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1. Genetic tool development in marine protists: emerging model organisms for experimental cell biology

Author

Faktorová, Drahomíra, Nisbet, R Ellen R, Fernández Robledo, José A, Casacuberta, Elena, Sudek, Lisa, Allen, Andrew E, Ares, Manuel, Aresté, Cristina, Balestreri, Cecilia, Barbrook, Adrian C, Beardslee, Patrick, Bender, Sara, Booth, David S, Bouget, François-Yves, Bowler, Chris, Breglia, Susana A, Brownlee, Colin, Burger, Gertraud, Cerutti, Heriberto, Cesaroni, Rachele, Chiurillo, Miguel A, Clemente, Thomas, Coles, Duncan B, Collier, Jackie L, Cooney, Elizabeth C, Coyne, Kathryn, Docampo, Roberto, Dupont, Christopher L, Edgcomb, Virginia, Einarsson, Elin, Elustondo, Pía A, Federici, Fernan, Freire-Beneitez, Veronica, Freyria, Nastasia J, Fukuda, Kodai, García, Paulo A, Girguis, Peter R, Gomaa, Fatma, Gornik, Sebastian G, Guo, Jian, Hampl, Vladimír, Hanawa, Yutaka, Haro-Contreras, Esteban R, Hehenberger, Elisabeth, Highfield, Andrea, Hirakawa, Yoshihisa, Hopes, Amanda, Howe, Christopher J, Hu, Ian, Ibañez, Jorge, Irwin, Nicholas AT, Ishii, Yuu, Janowicz, Natalia Ewa, Jones, Adam C, Kachale, Ambar, Fujimura-Kamada, Konomi, Kaur, Binnypreet, Kaye, Jonathan Z, Kazana, Eleanna, Keeling, Patrick J, King, Nicole, Klobutcher, Lawrence A, Lander, Noelia, Lassadi, Imen, Li, Zhuhong, Lin, Senjie, Lozano, Jean-Claude, Luan, Fulei, Maruyama, Shinichiro, Matute, Tamara, Miceli, Cristina, Minagawa, Jun, Moosburner, Mark, Najle, Sebastián R, Nanjappa, Deepak, Nimmo, Isabel C, Noble, Luke, Novák Vanclová, Anna MG, Nowacki, Mariusz, Nuñez, Isaac, Pain, Arnab, Piersanti, Angela, Pucciarelli, Sandra, Pyrih, Jan, Rest, Joshua S, Rius, Mariana, Robertson, Deborah, Ruaud, Albane, Ruiz-Trillo, Iñaki, Sigg, Monika A, Silver, Pamela A, Slamovits, Claudio H, Jason Smith, G, Sprecher, Brittany N, Stern, Rowena, Swart, Estienne C, Tsaousis, Anastasios D, Tsypin, Lev, Turkewitz, Aaron, and Turnšek, Jernej

Subjects
Genetics, Biotechnology, Life Below Water, Biodiversity, DNA, Ecosystem, Environment, Eukaryota, Green Fluorescent Proteins, Marine Biology, Models, Biological, Species Specificity, Transformation, Genetic, Biological Sciences, Technology, Medical and Health Sciences, Developmental Biology
Abstract

Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.

Published
2020

2. Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology

Author

Faktorová, Drahomíra, Nisbet, R Ellen R, Fernández Robledo, José A, Casacuberta, Elena, Sudek, Lisa, Allen, Andrew E, Ares, Manuel, Aresté, Cristina, Balestreri, Cecilia, Barbrook, Adrian C, Beardslee, Patrick, Bender, Sara, Booth, David S, Bouget, François-Yves, Bowler, Chris, Breglia, Susana A, Brownlee, Colin, Burger, Gertraud, Cerutti, Heriberto, Cesaroni, Rachele, Chiurillo, Miguel A, Clemente, Thomas, Coles, Duncan B, Collier, Jackie L, Cooney, Elizabeth C, Coyne, Kathryn, Docampo, Roberto, Dupont, Christopher L, Edgcomb, Virginia, Einarsson, Elin, Elustondo, Pía A, Federici, Fernan, Freire-Beneitez, Veronica, Freyria, Nastasia J, Fukuda, Kodai, García, Paulo A, Girguis, Peter R, Gomaa, Fatma, Gornik, Sebastian G, Guo, Jian, Hampl, Vladimír, Hanawa, Yutaka, Haro-Contreras, Esteban R, Hehenberger, Elisabeth, Highfield, Andrea, Hirakawa, Yoshihisa, Hopes, Amanda, Howe, Christopher J, Hu, Ian, Ibañez, Jorge, Irwin, Nicholas AT, Ishii, Yuu, Janowicz, Natalia Ewa, Jones, Adam C, Kachale, Ambar, Fujimura-Kamada, Konomi, Kaur, Binnypreet, Kaye, Jonathan Z, Kazana, Eleanna, Keeling, Patrick J, King, Nicole, Klobutcher, Lawrence A, Lander, Noelia, Lassadi, Imen, Li, Zhuhong, Lin, Senjie, Lozano, Jean-Claude, Luan, Fulei, Maruyama, Shinichiro, Matute, Tamara, Miceli, Cristina, Minagawa, Jun, Moosburner, Mark, Najle, Sebastián R, Nanjappa, Deepak, Nimmo, Isabel C, Noble, Luke, Novák Vanclová, Anna MG, Nowacki, Mariusz, Nuñez, Isaac, Pain, Arnab, Piersanti, Angela, Pucciarelli, Sandra, Pyrih, Jan, Rest, Joshua S, Rius, Mariana, Robertson, Deborah, Ruaud, Albane, Ruiz-Trillo, Iñaki, Sigg, Monika A, Silver, Pamela A, Slamovits, Claudio H, Jason Smith, G, Sprecher, Brittany N, Stern, Rowena, Swart, Estienne C, Tsaousis, Anastasios D, Tsypin, Lev, Turkewitz, Aaron, and Turnšek, Jernej

Subjects
Biological Sciences, Technology, Medical and Health Sciences, Developmental Biology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

3. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing

Author

Mary Ann Moran, Ronald P. Kiene, Matthew D. Johnson, Jennifer L. Jacobi, Gwenael Piganeau, Kjetill S. Jakobsen, Simon K. Davy, Edward C. Theriot, Uwe John, Alexander Kudryavtsev, Sarah R. Smith, Bente Edvardsen, Cristina Miceli, Adrian Marchetti, Karin Rengefors, Tatiana A. Rynearson, John M. Archibald, Matthew C. Posewitz, Brian Palenik, Alexandra Z. Worden, Pooja E. Umale, Boris Wawrik, Laura A. Katz, Satoshi Nagai, Anja Kamp, Lisa Campbell, Kathryn J. Coyne, Thomas Mock, E. Virginia Armbrust, Fabien Burki, Adriana Zingone, Sonya T. Dyhrman, Mary E. Rumpho, Bank Beszteri, Giovanna Romano, Declan C. Schroeder, Callum J. Bell, Yan Xu, Bassem Allam, Kay D. Bidle, Bethany D. Jenkins, Kelly B. Schilling, Giulio Petroni, David Roy Smith, Aurora M. Nedelcu, Arvind K. Bharti, Connie Lovejoy, Stephanie Guida, Spencer J. Greenwood, Peter Stief, David A. Caron, Senjie Lin, Marina Montresor, Denis H. Lynn, Patrick J. Keeling, Glen L. Wheeler, Linda A. Amaral-Zettler, Daniel Vaulot, Jan Pawlowski, Ruth D. Gates, Brian S. Leander, Heather M. Wilcox, Andrew R. Juhl, Govind Nadathur, Erick R. James, Rose Ann Cattolico, Alastair G. B. Simpson, Susanne Menden-Deuer, G. Jason Smith, George B. McManus, Christopher J. Gobler, Heidi M. Sosik, Connor Cameron, Jackie L. Collier, Shauna A. Murray, Scott N. Twary, William H. Wilson, Claudio H. Slamovits, Peter B. Ngam, Phillipe Deschamps, Eric E. Allen, Roberts, Roland G, Canadian Institute for Advanced Research (CIFAR), Department of Botany, University of British Columbia [Vancouver], Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, School of Marine and Atmospheric Sciences [Stony Brook] (SoMAS), Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY), Marine Biology Research Division, University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), The Josephine Bay Paul Center for comparative molecular biology and evolution, Department of Geological Sciences [Providence], Brown University, School of Oceanography [Seattle], University of Washington [Seattle], Department of biochemistry & molecular biology, Dalhousie University [Halifax], National center for genome resources (NCGR), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Institute of Marine and Coastal Science, Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), Department of Oceanography [College Station], Texas A&M University [College Station], Department of biology, University of Southern California (USC), University of Delaware [Newark], School of biological sciences, Victoria University of Wellington, Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Department of earth and environmental sciences and the Lamont-Doherty earth observatory, Columbia University [New York], Department of Molecular Biosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Hawai'i Institute of Marine Biology, Hawai'i Institute of Marine Biology (HIMB), Department of biomedical sciences, University of Prince Edward Island, Graduate School of Oceanography [Narragansett], University of Rhode Island (URI), Department of cell and molecular biology, University of Rhode Island, University of Rhode Island (URI)-University of Rhode Island (URI), Woods Hole Oceanographic Institution (WHOI), Jacobs University [Bremen], Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Department of biological sciences, Smith College [Northampton], University of South Alabama, Department of invertebrate zoology, Saint Petersburg State Technical University, Saint Petersburg State Polytechnical University (SPSPU)-Saint Petersburg State Polytechnical University (SPSPU), Department of genetics and evolution, Université de Genève = University of Geneva (UNIGE), Department of Marine sciences, University of Connecticut (UCONN), département de biologie, Université Laval [Québec] (ULaval), Department of Integrative Biology, University of Guelph, Department of zoology, University of British Columbia (UBC), Department of Marine, Earth, and Atmospheric Sciences [NCSU] (MEAS), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), University of New Brunswick (UNB), School of biosciences and biotechnology, Università degli Studi di Camerino = University of Camerino (UNICAM), School of Environmental Sciences [Norwich], University of East Anglia [Norwich] (UEA), Stazione Zoologica Anton Dohrn (SZN), Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney (UTS), Department of Marrine sciences, University of Puerto Rico (UPR), National Research Institute of Fisheries Science, University of Pisa - Università di Pisa, Biologie intégrative des organismes marins (BIOM), 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), Department of Chemistry and Geochemistry, Colorado School of Mines, department of biology, Lund University [Lund], Department of molecular and cell biology, Marine Biological Association of the UK, University of Western Ontario (UWO), Moss Landing Marine Laboratories, Section of Integrative Biology, University of Texas at Austin [Austin], Los Alamos National Laboratory (LANL), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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)-Station biologique de Roscoff [Roscoff] (SBR), department of microbiology and plant biology, University of Oklahoma (OU), Plymouth Marine Laboratory (PML), Bigelow Laboratory for Ocean Sciences, Princeton University, University of Britsh Columbia [Vancouver], University of California-University of California, University of Geneva [Switzerland], Università degli Studi di Camerino (UNICAM), Plymouth Marine Laboratory, and Roberts, Roland G.

Subjects
Genetics and Molecular Biology (all), Databases, Factual, animal genomics, Immunology and Microbiology (all), Biochemistry, Medical and Health Sciences, Transcriptome, transcriptome analysis, Community Page, sequence databases, Environmental Microbiology, Biology (General), Molecular Sequence Data, Sequence Analysis, Biodiversity, Eukaryota, Oceans and Seas, Agricultural and Biological Sciences (all), Biochemistry, Genetics and Molecular Biology (all), Neuroscience (all), Medicine (all), Genetics, General Neuroscience, marine ecology, Biological Sciences, genome sequencing, General Agricultural and Biological Sciences, Biologie, QH301-705.5, Sequence analysis, Ecology (disciplines), Marine Biology, Genomics, Biology, Microbiology, General Biochemistry, Genetics and Molecular Biology, DNA sequencing, Databases, Microbial ecology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], 14. Life underwater, Life Below Water, Factual, Comparative genomics, Marine biology, Evolutionary Biology, General Immunology and Microbiology, Agricultural and Veterinary Sciences, Ecology and Environmental Sciences, Human Genome, Biology and Life Sciences, 15. Life on land, Evolutionary biology, plant genomics, Generic health relevance, genomic library construction, Genomic databases, Developmental Biology
Abstract

Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes [1]. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well-curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics [2]. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases [3],[4], raising the question as to whether this is fit for purpose.

Published
2014
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4. Common genetic variation and the control of HIV-1 in humans

Author

Barton F. Haynes, Antonella Castagna, Kevin V. Shianna, Andrew J. McMichael, Simon Mallal, Curtis Gumbs, Steven M. Wolinsky, Huldrych F. Günthard, Joseph B. Margolick, Stylianos E. Antonarakis, Norman L. Letvin, Jacques S. Beckmann, Lisa P. Jacobson, David Goldstein, Jeremy J. Martinson, Andrea De Luca, Amalio Telenti, Stephen J. O'Brien, Roger Detels, Mary Carrington, Patrick Descombes, Sara Colombo, Kunlin Zhang, José M. Miró, Judith Dalmau, Niels Obel, Cristina Mussini, Bruno Ledergerber, Javier Martinez-Picado, Alessandro Cozzi-Lepri, Thomas J. Urban, Elizabeth T. Cirulli, Dongliang Ge, Jason Smith, Jacques Fellay, Philippa J. Easterbrook, Sheng Feng, University of Zurich, Fellay, J, McCarthy, Mark I, Universitat de Barcelona, NIAID Center for HIV/AIDS Vaccine Immunology (CHAVI), Fellay, Jacque, Ge, Dongliang, Shianna Kevin, V., Colombo, Sara, Ledergerber, Bruno, Cirulli Elizabeth, T., Urban Thomas, J., Zhang, Kunlin, Gumbs Curtis, E., Smith Jason, P., Castagna, Antonella, Cozzi Lepri, Alessandro, De Luca, Andrea, Easterbrook, Philippa, Guenthard Huldrych, F., Mallal, Simon, Mussini, Cristina, Dalmau, Judith, Martinez Picado, Javier, Miro Jose, M., Obel, Niel, Wolinsky Steven, M., Martinson Jeremy, J., Detels, Roger, Margolick Joseph, B., Jacobson Lisa, P., Descombes, Patrick, Antonarakis Stylianos, E., Beckmann Jacques, S., O'Brien Stephen, J., Letvin Norman, L., McMichael Andrew, J., Haynes Barton, F., Carrington, Mary, Feng, Sheng, Telenti, Amalio, Goldstein David, B., and Antonarakis, Stylianos

Subjects
Male, Cancer Research, Candidate gene, genetic control, Genome-wide association study, HIV Infections, Human genetic variation, Kaplan-Meier Estimate, Major Histocompatibility Complex/genetics, 10234 Clinic for Infectious Diseases, Major Histocompatibility Complex, 2.1 Biological and endogenous factors, ddc:576.5, 1306 Cancer Research, Molecular genetics, Aetiology, Genetics (clinical), Genetics and Genomics/Genetics of Disease, Genetics, HIV-1/ physiology, Single Nucleotide, Infectious Diseases/HIV Infection and AIDS, Viral Load, Polymorphism, Single Nucleotide/genetics, HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1), CD4(+) cells, Infectious Diseases, Phenotype, Adult, Alleles, Disease Progression, Female, Genetic Variation, Genotype, HIV Infections/virology, HIV-1/physiology, Humans, HIV/AIDS, Infection, Research Article, medicine.medical_specialty, 2716 Genetics (clinical), lcsh:QH426-470, Single-nucleotide polymorphism, 610 Medicine & health, Biology, Genetics and Genomics/Complex Traits, Polymorphism, Single Nucleotide, Genètica molecular, 1311 Genetics, Clinical Research, Genetic variation, medicine, VIH (Virus), 1312 Molecular Biology, Allele, Polymorphism, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Kaplan-Meiers Estimate, HIV (Viruses), Haplotype, Human Genome, HIV, Virology/Mechanisms of Resistance and Susceptibility, including Host Genetics, NIAID Center for HIV/AIDS Vaccine Immunology, lcsh:Genetics, 1105 Ecology, Evolution, Behavior and Systematics, HIV-1, Immunology/Genetics of the Immune System, Developmental Biology
Abstract

To extend the understanding of host genetic determinants of HIV-1 control, we performed a genome-wide association study in a cohort of 2,554 infected Caucasian subjects. The study was powered to detect common genetic variants explaining down to 1.3% of the variability in viral load at set point. We provide overwhelming confirmation of three associations previously reported in a genome-wide study and show further independent effects of both common and rare variants in the Major Histocompatibility Complex region (MHC). We also examined the polymorphisms reported in previous candidate gene studies and fail to support a role for any variant outside of the MHC or the chemokine receptor cluster on chromosome 3. In addition, we evaluated functional variants, copy-number polymorphisms, epistatic interactions, and biological pathways. This study thus represents a comprehensive assessment of common human genetic variation in HIV-1 control in Caucasians., Author Summary The ability to spontaneously control HIV-1 upon infection is highly variable between individuals. To evaluate the contribution of variation in human genes to differences in plasma viral load and in disease progression rates, we performed a genome-wide association study in >2,500 HIV–infected individuals. This study achieved two goals: it completed the analysis of common variation influencing viral control, and it re-assessed the majority of previously reported genetic associations. We show that genetic variants located near the HLA-B and HLA-C genes are the strongest determinants of viral control, and that other independent associations exist in the same region of chromosome 6, the Major Histocompatibility Complex, known to contain a large number of genes involved in immune defense. We could not replicate most of the previously published associations with HIV candidate genes in this large, well-characterized cohort. Overall, common human genetic variation, together with demographic variables, explains up to 22% of the variability in viral load in the Caucasian population.

Published
2009

5. Post-emergence herbicides are cost effective for vineyard floor management on the Central Coast

Author

Tiffany A. Bensen, Larry Bettiga, Richard Smith, Jason Smith, Darryl Salm, and Laura Tourte

Subjects
Integrated pest management, costs, Simazine, Vineyard, simazine, lcsh:Agriculture, chemistry.chemical_compound, vineyards, Yield (wine), Central Coast, post-emergence herbicides, groundwater, lcsh:Agriculture (General), Cover crop, Management practices, Pest Management, Agroforestry, General Engineering, lcsh:S, Weed control, lcsh:S1-972, Agronomy, chemistry, Environmental science, pre-emergence herbicides, cover crops, Bay
Abstract

Central Coast growers are under increasing scrutiny and regulatory pressure to manage herbicide use because of their farmland's proximity to the Monterey Bay and National Marine Sanctuary. Vineyard floor management practices typically consist of a combination of weed control strategies, including herbicide use and cover crops. We evaluated nine combinations of vineyard floor management practices for their impacts on fruit yield, quality and costs. We found that compared to the grower standard, post-emergence herbicide treatments generally used smaller amounts of chemicals and were less costly, with similar yields and quality.

Published
2008

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