Author: "The J. Craig Venter Institute" - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"The J. Craig Venter Institute"' showing total 254 results

Start Over Author "The J. Craig Venter Institute"

254 results on '"The J. Craig Venter Institute"'

1. Maternal carriage of Prevotella during pregnancy associates with protection against food allergy in the offspring

Author: Peter J. Vuillermin, Martin O’Hely, Fiona Collier, Katrina J. Allen, Mimi L. K. Tang, Leonard C. Harrison, John B. Carlin, Richard Saffery, Sarath Ranganathan, Peter D. Sly, Lawrence Gray, John Molloy, Angela Pezic, Michael Conlon, David Topping, Karen Nelson, Charles R. Mackay, Laurence Macia, Jennifer Koplin, Samantha L. Dawson, Margarita Moreno-Betancur, Anne-Louise Ponsonby, the J. Craig Venter Institute, and the BIS Investigator Group
Subjects: Science
Abstract: Incidence of food allergy in westernized populations is associated with low abundance of Prevotella. Here, the authors analyse the microbiome of a mother-infant prebirth cohort and find that maternal carriage, but not infant carriage, of P. copri during pregnancy predicts the absence of food allergy in the offspring.
Published: 2020
Full Text: View/download PDF

2. Xylitol and Sorbitol Effects on the Oral Microbiome

Author: J. Craig Venter Institute and Reisha Rafeek, Senior Lecturer
Published: 2021

3. Immunity to Hepatitis B Vaccine (HVP01)

Author: Vanderbilt University, J. Craig Venter Institute, The Scripps Research Institute, University of California, San Diego, Institut Pasteur, Human Vaccines Project, and Manish Sadarangani, Principle Investigator
Published: 2020

4. Biomarker Monitoring in TP53 Mutation Carriers

Author: J. Craig Venter Institute and Laura Goetz, Staff Surgeon
Published: 2019

5. Bacterial Composition and Immune Responses in the Nose and Oropharynx During Influenza Infection

Author: J. Craig Venter Institute
Published: 2016

6. Diagnosis of Subclinical Urinary Tract Infections Using Advanced Microbiome Survey Techniques in High Risk Trauma Patients

Author: J. Craig Venter Institute and Martin D. Zielinski, Assistant Professor of Surgery
Published: 2016

7. 20 years of the minimal cell's rise from theory to practice

Author: Assistant professor, Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, Founder, Chairman, and Chief executive officer, J. Craig Venter Institute, Suzuki, Yo, Venter, J. Craig, Assistant professor, Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, Founder, Chairman, and Chief executive officer, J. Craig Venter Institute, Suzuki, Yo, and Venter, J. Craig
Abstract: In any discipline, simple systems are desirable for understanding the basic workings in the groups of systems they represent. In biology, cells are established as units for life, but even the simplest cells in nature are complex systems with uncharacterized functions beyond simply living. Making a minimal model cell in the laboratory was therefore contemplated and then achieved. Many pioneering efforts, including those at Keio University, shaped the process. This endeavor created the synthetic genomics field and a worldwide community to understand the cell and explore its applications in biotechnology and medicine.
Published: 2022

8. Maternal carriage of Prevotella during pregnancy associates with protection against food allergy in the offspring

Author: Vuillermin, Peter J., O'Hely, Martin, Collier, Fiona, Allen, Katrina J., Tang, Mimi L. K., Harrison, Leonard C., Carlin, John B., Saffery, Richard, Ranganathan, Sarath, Sly, Peter D., Gray, Lawrence, Molloy, John, Pezic, Angela, Conlon, Michael, Topping, David, Nelson, Karen, Mackay, Charles R., Macia, Laurence, Koplin, Jennifer, Dawson, Samantha L., Moreno-Betancur, Margarita, Ponsonby, Anne-Louise, Vashee, Sanjay, Torralba, Manolito, Gomez, Andres, Dwyer, Terrence, Burgner, David, Forrester, Michael, Symeonides, Christos, Bandala Sanchez, Esther, The J. Craig Venter Institute, BIS Investigator Group, Vuillermin, Peter J., O'Hely, Martin, Collier, Fiona, Allen, Katrina J., Tang, Mimi L. K., Harrison, Leonard C., Carlin, John B., Saffery, Richard, Ranganathan, Sarath, Sly, Peter D., Gray, Lawrence, Molloy, John, Pezic, Angela, Conlon, Michael, Topping, David, Nelson, Karen, Mackay, Charles R., Macia, Laurence, Koplin, Jennifer, Dawson, Samantha L., Moreno-Betancur, Margarita, Ponsonby, Anne-Louise, Vashee, Sanjay, Torralba, Manolito, Gomez, Andres, Dwyer, Terrence, Burgner, David, Forrester, Michael, Symeonides, Christos, Bandala Sanchez, Esther, The J. Craig Venter Institute, and BIS Investigator Group
Published: 2020

9. Frequent MAGE mutations in human melanoma

Author: LICR NY - Memorial Sloan-Kettering Cancer Center, J. Craig Venter Institute, Rockville, Maryland, USA - J. Craig Venter Institute, Rockville, Maryland, USA, LICR Lausanne - LICR Lausanne, LICR Melbourne - Melbourne Centre for Clinical Sciences, Austin Health, Heidelberg, Victoria, Australie, LICR Ltd, Oxford Branch, Headington, Oxford, UK - Nuffield Department of Clinical Medicine, University of Oxford, LICR NY & Ludwig Center for Cancer Immunotherapy, New York, USA - Memorial Sloan-Kettering Cancer Center & Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, USA - Department of Medicine and Ludwig Center for Cancer Immunotherapy, Oregon Health & Science University, Portland, Oregon, USA - Division of Gynecologic Oncology and the Knight Cancer Institute, Roswell Park Cancer Institute, Buffalo, New York, USA - Department of Gynecological Oncology and Center for Immunotherapy, LICR NY - LICR NY, UCL - Autre, Caballero, Otavia L., Zhao, Qi, Rimoldi, Donata, Stevenson, Brian J., Svobodova, Suzanne, Devalle, Sylvie, Röhrig, Ute F., Pagotto, Anna, Michielin, Olivier, Speiser, Daniel, Wolchok, Jedd D., Liu, Cailian, Pejovic, Tanja, Odunsi, Kunle, Brasseur, Francis, Van den Eynde, Benoît, Old, Lloyd J., Lu, Xin, Cebon, Jonathan, Strausberg, Robert L., Simpson, Andrew J., LICR NY - Memorial Sloan-Kettering Cancer Center, J. Craig Venter Institute, Rockville, Maryland, USA - J. Craig Venter Institute, Rockville, Maryland, USA, LICR Lausanne - LICR Lausanne, LICR Melbourne - Melbourne Centre for Clinical Sciences, Austin Health, Heidelberg, Victoria, Australie, LICR Ltd, Oxford Branch, Headington, Oxford, UK - Nuffield Department of Clinical Medicine, University of Oxford, LICR NY & Ludwig Center for Cancer Immunotherapy, New York, USA - Memorial Sloan-Kettering Cancer Center & Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, USA - Department of Medicine and Ludwig Center for Cancer Immunotherapy, Oregon Health & Science University, Portland, Oregon, USA - Division of Gynecologic Oncology and the Knight Cancer Institute, Roswell Park Cancer Institute, Buffalo, New York, USA - Department of Gynecological Oncology and Center for Immunotherapy, LICR NY - LICR NY, UCL - Autre, Caballero, Otavia L., Zhao, Qi, Rimoldi, Donata, Stevenson, Brian J., Svobodova, Suzanne, Devalle, Sylvie, Röhrig, Ute F., Pagotto, Anna, Michielin, Olivier, Speiser, Daniel, Wolchok, Jedd D., Liu, Cailian, Pejovic, Tanja, Odunsi, Kunle, Brasseur, Francis, Van den Eynde, Benoît, Old, Lloyd J., Lu, Xin, Cebon, Jonathan, Strausberg, Robert L., and Simpson, Andrew J.
Abstract: BACKGROUND: Cancer/testis (CT) genes are expressed only in the germ line and certain tumors and are most frequently located on the X-chromosome (the CT-X genes). Amongst the best studied CT-X genes are those encoding several MAGE protein families. The function of MAGE proteins is not well understood, but several have been shown to potentially influence the tumorigenic phenotype. METHODOLOGY/PRINCIPAL FINDINGS: We undertook a mutational analysis of coding regions of four CT-X MAGE genes, MAGEA1, MAGEA4, MAGEC1, MAGEC2 and the ubiquitously expressed MAGEE1 in human melanoma samples. We first examined cell lines established from tumors and matching blood samples from 27 melanoma patients. We found that melanoma cell lines from 37% of patients contained at least one mutated MAGE gene. The frequency of mutations in the coding regions of individual MAGE genes varied from 3.7% for MAGEA1 and MAGEA4 to 14.8% for MAGEC2. We also examined 111 fresh melanoma samples collected from 86 patients. In this case, samples from 32% of the patients exhibited mutations in one or more MAGE genes with the frequency of mutations in individual MAGE genes ranging from 6% in MAGEA1 to 16% in MAGEC1. SIGNIFICANCE: These results demonstrate for the first time that the MAGE gene family is frequently mutated in melanoma.
Published: 2010

10. Accurate classification of MLH1/MSH2 missense variants with multivariate analysis of protein polymorphisms???mismatch repair (MAPP-MMR) Communicated by Marc Greenblatt

Author: Department of Internal Medicine, Epidemiology, and Human Genetics, University of Michigan, Ann Arbor, Michigan, Genetic Epidemiology Research Institute, University of California, Irvine, Irvine, California, J. Craig Venter Institute for Human Genetics, Rockville, Maryland, Hereditary Cancer Institute, Creighton University School of Medicine, Omaha, Nebraska, Department of Community Medicine and Epidemiology, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel ; CHS National Cancer Control Center, Haifa, Israel, Genetic Epidemiology Research Institute, University of California, Irvine, Irvine, California ; Cancer Genetics Clinic, Division of Hematology-Oncology, University of California, Irvine, 204 Sprague Hall, ZC 4038, Irvine, CA 92697, Chao, Elizabeth C., Velasquez, Jonathan L., Witherspoon, Mavee S. L., Rozek, Laura S., Peel, David, Ng, Pauline, Gruber, Stephen B., Watson, Patrice, Rennert, Gad, Anton-Culver, Hoda, Lynch, Henry, Lipkin, Steven M., Department of Internal Medicine, Epidemiology, and Human Genetics, University of Michigan, Ann Arbor, Michigan, Genetic Epidemiology Research Institute, University of California, Irvine, Irvine, California, J. Craig Venter Institute for Human Genetics, Rockville, Maryland, Hereditary Cancer Institute, Creighton University School of Medicine, Omaha, Nebraska, Department of Community Medicine and Epidemiology, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel ; CHS National Cancer Control Center, Haifa, Israel, Genetic Epidemiology Research Institute, University of California, Irvine, Irvine, California ; Cancer Genetics Clinic, Division of Hematology-Oncology, University of California, Irvine, 204 Sprague Hall, ZC 4038, Irvine, CA 92697, Chao, Elizabeth C., Velasquez, Jonathan L., Witherspoon, Mavee S. L., Rozek, Laura S., Peel, David, Ng, Pauline, Gruber, Stephen B., Watson, Patrice, Rennert, Gad, Anton-Culver, Hoda, Lynch, Henry, and Lipkin, Steven M.
Abstract: Lynch syndrome, also known as hereditary nonpolyposis colon cancer (HNPCC), is the most common known genetic syndrome for colorectal cancer (CRC). MLH1/MSH2 mutations underlie approximately 90% of Lynch syndrome families. A total of 24% of these mutations are missense. Interpreting missense variation is extremely challenging. We have therefore developed multivariate analysis of protein polymorphisms???mismatch repair (MAPP-MMR), a bioinformatic algorithm that effectively classifies MLH1/MSH2 deleterious and neutral missense variants. We compiled a large database (n>300) of MLH1/MSH2 missense variants with associated clinical and molecular characteristics. We divided this database into nonoverlapping training and validation sets and tested MAPP-MMR. MAPP-MMR significantly outperformed other missense variant classification algorithms (sensitivity, 94%; specificity, 96%; positive predictive value [PPV] 98%; negative predictive value [NPV], 89%), such as SIFT and PolyPhen. MAPP-MMR is an effective bioinformatic tool for missense variant interpretation that accurately distinguishes MLH1 / MSH2 deleterious variants from neutral variants. Hum Mutat 29(6), 852???860, 2008. ?? 2008 Wiley-Liss, Inc.
Published: 2008

11. Traditional protocols and optimization methods lead to absent expression in a mycoplasma cell-tree gene expression platform

Author: Andrei Sakai, Christopher R Deich, Frank H T Nelissen, Aafke J Jonker, Daniela M de C Bittencourt, Christopher P Kempes, Kim S Wise, Hans A Heus, Wilhelm T S Huck, Katarzyna P Adamala, John I Glass, ANDREI SAKAI, Institute for Molecules and Materials, Radboud University, Netherlands., CHRISTOPHER R. DEICH, University of Minnesota, Minneapolis, USA., FRANK H. T. NELISSEN, Institute for Molecules and Materials, Radboud University, Netherlands., AAFKE J. JONKER, Institute for Molecules and Materials, Radboud University, Netherlands., DANIELA MATIAS DE C BITTENCOURT, Cenargen, CHRISTOPHER P. KEMPES, Santa Fe Institute, Santa Fe, USA., KIM S. WISE, The J. Craig Venter Institute, La Jolla, USA., HANS A. HEUS, Institute for Molecules and Materials, Radboud University, Netherlands., WILHELM T. S. HUCK, Institute for Molecules and Materials, Radboud University, Netherlands., KATARZYNA P. ADAMALA, University of Minnesota, Minneapolis, USA., and JOHN I. GLASS, The J. Craig Venter Institute, La Jolla, USA.
Subjects: Biomaterials, Mycoplasma, Ribonucleases, In vitro transcription, Biomedical Engineering, Cell-free expression system, Bioengineering, Biophysical Chemistry, Agricultural and Biological Sciences (miscellaneous), In vitro translation, Physical Organic Chemistry, Biotechnology
Abstract: Cell-free expression (CFE) systems are one of the main platforms for building synthetic cells. A major drawback is the orthogonality of cell-free systems across species. To generate a CFE system compatible with recently established minimal cell constructs, we attempted to optimize a Mycoplasma bacterium-based CFE system using lysates of the genomeminimized cell JCVI-syn3A (Syn3A) and its close phylogenetic relative Mycoplasma capricolum (Mcap). To produce mycoplasma-derived crude lysates, we systematically tested methods commonly used for bacteria, based on the S30 protocol of E. coli. Unexpectedly, after numerous attempts to optimize lysate production methods or composition of feeding buffer, none of the Mcap or Syn3A lysates supported cell-free gene expression. Only modest levels of in vitro transcription of RNA aptamers were observed. While our experimental systems were intended to perform transcription and translation, our assays focused on RNA. Further investigations identified persistently high ribonuclease activity in all lysates, despite removal of recognizable nucleases from the respective genomes and attempts to inhibit nuclease activities in assorted CFE preparations. An alternative method using digitonin to permeabilize the mycoplasma cell membrane produced a lysate with diminished RNAse activity, yet still was unable to support cell-free gene expression. We found that intact mycoplasma cells poisoned E. coli cell free extracts by degrading ribosomal RNAs, indicating that the mycoplasma cells, even the minimal cell, have a surface-associated RNAse activity. However, it is not clear which gene encodes the ribonuclease. This work summarizes attempts to produce mycoplasma-based CFE and serves as a cautionary tale for researchers entering this field. Made available in DSpace on 2022-09-14T10:05:22Z (GMT). No. of bitstreams: 1 ysac008.pdf: 1730093 bytes, checksum: 3e9cfc7a0da3bd42af172a8053fad886 (MD5) Previous issue date: 2022
Published: 2022

12. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author: Seth R. Bordenstein, Frederik Schulz, Pelin Yilmaz, Rebecca Vega Thurber, Natalia Ivanova, Christelle Desnues, Shinichi Sunagawa, Karyna Rosario, Simon Roux, Steven W. Wilhelm, Nicole S. Webster, Mart Krupovic, Lisa Zeigler Allen, Catherine Putonti, K. Eric Wommack, Tanja Woyke, Eugene V. Koonin, Joanne B. Emerson, Jed A. Fuhrman, Hiroyuki Ogata, Ramy K. Aziz, Arvind Varsani, Marie-Agnès Petit, Bonnie L. Hurwitz, Evelien M. Adriaenssens, Andrew M. Kropinski, Katrine Whiteson, Thomas Rattei, Kyung Bum Lee, Peer Bork, David Paez-Espino, Mark J. Young, Jens H. Kuhn, Ben Temperton, Rebecca A. Daly, Natalya Yutin, Emiley A. Eloe-Fadrosh, Manuel Martinez-Garcia, Curtis A. Suttle, Susannah G. Tringe, Alejandro Reyes, Bas E. Dutilh, Nikos C. Kyrpides, Rex R. Malmstrom, Ilene Karsch Mizrachi, Kelly C. Wrighton, Rob Lavigne, Mya Breitbart, Lynn M. Schriml, Philip Hugenholtz, Melissa B. Duhaime, François Enault, Pascal Hingamp, Francisco Rodriguez-Valera, Clara Amid, Matthew B. Sullivan, Jessica M. Labonté, Grieg F. Steward, J. Rodney Brister, Takashi Yoshida, Guy Cochrane, DOE Joint Genome Institute [Walnut Creek], University of Liverpool, Theoretical Biology & Bioinformatics [Utrecht], University Medical Center [Utrecht], Radboud University Medical Center [Nijmegen], National Center for Biotechnology Information (NCBI), University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Arizona State University [Tempe] (ASU), University of Cape Town, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Cairo University, Vanderbilt University [Nashville], European Molecular Biology Laboratory [Heidelberg] (EMBL), University of South Florida [Tampa] (USF), Colorado State University [Fort Collins] (CSU), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), University of Michigan [Ann Arbor], University of Michigan System, University of California [Davis] (UC Davis), University of California (UC), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), University of Southern California (USC), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), University of Queensland [Brisbane], University of Arizona, Texas A&M University [Galveston], National Institute of Genetics (NIG), Universidad de Alicante, Kyoto University, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, University of Chicago, Department of Microbiology and Ecosystem Science [Vienna], University of Vienna [Vienna], Universidad de los Andes [Bogota] (UNIANDES), Universidad Miguel Hernández [Elche] (UMH), University of Maryland School of Medicine, University of Maryland System, University of Hawai‘i [Mānoa] (UHM), Ohio State University [Columbus] (OSU), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), University of British Columbia (UBC), University of Exeter, Oregon State University (OSU), Australian Institute of Marine Science [Townsville] (AIMS Townsville), Australian Institute of Marine Science (AIMS), University of California [Irvine] (UC Irvine), The University of Tennessee [Knoxville], University of Delaware [Newark], Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Montana State University (MSU), J. Craig Venter Institute, University of California [San Diego] (UC San Diego), This work was supported by the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under US Department of Energy Contract No. DE-AC02-05CH11231 for S.R., the Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004 for B.E.D., the Intramural Research Program of the National Library of Medicine, National Institutes of Health for E.V.K., I.K.M., J.R.B. and N.Y., the Virus-X project (EU Horizon 2020, No. 685778) for F.E. and M.K., Battelle Memorial Institute's prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I for J.H.K., the GOA grant 'Bacteriophage Biosystems' from KU Leuven for R.L., the European Molecular Biology Laboratory for C.A. and G.R.C., Cairo University Grant 2016-57 for R.K.A., National Science Foundation award 1456778, National Institutes of Health awards R01 AI132581 and R21 HD086833, and The Vanderbilt Microbiome Initiative award for S.R.B., National Science Foundation awards DEB-1239976 for M.B. and K.R. and DEB-1555854 for M.B., the NSF Early Career award DEB-1555854 and NSF Dimensions of Biodiversity #1342701 for K.C.W. and R.A.D., the Agence Nationale de la Recherche JCJC grant ANR-13-JSV6-0004 and Investissements d'Avenir Méditerranée Infection 10-IAHU-03 for C.D., the Gordon and Betty Moore Foundation Marine Microbiology Initiative No. 3779 and the Simons Foundation for J.A.F., the French government 'Investissements d'Avenir' program OCEANOMICS ANR-11-BTBR-0008 and European FEDER Fund 1166-39417 for P. Hingamp, Australian Research Council Laureate Fellowship FL150100038 to P. Hugenholtz the National Science Foundation award 1801367 and C-DEBI Research Grant for J.M.L., the Gordon and Betty Moore Foundation grant 5334 and Ministry of Economy and Competitivity refs. CGL2013-40564-R and SAF2013-49267-EXP for M.M.-G., the Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Science, Sports, and Technology (MEXT) of Japan No. 16H06429, 16K21723, and 16H06437 for H.O. and T.Y., National Science Foundation award DBI-1661357 to C.P., the Ministry of Economy and Competitivity ref CGL2016-76273-P (cofunded with FEDER funds) for F.R.-V., the Gordon and Betty Moore Foundation awards 3305 and 3790 and NSF Biological Oceanography OCE 1536989 for M.B.S., the ETH Zurich and Helmut Horten Foundation and the Novartis Foundation for Medical-Biological Research (17B077) for S.S., a BIOS-SCOPE award from Simons Foundation International and NERC award NE/P008534/1 to B.T., NSF Biological Oceanography Grant 1635913 for R.V.T., the Australian Research Council Future Fellowship FT120100480 for N.S.W., a Gilead Sciences Cystic Fibrosis Research Scholarship for K.L.W., Gordon and Better Moore Foundation Grant 4971 for S.W.W., the NSF EPSCoR grant 1736030 for K.E.W., the National Science Foundation award DEB-4W4596 and National Institutes of Health award R01 GM117361 for M.J.Y., the Gordon and Betty Moore Foundation No. 7000 and the National Oceanic and Atmospheric Administration (NOAA) under award NA15OAR4320071 for L.Z.A. DDBJ is supported by ROIS and MEXT. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors. B.E.D., A.K., M.K., J.H.K., R.L. and A.V. are members of the ICTV Executive Committee, but the views and opinions expressed are those of the authors and not those of the ICTV., Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Ecología Microbiana Molecular, Institut Pasteur [Paris], University of South Florida (USF), University of California, Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Kyoto University [Kyoto], Universidad de los Andes [Bogota], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), University of California [Irvine] (UCI), J Craig Venter Institute, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Sub Bioinformatics, and Theoretical Biology and Bioinformatics
Subjects: [SDV]Life Sciences [q-bio], Microbiología, 2.2 Factors relating to physical environment, Applied Microbiology and Biotechnology, Genome, 0302 clinical medicine, Databases, Genetic, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], phage, Viral, 0303 health sciences, Genetic Databases, Environmental microbiology, pipeline, Genome project, dynamics, Genomics, annotation, Viruses, Molecular Medicine, tacomony, Infection, Genetic databases, Biotechnology, Virus Cultivation, In silico, Biomedical Engineering, Phage biology, Bioengineering, Computational biology, Genome, Viral, Biology, Virus, dna viruses, Article, Uncultivated virus genomes, Databases, 03 medical and health sciences, Annotation, Genetic, Virology, MD Multidisciplinary, Genetics, 030304 developmental biology, Human Genome, Biological classification, commitee, prediction, Metagenomics, Minimum Information about any (x) Sequence (MIxS), 030217 neurology & neurosurgery, discovery
Abstract: We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere., Nature Biotechnology, 37 (1), ISSN:1546-1696, ISSN:1087-0156
Published: 2018
Full Text: View/download PDF

13. Interrogation of the Burkholderia pseudomallei genome to address differential virulence among isolates

Author: Badger, Jonathan [J. Craig Venter Institute, Rockville, MD (United States)]
Published: 2014
Full Text: View/download PDF

14. A comprehensive collection of systems biology data characterizing the host response to viral infection

Author: Scheuermann, Richard [J. Craig Venter Institute, La Jolla, CA (United States); Univ. of California, San Diego, CA (United States)]
Published: 2014
Full Text: View/download PDF

15. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

Author: Eichiro Ichiishi, Dmitri Beglov, Bernard Maigret, Gyu Rie Lee, Artem B. Mamonov, Shoshana J. Wodak, Jonathan C. Fuller, Dima Kozakov, Jong Young Joung, Petr Popov, Xiaofeng Yu, Keehyoung Joo, João P. G. L. M. Rodrigues, Anna Vangone, Koen M. Visscher, Xiaoqin Zou, Paul A. Bates, Andriy Kryshtafovych, Shourya S. Roy Burman, Daisuke Kihara, Romina Oliva, Efrat Ben-Zeev, Jeffrey J. Gray, Yang Shen, Li C. Xue, Sameer Velankar, Emilie Neveu, Shruthi Viswanath, Dina Schneidman-Duhovny, Juan Esquivel-Rodríguez, Mieczyslaw Torchala, Amit Roy, Alexandre M. J. J. Bonvin, David R. Hall, Tanggis Bohnuud, Xusi Han, David W. Ritchie, Ron Elber, Daisuke Kuroda, Zhiwei Ma, Joan Segura, Carlos A. Del Carpio, Nicholas A. Marze, Jong Yun Kim, Andrej Sali, Petras J. Kundrotas, Ezgi Karaca, Neil J. Bruce, Chaok Seok, Panagiotis L. Kastritis, Shen You Huang, Ilya A. Vakser, Lim Heo, Sanbo Qin, Raphael A. G. Chaleil, Adrien S. J. Melquiond, Miguel Romero-Durana, Anisah W. Ghoorah, Surendra S. Negi, Andrey Tovchigrechko, Françoise Ochsenbein, Narcis Fernandez-Fuentes, Liming Qiu, Miriam Eisenstein, Mehdi Nellen, Marie-Dominique Devignes, Lenna X. Peterson, Jinchao Yu, Minkyung Baek, Brian G. Pierce, Hasup Lee, Toshiyuki Oda, Rebecca C. Wade, Raphael Guerois, Juan Fernández-Recio, Iain H. Moal, Edrisse Chermak, Sergei Grudinin, Sangwoo Park, Ivan Anishchenko, Chengfei Yan, Thom Vreven, Kentaro Tomii, Bing Xia, Hyung Rae Kim, Chiara Pallara, Jooyoung Lee, Kazunori D. Yamada, Xianjin Xu, Kenichiro Imai, Zhiping Weng, Luigi Cavallo, Tyler M. Borrman, Jianlin Cheng, Marc F. Lensink, Huan-Xiang Zhou, Jilong Li, Gydo C. P. van Zundert, Brian Jiménez-García, Tsukasa Nakamura, Scott E. Mottarella, Sandor Vajda, Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] ( IRI ), Université de Lille, Sciences et Technologies-Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique ( CNRS ), European Molecular Biology Laboratory, European Bioinformatics Institute, Genome Center [UC Davis], University of California at Davis, Research Support Computing [Columbia], University of Missouri-Columbia, Bioinformatics Consortium and Department of Computer Science [Columbia], Department of Bioengineering and Therapeutic Sciences, University of California [San Francisco] ( UCSF ), Department of Pharmaceutical Chemistry, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California [San Francisco] ( UCSF ) -California Institute for Quantitative Biosciences, GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit, Centro Nacional de Biotecnología (CSIC), Institute of Biological, Environmental and Rural Sciences ( IBERS ), Institute for Computational Engineering and Sciences [Austin] ( ICES ), University of Texas at Austin [Austin], Department of Computer Science, Department of Chemistry, Algorithms for Modeling and Simulation of Nanosystems ( NANO-D ), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Laboratoire Jean Kuntzmann ( LJK ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Institut National Polytechnique de Grenoble ( INPG ), Moscow Institute of Physics and Technology [Moscow] ( MIPT ), Seoul National University [Seoul], Florida State University [Tallahassee] ( FSU ), Computational Algorithms for Protein Structures and Interactions ( CAPSID ), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Department of Complex Systems, Artificial Intelligence & Robotics ( LORIA - AIS ), Laboratoire Lorrain de Recherche en Informatique et ses Applications ( LORIA ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Laboratoire Lorrain de Recherche en Informatique et ses Applications ( LORIA ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ), University of Mauritius, Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, G-INCPM, Weizmann Institute of Science, Chemical Research Support [Rehovot], Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch ( UTMB ), Program in Bioinformatics and Integrative Biology [Worcester], University of Massachusetts Medical School [Worcester] ( UMASS ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Bijvoet Center for Biomolecular Research [Utrecht], Utrecht University [Utrecht], Dalton Cardiovascular Research Center [Columbia], Department of Computer Science [Columbia], Informatics Intitute, Department of Biochemistry, University of Missouri, UNIVERSITY OF MISSOURI, Toyota Technological Institute at Chicago [Chicago] ( TTIC ), Department of Biological Sciences, Purdue University, Purdue University [West Lafayette], Department of Computer Science [Purdue], Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, Molecular and Cellular Modeling Group, Heidelberg Institute of Theoretical Studies, Center for Molecular Biology ( ZMBH ), Universität Heidelberg [Heidelberg], Interdisciplinary Center for Scientiﬁc Computing ( IWR ), Department of Molecular Biosciences [Lawrence], University of Kansas [Lawrence] ( KU ), Computational Biology Research Center ( CBRC ), National Institute of Advanced Industrial Science and Technology ( AIST ), Graduate School of Frontier Sciences, The University of Tokyo, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center - Centro Nacional de Supercomputacion ( BSC - CNS ), Center for In-Silico Protein Science, Korea Institute for Advanced Study ( KIAS ), Center for Advanced Computation, Department of Biomedical Engineering [Boston], Boston University [Boston] ( BU ), Institute of Biological Diversity, International Pacific Institute of Indiana, Drosophila Genetic Resource Center, Kyoto Institute of Technology, International University of Health and Welfare Hospital ( IUHW Hospital ), International University of Health and Welfare Hospital, Department of Chemical and Biomolecular Engineering [Baltimore], Johns Hopkins University ( JHU ), Program in Molecular Biophysics [Baltimore], King Abdullah University of Science and Technology ( KAUST ), University of Naples, J Craig Venter Institute, Structural Biology Research Center, VIB, 1050 Brussels, Belgium, Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] (IRI), Université de Lille, Sciences et Technologies-Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), University of Missouri [Columbia] (Mizzou), University of Missouri System, University of California [San Francisco] (UC San Francisco), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute of Biological, Environmental and Rural Sciences (IBERS), Institute for Computational Engineering and Sciences [Austin] (ICES), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Moscow Institute of Physics and Technology [Moscow] (MIPT), Seoul National University [Seoul] (SNU), Florida State University [Tallahassee] (FSU), Computational Algorithms for Protein Structures and Interactions (CAPSID), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Biomolecular Modelling Laboratory [London], The Francis Crick Institute [London], Weizmann Institute of Science [Rehovot, Israël], The University of Texas Medical Branch (UTMB), University of Massachusetts Medical School [Worcester] (UMASS), University of Massachusetts System (UMASS)-University of Massachusetts System (UMASS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Assemblage moléculaire et intégrité du génome (AMIG), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), University of Missouri System-University of Missouri System, Toyota Technological Institute at Chicago [Chicago] (TTIC), Department of Biological Sciences [Lafayette IN], Heidelberg Institute for Theoretical Studies (HITS ), Center for Molecular Biology (ZMBH), Universität Heidelberg [Heidelberg] = Heidelberg University, Interdisciplinary Center for Scientiﬁc Computing (IWR), University of Kansas [Lawrence] (KU), Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), The University of Tokyo (UTokyo), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Korea Institute for Advanced Study (KIAS), Boston University [Boston] (BU), International University of Health and Welfare Hospital (IUHW Hospital), Johns Hopkins University (JHU), King Abdullah University of Science and Technology (KAUST), University of Naples Federico II = Università degli studi di Napoli Federico II, J. Craig Venter Institute, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Droit et Santé-Université de Lille, Sciences et Technologies, University of California-University of California, University of California [San Francisco] (UCSF), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), University of Naples Federico II, Barcelona Supercomputing Center, NMR Spectroscopy, and Sub NMR Spectroscopy
Subjects: 0301 basic medicine, Protein Conformation, alpha-Helical, Protein Folding, Computer science, International Cooperation, Amino Acid Motifs, Oligomer state, Homoprotein, DATA-BANK, computer.software_genre, Molecular Docking Simulation, Biochemistry, CAPRI Round 30, DESIGN, Structural Biology, ALIGN, Blind prediction, AFFINITY, Protein interaction, Enginyeria biomèdica [Àrees temàtiques de la UPC], ZDOCK, Oligomer State, computer.file_format, Articles, Protein structure prediction, Proteïnes--Investigació, 3. Good health, WEB SERVER, CASP, Thermodynamics, Data mining, CAPRI, Protein docking, Molecular Biology, Algorithms, INTERFACES, Protein Binding, [ INFO.INFO-MO ] Computer Science [cs]/Modeling and Simulation, Bioinformatics, STRUCTURAL BIOLOGY, Computational biology, Molecular Dynamics Simulation, Article, 03 medical and health sciences, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], Heteroprotein, Humans, Protein binding, Macromolecular docking, Protein Interaction Domains and Motifs, Homology modeling, ALGORITHM, Protein-protein docking, Internet, Binding Sites, Models, Statistical, 030102 biochemistry & molecular biology, Bacteria, Sequence Homology, Amino Acid, Computational Biology, Proteins, Protein Data Bank, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Protein Structure, Tertiary, 030104 developmental biology, Structural biology, Docking (molecular), Protein structure, Protein Conformation, beta-Strand, Protein Multimerization, oligomer state, blind prediction, protein interaction, protein docking, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Software
Abstract: We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein–protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. We are most grateful to the PDBe at the European Bioinformatics Institute in Hinxton, UK, for hosting the CAPRI website. Our deepest thanks go to all the structural biologists and to the following structural genomics initiatives: Northeast Structural Genomics Consortium, Joint Center for Structural Genomics, NatPro PSI:Biology, New York Structural Genomics Research Center, Midwest Center for Structural Genomics, Structural Genomics Consortium, for contributing the targets for this joint CASP-CAPRI experiment. MFL acknowledges support from the FRABio FR3688 Research Federation “Structural & Functional Biochemistry of Biomolecular Assemblies.”
Published: 2016
Full Text: View/download PDF

16. MIB–MIP is a mycoplasma system that captures and cleaves immunoglobulin G

Author: Alain Blanchard, Laurent Coquet, Pascal Sirand-Pugnet, Joerg Jores, Yonathan Arfi, Sanjay Vashee, Stéphane Claverol, Carmelo Di Primo, Laetitia Minder, Aline Le Roy, Christine Ebel, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Institut Européen de Chimie et de Biologie, Institut de biologie structurale (IBS - UMR 5075), 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)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Polymères Biopolymères Surfaces (PBS), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Centre Génomique Fonctionnelle Bordeaux [Bordeaux] (CGFB), Institut Polytechnique de Bordeaux-Université de Bordeaux Ségalen [Bordeaux 2], J Craig Venter Institute, International Livestock Research Institute, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-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), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), J. Craig Venter Institute, Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-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)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), and Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2
Subjects: 0301 basic medicine, medicine.medical_treatment, 030106 microbiology, mycoplasmas, medicine.disease_cause, Immunoglobulin G, Microbiology, 03 medical and health sciences, Immune system, Bacterial Proteins, medicine, Gene, neoplasms, Serine protease, Multidisciplinary, Protease, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Mycoplasma mycoides, protease, Mycoplasma, Biological Sciences, biology.organism_classification, Virology, 3. Good health, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 030104 developmental biology, Multiprotein Complexes, biology.protein, Antibody, immunoglobulin, Protein Binding
Abstract: International audience; Mycoplasmas are "minimal" bacteria able to infect humans, wildlife, and a large number of economically important livestock species. Mycoplasma infections include a spectrum of clinical manifestations ranging from simple fever to fulminant inflammatory diseases with high mortality rates. These infections are mostly chronic, suggesting that mycoplasmas have developed means to evade the host immune response. Here we present and functionally characterize a two-protein system from Mycoplasma mycoides subspecies capri that is involved in the capture and cleavage of IgG. The first component, Mycoplasma Ig binding protein (MIB), is an 83-kDa protein that is able to tightly bind to the Fv region of a wide range of IgG. The second component, Mycoplasma Ig protease (MIP), is a 97-kDa serine protease that is able to cleave off the VH domain of IgG. We demonstrate that MIB is necessary for the proteolytic activity of MIP. Cleavage of IgG requires a sequential interaction of the different partners of the system: first MIB captures the IgG, and then MIP is recruited to the MIB-IgG complex, enabling protease activity. MIB and MIP are encoded by two genes organized in tandem, with homologs found in the majority of pathogenic mycoplasmas and often in multiple copies. Phylogenetic studies suggest that genes encoding the MIB-MIP system are specific to mycoplasmas and have been disseminated by horizontal gene transfer. These results highlight an original and complex system targeting the host immunoglobulins, playing a potentially key role in the immunity evasion by mycoplasmas.
Published: 2016
Full Text: View/download PDF

17. Complete Genome Sequence of Mycoplasma mycoides subsp. mycoides T1/44, a Vaccine Strain against Contagious Bovine Pleuropneumonia

Author: Valérie Barbe, Joerg Jores, Ghislaine Magdelenat, Pascal Sirand-Pugnet, Carole Lartigue, Alain Blanchard, Emmanuel Beaudoing, Géraldine Gourgues, Johann Weber, Elise Schieck, Aurélien Barré, Sanjay Vashee, Centre de Bioinformatique de Bordeaux (CBIB), CGFB, University of Victoria [Canada] (UVIC), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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), International Livestock Research Institute, J. Craig Venter Institute, Deuxième labo, Laboratoire Universitaire de Recherche en Production Automatisée (LURPA), Université Paris-Sud - Paris 11 (UP11)-École normale supérieure - Cachan (ENS Cachan), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, J Craig Venter Institute, École normale supérieure - Cachan (ENS Cachan)-Université Paris-Sud - Paris 11 (UP11), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB)
Subjects: 0301 basic medicine, 030106 microbiology, 610 Medicine & health, medicine.disease_cause, Microbiology, 03 medical and health sciences, Vaccine strain, Contagious bovine pleuropneumonia, Genetics, medicine, Prokaryotes, Molecular Biology, Whole genome sequencing, Attenuated vaccine, biology, 630 Agriculture, Strain (biology), Mycoplasma, biology.organism_classification, medicine.disease, Virology, 3. Good health, 030104 developmental biology, 570 Life sciences, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Mycoplasma mycoides
Abstract: Mycoplasma mycoides subsp. mycoides is the etiologic agent of contagious bovine pleuropneumonia. We report here the complete genome sequence of the strain T1/44, which is widely used as a live vaccine in Africa.
Published: 2016
Full Text: View/download PDF

18. Insights into the Musa genome: Syntenic relationships to rice and between Musa species

Author: Olivier Garsmeur, Felipe Rodrigues da Silva, Georgios J. Pappas, Foo Cheung, Ang lique D'Hont, Christopher D. Town, Ryan Althoff, Manoel Souza, C. M. R. Santos, Tammy Arbogast, Catherine M. Ronning, Ana Y. Ciampi, Guillaume Blanc, Jim Leebens-Mack, Alberto Duarte Vilarinhos, Brian J. Haas, Pietro Piffanelli, Jean-Christophe Glaszmann, Magali Lescot, Manuel Ruiz, Robert N.G. Miller, Hiroyuki Kanamori, Takashi Matsumoto, Takuji Sasaki, Erin Hine, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Magali Lescot, CIRAD/IBSM, Pietro Piffanelli, CIRAD/PADANO, Ana Yamaguishi Ciampi, Embrapa Recursos Genéticos e Biotecnologia, Manuel Ruiz, CIRAD, Guillaume Blanc, IGS, Jim Leebens-Mack, University of Georgia, Felipe Rodrigues da Silva, Embrapa Recursos Genéticos e Biotecnologia, Candice Mello Romero Santos bolsista Embrapa Recursos Genéticos e Biotecnologia, Angélique D'Hont, CIRAD, Olivier Garsmeur, CIRAD, Alberto Duarte Vilarinhos, CNPMF, Hiroyuki Kanamori, RGP, Takashi Matsumoto, RGP, Catherine M. Ronning, J. Craig Venter Institute, Foo Cheung, J. Craig Venter Institute, Brian J. Haas, J. Craig Venter Institute, Ryan Althoff, J. Craig Venter Institute, Tammy Arbogast, J. Craig Venter Institute, Erin Hine, J. Craig Venter Institute, Georgios Joannis Pappas Junior, Embrapa Recursos Genéticos e Biotecnologia, Takuji Sasaki, RGP, Manoel Teixeira Souza Junior, Embrapa Recursos Genéticos e Biotecnologia, Robert N. G. Miller, UCB, Jean-Christophe Glaszmann, CIRAD, and Christopher D. Town, J. Craig Venter Institute.
Subjects: 0106 biological sciences, Chromosomes, Artificial, Bacterial, Phylogénie, Arabidopsis, comparative sequence-analysis, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, Banana, Gene Duplication, Musa balbisiana, ComputingMilieux_MISCELLANEOUS, Expressed Sequence Tags, 2. Zero hunger, Genetics, Base Composition, 0303 health sciences, gibberellin 20-oxidase, food and beverages, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], genetic-recombination map, duplicate genes, Genome, Plant, Polymorphism, Restriction Fragment Length, Research Article, Biotechnology, Genome evolution, DNA, Complementary, Séquence nucléotidique, lcsh:QH426-470, lcsh:Biotechnology, Zingiberales, Genomics, arabidopsis-thaliana, Biology, Genes, Plant, Synteny, Evolution, Molecular, 03 medical and health sciences, Species Specificity, Zingiberaceae, lcsh:TP248.13-248.65, Musa acuminata, acuminata colla, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Musa species, splice-site prediction, Sorghum, Repetitive Sequences, Nucleic Acid, 030304 developmental biology, Comparative genomics, Whole genome sequencing, molecular evidence, flowering plants, Génome, Biointeracties and Plant Health, Musa, Oryza, 15. Life on land, biology.organism_classification, lcsh:Genetics, DNA Transposable Elements, PRI Biointeractions en Plantgezondheid, nuclear-dna content, 010606 plant biology & botany
Abstract: Background Musa species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale analyses of Musa genomic sequence have been conducted. This study compares genomic sequence in two Musa species with orthologous regions in the rice genome. Results We produced 1.4 Mb of Musa sequence from 13 BAC clones, annotated and analyzed them along with 4 previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with eudicot and Poaceae genomes. Comparison with rice revealed microsynteny regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The divergence time distributions for Musa-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong evidence for a large-scale duplication event in the Musa lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from M. acuminata and M. balbisiana revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya. Conclusion These results point to the utility of comparative analyses between distantly-related monocot species such as rice and Musa for improving our understanding of monocot genome evolution. Sequencing the genome of M. acuminata would provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivated Musa polyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic traits for breeding purposes.
Published: 2008
Full Text: View/download PDF

19. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

Author: Joseph M. Vinetz, X. Frank Yang, Derrick E. Fouts, Douglas E. Berg, Rudy A. Hartskeerl, Alejandro Buschiazzo, Daniel H. Haft, Albert I. Ko, Dieter M. Bulach, Jun-Jie Zhang, Ana L. T. O. Nascimento, Janjira Thaipandungpanit, Luciane Amorim-Santos, Bernhard O. Palsson, Sharon J. Peacock, Mathieu Picardeau, Ariel E. Mechaly, Jonathan M. Monk, Ben Adler, David A. Haake, Haritha Adhikarla, James Matsunaga, Elsio A. Wunder, Karen E. Nelson, Michael A. Matthias, Yung Fu Chang, Paul N. Levett, Jessica N. Ricaldi, Renee L. Galloway, J. Craig Venter Institute [La Jolla, USA] (JCVI), Division of Infectious Diseases - Department of Medicine, University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Department of Epidemiology of Microbial Disease [New Haven], Yale School of Public Health (YSPH), Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University [Clayton], Instituto Gonçalo Moniz / Gonçalo Moniz Research Centre - Fiocruz Bahia [Salvador, Brésil] (IGM), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Victorian Bioinformatics Consortium [Clayton], Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP), Département de Biologie structurale et Chimie - Department of Structural Biology and Chemistry, Institut Pasteur [Paris] (IP), Department of Population Medicine and Diagnostic Sciences, Cornell University [New York], Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, David Geffen School of Medicine [Los Angeles], University of California [Los Angeles] (UCLA), Veterans Affairs Greater Los Angeles Health Care System, National Collaborating Centre for Reference and Research on Leptospirosis [Pays-bas], The Royal Tropical Institute (KIT), Disease Control Laboratory Regina, Government of Saskatchewan, Department of Bioengineering, Centro de Biotecnologia [Sao Paulo], Instituto Butantan [São Paulo], Instituto de ciencias biomedicas (ICB-USP), Universidade de São Paulo = University of São Paulo (USP), Department of Medicine [Cambridge], University of Cambridge [UK] (CAM), Biologie des Spirochètes / Biology of Spirochetes, Instituto de Medicina Tropical 'Alexander von Humboldt' (IMT AvH), Universidad Peruana Cayetano Heredia (UPCH), Faculty of Tropical Medicine, Mahidol University [Bangkok], Department of Microbiology and Immunology [Indianapolis], Indiana University School of Medicine, Indiana University System-Indiana University System, This project has been funded in whole or part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under Contract Number HHSN272200900007C. Thiswork was also supported in part by the following U.S. Public Health Service grants: U19AI115658 (JMV), R01AI108276 (JMV), D43TW007120 (JMV), K24AI068903 (JMV), R21AI115273 (MAM), R01AI052473 (AIK), U01AI088752 (AIK), R25TW009338 (AIK), R01TW009504 (AIK), and R01AI121207 (AIK). In addition, support to the A. Buschiazzo team was provided in part by grantsFSA_1_2013_1_12557 and ALI_1_2014_1_4982 from ANII (Uruguay). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., We are grateful to the J. Craig Venter Institute sequencing, bioinformatics and IT departments for supporting the infrastructure required to determine the genome sequences, annotation and pan-genome and other analyses carried out in this project., University of California-University of California, Fundação Oswaldo Cruz (FIOCRUZ), Institut Pasteur [Paris], Universidade de São Paulo (USP), and Small, Pamela LC
Subjects: 0301 basic medicine, animal diseases, [SDV]Life Sciences [q-bio], Pathology and Laboratory Medicine, Medical and Health Sciences, Biochemistry, Genome, Medicine and Health Sciences, 2.2 Factors relating to the physical environment, CRISPR, Bacteriophages, Aetiology, Bacterial Secretion Systems, Phylogeny, Leptospira, Virulence, biology, lcsh:Public aspects of medicine, Bacterial, Genomics, Biological Sciences, 3. Good health, Leptospira/classification/genetics/isolation & purification/pathogenicity, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Medical Microbiology, Viruses, Bacterial Proteins/genetics/metabolism, Host adaptation, Pathogens, Infection, Sequence Analysis, Leptospira interrogans, purl.org/pe-repo/ocde/ford#3.03.06 [https], Biotechnology, Research Article, lcsh:Arctic medicine. Tropical medicine, lcsh:RC955-962, Evolution, Molecular Sequence Data, 030106 microbiology, Protein Sorting Signals, Research and Analysis Methods, Biosynthesis, Microbiology, Evolution, Molecular, 03 medical and health sciences, Bacterial Proteins, Tropical Medicine, Genetics, Animals, Humans, Leptospirosis, Molecular Biology Techniques, Sequencing Techniques, Microbial Pathogens, Molecular Biology, Comparative genomics, Bacteria, Base Sequence, Organisms, Public Health, Environmental and Occupational Health, Molecular, Biology and Life Sciences, Computational Biology, lcsh:RA1-1270, Genome analysis, biology.organism_classification, bacterial infections and mycoses, Bacterial adhesin, Emerging Infectious Diseases, Good Health and Well Being, Leptospirosis/microbiology/veterinary, bacteria, Bacterial pathogens, Sequence Alignment, Genome, Bacterial
Abstract: Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field. Infectious Leptospira, comprised of pathogenic and intermediately pathogenic Leptospira, evolutionarily diverged from non-infectious, saprophytic Leptospira, as demonstrated by the following computational biology analyses: 1) the definitive taxonomy and evolutionary relatedness among all known Leptospira species; 2) genomically-predicted metabolic reconstructions that indicate novel adaptation of infectious Leptospira to mammals, including sialic acid biosynthesis, pathogen-specific porphyrin metabolism and the first-time demonstration of cobalamin (B12) autotrophy as a bacterial virulence factor; 3) CRISPR/Cas systems demonstrated only to be present in pathogenic Leptospira, suggesting a potential mechanism for this clade’s refractoriness to gene targeting; 4) finding Leptospira pathogen-specific specialized protein secretion systems; 5) novel virulence-related genes/gene families such as the Virulence Modifying (VM) (PF07598 paralogs) proteins and pathogen-specific adhesins; 6) discovery of novel, pathogen-specific protein modification and secretion mechanisms including unique lipoprotein signal peptide motifs, Sec-independent twin arginine protein secretion motifs, and the absence of certain canonical signal recognition particle proteins from all Leptospira; and 7) and demonstration of infectious Leptospira-specific signal-responsive gene expression, motility and chemotaxis systems. By identifying large scale changes in infectious (pathogenic and intermediately pathogenic) vs. non-infectious Leptospira, this work provides new insights into the evolution of a genus of bacterial pathogens. This work will be a comprehensive roadmap for understanding leptospirosis pathogenesis. More generally, it provides new insights into mechanisms by which bacterial pathogens adapt to mammalian hosts., Author Summary Leptospirosis is an emerging and re-emerging globally important zoonotic infectious disease caused by spirochetes of the genus Leptospira. This genus is complex, with members that cause lethal human disease, yet mechanisms that underlie pathogenesis remain obscure. Leptospira species are divided into those that are infectious for mammals, and those that are non-infectious environmental saprophytes. Based on biological characteristics and molecular phylogeny, infectious Leptospira are further divided into pathogenic and intermediately pathogenic members. The pan-genus genomic analysis of 20 Leptospira species reported here shows the evolutionary relationship of the different Leptospira clades, and various genetic factors related to virulence and pathogenesis. Infectious Leptospira show key adaptations to mammals, for example sialic acid biosynthesis, pathogen-specific porphyrin metabolism, and the observation that pathogenic Leptospira are vitamin B12 autotrophs, able to synthesize it from a simple amino acid precursor, L-glutamine. A large novel protein family of unknown function—the Virulence Modifying proteins—is found uniquely in pathogenic Leptospira. Similarly, the CRISPR/Cas system was only found in pathogenic Leptospira. A comparative genomic analysis of a complex bacterial genus allowed us to identify large-scale changes that provides new insights into general processes by which bacteria evolve to become pathogenic.
Published: 2016
Full Text: View/download PDF

20. A novel protein, ubiquitous in marine phytoplankton, concentrates iron at the cell surface and facilitates uptake

Author: Chris Bowler, Ahmed A. Moustafa, Andrew E. Allen, Atsuko Tanaka, Javier Paz-Yepes, Alaguraj Veluchamy, Yann Thomas, Emmanuel Lesuisse, Hugo Botebol, Robert Sutak, Leila Tirichine, Jeffrey B. McQuaid, François-Yves Bouget, Joe Morrissey, Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Parasitology, Faculty of Science, Charles University [Prague] (CU), Department of Biology and Biotechnology Graduate Program, American University in Cairo, American University in Cairo, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Microbial and Environmental Genomics, J. Craig Venter Institute [La Jolla, USA] (JCVI), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), ERC 'Diatomite', ANR 'PhytoIron' (ANR 11 BSV7 018 02) projects, Fondation Pierre Gilles de Gennes, People Programme (Marie Curie Actions), European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement number 275289, National Science Foundation (NSF-ANT 1043671), Department of Energy (DOE-DE-SC0008593), Gordon and Betty Moore Foundation (GBMF3828), EU MicroB3 project, French Government 'Investissements d'Avenir' programmes MEMO LIFE (ANR-10-LABX-54), Research University (ANR-11-IDEX-0001-02), Czech Science Foundation (13-25349S), project BIOCEV (CZ.1.05/1.1.00/02.0109), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Charles University [Prague], and J. Craig Venter Institute
Subjects: Iron, Iron fertilization, Marine Biology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, General Biochemistry, Genetics and Molecular Biology, Nutrient, Species Specificity, Phytoplankton, Botany, Seawater, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, Phaeodactylum tricornutum, Diatoms, Chlorosis, biology, Agricultural and Biological Sciences(all), Biochemistry, Genetics and Molecular Biology(all), Gene Expression Profiling, fungi, Membrane Proteins, biology.organism_classification, Protein Structure, Tertiary, Bioavailability, Diatom, 13. Climate action, Biophysics, Composition (visual arts), General Agricultural and Biological Sciences
Abstract: International audience; Numerous cellular functions including respiration require iron. Plants and phytoplankton must also maintain the iron-rich photosynthetic electron transport chain, which most likely evolved in the iron-replete reducing environments of the Proterozoic ocean [1]. Iron bioavailability has drastically decreased in the contemporary ocean [1], most likely selecting for the evolution of efficient iron acquisition mechanisms among modern phytoplankton. Mesoscale iron fertilization experiments often result in blooms dominated by diatoms [2], indicating that diatoms have adaptations that allow survival in iron-limited waters and rapid multiplication when iron becomes available. Yet the genetic and molecular bases are unclear, as very few iron uptake genes have been functionally characterized from marine eukaryotic phytoplankton, and large portions of diatom iron starvation transcriptomes are genes encoding unknown functions [3-5]. Here we show that the marine diatom Phaeodactylum tricornutum utilizes ISIP2a to concentrate Fe(III) at the cell surface as part of a novel, copper-independent and thermodynamically controlled iron uptake system. ISIP2a is expressed in response to iron limitation several days prior to the induction of ferrireductase activity, and it facilitates significant Fe(III) uptake during the initial response to Fe limitation. ISIP2a is able to directly bind Fe(III) and increase iron uptake when heterologously expressed, whereas knockdown of ISIP2a in P. tricornutum decreases iron uptake, resulting in impaired growth and chlorosis during iron limitation. ISIP2a is expressed by diverse marine phytoplankton, indicating that it is an ecologically significant adaptation to the unique nutrient composition of marine environments.
Published: 2015
Full Text: View/download PDF

21. Early allopolyploid evolution in the post-Neolithic[i] Brassica napus[/i] oilseed genome

Author: Patrick Wincker, Pascal Bento, Sahana Manoli, Agnieszka A. Golicz, G. Deniot, Shengyi Liu, Christine Sidebottom, Chu Shin Koh, Ian Bancroft, Christian Daviaud, David C. Tack, Rod J. Snowdon, Jörg Tost, Guangyi Fan, Hui Guo, Smahane Chalabi, Boulos Chalhoub, Xinfa Wang, Harry Belcram, Aurélie Chauveau, Gilles Lassalle, Jean-Marc Aury, Tae-Ho Lee, Houda Chelaifa, Jinling Meng, Christopher D. Town, Haibao Tang, Zhongsong Liu, Julien Chiquet, Andrew G. Sharpe, Salman Alamery, Chunyun Guan, Mathieu Charles, Qiong Hu, Xiyin Wang, Xiaowu Wang, Jianxin Ma, Régine Delourme, Mei Guan, Eric Lyons, Chaobo Tong, Margot Correa, Adriana Alberti, Keith L. Adams, Patrick P. Edger, Marie-Christine Le Paslier, Yunhai Lu, Corinne Da Silva, Christophe Battail, Andrew H. Paterson, Isabelle Le Clainche, Benjamin Noel, Jérémy Just, Jacqueline Batley, Jinxiong Shen, Fengming Sun, Kamel Jabbari, Karine Labadie, Michel Renard, Maria Bernard, Birgit Samans, Aurélie Canaguier, Isobel A. P. Parkin, Yong Pyo Lim, Vinh Ha Dinh Thi, Victor Renault, Meixia Zhao, David Edwards, Graham J.W. King, Nicolas Schnel, Dominique Brunel, Cyril Falentin, Reece Tollenaere, Aurélie Bérard, Yongming Zhou, Dominique Arnaud, Imen Mestiri, Philippe E. Bayer, Chuchuan Fan, Wei Hua, J. Chris Pires, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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)-Université Paris-Saclay-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture-Chinese Academy of Agricultural Sciences (CAAS), Agriculture and Agri-Food (AAFC), J. Craig Venter Institute [La Jolla, USA] (JCVI), Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University (FAFU), University of Georgia [USA], School of Life Sciences, Center of Genomics and Computational Biology, Hebei United University, Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Research Center for Biosystems, Land Use and Nutrition, Department of Plant Breeding, Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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 de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, National Research Council of Canada (NRC), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Centre National de Genotypage, Plant Genome Mapping Laboratory, Laboratoire épigénétique et environnement, School of Agriculture and Food Sciences, Australian Centre for Plant Functional Genomics, University of Queensland [Brisbane], Cologne Center for Genomics, University of Cologne, Department of Agronomy, Purdue University [West Lafayette], Department of Plant and Microbial Biology, University of California (UC), Department of Botany [Vancouver] (UBC Botany), University of British Columbia (UBC), National Key Laboratory of Crop Genetic Improvement [China], Huazhong Agricultural University [Wuhan] (HZAU), Beijing Genome Institute, Fondation Jean Dausset - Centre d’Étude du Polymorphisme Humain, College of Agronomy, Hunan Agricultural University [Changsha], Department of Horticulture, Molecular Genetics and Genomics Laboratory, Chungnam National University (CNU), School of Plant Sciences, iPlant Collaborative, University of Arizona, Department of Biology, University of York [York, UK], Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS), Division of Biological Sciences, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Southern Cross Plant Science, Southern Cross University (SCU), School of Plant Biology, The University of Western Australia (UWA), Laboratory for Epigenetics and Environment, Agriculture and Agri-Food [Ottawa] (AAFC), Laboratoire de Mathématiques et Modélisation d'Evry, Justus-Liebig-Universität Gießen (JLU), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, 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), University of California, Huazhong Agricultural University, Euralis Semences, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), BIOGEMMA, Unité de Recherches Zootechniques (URZ), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Institut national de recherches archéologiques préventives (Inrap), Limagrain, J. Craig Venter Institute, Fujian Agriculture and Forestry University, Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Department of Botany, University of Missouri [Columbia], Southern Cross University, Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), UMR 1165 Unité de Recherche en Génomique Végétale, Institut National de la Recherche Agronomique ( INRA ) -Université d'Evry Val d'Essonne, Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Ministry of Agriculture-Chinese Academy of Agricultural Sciences ( CAAS ), Agriculture and Agri-Food [Ottawa] ( AAFC ), University of Georgia, Laboratoire de Mathématiques et Modélisation d'Evry ( LaMME ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -ENSIIE-Centre National de la Recherche Scientifique ( CNRS ), Unité de recherche en génomique végétale ( URGV ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Justus Liebig University Giessen, Institut de Génomique d'Evry ( IG ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, National Research Council of Canada ( NRC ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), Institut National de la Recherche Agronomique ( INRA ), University of British Columbia ( UBC ), National Key Laboratory of Crop Genetic Improvement, Chungnam National University, Institute of Vegetables and Flowers ( IVF ), Chinese Academy of Agricultural Sciences ( CAAS ), University of Missouri ( Saisissez le sigle en majuscules sans points ), The University of Western Australia ( UWA ), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, plant genome, [SDV]Life Sciences [q-bio], Brassica, rapeseed, Biology, 01 natural sciences, Genome, Evolution, Molecular, Polyploidy, 03 medical and health sciences, chemistry.chemical_compound, Gene duplication, genetics, Epigenetics, Domestication, Gene, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, [ SDV ] Life Sciences [q-bio], molecular evolution, Brassica napus, chromosome duplication, food and beverages, plant seed, biology.organism_classification, chemistry, Glucosinolate, Seeds, cytology, Genome, Plant, 010606 plant biology & botany
Abstract: Oilseed rape (Brassica napus L.) was formed ∼7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72x genome multiplication since the origin of angiosperms and high gene content.We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement., Erratum published in Vol 345, no. 6202 September 2014 DOI: 10.1126/science.1260782
Published: 2014
Full Text: View/download PDF

22. BREAD: Toward Development of an effective vaccine vaccine for contagious bovine pleuropneumoniae

Author: Vashee, Sanjay, Lartigue, Carole, Jores, Joerg, Blanchard, Alain, Schieck, Elise, Lebaudy, Anne, Nene, Vishvanath, Sirand-Pugnet, Pascal, Glass, John I., Lartigue, Carole, The J. Craig Venter Institute (JCVI), The J. Craig Venter Institute, Biologie du fruit et pathologie (BFP), and Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2012

23. HIV-PDI: A Protein-Drug Interaction Resource for Structural Analyses of HIV Drug Resistance: 1. Concepts and Associated Database

Author: Ouwe-Missi-Oukem-Boyer Odile, Kelbert Patricia, Djikeng Appolinaire, Maigret Bernard, Keminse Lionel, Fokam Joseph, Devignes Marie-Dominique, Sma L-Tabbone Malika, Ghemtio Leo, Knowledge representation, reasonning (ORPAILLEUR), INRIA Lorraine, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS), The J. Craig Venter Institute (JCVI), The J. Craig Venter Institute, Centre international de référence Chantal Biya pour la recherche sur la prévention et la prise en charge du VIH/SIDA (CIRCB), Fondation Chantal Biya (FCB), and Harmonic Phama
Subjects: Drug, 0303 health sciences, 030306 microbiology, Viral protein, business.industry, media_common.quotation_subject, virus diseases, Drug interaction, Bioinformatics, medicine.disease_cause, medicine.disease, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, 03 medical and health sciences, Antibiotic resistance, Resource (project management), Acquired immunodeficiency syndrome (AIDS), medicine, Identification (biology), [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, HIV drug resistance, 030304 developmental biology, media_common
Abstract: International audience; Overcoming the problem of resistance to antiretroviral drugs (ARVs) in HIV-infected patients is a major issue in AIDS research today. Advances in genome sequencing have facilitated the identification of a growing number of individual genotypes. Hence, it is now possible to understand HIV drug resistance at the molecular level by considering the three-dimensional (3D) structural interactions between ARVs and the mutated viral proteins of patients. Therefore, identification of the critical interactions lost further to one or several HIV mutations, and consequently the modifications of other molecular factors, could be indicators to propose appropriate ARVs escaping the resistance. This paper introduces the HIV-PDI (Protein-Drug Interactions) resource designed to be a decision making tool to propose alternative ARVs against a particular mutated viral protein, and thus to provide a personalized antiretroviral treatment. The HIV-PDI was conceived to serve as an integrated resource for studying HIV drug resistance at the structural level of the protein-drug interaction, with a special emphasis on the active site of the HIV drug target. As a first step, we focus on the well documented protease and related drugs. The HIV-PDI includes clinical information on patients, resistance to given ARVs treatments, HIV proteins structures and mutations, HIV protein/ARV drugs and their 3D interactions. The HIV-PDI may be queried using multiple combinations of fields including protein, drug and treatment conditions and coupled to visualization/analysis tools of 3D Protein-Drug interactions. The HIV-PDI resource can be used in order to help understand the appearance of resistance and to promote further novel drug and treatment developments based on analyses of 3D pattern of protein-drug interactions. A web-based version of HIV-PDI is available at http://hiv-pdi.loria.fr.
Published: 2011
Full Text: View/download PDF

24. HIV-PDI: A Protein Drug Interaction Resource for Structural Analyses of HIV Drug Resistance: 2. Examples of Use and Proof-of-Concept

Author: Souchet Michel, Kelbert Patricia, Ritchie W David, Ghemtio Leo, Keminse Lionel, Djikeng Appolinaire, Ouwe-Missioukem Boyer Odile, Maigret Bernard, Knowledge representation, reasonning (ORPAILLEUR), INRIA Lorraine, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS), Harmonic Phama, The J. Craig Venter Institute (JCVI), The J. Craig Venter Institute, Centre international de référence Chantal Biya pour la recherche sur la prévention et la prise en charge du VIH/SIDA (CIRCB), and Fondation Chantal Biya (FCB)
Subjects: 0303 health sciences, Biological data, Decision support system, Data collection, 030306 microbiology, business.industry, Drug resistance, Drug interaction, Bioinformatics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, 03 medical and health sciences, Medicine, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Medical prescription, business, Set (psychology), HIV drug resistance, 030304 developmental biology
Abstract: International audience; The HIV-PDI resource was designed and implemented to address the problems of drug resistance with a central focus on the 3D structure of the target-drug interaction. Clinical and biological data, structural and physico-chemical information and 3D interaction data concerning the targets (HIV protease) and the drugs (ARVs) were meticulously integrated and combined with tools dedicated to study HIV mutations and their consequences on the efficacy of drugs. Here, the capabilities of the HIV-PDI resource are demonstrated for several different scenarios ranging from retrieving information associated with patients to analyzing structural data relating cognate proteins and ligands. HIV-PDI allows such diverse data to be correlated, especially data linking antiretroviral drug (ARV) resistance to a given treatment with changes in three-dimensional interactions between a drug molecule and the mutated protease. Our work is based on the assumption that ARV resistance results from a loss of affinity between the mutated HIV protease and a drug molecule due to subtle changes in the nature of the protein-ligand interaction. Therefore, a set of patients whose resistance to first line treatment was corrected by a second line treatment was selected from the HIV-PDI database for detailed study, and several queries regarding these patients are processed via its graphical user interface. Considering the protease mutations found in the selected set of patients, our retrospective analysis was able to establish in most cases that the first line treatment was not suitable, and it predicted a second line treatment which agreed perfectly with the clincian's prescription. The present study demonstrates the capabilities of HIV-PDI. We anticipate that this decision support tool will help clinicians and researchers find suitable HIV treatments for individual patients. The HIVPDI database is thereby useful as a system of data collection allowing interpretation on the basis of all available information, thus helping in possible decision-makings.
Published: 2011
Full Text: View/download PDF

25. Toward the development of an effective vaccine against contagious bovine pleuropneumoniae (CBPP) using synthetic genomics approaches

Author: Vashee, Sanjay, Lartigue, Carole, Jores, Joerg, Chandran, Suchismita, Schieck, Elise, Ssajjakambwe, Paul, Glass, John I., Sirand-Pugnet, Pascal, Nene, Vishvanath, Blanchard, Alain, The J. Craig Venter Institute (JCVI), The J. Craig Venter Institute, Génomique, développement et pouvoir pathogène (GD2P), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), International Livestock Research Institute [CGIAR, Nairobi] (ILRI), International Livestock Research Institute [CGIAR, Ethiopie] (ILRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), and Lartigue, Carole
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2010

26. The Ectocarpus genome and the independent evolution of multicellularity in brown algae

Author: Jean-Marc Aury, Frithjof C. Küpper, Diego Miranda-Saavedra, John H. F. Bothwell, Claire Jubin, Chris Bowler, Bernhard Gschloessl, James W. Tregear, Andrés Ritter, Andrew E. Allen, Carolyn A. Napoli, Ludovic Delage, Bernard Kloareg, Takahiro Yamagishi, Pi Nyvall-Collén, Svenja Heesch, Julia Morales, Gaelle Samson, Kei Kimura, Ga Youn Cho, Grigoris D. Amoutzias, Yves Van de Peer, Simon M. Dittami, Kenny Billiau, Julie Poulain, François Artiguenave, Sylvie Doulbeau, Marek Eliáš, Bank Beszteri, Carl J. Carrano, Daniel Lang, Florian Maumus, Stefan A. Rensing, Jonathan H. Badger, Béatrice Segurens, Martina Strittmatter, Sylvie Rousvoal, Hervé Moreau, Patrice Lerouge, Colin Brownlee, Betsy Read, Akira F. Peters, J. Mark Cock, Corinne Da Silva, Declan C. Schroeder, Catherine Boyen, Pierre Rouzé, Eric Bonnet, Jonas Collén, Susana M. Coelho, Aude Le Bail, Kamel Jabbari, David R. Nelson, Thierry Tonon, Pascal J. Lopez, Véronique Anthouard, Hadi Quesneville, Manoj P. Samanta, Delphine Scornet, Klaus Valentin, Nicolas Delaroque, Bénédicte Charrier, Cindy Martens, Peter von Dassow, Martin Lohr, Garry Farnham, Chikako Nagasato, Claire M. M. Gachon, Gurvan Michel, Lieven Sterck, Philippe Potin, Erwan Corre, Catherine Leblanc, Taizo Motomura, Cyril Pommier, Patrick Wincker, Hiroshi Kawai, Publica, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, State University of Ghent, J Craig Venter Institute, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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)-Université Paris-Saclay, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Marine Biological Association, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), San Diego State University (SDSU), Phophorylation de protéines et Pathologies Humaines (P3H), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Diversité et adaptation des plantes cultivées (UMR DIAPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Charles University [Prague], Scottish Association for Marine Science (SAMS), Kobe University, Institute of Algological Research [Muroran], Hokkaido University, Fakultät für Biologie = Faculty of Biology [Freiburg], Albert-Ludwigs-Universität Freiburg, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Johannes Gutenberg - Universität Mainz (JGU), École normale supérieure - Paris (ENS Paris), Institut de biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Haematology, University of Cambridge [UK] (CAM), Mer et santé (MS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Arizona, The University of Tennessee Health Science Center [Memphis] (UTHSC), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), California State University [Los Angeles] (CAL STATE LA), Laboratoire de Biotechnologie et Chimie Marines (LBCM), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Systemix Institute, Savelli, Bruno, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), J. Craig Venter Institute, Université Paris-Saclay-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 de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Fraunhofer Institute for Cell Therapy and Immunology (Fraunhofer IZI), Fraunhofer (Fraunhofer-Gesellschaft), Charles University [Prague] (CU), Hokkaido University [Sapporo, Japan], Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Université Paris sciences et lettres (PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris
Subjects: 0106 biological sciences, Lineage (evolution), Molecular Sequence Data, Phaeophyta, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, Algae, [SDV.BDD] Life Sciences [q-bio]/Development Biology, Botany, BIOLOGIE CELLULAIRE, Animals, 14. Life underwater, [SDV.BDD]Life Sciences [q-bio]/Development Biology, flore marine, Phylogeny, Organism, ComputingMilieux_MISCELLANEOUS, phéophycées, 030304 developmental biology, 0303 health sciences, Multidisciplinary, biology, Ectocarpus siliculosus, Algal Proteins, Eukaryota, Pigments, Biological, Ectocarpus, 15. Life on land, biology.organism_classification, Biological Evolution, Brown algae, Multicellular organism, Evolutionary biology, algues brunes, Biologie, Signal Transduction, 010606 plant biology & botany
Abstract: Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further. © 2010 Macmillan Publishers Limited. All rights reserved.
Published: 2010
Full Text: View/download PDF

27. A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite, Plasmodium falciparum

Author: Jacques Prudhomme, Henri Vial, Choukri Ben Mamoun, Hugues Ahiboh, Jeffrey R. Johnson, Karine G. Le Roch, Kerstin Henson, David Plouffe, William H. Witola, Elizabeth A. Winzeler, John R. Yates, Duk Won D. Chung, Yingyao Zhou, instituto Geofísico, Escuela Politécnica Nacional (EPN), British Antarctic Survey (BAS), Natural Environment Research Council (NERC), J Craig Venter Institute, J. Craig Venter Institute, Centre de génétique et de physiologie moléculaire et cellulaire (CGPhiMC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences [Beijing] (CAS), Department of Ecology and Evolutionary Biology, University of Kansas [Lawrence] (KU), Ningbo Institute of Technology (NIT), Department of Molecular Biology [San Diego], The Scripps Research Institute [La Jolla], University of California [San Diego] (UC San Diego), University of California-University of California-University of California [San Diego] (UC San Diego), University of California-University of California, Dynamique des interactions membranaires normales et pathologiques (DIMNP), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Montpellier 1 (UM1), Dynamique moléculaire des interactions membranaires (DMIM), and Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)
Subjects: Erythrocytes, Proteome, Transcription, Genetic, Transferases (Other Substituted Phosphate Groups), MESH: Cell Cycle, Drug resistance, Medical and Health Sciences, Choline, Transcriptome, chemistry.chemical_compound, Tandem Mass Spectrometry, MESH: Reverse Transcriptase Polymerase Chain Reaction, 2.2 Factors relating to the physical environment, Parasite hosting, MESH: Animals, Aetiology, MESH: Plasmodium falciparum, Cells, Cultured, Oligonucleotide Array Sequence Analysis, 0303 health sciences, Cultured, Reverse Transcriptase Polymerase Chain Reaction, MESH: Erythrocytes, Cell Cycle, MESH: Choline, Biological Sciences, 3. Good health, MESH: Proteome, Infectious Diseases, Biochemistry, 5.1 Pharmaceuticals, Ethanolamines, Protozoan, Phosphatidylcholines, MESH: RNA, Protozoan, Development of treatments and therapeutic interventions, medicine.symptom, Infection, Transcription, Algorithms, RNA, Protozoan, Biotechnology, MESH: Cells, Cultured, Research Article, lcsh:QH426-470, Bioinformatics, lcsh:Biotechnology, Cells, Plasmodium falciparum, MESH: Thiazoles, MESH: Algorithms, Biology, MESH: Ethanolamines, 03 medical and health sciences, MESH: Gene Expression Profiling, Antimalarials, Rare Diseases, Genetic, Transferases, Phosphatidylcholine, lcsh:TP248.13-248.65, Information and Computing Sciences, Genetics, medicine, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Nutrition, 030304 developmental biology, MESH: Humans, 030306 microbiology, MESH: Transcription, Genetic, Gene Expression Profiling, MESH: Tandem Mass Spectrometry, Lipid metabolism, MESH: Phosphatidylcholines, biology.organism_classification, MESH: Antimalarials, Malaria, Vector-Borne Diseases, lcsh:Genetics, Thiazoles, Good Health and Well Being, chemistry, Mechanism of action, MESH: Oligonucleotide Array Sequence Analysis, RNA, MESH: Transferases (Other Substituted Phosphate Groups)
Abstract: Background In recent years, a major increase in the occurrence of drug resistant falciparum malaria has been reported. Choline analogs, such as the bisthiazolium T4, represent a novel class of compounds with strong potency against drug sensitive and resistant P. falciparum clones. Although T4 and its analogs are presumed to target the parasite's lipid metabolism, their exact mechanism of action remains unknown. Here we have employed transcriptome and proteome profiling analyses to characterize the global response of P. falciparum to T4 during the intraerythrocytic cycle of this parasite. Results No significant transcriptional changes were detected immediately after addition of T4 despite the drug's effect on the parasite metabolism. Using the Ontology-based Pattern Identification (OPI) algorithm with an increased T4 incubation time, we demonstrated cell cycle arrest and a general induction of genes involved in gametocytogenesis. Proteomic analysis revealed a significant decrease in the level of the choline/ethanolamine-phosphotransferase (PfCEPT), a key enzyme involved in the final step of synthesis of phosphatidylcholine (PC). This effect was further supported by metabolic studies, which showed a major alteration in the synthesis of PC from choline and ethanolamine by the compound. Conclusion Our studies demonstrate that the bisthiazolium compound T4 inhibits the pathways of synthesis of phosphatidylcholine from choline and ethanolamine in P. falciparum, and provide evidence for post-transcriptional regulations of parasite metabolism in response to external stimuli.
Published: 2008
Full Text: View/download PDF

28. Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria

Author: Carole Dossat, David J. Scanlan, Sophie Mazard, Steve Ferriera, Frédéric Partensky, Patrick Wincker, Martin Ostrowski, Brian Palenik, Justin Johnson, Ian T. Paulsen, Alexis Dufresne, Laurence Garczarek, Anton F. Post, Wolfgang R. Hess, Nicole Tandeau de Marsac, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Department of Biological Sciences, Warwick, University of Warwick [Coventry], Scripps Institution of Oceanography (SIO - UC San Diego), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Department of Chemistry and Biomolecular Sciences, Macquarie University, Collection des Cyanobactéries, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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)-Université Paris-Saclay-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), J Craig Venter Institute, J. Craig Venter Institute, Interuniversity Institute for Marine Science, Hebrew University, Faculty of Biology, Freiburg, University of Freiburg [Freiburg], Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Scripps Institution of Oceanography (SIO), University of California-University of California, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and 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)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: Cyanobacteria, Gene Transfer, Horizontal, Bioinformatics, [SDE.MCG]Environmental Sciences/Global Changes, DIVERSITY, Biology, SYNECHOCOCCUS ECOTYPES, MESH: Genome, Bacterial, 03 medical and health sciences, Genus, Photic zone, Seawater, PHYLOGENETIC ANALYSIS, 14. Life underwater, Clade, MAXIMUM-LIKELIHOOD, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, 030304 developmental biology, ATLANTIC-OCEAN, Ecological niche, Synechococcus, 0303 health sciences, SEA, 030306 microbiology, Ecology, Research, fungi, QK, Niche differentiation, MESH: Seawater, biology.organism_classification, NORTH-ATLANTIC, PROCHLOROCOCCUS ECOTYPES, MESH: Gene Transfer, Horizontal, MESH: Synechococcus, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Habitat, Evolutionary biology, NE ATLANTIC, COMMUNITY STRUCTURE, Genome, Bacterial
Abstract: Local niche occupancy of marine Synechococcus lineages is facilitated by lateral gene transfers. Genomic islands act as repositories for these transferred genes., Background The picocyanobacterial genus Synechococcus occurs over wide oceanic expanses, having colonized most available niches in the photic zone. Large scale distribution patterns of the different Synechococcus clades (based on 16S rRNA gene markers) suggest the occurrence of two major lifestyles ('opportunists'/'specialists'), corresponding to two distinct broad habitats ('coastal'/'open ocean'). Yet, the genetic basis of niche partitioning is still poorly understood in this ecologically important group. Results Here, we compare the genomes of 11 marine Synechococcus isolates, representing 10 distinct lineages. Phylogenies inferred from the core genome allowed us to refine the taxonomic relationships between clades by revealing a clear dichotomy within the main subcluster, reminiscent of the two aforementioned lifestyles. Genome size is strongly correlated with the cumulative lengths of hypervariable regions (or 'islands'). One of these, encompassing most genes encoding the light-harvesting phycobilisome rod complexes, is involved in adaptation to changes in light quality and has clearly been transferred between members of different Synechococcus lineages. Furthermore, we observed that two strains (RS9917 and WH5701) that have similar pigmentation and physiology have an unusually high number of genes in common, given their phylogenetic distance. Conclusion We propose that while members of a given marine Synechococcus lineage may have the same broad geographical distribution, local niche occupancy is facilitated by lateral gene transfers, a process in which genomic islands play a key role as a repository for transferred genes. Our work also highlights the need for developing picocyanobacterial systematics based on genome-derived parameters combined with ecological and physiological data.
Published: 2008
Full Text: View/download PDF

29. The $Phaeodactylum$ genome reveals the evolutionary history of diatom genomes

Author: Yves Van de Peer, Michael R. Sussman, Frédéric Verret, Miyoshi Haruta, Angela Falciatore, John A. Berges, Leszek Rychlewski, Anusuya Willis, Richard E. Jorgensen, Michael Katinka, Jane Grimwood, Betina M. Porcel, Magali Siaut, Klaus Valentin, Pascal J. Lopez, Marc Heijde, Véronique Martin-Jézéquel, Jean-Louis Petit, Wim Vyverman, Edda Rayko, Klaas Vandepoele, Miroslav Oborník, Anthony Chiovitti, Alan Kuo, E. Virginia Armbrust, Matthew Robison, Alessandra De Martino, Nils Kröger, Susan Lucas, Colin Brownlee, Alison Taylor, Igor V. Grigoriev, Jonathan H. Badger, Kamel Jabbari, Jérome Fournet, Jeremy Schmutz, Uma Maheswari, Sacha Coesel, Michele S. Stanley, J. Chris Detter, Chang Jae Choi, Thomas Mock, Assaf Vardi, Markus Lommer, Aaron Kaplan, Yolaine Joubert, Florian Maumus, Katerina Jiroutova, Anton Montsant, Colleen A. Durkin, Cindy Martens, Bank Beszteri, Micaela S. Parker, Asaf Salamov, Linda K. Medlin, Karen M. McGinnis, Ansgar Gruber, Marie J. J. Huysman, Manuela Mangogna, Lucyan S. Wyrwicz, Jean-Paul Cadoret, Peter von Dassow, Daniel S. Rokhsar, Marie-Pierre Oudot-Le Secq, Carolyn A. Napoli, Beverley R. Green, Erica Lindquist, Peter G. Kroth, Chris Bowler, Andrew E. Allen, Tatiana A. Rynearson, Nicole Poulsen, Bethany D. Jenkins, Harris Shapiro, Robert Otillar, Jean Weissenbach, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL), J. Craig Venter Institute, J. Craig Venter Institute [La Jolla, USA] (JCVI), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), DOE Joint Genome Institute [Walnut Creek], Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Institut de biologie de l'Ecole Normale Supérieure (IBENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Biologie moléculaire des organismes photosynthétiques (UMR8186), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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), Environnement, Bioénergie, Microalgues et Plantes (EBMP), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), 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)), Marine Biological Association, Physiologie et biotechnologie des Algues (PBA), Biotechnologies et Ressources Marines (BRM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratory of Ecology and Evolution of Plankton, Stazione Zoologica Anton Dohrn (SZN), Génomique des Microorganismes (LGM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Marine Biogeochemistry, Leibniz-Institut für Meereswissenschaften (IFM-GEOMAR), Biology Institute, University of Arizona, School of Oceanography [Seattle], University of Washington [Seattle], Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Station biologique de Roscoff [Roscoff] (SBR), European Project: 29849,DIATOMICS, Savelli, Bruno, Understanding Diatom Biology by Functional Genomics Approaches - DIATOMICS - 29849 - OLD, École normale supérieure - Paris (ENS Paris), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Bioénergie et Microalgues (EBM), 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), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Génomique des microorganismes, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)
Subjects: 0106 biological sciences, Thalassiosira pseudonana, Molecular Sequence Data, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, DNA, Algal, Phylogenetics, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, 14. Life underwater, Phaeodactylum tricornutum, Gene, 030304 developmental biology, Genetics, Diatoms, 0303 health sciences, Multidisciplinary, biology, Sequence Homology, Amino Acid, Heterokont, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, biology.organism_classification, Protein Structure, Tertiary, Diatom, Genes, Bacterial, Biologie, 010606 plant biology & botany, Signal Transduction
Abstract: Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (
Published: 2008
Full Text: View/download PDF

30. Functional metagenomic profiling of nine biomes

Author: Mary Ann Moran, Christina Nilsson, Beltran Rodriguez Brito, Rebecca Vega Thurber, Matthew Haynes, Forest Rohwer, Brandon K. Swan, Karen E. Nelson, Bryan A. White, Elizabeth A. Dinsdale, Yijun Ruan, Linda Wegley, Mya Breitbart, Robert Olson, Dana Hall, Rick Stevens, Christelle Desnues, Lauren D. McDaniel, Linlin Li, David L. Valentine, John H. Paul, Robert Edwards, Mike Furlan, Jennifer M. Brulc, Florent E. Angly, San Diego State University (SDSU), College of Marine Science [St Petersburg, FL], University of South Florida [Tampa] (USF), Department of Marine Sciences [Athens], University of Georgia [USA], The J. Craig Venter Institute (JCVI), The J. Craig Venter Institute, Genome Institute of Singapore (GIS), Mathematics and Computer Science Division [ANL] (MCS), Argonne National Laboratory [Lemont] (ANL), Department of Earth Science [Santa Barbara), University of California [Santa Barbara] (UC Santa Barbara), University of California (UC)-University of California (UC), University of Illinois, University of Illinois System, University of California [Santa Barbara] (UCSB), and University of California-University of California
Subjects: [SDV]Life Sciences [q-bio], Microbial metabolism, Genomics, Fresh Water, Genome, Viral, Biology, Genome, Microbiology, 03 medical and health sciences, Microbial ecology, Genome, Archaeal, Animals, Ecosystem, Seawater, Microbiome, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Bacteria, 030306 microbiology, Ecology, Chemotaxis, Gene Expression Profiling, Fishes, Biogeochemistry, Computational Biology, 15. Life on land, Anthozoa, Archaea, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Culicidae, Evolutionary biology, Metagenomics, Viruses, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genome, Bacterial
Abstract: Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.
Published: 2007

31. Genome transplantation in bacteria

Author: Lartigue, Carole, Glass, John I., Alperovitch, Nina, Pieper, Rembert, Parmar, Prashanth P., Hutchison 3rd, Clyde A, Smith, Hamilton O., Venter, J. Craig, The J. Craig Venter Institute (JCVI), The J. Craig Venter Institute, and Lartigue, Carole
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2007

32. Assessing diversity and biogeography of aerobic anoxygenic phototrophic bacteria in surface waters of the Atlantic and Pacific Oceans using the Global Ocean Sampling expedition metagenomes

Author: Oded Béjà, M. Weber, Marcelino T. Suzuki, Douglas B. Rusch, Hanno Teeling, Natalya Yutin, J. Craig Venter, National Center for Biotechnology Information (NCBI), Technion - Israel Institute of Technology [Haifa], University of Maryland Center for Environmental Science (UMCES), University of Maryland System, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), PIERRE FABRE-EDF (EDF)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, The J. Craig Venter Institute (JCVI), and The J. Craig Venter Institute
Subjects: Biogeography, Biodiversity, Biology, Bacterial Physiological Phenomena, Microbiology, 03 medical and health sciences, Abundance (ecology), [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Seawater, 14. Life underwater, Atlantic Ocean, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Pacific Ocean, 030306 microbiology, Ecology, Pelagic zone, Bacterioplankton, Pigments, Biological, Sequence Analysis, DNA, Anoxygenic photosynthesis, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Aerobiosis, Bacteria, Aerobic, Phototrophic Processes, 13. Climate action, Aerobic anoxygenic phototrophic bacteria, Photosynthetic bacteria, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Aerobic anoxygenic photosynthetic bacteria (AAnP) were recently proposed to be significant contributors to global oceanic carbon and energy cycles. However, AAnP abundance, spatial distribution, diversity and potential ecological importance remain poorly understood. Here we present metagenomic data from the Global Ocean Sampling expedition indicating that AAnP diversity and abundance vary in different oceanic regions. Furthermore, we show for the first time that the composition of AAnP assemblages change between different oceanic regions with specific bacterial assemblages adapted to open ocean or coastal areas respectively. Our results support the notion that marine AAnP populations are complex and dynamic and compose an important fraction of bacterioplankton assemblages in certain oceanic areas.
Published: 2007
Full Text: View/download PDF

33. Genetic Engineering in Marine Diatoms: Current Practices and Emerging Technologies

Author: Mark Moosburner, Andrew E. Allen, Fayza Daboussi, University of California [San Diego] (UC San Diego), University of California (UC), J. Craig Venter Institute [La Jolla, USA] (JCVI), Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Génie génétique, Diatomées, [SDV]Life Sciences [q-bio], Biologie synthétique
Abstract: International audience; Diatom ecology, physiology, and biotechnology research has been bolstered by the development of genetic engineering practices. The whole genome sequencing of two diatom species, Thalassiosira pseudonana and Phaeodactylum tricornutum, has greatly aided in shaping these into laboratory models by allowing researchers to characterize gene-expression and regulatory elements that are essential tools for synthetic biology and genetic engineering technologies. Tools that have been previously developed for other model organisms (yeasts, plants, animals), including gene overexpression, gene silencing, and targeted mutagenesis methods such as CRISPR-Cas9 have been quickly adapted for diatom research. Implementation of these tools relies on nucleic acid transformation methods to deliver the genetic payload to the diatom, be it particle bombardment or bacterial-mediated conjugation. Currently, more diatom species that may have alternative ecological relevance or attractive physiological or biochemical attributes in diatom biology, such as cold-adaptation or a benthic life-cycle are entering the genetic engineering fold. The breadth of molecular and genetic engineering tools employed in diatoms are reviewed here.
Published: 2022
Full Text: View/download PDF

34. Plankton Planet: A frugal, cooperative measure of aquatic life at the planetary scale

Author: de Vargas, Colomban, Le Bescot, Noan, Pollina, Thibaut, Henry, Nicolas, Romac, Sarah, Colin, Sébastien, Haëntjens, Nils, Carmichael, Margaux, Berger, Calixte, Le Guen, David, Decelle, Johan, Mahé, Frédéric, Poulain, Julie, Malpot, Emmanuel, Beaumont, Carole, Hardy, Michel, Guiffant, Damien, Probert, Ian, Gruber, David, Allen, Andrew, Gorsky, Gabriel, Follows, Michael, Pochon, Xavier, Troublé, Romain, Cael, B., Lombard, Fabien, Boss, Emmanuel, Prakash, Manu, Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), ECOlogy of MArine Plankton (ECOMAP), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Bioengineering, Stanford University, Stanford University, Max-Planck-Institut fur Biologie = Max Planck Institute for Biology [Tübingen], Max-Planck-Gesellschaft, University of Maine, Photosymbiose, 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), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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 de Montpellier (UM), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Moana New Zealand, Cawthron Aquaculture Park, On board ‘Folligou’, On board 'Taravana', Baruch College [CUNY], City University of New York [New York] (CUNY), J. Craig Venter Institute [La Jolla, USA] (JCVI), Scripps Institution of Oceanography (SIO - UC San Diego), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Massachusetts Institute of Technology (MIT), University of Auckland [Auckland], Cawthron Institute, Fondation Tara Ocean, National Oceanography Centre [Southampton] (NOC), University of Southampton, Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), The ‘Plankton Arts’ grant from the Fondation d’Entreprise Total, The New Zealand Royal Society Dumont-D’Urville (DDU-CAW1501), Strategic Seeding (16-CAW-008-CSG) Funds, The Cawthron Institute, Okeanos Foundation, Tara Ocean Foundation, Schmidt Futures Foundation, ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), and ANR-17-CE02-0020,CORALGENE,Complexité génomique de l'holobionte ' corail ' à l'échelle du Pacifique(2017)
Subjects: Global and Planetary Change, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Ocean Engineering, Aquatic Science, Oceanography, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Water Science and Technology
Abstract: In every liter of seawater there are between 10 and 100 billion life forms, mostly invisible, called marine plankton or marine microbiome, which form the largest and most dynamic ecosystem on our planet, at the heart of global ecological and economic processes. While physical and chemical parameters of planktonic ecosystems are fairly well measured and modeled at the planetary scale, biological data are still scarce due to the extreme cost and relative inflexibility of the classical vessels and instruments used to explore marine biodiversity. Here we introduce ‘Plankton Planet’, an initiative whose goal is to engage the curiosity and creativity of researchers, makers, and mariners to (i) co-develop a new generation of cost-effective (frugal) universal scientific instrumentation to measure the genetic and morphological diversity of marine microbiomes in context, (ii) organize their systematic deployment through coastal or open ocean communities of sea-users/farers, to generate uniform plankton data across global and long-term spatio-temporal scales, and (iii) setup tools to flow the data without embargo into public and explorable databases. As proof-of-concept, we show how 20 crews of sailors were able to sample plankton biomass from the world surface ocean in a single year, generating the first seatizen-based, planetary dataset of marine plankton biodiversity based on DNA barcodes. The quality of this dataset is comparable to that generated by Tara Oceans and is not biased by the multiplication of samplers. The data unveil significant genetic novelty and can be used to explore the taxonomic and ecological diversity of plankton at both regional and global scales. This pilot project paves the way for construction of a miniaturized, modular, evolvable, affordable and open-source citizen field-platform that will allow systematic assessment of the eco/morpho/genetic variation of aquatic ecosystems and microbiomes across the dimensions of the Earth system.
Published: 2022
Full Text: View/download PDF

35. Can direct extracellular electron transfer occur in the absence of outer membrane cytochromes in Desulfovibrio vulgaris?

Author: Gorby, Dr. [J. Craig Venter Institute]
Published: 2010

36. Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis

Author: Dupont, Christopher [Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla CA USA]
Published: 2014
Full Text: View/download PDF

37. Multiplex CRISPR/Cas9 editing of the long‐chain acyl‐CoA synthetase family in the diatom Phaeodactylum tricornutum reveals that mitochondrial ptACSL3 is involved in the synthesis of storage lipids

Author: Xiahui Hao, Wenchao Chen, Alberto Amato, Juliette Jouhet, Eric Maréchal, Daniel Moog, Hanhua Hu, Hu Jin, Lingjie You, Fenghong Huang, Mark Moosburner, Andrew E. Allen, Yangmin Gong, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Oil Crops, LIPID, 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), Laboratory for Cell Biology, Philipps-University Marburg, Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Scripps Institution of Oceanography (SIO), University of California [San Diego] (UC San Diego), University of California-University of California, J. Craig Venter Institute [La Jolla, USA] (JCVI), National Natural Science Foundation of China (41776175 and 31961133008), Agricultural Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences (CAAS-ASTIP-2013-OCRI), 2021 CEA-CAS bilateral program, Institut Carnot 3BCAR, Grants from the United States Department of Energy Genomics Science program, US National Science Foundation, NSF-MCB-1818390, Gordon and Betty Moore Foundation GBMF3828, ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-15-IDEX-0002,UGA,IDEX UGA(2015), Scripps Institution of Oceanography (SIO - UC San Diego), and University of California (UC)-University of California (UC)
Subjects: 0106 biological sciences, Diatoms, 0303 health sciences, Physiology, Fatty Acids, Multiplexed CRISPR/Cas9, Plant Science, Fatty acid, Long-chain acyl-CoA synthetase, 01 natural sciences, Phaeodactylum tricornutum, Triacylglycerol, Mitochondria, 03 medical and health sciences, Coenzyme A Ligases, Coenzyme A, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, CRISPR-Cas Systems, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; Long-chain acyl-CoA synthetases (LACSs) play diverse and fundamentally important roles in lipid metabolism. While their functions have been well-established in bacteria, yeast and plants, the mechanisms by which LACS isozymes regulate lipid metabolism in unicellular oil-producing microalgae, including the diatom Phaeodactylum tricornutum, remain largely unknown. In P. tricornutum, a family of five genes (ptACSL1~5) encodes LACS activities. We generated single lacs knockout/knockdown mutants using multiplexed CRISPR/Cas9 method, and determined their substrate specificities towards different fatty acids (FAs) and subcellular localizations. ptACSL3 is localized in the mitochondria and its disruption led to compromised growth and reduced triacylglycerol (TAG) content when cells were bubbled with air. The ptACSL3 mutants showed altered FA profiles in two galactoglycerolipids and phosphatidylcholine (PC) with significantly reduced distribution of 16:0 and 16:1. ptACSL5 is localized in the peroxisome and its knockdown resulted in reduced growth rate and altered molecular species of PC and TAG, indicating a role in controlling the composition of acyl-CoAs for lipid synthesis. Our work demonstrates the potential of generating gene knockout mutants with the mutation of large fragment deletion using multiplexed CRISPR/Cas9 and provides insight into the functions of LACS isozymes in lipid metabolism in the oleaginous microalgae.
Published: 2021
Full Text: View/download PDF

38. Machine Learning-Based Single Cell and Integrative Analysis Reveals That Baseline mDC Predisposition Correlates With Hepatitis B Vaccine Antibody Response

Author: Brian D. Aevermann, Casey P. Shannon, Mark Novotny, Rym Ben-Othman, Bing Cai, Yun Zhang, Jamie C. Ye, Michael S. Kobor, Nicole Gladish, Amy Huei-Yi Lee, Travis M. Blimkie, Robert E. Hancock, Alba Llibre, Darragh Duffy, Wayne C. Koff, Manish Sadarangani, Scott J. Tebbutt, Tobias R. Kollmann, Richard H. Scheuermann, J. Craig Venter Institute [La Jolla, USA] (JCVI), St. Paul’s Hospital - University of British Columbia [Vancouver, BC, Canada], University of British Columbia (UBC), The University of Western Australia (UWA), Simon Fraser University (SFU.ca), Immunologie Translationnelle - Translational Immunology lab, Institut Pasteur [Paris], Human Vaccines Project [New York], BC Children's Hospital Research Institute [Vancouver, BC, Canada] (BCCHR), University of California [San Diego] (UC San Diego), University of California, La Jolla Institute for Immunology [La Jolla, CA, États-Unis], This work was supported by the Human Vaccines Project. Additional funding from the Canadian Institutes for Health Research FDN-154287 to RH is gratefully acknowledged. RH holds a Canada Research Chair and a UBC Killam Professorship. DD acknowledges support from the Milieu Interieur Consortium., St. Paul’s Hospital - University of British Columbia [Vancouver, BC, Canada] (SPH-UBC), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), and University of California (UC)
Subjects: Male, Endotype, medicine.disease_cause, computer.software_genre, 0302 clinical medicine, baseline correlates, Immunology and Allergy, Medicine, MESH: High-Throughput Nucleotide Sequencing, MESH: Hepatitis B Antibodies, Original Research, canonical correlation analysis, MESH: Aged, 0303 health sciences, MESH: Middle Aged, MESH: Machine Learning, MESH: Dendritic Cells, Vaccination, High-Throughput Nucleotide Sequencing, Middle Aged, vaccines, Hepatitis B, 3. Good health, MESH: Canonical Correlation Analysis, machine learning, endotypes, 030220 oncology & carcinogenesis, Host-Pathogen Interactions, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, Single-Cell Analysis, MESH: Vaccine Efficacy, Adult, Hepatitis B vaccine, Immunology, Vaccine Efficacy, Machine learning, 03 medical and health sciences, MESH: Gene Expression Profiling, Immune system, single cell RNA sequencing, Humans, Hepatitis B Vaccines, dendritic cells, Hepatitis B Antibodies, 030304 developmental biology, Aged, Hepatitis B virus, MESH: Hepatitis B Vaccines, Innate immune system, MESH: Humans, MESH: Hepatitis B, business.industry, Gene Expression Profiling, MESH: Host-Pathogen Interactions, MESH: Adult, Dendritic cell, MESH: Vaccination, RC581-607, MESH: Male, Immunization, Artificial intelligence, Immunologic diseases. Allergy, business, computer, MESH: Female, MESH: Single-Cell Analysis
Abstract: International audience; Vaccination to prevent infectious disease is one of the most successful public health interventions ever developed. And yet, variability in individual vaccine effectiveness suggests that a better mechanistic understanding of vaccine-induced immune responses could improve vaccine design and efficacy. We have previously shown that protective antibody levels could be elicited in a subset of recipients with only a single dose of the hepatitis B virus (HBV) vaccine and that a wide range of antibody levels were elicited after three doses. The immune mechanisms responsible for this vaccine response variability is unclear. Using single cell RNA sequencing of sorted innate immune cell subsets, we identified two distinct myeloid dendritic cell subsets (NDRG1-expressing mDC2 and CDKN1C-expressing mDC4), the ratio of which at baseline (pre-vaccination) correlated with the immune response to a single dose of HBV vaccine. Our results suggest that the participants in our vaccine study were in one of two different dendritic cell dispositional states at baseline – an NDRG2-mDC2 state in which the vaccine elicited an antibody response after a single immunization or a CDKN1C-mDC4 state in which the vaccine required two or three doses for induction of antibody responses. To explore this correlation further, genes expressed in these mDC subsets were used for feature selection prior to the construction of predictive models using supervised canonical correlation machine learning. The resulting models showed an improved correlation with serum antibody titers in response to full vaccination. Taken together, these results suggest that the propensity of circulating dendritic cells toward either activation or suppression, their “dispositional endotype” at pre-vaccination baseline, could dictate response to vaccination.
Published: 2021
Full Text: View/download PDF

39. Advancing respiratory-cardiovascular physiology with the working heart-brainstem preparation over 25 years

Author: Julian F. R. Paton, Benedito H. Machado, Davi J. A. Moraes, Daniel B. Zoccal, Ana P. Abdala, Jeffrey C. Smith, Vagner R. Antunes, David Murphy, Mathias Dutschmann, Rishi R. Dhingra, Robin McAllen, Anthony E. Pickering, Richard J. A. Wilson, Trevor A. Day, Nicole O. Barioni, Andrew M. Allen, Clément Menuet, Joseph Donnelly, Igor Felippe, Walter M. St‐John, Department of Economics, University of Wisconsin, UCL, Institute of Neurology [London], Centre de recherche en neurobiologie - neurophysiologie de Marseille (CRN2M), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Mount Royal/Mount Royal University [Calgary, AB, Canada] (MRU), J. Craig Venter Institute [La Jolla, USA] (JCVI), University of California [San Diego] (UC San Diego), University of California (UC), Institut de Neurobiologie de la Méditerranée [Aix-Marseille Université] (INMED - INSERM U1249), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), and A.P.A. -R01 AT008632 -CRCNS. A.M.A. -Australian Research Council (DP170104582) and Australian National Health and Medical Research Council (APP1156727). V.R.A. Sao Paulo Research Foundation (FAPESP 2019/19894-8) and National Council for Development of Science and Technology (CNPq -Research Fellow: no. 304970/2017-4). R.R.D. -National Institutes of Health (U01 EB021960). J.D. -Clinical Fellowship from the Neurological Foundation of New Zealand. I.S.A.F. -University of Auckland PhD scholarship. B.H.M. Sao Paulo Research Foundation (FAPESP-2018/15957-2) and the National Council for Development of Science and Technology (CNPq-309338/2020-4). C.M. -Agence Nationale de la Recherche (ANR-21-CE14-0009-01). D.J.A.M. -FAPESP (2019/11863-6 and 2021/06886-7) and CNPq (437375/2018-8 and 313719/2020-9). J.F.R.P. -Health Research Council of New Zealand (19/687) and the Sidney Taylor Trust. A.E.P. was funded by a Wellcome Trust Clinical research fellowship. J.C.S. -Intramural Research Program of the NIH, NINDS. T.A.D. -Natural Sciences and Engineering Research Council of Canada Discovery grants (NSERC RGPIN-2016-04915). R.J.A. W. -Canada Institute of Health Research (CIHR201603PJT/366421). N.O.B. -SIDS Calgary Society.
Subjects: gasp, hypertension, hypoxia, Physiology, [SDV]Life Sciences [q-bio], chemoreceptor, Respiration, respiratory rhythm generation, Kölliker–Fuse, Heart, cardiac ganglion, sympathetic, sympathetic-respiratory coupling, Rats, RATOS, Cardiovascular Physiological Phenomena, Mice, eupnoea, Animals, cardiac vagus, pre-Bötzingercomplex, Lung, Anaesthesia Pain and Critical Care, Brain Stem
Abstract: Twenty-five years ago, a new physiological preparation called the working heart–brainstem preparation (WHBP) was introduced with the claim it would provide a new platform allowing studies not possible before in cardiovascular, neuroendocrine, autonomic and respiratory research. Herein, we review some of the progress made with the WHBP, some advantages and disadvantages along with potential future applications, and provide photographs and technical drawings of all the customised equipment used for the preparation. Using mice or rats, the WHBP is an in situ experimental model that is perfused via an extracorporeal circuit benefitting from unprecedented surgical access, mechanical stability of the brain for whole cell recording and an uncompromised use of pharmacological agents akin to in vitro approaches. The preparation has revealed novel mechanistic insights into, for example, the generation of distinct respiratory rhythms, the neurogenesis of sympathetic activity, coupling between respiration and the heart and circulation, hypothalamic and spinal control mechanisms, and peripheral and central chemoreceptor mechanisms. Insights have been gleaned into diseases such as hypertension, heart failure and sleep apnoea. Findings from the in situ preparation have been ratified in conscious in vivo animals and when tested have translated to humans. We conclude by discussing potential future applications of the WHBP including two-photon imaging of peripheral and central nervous systems and adoption of pharmacogenetic tools that will improve our understanding of physiological mechanisms and reveal novel mechanisms that may guide new treatment strategies for cardiorespiratory diseases.
Published: 2021
Full Text: View/download PDF

40. A community resource for paired genomic and metabolomic data mining

Author: Lars Ridder, Tim S. Bugni, Jamshid Amiri Moghaddam, Florian Huber, Elke Dittmann, Kelly C. Weldon, Louis-Félix Nothias, Douglas Sweeney, Mingxun Wang, Paul R. Jensen, Letícia V. Costa-Lotufo, Christine Beemelmanns, Katherine R. Duncan, Nadine Ziemert, Xuanji Li, Dulce G. Guillén Matus, Chao Du, Neha Garg, Jae Seoun Hur, Elizabeth I. Parkinson, Raphael Reher, Nicholas J. Tobias, Alex A. Blacutt, Emily C Pierce, Michelle Schorn, J. Michael Beman, Simon Rogers, María Victoria Berlanga-Clavero, Martin Baunach, Fan Zhang, Deepa D. Acharya, Harald Gross, Hamada Saad, M. Caroline Roper, Anna Edlund, Jason M. Crawford, Daniel Petras, Alexandra Calteau, Benjamin-Florian Hempel, Seoung Rak Lee, Max Crüsemann, Neil L. Kelleher, Hosein Mohimani, David P. Fewer, Shaurya Chanana, Carmen Saenz, Lena Gerwick, Ki-Hyun Kim, Roderich D. Süssmuth, Jörn Piel, Diego Romero, Marnix H. Medema, Anelize Bauermeister, Christopher Drozd, Regan J. Thomson, Anne Boullie, Michael W. Mullowney, Karine Pires, Andrew C. McAvoy, Alexander A. Aksenov, Saefuddin Aziz, Raquel Castelo-Branco, Julia M. Gauglitz, Mitchell N. Muskat, Bart Cuypers, Emily C. Gentry, Yi Yuan Lee, Eric J. N. Helfrich, Tam Dang, Pieter C. Dorrestein, Liu Cao, Rachel J. Dutton, Gilles P. van Wezel, Helge B. Bode, Margherita Sosio, Asker Daniel Brejnrod, Gajender Aleti, Leonard Kaysser, Amaro E. Trindade-Silva, Willam W. Metcalf, Irina Koester, Tiago Leao, Katherine D. Bauman, Jessica C. Little, Evgenia Glukhov, Ellis C. O’Neill, Justin J. J. van der Hooft, Alyssa M. Demko, Alexander B. Chase, Marc G. Chevrette, Bradley S. Moore, Christian Martin H, Kapil Tahlan, Cameron R. Currie, Allegra T. Aron, Muriel Gugger, Kyo Bin Kang, Víctor J. Carrión, Michael J. Rust, Gabriele M. König, Carlos Molina-Santiago, Søren J. Sørensen, Marianna Iorio, Jean-Claude Dujardin, Daniel Männle, Chung Sub Kim, Laura M. Sanchez, Katherine N. Maloney, Stefan Verhoeven, Tristan de Rond, Wageningen University and Research [Wageningen] (WUR), Netherlands eScience Center, University of Wisconsin-Madison, University of California [San Diego] (UC San Diego), University of California, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knoell Institute), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Jenderal Soedirman University [Purwokerto, Indonesia], Universidade de São Paulo (USP), University of Potsdam, University of California [Merced], Universidad de Málaga [Málaga] = University of Málaga [Málaga], University of California [Riverside] (UCR), Goethe-University Frankfurt am Main, Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association, Max Planck Institute for Terrestrial Microbiology, Max-Planck-Gesellschaft, Collection des Cyanobactéries, Institut Pasteur [Paris], Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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)-Université Paris-Saclay, Carnegie Mellon University [Pittsburgh] (CMU), Leiden University, Netherlands Institute of Ecology (NIOO-KNAW), Universidade do Porto, University of Helsinki, Yale University [New Haven], Yale University School of Medicine, University of Antwerp (UA), Institute of Tropical Medicine [Antwerp] (ITM), Technische Universität Berlin (TU), J. Craig Venter Institute [La Jolla, USA] (JCVI), Instituto de Investigaciones Científicas y Servicios de Alta Tecnología [Panama], The research reported in this publication was supported by an ASDI eScience Grant (ASDI.2017.030) fromthe Netherlands eScience Center (to J.J.J.v.d.H. and M.H.M.), a National Institutes of Health (NIH) Genometo Natural Products Network supplementary award (no. U01GM110706 to M.H.M.), a Wageningen GraduateSchool Postdoc Talent Program fellowship (to M.A.S.), a Marie Sklodowska-Curie Individual Fellowship from the European Union (MSCA-IF-EF-ST-897121 to M.A.S.), the National Science Foundation (NSF) (1817955 to L.M.S. and 1817887 to R.J.D.), a Fundaçao para a Ciencia e Tecnologia (FCT) fellowship (SFRH/BD/136367/2018 to R.C.B.), the National Cancer Institute of the NIH (award no. F32CA221327 to M.W.M.), the University of California, San Diego, Scripps Institution of Oceanography, and two grant from the NIH (Awards GM118815 and 107550 to L.G.), and the National Center for Complementary and Integrative Health of the NIH (award no. R01AT009143 to R.J.T. and N.L.K.)., Microbial Ecology (ME), Department of Food and Nutrition, Department of Microbiology, Helsinki Institute of Sustainability Science (HELSUS), Microbial Natural Products, University of California (UC), Universidade de São Paulo = University of São Paulo (USP), University of Potsdam = Universität Potsdam, University of California [Merced] (UC Merced), University of California [Riverside] (UC Riverside), Institut Pasteur [Paris] (IP), Université Paris-Saclay-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), Universiteit Leiden, Universidade do Porto = University of Porto, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Yale School of Medicine [New Haven, Connecticut] (YSM), and Technical University of Berlin / Technische Universität Berlin (TU)
Subjects: Databases, Factual, Bioinformatics, Systems biology, Metabolite, [SDV]Life Sciences [q-bio], Genomics, Computational biology, Biology, Genome, Plan_S-Compliant-OA, 03 medical and health sciences, chemistry.chemical_compound, Databases, Metabolomics, Bioinformatica, Metabolome, Data Mining, Life Science, MolEco, Molecular Biology, QH426, 030304 developmental biology, 0303 health sciences, METABOLÔMICA, 030302 biochemistry & molecular biology, Comment, Cell Biology, DNA, Computational biology and bioinformatics, Chemistry, chemistry, international, Community resource, 1182 Biochemistry, cell and molecular biology, Identification (biology)
Abstract: International audience; Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.
Published: 2021
Full Text: View/download PDF

41. Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults

Author: Rym Ben-Othman, Bing Cai, Aaron C. Liu, Natallia Varankovich, Daniel He, Travis M. Blimkie, Amy H. Lee, Erin E. Gill, Mark Novotny, Brian Aevermann, Sibyl Drissler, Casey P. Shannon, Sarah McCann, Kim Marty, Gordean Bjornson, Rachel D. Edgar, David Tse Shen Lin, Nicole Gladish, Julia Maclsaac, Nelly Amenyogbe, Queenie Chan, Alba Llibre, Joyce Collin, Elise Landais, Khoa Le, Samantha M. Reiss, Wayne C. Koff, Colin Havenar-Daughton, Manraj Heran, Bippan Sangha, David Walt, Mel Krajden, Shane Crotty, Devin Sok, Bryan Briney, Dennis R. Burton, Darragh Duffy, Leonard J. Foster, William W. Mohn, Michael S. Kobor, Scott J. Tebbutt, Ryan R. Brinkman, Richard H. Scheuermann, Robert E. W. Hancock, Tobias R. Kollmann, Manish Sadarangani, BC Children's Hospital Research Institute [Vancouver, BC, Canada] (BCCHR), University of British Columbia (UBC), The University of Western Australia (UWA), Simon Fraser University (SFU.ca), J. Craig Venter Institute [La Jolla, USA] (JCVI), St. Paul’s Hospital - University of British Columbia [Vancouver, BC, Canada] (SPH-UBC), Immunologie Translationnelle - Translational Immunology lab, Institut Pasteur [Paris] (IP), The Scripps Research Institute [La Jolla, San Diego], La Jolla Institute for Immunology [La Jolla, CA, États-Unis], Human Vaccines Project [New York], Harvard Medical School [Boston] (HMS), St. Paul’s Hospital - University of British Columbia [Vancouver, BC, Canada], Institut Pasteur [Paris], The Scripps Research Institute [La Jolla], University of California [San Diego] (UC San Diego), and University of California-University of California
Subjects: lcsh:Immunologic diseases. Allergy, Adult, Male, 0301 basic medicine, Hepatitis B virus, Hepatitis B vaccine, Systems biology, Immunology, Computational biology, 03 medical and health sciences, 0302 clinical medicine, Immune system, Antibody Repertoire, Monitoring, Immunologic, Immunity, vaccine, Methods, Humans, Immunology and Allergy, Medicine, Hepatitis B Vaccines, Prospective Studies, Microbiome, bio-informatic, Aged, Whole blood, Aged, 80 and over, multi-omic, business.industry, Systems Biology, Vaccination, Middle Aged, lymph node, Hepatitis B, 3. Good health, single cell, Treatment Outcome, 030104 developmental biology, immunimonitoring, gene expression, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, lcsh:RC581-607, business, 030215 immunology
Abstract: International audience; Conventional vaccine design has been based on trial-and-error approaches, which have been generally successful. However, there have been some major failures in vaccine development and we still do not have highly effective licensed vaccines for tuberculosis, HIV, respiratory syncytial virus, and other major infections of global significance. Approaches at rational vaccine design have been limited by our understanding of the immune response to vaccination at the molecular level. Tools now exist to undertake in-depth analysis using systems biology approaches, but to be fully realized, studies are required in humans with intensive blood and tissue sampling. Methods that support this intensive sampling need to be developed and validated as feasible. To this end, we describe here a detailed approach that was applied in a study of 15 healthy adults, who were immunized with hepatitis B vaccine. Sampling included ~350 mL of blood, 12 microbiome samples, and lymph node fine needle aspirates obtained over a ~7-month period, enabling comprehensive analysis of the immune response at the molecular level, including single cell and tissue sample analysis. Samples were collected for analysis of immune phenotyping, whole blood and single cell gene expression, proteomics, lipidomics, epigenetics, whole blood response to key immune stimuli, cytokine responses, in vitro T cell responses, antibody repertoire analysis and the microbiome. Data integration was undertaken using different approaches-NetworkAnalyst and DIABLO. Our results demonstrate that such intensive sampling studies are feasible in healthy adults, and data integration tools exist to analyze the vast amount of data generated from a multi-omics systems biology approach. This will provide the basis for a better understanding of vaccine-induced immunity and accelerate future rational vaccine design.
Published: 2020
Full Text: View/download PDF

42. Mitochondrial fatty acid β‐oxidation is required for storage‐lipid catabolism in a marine diatom

Author: Andrew E. Allen, Denghui Xing, Mark Moosburner, Alexander R. Hughes, Denis Jallet, Graham Peers, Mark P. Simmons, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Colorado State University [Fort Collins] (CSU), Scripps Institution of Oceanography (SIO), University of California [San Diego] (UC San Diego), University of California-University of California, J. Craig Venter Institute, United States Department of Energy (DOE)DOE-DE-SC0008595DOE-DE-SC0018344, Fondation Bettencourt Schueller, Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Scripps Institution of Oceanography (SIO - UC San Diego), and University of California (UC)-University of California (UC)
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, Plant Science, Photosynthesis, 01 natural sciences, Phaeodactylum tricornutum, beta-oxidation, 03 medical and health sciences, lipid, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plastid, chemistry.chemical_classification, Diatoms, biology, Endosymbiosis, Catabolism, Fatty Acids, fungi, Fatty acid, Peroxisome, biology.organism_classification, Lipids, diatom, Mitochondria, 030104 developmental biology, Diatom, Biochemistry, chemistry, biofuel, Oxidation-Reduction, 010606 plant biology & botany
Abstract: International audience; Photoautotrophic growth in nature requires the accumulation of energy-containing molecules via photosynthesis during daylight to fuel nighttime catabolism. Many diatoms store photosynthate as the neutral lipid triacylglycerol (TAG). While the pathways of diatom fatty acid and TAG synthesis appear to be well conserved with plants, the pathways of TAG catabolism and downstream fatty acid beta-oxidation have not been characterised in diatoms.We identified a putative mitochondria-targeted, bacterial-type acyl-CoA dehydrogenase (PtMACAD1) that is present in Stramenopile and Hacrobian eukaryotes, but not found in plants, animals or fungi. Gene knockout, protein-YFP tags and physiological assays were used to determine PtMACAD1's role in the diatom Phaeodactylum tricornutum.PtMACAD1 is located in the mitochondria. Absence of PtMACAD1 led to no consumption of TAG at night and slower growth in light : dark cycles compared with wild-type. Accumulation of transcripts encoding peroxisomal-based beta-oxidation did not change in response to day : night cycles or to PtMACAD1 knockout. Mutants also hyperaccumulated TAG after the amelioration of N limitation.We conclude that diatoms utilise mitochondrial beta-oxidation; this is in stark contrast to the peroxisomal-based pathways observed in plants and green algae. We infer that this pattern is caused by retention of catabolic pathways from the host during plastid secondary endosymbiosis.
Published: 2020
Full Text: View/download PDF

43. Development of microsatellite markers for the carnivorous plant Genlisea aurea (Lentibulariaceae) using genomics data of NGS

Author: Alessandro M. Varani, Yani C. Aranguren-Díaz, Todd P. Michael, Vitor F. O. Miranda, Universidade Estadual Paulista (Unesp), Universidad Simón Bolívar, and J. Craig Venter Institute
Subjects: 0301 basic medicine, Lentibulariaceae, Plant genetics, Population, Conservation, Biology, Genetic diversity, Magnoliopsida, 03 medical and health sciences, Genetics, Computer Simulation, education, Molecular Biology, Phylogeny, education.field_of_study, High-Throughput Nucleotide Sequencing, Molecular markers, Genomics, Sequence Analysis, DNA, General Medicine, biology.organism_classification, SSR, Carnivory, Genetics, Population, 030104 developmental biology, Evolutionary biology, Genetic structure, Genlisea aurea, Microsatellite, Endemic species, Brazil, Genome, Plant, Genlisea, Microsatellite Repeats
Abstract: Made available in DSpace on 2018-12-11T17:17:02Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-02-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Genlisea aurea A.St.-Hil. is a carnivorous plant endemic species to Brazil in the Lentibulariaceae family. Very few studies have addressed the genetic structure and conservation status of G. aurea and the Lentibulariaceae. Microsatellites markers are advantageous tools that can be employed to predict the vulnerability of Lentibulariaceae species. Therefore, the development of molecular markers focusing the population analyses of Genlisea for future genetic studies and conservation actions are essential. Thus, we developed simple sequence repeats (SSRs) based on in silico analyses of G. aurea draft genome assembly. We characterized 40 individuals from several populations and identified 12 loci that were polymorphic, with heterozygosity between 0.123 and 0.650. We demonstrated that the G. aurea SSR markers work cross-species in Genlisea filiformis, G. repens, G. tuberosa and G. violacea. These markers will be important for future population, phylogeographic and conservation studies in G. aurea and other Genlisea species. Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias Jaboticabal Departamento de Biologia Aplicada à Agropecuária, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal Universidad Simón Bolívar Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias Jaboticabal Departamento de Tecnologia J. Craig Venter Institute, 4120 Capricorn Ln. Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias Jaboticabal Departamento de Biologia Aplicada à Agropecuária, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias Jaboticabal Departamento de Tecnologia CNPq: #309040/2014-0
Published: 2017
Full Text: View/download PDF

44. Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework

Author: Bram Vrancken, Alexander A. Fisher, Simon Dellicour, Sebastian Lequime, Louis du Plessis, Karthik Gangavarapu, Kristian G. Andersen, Mandev S. Gill, Nathan D. Grubaugh, Marius Gilbert, Paul Bastide, Oliver G. Pybus, Philippe Lemey, Marc A. Suchard, Nathaniel L. Matteson, Yi Tan, Martha I. Nelson, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, KU Leuven (KU Leuven), Spatial Epidemiology Lab (SpELL), Université libre de Bruxelles (ULB), Department of Immunology and Microbiology, The Scripps Research Institute, Scripps Research Institute, Infectious Diseases Group, J. Craig Venter Institute, Department of Medicine, Vanderbilt University [Nashville], Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK, Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, University of California [Los Angeles] (UCLA), University of California-University of California, Fogarty International Center, National Institutes of Health, Bethesda, MD, 20894, USA, Fielding School of Public Health, Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, The Scripps Translational Science Institute and The Scripps Research Institute, Department of Epidemiology of Microbial Diseases, and Yale School of Public Health (YSPH)
Subjects: 0106 biological sciences, 0301 basic medicine, viruses, General Physics and Astronomy, 01 natural sciences, Flyway, 2.2 Factors relating to the physical environment, Viral, Aetiology, lcsh:Science, Phylogeny, education.field_of_study, [STAT.AP]Statistics [stat]/Applications [stat.AP], Multidisciplinary, Genome, Viral Epidemiology, West nile virus, Sciences bio-médicales et agricoles, 3. Good health, Phylogenetics, Phylogeography, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Molecular ecology, Infection, West Nile virus, Viral epidemiology, Science, Population, Wildlife, Genome, Viral, Biology, Environment, 010603 evolutionary biology, Article, General Biochemistry, Genetics and Molecular Biology, Vaccine Related, 03 medical and health sciences, Rare Diseases, Biodefense, Genetics, Animals, Humans, education, Ecosystem, Ecological epidemiology, Genetic diversity, Bird Diseases, Prevention, Genetic Variation, General Chemistry, Vector-Borne Diseases, Emerging Infectious Diseases, Good Health and Well Being, 030104 developmental biology, Evolutionary biology, North America, Biological dispersal, lcsh:Q, West Nile Fever
Abstract: Computational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond historical reconstructions and use spatially-explicit phylogeographic and phylodynamic approaches to formally test epidemiological hypotheses. We illustrate our approach by focusing on the West Nile virus (WNV) spread in North America that has substantially impacted public, veterinary, and wildlife health. We apply an analytical workflow to a comprehensive WNV genome collection to test the impact of environmental factors on the dispersal of viral lineages and on viral population genetic diversity through time. We find that WNV lineages tend to disperse faster in areas with higher temperatures and we identify temporal variation in temperature as a main predictor of viral genetic diversity through time. By contrasting inference with simulation, we find no evidence for viral lineages to preferentially circulate within the same migratory bird flyway, suggesting a substantial role for non-migratory birds or mosquito dispersal along the longitudinal gradient., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2020
Full Text: View/download PDF

45. Budding yeast as a factory to engineer partial and complete microbial genomes

Author: Sanjay Vashee, Carole Lartigue, Yonathan Arfi, J. Craig Venter Institute, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and This work was supported in part by the National Institutes of Health [Grant numbers 1R01AI137365, R03AI146632], the IDRC [Grant number 109212] and the French National Funding Research Agency [No ANR-18-CE44-0003-02]
Subjects: Genome transfection, [SDV]Life Sciences [q-bio], Saccharomyces cerevisiae, Bacterial genome size, Computational biology, General Biochemistry, Genetics and Molecular Biology, Article, Genome Engineering, Genome engineering, 03 medical and health sciences, chemistry.chemical_compound, Synthetic biology, 0302 clinical medicine, Genome editing, Drug Discovery, 030304 developmental biology, 0303 health sciences, Genome transplantation, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, biology, Applied Mathematics, [SDV.BA]Life Sciences [q-bio]/Animal biology, biology.organism_classification, Yeast, Computer Science Applications, chemistry, Modeling and Simulation, Exogenous DNA, 030217 neurology & neurosurgery, DNA, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: Yeast cells have long been used as hosts to propagate exogenous DNA. Recent progress in genome editing opens new avenues in synthetic biology. These developments allow the efficient engineering of microbial genomes in Saccharomyces cerevisiae that can then be rescued to yield modified bacteria/viruses. Recent examples show that the ability to quickly synthesize, assemble and/or modify viral and bacterial genomes may be a critical factor to respond to emerging pathogens. However, this process has some limitations. DNA molecules much larger than two megabase pairs are complex to clone, bacterial genomes have proven difficult to rescue, and the dual-use potential of these technologies must be carefully considered. Regardless, the use of yeast as a factory has enormous appeal for biological applications., Graphical abstract Image 1, Highlights • Saccharomyces cerevisiae is a robust and efficient host for cloning microbial genomes. • Recent developments allow the efficient engineering of microbial genomes in yeast that can then be rescued using transplantation/transfection to yield modified bacteria/viruses. • Overcoming bottlenecks is key to expand use of yeast as a factory and to offer new possibilities in the synthetic biology field. • Rapid synthesis, assembly or modification of viral and bacterial genomes may be a critical factor to respond to emerging pathogens.
Published: 2020
Full Text: View/download PDF

46. A Novel Mouse Model of Acute-on-Chronic Cholestatic Alcoholic Liver Disease: A Systems Biology Comparison With Human Alcoholic Hepatitis

Author: Ramon Bataller, Takeki Uehara, Yuuki Katou, Laurent Dubuquoy, Shinji Furuya, Ivan Rusyn, Bernd Schnabl, Rajanikanth Vadigepalli, Derrick E. Fouts, Hiroshi Kono, Josepmaria Argemi, Abha Belorkar, Texas A&M University [College Station], University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), Osaka Prefecture University, J. Craig Venter Institute, University of California [San Diego] (UC San Diego), University of California, Lille Inflammation Research International Center - U 995 (LIRIC), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Jefferson University Hospitals, Yamanashi University, University of California (UC), Université de Lille, LillOA, Université de Lille, Inserm, CHU Lille, University of Pittsburgh [PITT], University of California [San Diego] [UC San Diego], and Lille Inflammation Research International Center - U 995 [LIRIC]
Subjects: Liver Cirrhosis, Male, Alcoholic liver disease, medicine.medical_specialty, Acute-on-Chronic, Alcoholic Hepatitis, Mouse Model, Pyridines, [SDV]Life Sciences [q-bio], 030508 substance abuse, Medicine (miscellaneous), Alcoholic hepatitis, Pharmacology, Diet, High-Fat, Toxicology, Article, Mice, 03 medical and health sciences, Liver disease, 0302 clinical medicine, Cholestasis, Fibrosis, medicine, Animals, Humans, Liver injury, Ethanol, Hepatitis, Alcoholic, Systems Biology, medicine.disease, Pathophysiology, 3. Good health, [SDV] Life Sciences [q-bio], Mice, Inbred C57BL, Disease Models, Animal, Psychiatry and Mental health, Acute Disease, Chronic Disease, Histopathology, 0305 other medical science, 030217 neurology & neurosurgery
Abstract: Background Alcohol-related liver disease is the main cause of liver-related mortality worldwide. The development of novel targeted therapies for patients with advanced forms (i.e., alcoholic hepatitis, AH) is hampered by the lack of suitable animal models. Here, we developed a novel mouse model of acute-on-chronic alcohol liver injury with cholestasis and fibrosis and performed an extensive molecular comparative analysis with human AH. Methods For the mouse model of acute-on-chronic liver injury, we used 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC, 0.05% w/w) diet for 8 weeks to establish cholestatic liver fibrosis. After 1-week washout period, male mice were fed intragastrically for 4 weeks with up to 24 g/kg of ethyl alcohol in a high-fat diet. This animal model was phenotyped using histopathology, clinical chemistry, microbiome, and gene expression approaches. Data were compared to the phenotypes of human alcohol-related liver disease, including AH. Results Mice with cholestatic liver fibrosis and subsequent alcohol exposure (DDC + EtOH) exhibited exacerbated liver fibrosis with a pericellular pattern, increased neutrophil infiltration, and ductular proliferation, all characteristics of human AH. DDC administration had no effect on urine alcohol concentration or liver steatosis. Importantly, DDC- and alcohol-treated mice showed a transcriptomic signature that resembled that of patients with AH. Finally, we show that mice in the DDC + EtOH group had an increased gut barrier dysfunction, mimicking an important pathophysiological mechanism of human AH. Conclusions We developed a novel mouse model of acute-on-chronic cholestatic alcoholic liver injury that has considerable translational potential and can be used to test novel therapeutic modalities for AH.
Published: 2020
Full Text: View/download PDF

47. Contagious Bovine and Caprine Pleuropneumonia: A research community's recommendations for the development of better vaccines

Author: Nick Juleff, Ran Nir-Paz, Artur Summerfield, Xiumei Wang, François Thiaucourt, Vish Nene, Cynthia L. Baldwin, Anne Liljander, Joerg Jores, Hermann Unger, Sanjay Vashee, Geoffrey Munkombwe Muuka, Flavio Sacchini, Jeremy Salt, Fabien Labroussaa, Glenn F. Browning, Alain Blanchard, Danny Goovaerts, Martin Heller, Volker Gerdts, Angie Colston, University of Bern, University of Massachusetts [Amherst] (UMass Amherst), University of Massachusetts System (UMASS), Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Melbourne, Global Alliance for Livestock Veterinary Medicines, Partenaires INRAE, Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan [Saskatoon] (U of S), Federal Research Institute for Animal Health - Friedrich-Loeffler-Institut, Bill & Melinda Gates Foundation [Seattle], International Livestock Research Institute [CGIAR, Nairobi] (ILRI), International Livestock Research Institute [CGIAR, Ethiopie] (ILRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), University of Zambia [Lusaka] (UNZA), Hadassah Hebrew University Medical Center [Jerusalem], Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise Guiseppe Caporale (IZSAM), Institute of Virology and Immunology [Mittelhäusern] (IVI), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Joint FAO/IAEA Programme - Nuclear Techniques in Food and Agriculture, Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO)-International Atomic Energy Agency [Vienna] (IAEA), J. Craig Venter Institute, and Chinese Academy of Agricultural Sciences (CAAS)
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], ruminant, Pleuropneumonie bobine, Review Article, medicine.disease_cause, L73 - Maladies des animaux, Mycoplasma capricolum, Péripneumonie contagieuse bovine, Contagious bovine pleuropneumonia, Mycoplasma, Mycoplasme, Immunologie, Pharmacology (medical), Vaccines, Mycoplasma capricolum subsp capripneumoniae, 630 Agriculture, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Santé animale, Mycoplasma mycoides, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, Pleuropneumonie, 3. Good health, Vaccination, Infectious Diseases, Maladie des animaux, Pleuropneumonia, Pleuropneumonie caprine, lcsh:Immunologic diseases. Allergy, Vaccin, 030106 microbiology, Immunology, 610 Medicine & health, lcsh:RC254-282, 03 medical and health sciences, Contagious caprine pleuropneumonia, Immunity, medicine, pathologie animale, Pleuropneumonie contagieuse caprine, Pharmacology, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, business.industry, L70 - Sciences et hygiène vétérinaires - Considérations générales, biology.organism_classification, medicine.disease, Virology, Mycoplasma mycoides subspecies mycoides, 030104 developmental biology, 13. Climate action, Maladie infectieuse, 570 Life sciences, Bacterial infection, lcsh:RC581-607, business
Abstract: Contagious bovine pleuropneumonia (CBPP) and contagious caprine pleuropneumonia (CCPP) are major infectious diseases of ruminants caused by mycoplasmas in Africa and Asia. In contrast with the limited pathology in the respiratory tract of humans infected with mycoplasmas, CBPP and CCPP are devastating diseases associated with high morbidity and mortality. Beyond their obvious impact on animal health, CBPP and CCPP negatively impact the livelihood and wellbeing of a substantial proportion of livestock-dependent people affecting their culture, economy, trade and nutrition. The causative agents of CBPP and CCPP are Mycoplasma mycoides subspecies mycoides and Mycoplasma capricolum subspecies capripneumoniae, respectively, which have been eradicated in most of the developed world. The current vaccines used for disease control consist of a live attenuated CBPP vaccine and a bacterin vaccine for CCPP, which were developed in the 1960s and 1980s, respectively. Both of these vaccines have many limitations, so better vaccines are urgently needed to improve disease control. In this article the research community prioritized biomedical research needs related to challenge models, rational vaccine design and protective immune responses. Therefore, we scrutinized the current vaccines as well as the challenge-, pathogenicity- and immunity models. We highlight research gaps and provide recommendations towards developing safer and more efficacious vaccines against CBPP and CCPP.
Published: 2020
Full Text: View/download PDF

48. The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity

Author: Maria H. M. Julião, Vitor F. O. Miranda, Ana Paula Moraes, Helen A. Penha, Todd P. Michael, Douglas Silva Domingues, Saura R. Silva, Alessandro M. Varani, Universidade Estadual Paulista (Unesp), Universidade Federal do ABC (UFABC), and J. Craig Venter Institute
Subjects: 0106 biological sciences, 0301 basic medicine, Transposable element, Evolution, Lentibulariaceae, 01 natural sciences, Genome, Catalysis, Inorganic Chemistry, 03 medical and health sciences, genome fractionation, transcription factors, evolution, Transcription factors, Physical and Theoretical Chemistry, Whole-genome duplication, Molecular Biology, Gene, Genome size, Spectroscopy, Comparative genomics, Utricularia, biology, Organic Chemistry, General Medicine, biology.organism_classification, Computer Science Applications, 030104 developmental biology, ABC transporters, Evolutionary biology, whole-genome duplication, Genome fractionation, transposable elements, Transposable elements, Utricularia reniformis, 010606 plant biology & botany
Abstract: Utricularia belongs to Lentibulariaceae, a widespread family of carnivorous plants that possess ultra-small and highly dynamic nuclear genomes. It has been shown that the Lentibulariaceae genomes have been shaped by transposable elements expansion and loss, and multiple rounds of whole-genome duplications (WGD), making the family a platform for evolutionary and comparative genomics studies. To explore the evolution of Utricularia, we estimated the chromosome number and genome size, as well as sequenced the terrestrial bladderwort Utricularia reniformis (2n = 40, 1C = 317.1-Mpb). Here, we report a high quality 304 Mb draft genome, with a scaffold NG50 of 466-Kb, a BUSCO completeness of 87.8%, and 42,582 predicted genes. Compared to the smaller and aquatic U. gibba genome (101 Mb) that has a 32% repetitive sequence, the U. reniformis genome is highly repetitive (56%). The structural differences between the two genomes are the result of distinct fractionation and rearrangements after WGD, and massive proliferation of LTR-retrotransposons. Moreover, GO enrichment analyses suggest an ongoing gene birth&ndash, death&ndash, innovation process occurring among the tandem duplicated genes, shaping the evolution of carnivory-associated functions. We also identified unique patterns of developmentally related genes that support the terrestrial life-form and body plan of U. reniformis. Collectively, our results provided additional insights into the evolution of the plastic and specialized Lentibulariaceae genomes.
Published: 2019
Full Text: View/download PDF

49. Specific Immunologic Countermeasure Protocol for Deep-Space Exploration Missions

Author: George Makedonas, Satish Mehta, Alexander Choukèr, Richard J. Simpson, Gailen Marshall, Jordan S. Orange, Serena Aunon-Chancellor, Scott M. Smith, Sara R. Zwart, Raymond P. Stowe, Martina Heer, Sergey Ponomarev, Alexandra Whitmire, Jean P. Frippiat, Grace L. Douglas, Stephanie S. Krieger, Hernan Lorenzi, Judith-Irina Buchheim, Geoffrey S. Ginsburg, C. Mark Ott, Meghan Downs, Duane Pierson, Natalie Baecker, Clarence Sams, Brian Crucian, JES Tech, University Hospital of the Ludwig-Maximilians University, The University of Arizona Medical Center, University of Arizona, University of Mississippi Medical Center (UMMC), Department of Pediatrics (University of British Columbia), NASA Johnson Space Center (JSC), NASA, The University of Texas Medical Branch (UTMB), Institute of Human Nutrition and Food Science, Rheinische Friedrich-Wilhelms-Universität Bonn, Institute of biomedical problems, Russian Academy of Sciences [Moscow] (RAS), Stress, Immunité, Pathogènes (SIMPA), Université de Lorraine (UL), J. Craig Venter Institute, Duke Center for Applied Genomics and Precision Medicine [Durham, NC, USA], Duke University School of Medicine [Durham, NC, USA], Aerospace Medical Institute, and German Aerospace Center (DLR)
Subjects: 0301 basic medicine, lcsh:Immunologic diseases. Allergy, Opinion, stress management, T-Lymphocytes, Immunology, 03 medical and health sciences, 0302 clinical medicine, Aeronautics, Political science, Herpesvirus reactivation, Agency (sociology), Humans, Immunology and Allergy, Protocol (object-oriented programming), ComputingMilieux_MISCELLANEOUS, Inflammation, Immunity, Cellular, immune countermeasures, immune surveillance, DNA Methylation, Space Flight, Immune surveillance, 3. Good health, 030104 developmental biology, Deep space exploration, Twin Studies as Topic, Space program, [SDV.IMM]Life Sciences [q-bio]/Immunology, space immunology, lcsh:RC581-607, Countermeasure (computer), 030215 immunology
Abstract: German National Space Program [50WB1622]; European Space Agency (ESA)'s Topical Team Stress and Immunity - ESA ELIPS 4 program; European Space Agency (ESA)'s Topical Team Stress and Immunity - ESA SciSpacE program
Published: 2019
Full Text: View/download PDF

50. Sweet mycoplasmas: characterization of the polysaccharide pathway of Mycoplasma mycoides subsp. capri (Mmc) using synthetic genomics

Author: Labroussaa, Fabien, Schieck, Elise, Daupenspeck, James, Oberhansli, Simone, Schumacher, Mélanie, Nicholson, Pamela, Vashee, Sanjay, Lartigue, Carole, Stoffel, Michael H., Dybvig, Kevin, Jores, Joerg, Institute of Veterinary Bacteriology, Partenaires INRAE, International Livestock Research Institute [CGIAR, Nairobi] (ILRI), International Livestock Research Institute [CGIAR, Ethiopie] (ILRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), University of Alabama at Birmingham (UAB), Universität Bern- University of Bern [Bern], J. Craig Venter Institute [La Jolla, USA] (JCVI), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, and ProdInra, Migration
Subjects: [SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Publication Type

Journal

Region

Database

Publisher

254 results on '"The J. Craig Venter Institute"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources