H.T. Harvey & Associates [CA, USA), Department of Primary Industries [Australia], Department of Primary Industries, Parks, Water and Environment, PRBO Conservation Science, Department of Zoology and Entomology [Pretoria], University of Pretoria [South Africa], Mammal Research Institute - Department Zoology and Entomology, University of Pretoria (UPSpace), University of Tromsø (UiT), Scottish Oceans Institute, University of St Andrews [Scotland], School of Biological Sciences [Auckland, New Zealand], University of Auckland [Auckland], Department of Environmental Affairs [South Africa] (Oceans and Coasts), Laboratório de Ecologia e Conservação da Megafauna Marinha [Rio Grande, Brazil], Universidade Federal do Rio Grande do Sul (UFRGS), Norwegian Polar Institute, Fram Centre, Australian Antarctic Division (AAD), Australian Government, Department of the Environment and Energy, Antarctic Ecosystem Research Division, Southwest Fisheries Science Center (SWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), South Australian Research and Development Institute (SARDI), South Australian Research and Development Institute, Department of Biological Sciences [North Ryde], Center for Marine Biology and Biomedicine [La Jolla], Scripps Institution of Oceanography (SIO), University of California [San Diego] (UC San Diego), University of California-University of California-University of California [San Diego] (UC San Diego), FRAM Centre, Norwegian Polar Institute, Biodiversity Section [Norway], Manaaki Whenua – Landcare Research [Lincoln], Oceans & Coasts Branch, Instituto Antártico Argentino, Moss Landing Marine Laboratories [CA, USA] (San José State University), San Jose State University [San José] (SJSU), University of Sydney Institute of Marine Science (USIMS), The University of Sydney, Instituto de Oceanografia, Universidade Federal do Rio Grande, Dipartimento di Scienze Fisiche [Siena, Italy] (Università di Siena), Università di Siena, National Research Foundation Centre of Excellence at the Percy FitzPatrick Institute, Antarctic Research Trust, British Antarctic Survey NERC [UK], Percy FitzPatrick Institute of African Ornithology, University of Cape Town, National Institute of Polar Research [Tokyo] (NiPR), Institute of Biodiversity, Animal Health and Comparative Medicine, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Marine and Environmental Sciences Centre (MARE UC), Universidade de Coimbra [Coimbra], La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC)-University of California (UC), Department of Biological Sciences [Sydney], Institute for Marine and Antarctic Studies [Hobart] (IMAS), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), Scripps Institution of Oceanography (SIO - UC San Diego), University of California (UC)-University of California (UC)-University of California [San Diego] (UC San Diego), San Jose State University [San Jose] (SJSU), and Università degli Studi di Siena = University of Siena (UNISI)

Subjects
0106 biological sciences, Statistics and Probability, Data Descriptor, bird, Ecosystem ecology, animal experiment, Library and Information Sciences, Biodiversity informatics, animal experiment, Antarctica, biodiversity, bird, climate data,ecosystem, Southern Ocean, 010603 evolutionary biology, 01 natural sciences, Education, Information system, VDP::Mathematics and natural science: 400::Zoology and botany: 480, Tracking data, Ecosystem, 14. Life underwater, Southern Ocean, lcsh:Science, Life Below Water, biodiversity, Apex predator, ecosystem, Science & Technology, CLIMATE-CHANGE, business.industry, Conservation biology, 010604 marine biology & hydrobiology, Environmental resource management, 15. Life on land, Computer Science Applications, Multidisciplinary Sciences, MODEL, Ocean Biogeographic Information System, Geography, 13. Climate action, [SDE]Environmental Sciences, Antarctica, Science & Technology - Other Topics, ECOSYSTEM, lcsh:Q, Statistics, Probability and Uncertainty, business, climate data, Information Systems, Sciences exactes et naturelles, VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480
Abstract

The Retrospective Analysis of Antarctic Tracking Data (RAATD) is a Scientific Committee for Antarctic Research project led jointly by the Expert Groups on Birds and Marine Mammals and Antarctic Biodiversity Informatics, and endorsed by the Commission for the Conservation of Antarctic Marine Living Resources. RAATD consolidated tracking data for multiple species of Antarctic meso- and top-predators to identify Areas of Ecological Significance. These datasets and accompanying syntheses provide a greater understanding of fundamental ecosystem processes in the Southern Ocean, support modelling of predator distributions under future climate scenarios and create inputs that can be incorporated into decision making processes by management authorities. In this data paper, we present the compiled tracking data from research groups that have worked in the Antarctic since the 1990s. The data are publicly available through biodiversity.aq and the Ocean Biogeographic Information System. The archive includes tracking data from over 70 contributors across 12 national Antarctic programs, and includes data from 17 predator species, 4060 individual animals, and over 2.9 million observed locations., Measurement(s)geographic locationTechnology Type(s)digital curationFactor Type(s)temporal interval • geographic locationSample Characteristic – OrganismAptenodytes forsteri • Lobodon carcinophaga • Eudyptes chrysolophus • Thalassarche melanophrys • Phoebetria palpebrata • Aptenodytes patagonicus • Pygoscelis adeliae • Leptonychotes weddellii • Megaptera novaeangliae • Mirounga leonina • Arctocephalus gazella • Thalassoica antarctica • Eudyptes schlegeli • Diomedea exulans • Phoebetria fusca • Diomedea chrysostoma • Procellaria aequinoctialisSample Characteristic – Environmentpolar biomeSample Characteristic – LocationAntarctica Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11688876

Published
2018
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5. Two genes, ANS and UFGT2, from Vaccinium spp. are key steps for modulating anthocyanin production.

Author

Nguyen HM, Putterill J, Dare AP, Plunkett BJ, Cooney J, Peng Y, Souleyre EJF, Albert NW, Espley RV, and Günther CS

Abstract

Anthocyanins are a major group of red to blue spectrum plant pigments with many consumer health benefits. Anthocyanins are derived from the flavonoid pathway and diversified by glycosylation and methylation, involving the concerted action of specific enzymes. Blueberry and bilberry ( Vaccinium spp.) are regarded as 'superfruits' owing to their high content of flavonoids, especially anthocyanins. While ripening-related anthocyanin production in bilberry ( V. myrtillus ) and blueberry ( V. corymbosum ) is regulated by the transcriptional activator MYBA1, the role of specific structural genes in determining the concentration and composition of anthocyanins has not been functionally elucidated. We isolated three candidate genes, CHALCONE SYNTHASE ( VmCHS1 ), ANTHOCYANIDIN SYNTHASE ( VmANS ) and UDP-GLUCOSE : FLAVONOID-3-O-GLYCOSYLTRANSFERASE ( VcUFGT2 ), from Vaccinium , which were predominantly expressed in pigmented fruit skin tissue and showed high homology between bilberry and blueberry. Agrobacterium -mediated transient expression of Nicotiana benthamiana showed that overexpression of VcMYBA1 in combination with VmANS significantly increased anthocyanin concentration (3-fold). Overexpression of VmCHS1 showed no effect above that induced by VcMYBA1 , while VcUFGT2 modulated anthocyanin composition to produce delphinidin-3-galactosylrhamnoside, not naturally produced in tobacco. In strawberry ( Fragaria × ananassa ), combined transient overexpression of VcUFGT2 with a FLAVONOID 3 ´ ,5´-HYDROXYLASE from kiwifruit ( Actinidia melanandra ) modulated the anthocyanin profile to include galactosides and arabinosides of delphinidin and cyanidin, major anthocyanins in blueberry and bilberry. These findings provide insight into the role of the final steps of biosynthesis in modulating anthocyanin production in Vaccinium and may contribute to the targeted breeding of new cultivars with improved nutritional properties., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Nguyen, Putterill, Dare, Plunkett, Cooney, Peng, Souleyre, Albert, Espley and Günther.)

Published
2023
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6. Does plastic type matter? Insights into non-indigenous marine larvae recruitment under controlled conditions.

Author

Audrézet F, Zaiko A, Cahill P, Champeau O, Tremblay LA, Smith D, Wood SA, Lear G, and Pochon X

Subjects
Animals, Larva, RNA, Ribosomal, 16S genetics, Polyethylene, Polyesters, Plastics chemistry, Microbiota
Abstract

Marine plastic debris (MPD) are a global threat to marine ecosystems. Among countless ecosystem impacts, MPD can serve as a vector for marine 'hitchhikers' by facilitating transport and subsequent spread of unwanted pests and pathogens. The transport and spread of these non-indigenous species (NIS) can have substantial impacts on native biodiversity, ecosystem services/functions and hence, important economic consequences. Over the past decade, increasing research interest has been directed towards the characterization of biological communities colonizing plastic debris, the so called Plastisphere. Despite remarkable advances in this field, little is known regarding the recruitment patterns of NIS larvae and propagules on MPD, and the factors influencing these patterns. To address this knowledge gap, we used custom-made bioassay chambers and ran four consecutive bioassays to compare the settlement patterns of four distinct model biofouling organisms' larvae, including the three notorious invaders Crassostrea gigas , Ciona savignyi and Mytilus galloprovincialis , along with one sessile macro-invertebrate Spirobranchus cariniferus , on three different types of polymers, namely Low-Linear Density Polyethylene (LLDPE), Polylactic Acid (PLA), Nylon-6, and a glass control. Control bioassay chambers were included to investigate the microbial community composition colonizing the different substrates using 16S rRNA metabarcoding. We observed species-specific settlement patterns, with larvae aggregating on different locations on the substrates. Furthermore, our results revealed that C. savignyi and S. cariniferus generally favoured Nylon and PLA, whereas no specific preferences were observed for C. gigas and M. galloprovincialis . We did not detect significant differences in bacterial community composition between the tested substrates. Taken together, our results highlight the complexity of interactions between NIS larvae and plastic polymers. We conclude that several factors and their potential interactions influenced the results of this investigation, including: (i) species-specific larval biological traits and ecology; (ii) physical and chemical composition of the substrates; and (iii) biological cues emitted by bacterial biofilm and the level of chemosensitivity of the different NIS larvae. To mitigate the biosecurity risks associated with drifting plastic debris, additional research effort is critical to effectively decipher the mechanisms involved in the recruitment of NIS on MPD., Competing Interests: Susanna Wood, Anastasija Zaiko and Xavier Pochon are Academic Editors for PeerJ., (© 2022 Audrezet et al.)

Published
2022
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7. Investigating the Process of Sheath Maturation in Antifeeding Prophage: a Phage Tail-Like Protein Translocation Structure.

Author

Bhardwaj P, Mitra AK, and Hurst MRH

Subjects
Gene Expression Regulation, Viral, Humans, Molecular Chaperones, Mutagenesis, Viral Proteins chemistry, Viral Proteins genetics, Virus Replication, Prophages growth & development, Prophages physiology, Serratia virology, Viral Proteins metabolism
Abstract

The antifeeding prophage (Afp) produced by the bacterium Serratia entomophila is the archetypical external contractile injection system (eCIS). Afp and its orthologues are characterized by three sheath proteins, while contractile bacteriophages and pyocins encode only one. Using targeted mutagenesis, transmission electron microscopy (TEM), and pulldown studies, we interrogated the roles of the three sheath proteins (Afp2, Afp3, and Afp4) in Afp assembly, in particular the interaction between the two sequence-related helical-sheath-forming proteins Afp2 and Afp3 and their cross talk with the tail termination sheath capping protein (TrP) Afp16 in the sheath maturation process. The expressed assemblies for the afp2 -deficient mutant were mostly a mixture of isolated tail fibers, detached baseplates without tail fibers, and sheathless inner tube baseplate complexes (TBCs) with a length similar to that of mature Afp, which were surrounded in many cases by fibrillar polymerized material. In the afp3 -deficient mutant, variable-length TBCs with similar but shorter fibrillar polymerized material, largely bereft of tail fibers, were observed, while only detached baseplate assemblies were seen for the afp4 -deficient mutant. Furthermore, we found that (i) only trans complementation of afp2 with its mutated counterpart restored mature Afp particles with full biological activity, (ii) purified Afp3 pulled down Afp2 by forming a sodium dodecyl sulfate (SDS)-resistant complex but not vice versa, (iii) Afp16 had a higher affinity for binding Afp2 or Afp3 than Afp4, and (iv) Afp4 is required for the association of the polymerized sheath on the baseplate via Afp2. A proposed model for sheath maturation and assembly in Afp is presented. IMPORTANCE Members of the contractile bacteriophage-related but evolutionarily divergent eCIS contain not one but three sheath proteins, two of which, namely, Afp2 and Afp3 in the Afp, arranged as alternate hexameric stacks constitute the helical sheath. We revealed that Afp2 and Afp3, even though they are highly similar, possess markedly distinct, crucial roles in Afp assembly. We find that Afp3, by virtue of its interaction with the tail-terminating protein Afp16, regulates tube and sheath length, while Afp2 is critical for proper sheath polymerization and the assembly of the baseplate. The resulting model for the Afp assembly will further guide the manipulation of Afp and its related eCISs as nanodelivery vehicles for pest control and phage therapy.

Published
2021
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8. Automated annotation and visualisation of high-resolution spatial proteomic mass spectrometry imaging data using HIT-MAP.

Author

Guo G, Papanicolaou M, Demarais NJ, Wang Z, Schey KL, Timpson P, Cox TR, and Grey AC

Subjects
Animals, Brain Chemistry, Cattle, Lens, Crystalline chemistry, Mice, Peptides analysis, Peptides chemistry, Software, Proteomics methods, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Abstract

Spatial proteomics has the potential to significantly advance our understanding of biology, physiology and medicine. Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) is a powerful tool in the spatial proteomics field, enabling direct detection and registration of protein abundance and distribution across tissues. MALDI-MSI preserves spatial distribution and histology allowing unbiased analysis of complex, heterogeneous tissues. However, MALDI-MSI faces the challenge of simultaneous peptide quantification and identification. To overcome this, we develop and validate HIT-MAP (High-resolution Informatics Toolbox in MALDI-MSI Proteomics), an open-source bioinformatics workflow using peptide mass fingerprint analysis and a dual scoring system to computationally assign peptide and protein annotations to high mass resolution MSI datasets and generate customisable spatial distribution maps. HIT-MAP will be a valuable resource for the spatial proteomics community for analysing newly generated and retrospective datasets, enabling robust peptide and protein annotation and visualisation in a wide array of normal and disease contexts.

Published
2021
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9. Flow-Cytometric Method for Viability Analysis of Mycoplasma gallisepticum and Other Cell-Culture-Contaminant Mollicutes.

Author

Lawson-Ferreira R, Santiago MA, Chometon TQ, Costa VA, Silva SA, Bertho AL, and de Filippis I

Subjects
Cell Culture Techniques, Flow Cytometry, Mycoplasma, Mycoplasma gallisepticum, Tenericutes
Abstract

Mycoplasma is the smallest self-replicating bacteria, figuring as common contaminant of eukaryotic cell cultures. Production inputs and operator's manipulation seem to be the main sources of such contamination. Many analytical approaches have been applied for mycoplasma detection in cell cultures and also in biological products. However, unless they were validated, only indicator cell culture and bacteriological culture are considered as compendial methods for quality control of biological products. Nano-flow cytometry has been pointed out as an alternative technique for addressing prokaryotic and eukaryotic cell viability being a substantial tool for reference material production. In this study, a viability-flow-cytometry assay was standardized for M. gallisepticum and then applied to other cell-culture-contaminant mycoplasmas. For this, M. galliseticum's growth rate was observed and different treatments were evaluated to establish low viability cultures (cell death-induced control). Distinct viability markers and their ideal concentrations (titration) were appraised. Ethanol treatment showed to be the best death-inducing control. CFDA and TOPRO markers revealed to be the best choice for detecting live and dead mycoplasma frequencies, respectively. The standardized methodology was applied to Mycoplasma arginini, M. hyorhinis, M. orale, Spiroplasma citri and Acholeplasma laidlawii. Significant statistical difference was observed in the percentage of viable cells in comparison to ethanol treatment for A. laidlawii in CFDA and in both markers for M. gallisepticum, M. hyorhinis and S. citri. In summary, we standardized a flow cytometry assay for assessing M. gallisepticum - and potentially other species - viability and ultimately applied for reference material production improving the quality control of biological products.

Published
2021
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10. Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring.

Author

Ward L, Taylor MW, Power JF, Scott BJ, McDonald IR, and Stott MB

Subjects
Archaea genetics, Archaea metabolism, Bacteria genetics, Bacteria metabolism, Chemoautotrophic Growth, Ecosystem, Hot Temperature, Lakes microbiology, New Zealand, RNA, Ribosomal, 16S genetics, Sulfur metabolism, Temperature, Archaea isolation & purification, Bacteria isolation & purification, Hot Springs microbiology
Abstract

Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40-60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle. At temperatures >65 °C, the microbial community was dominated almost exclusively by sulphur-oxidising archaea (Sulfolobus-like spp.). By contrast, at mesophilic temperatures the community structure was more mixed, comprising both archaea and bacteria but dominated primarily by chemolithotrophic sulphur and hydrogen oxidisers. Multivariate analysis of physicochemical data confirmed that temperature was the only significant variable associated with community turnover. This research contributes to our understanding of microbial community dynamics in variable environments, using a naturally alternating system as a model and extends our limited knowledge of acidophile ecology in geothermal habitats.

Published
2017
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11. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species.

Author

Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete Jde J, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, and Herrera-Estrella A

Subjects
Chromatin Assembly and Disassembly, Fungal Proteins metabolism, Histone Acetyltransferases genetics, Histone Acetyltransferases metabolism, Histone Deacetylases genetics, Histone Deacetylases metabolism, Histones genetics, Histones metabolism, Metabolic Networks and Pathways genetics, Phylogeny, Protein Structure, Tertiary, Signal Transduction, Transcription Factors genetics, Transcription Factors metabolism, Trichoderma classification, Trichoderma metabolism, Fungal Proteins genetics, Gene Expression Regulation, Fungal, Genome, Fungal, Protein Processing, Post-Translational, Trichoderma genetics
Abstract

The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway., (Copyright © 2016, American Society for Microbiology. All Rights Reserved.)

Published
2016
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12. Transcriptional control of fleshy fruit development and ripening.

Author

Karlova R, Chapman N, David K, Angenent GC, Seymour GB, and de Maagd RA

Subjects
Fruit drug effects, Fruit metabolism, Solanum lycopersicum drug effects, Pigmentation drug effects, Pigmentation genetics, Plant Growth Regulators pharmacology, Transcription Factors metabolism, Fruit genetics, Fruit growth & development, Solanum lycopersicum genetics, Solanum lycopersicum growth & development, Transcription, Genetic drug effects
Abstract

Fleshy fruits have evolved to be attractive to frugivores in order to enhance seed dispersal, and have become an indispensable part of the human diet. Here we review the recent advances in the understanding of transcriptional regulation of fleshy fruit development and ripening with a focus on tomato. While aspects of fruit development are probably conserved throughout the angiosperms, including the model plant Arabidopsis thaliana, it is shown that the likely orthologues of Arabidopsis genes have distinct functions in fleshy fruits. The model for the study of fleshy fruit development is tomato, because of the availability of single gene mutants and transgenic knock-down lines. In other species, our knowledge is often incomplete or absent. Tomato fruit size and shape are co-determined by transcription factors acting during formation of the ovary. Other transcription factors play a role in fruit chloroplast formation, and upon ripening impact quality aspects such as secondary metabolite content. In tomato, the transcription factors NON-RIPENING (NOR), COLORLESS NON-RIPENING (CNR), and RIPENING INHIBITOR (MADS-RIN) in concert with ethylene signalling regulate ripening, possibly in response to a developmental switch. Additional components include TOMATO AGAMOUS-LIKE1 (TAGL1), APETALA2a (AP2a), and FRUITFULL (FUL1 and FUL2). The links between this highly connected regulatory network and downstream effectors modulating colour, texture, and flavour are still relatively poorly understood. Intertwined with this network is post-transcriptional regulation by fruit-expressed microRNAs targeting several of these transcription factors. This important developmental process is also governed by changes in DNA methylation levels and possibly chromatin remodelling., (© The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Published
2014
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13. Mechanical filtering for narrow-band hearing in the weta.

Author

Lomas K, Montealegre-Z F, Parsons S, Field LH, and Robert D

Subjects
Animals, Ear anatomy & histology, Ear physiology, Ear, Middle anatomy & histology, Ear, Middle physiology, Female, Hearing, Male, Tympanic Membrane anatomy & histology, Tympanic Membrane physiology, Orthoptera anatomy & histology, Orthoptera physiology
Abstract

This paper constitutes a major attempt to associate tympanic deflections with the mechanoreceptor organ location in an acoustic insect. The New Zealand tree weta (Hemideina thoracica) has tympanal ears located on each of the prothoracic tibiae. The tympana exhibit a sclerotized oval plate, membranous processes bulging out from the tibial cuticle and many loosely suspended ripples. We used microscanning laser Doppler vibrometry to determine how such a tympanal membrane vibrates in response to sound and whether the sclerotized region plays a role in hearing. The tympanum displays a single resonance at the calling frequency of the male, an unusual example of an insect tympana acting as a narrow bandpass filter. Both tympana resonate in phase with the stimulus and with each other. Histological sections show that the tympanal area is divided into two distinct regions, as in other ensiferans. An oval plate lies in the middle of a thickened region and is surrounded by a transparent and uniformly thin region. It is hinged dorsally to the tympanal rim and thus resembles the model of a 'hinged flap'. The thickened region appears to act as a damping mass on the oscillation of the thin region, and vibration displacement is reduced in this area. The thinner area vibrates with higher amplitude, inducing mechanical pressure on the dorsal area adjacent to the crista acustica. We present a new model showing how the thickened region might confer a mechanical gain onto the activation of the crista acustica sensory neurons during the sound-induced oscillations.

Published
2011
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