Lin Senjie

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Lin
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Senjie
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  • Article
    The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) : illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing
    (Public Library of Science, 2014-06-24) Keeling, Patrick J. ; Burki, Fabien ; Wilcox, Heather M. ; Allam, Bassem ; Allen, Eric E. ; Amaral-Zettler, Linda A. ; Armbrust, E. Virginia ; Archibald, John M. ; Bharti, Arvind K. ; Bell, Callum J. ; Beszteri, Bank ; Bidle, Kay D. ; Cameron, Connor T. ; Campbell, Lisa ; Caron, David A. ; Cattolico, Rose Ann ; Collier, Jackie L. ; Coyne, Kathryn J. ; Davy, Simon K. ; Deschamps, Phillipe ; Dyhrman, Sonya T. ; Edvardsen, Bente ; Gates, Ruth D. ; Gobler, Christopher J. ; Greenwood, Spencer J. ; Guida, Stephanie M. ; Jacobi, Jennifer L. ; Jakobsen, Kjetill S. ; James, Erick R. ; Jenkins, Bethany D. ; John, Uwe ; Johnson, Matthew D. ; Juhl, Andrew R. ; Kamp, Anja ; Katz, Laura A. ; Kiene, Ronald P. ; Kudryavtsev, Alexander N. ; Leander, Brian S. ; Lin, Senjie ; Lovejoy, Connie ; Lynn, Denis ; Marchetti, Adrian ; McManus, George ; Nedelcu, Aurora M. ; Menden-Deuer, Susanne ; Miceli, Cristina ; Mock, Thomas ; Montresor, Marina ; Moran, Mary Ann ; Murray, Shauna A. ; Nadathur, Govind ; Nagai, Satoshi ; Ngam, Peter B. ; Palenik, Brian ; Pawlowski, Jan ; Petroni, Giulio ; Piganeau, Gwenael ; Posewitz, Matthew C. ; Rengefors, Karin ; Romano, Giovanna ; Rumpho, Mary E. ; Rynearson, Tatiana A. ; Schilling, Kelly B. ; Schroeder, Declan C. ; Simpson, Alastair G. B. ; Slamovits, Claudio H. ; Smith, David R. ; Smith, G. Jason ; Smith, Sarah R. ; Sosik, Heidi M. ; Stief, Peter ; Theriot, Edward ; Twary, Scott N. ; Umale, Pooja E. ; Vaulot, Daniel ; Wawrik, Boris ; Wheeler, Glen L. ; Wilson, William H. ; Xu, Yan ; Zingone, Adriana ; Worden, Alexandra Z.
    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. 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. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases, raising the question as to whether this is fit for purpose.
  • Article
    The genetic diversity of Mesodinium and associated cryptophytes
    (Frontiers Media, 2016-12-20) Johnson, Matthew D. ; Beaudoin, David J. ; Laza-Martinez, Aitor ; Dyhrman, Sonya T. ; Fensin, Elizabeth ; Lin, Senjie ; Merculief, Aaron ; Nagai, Satoshi ; Pompeu, Mayza ; Setala, Outi ; Stoecker, Diane K.
    Ciliates from the genus Mesodinium are globally distributed in marine and freshwater ecosystems and may possess either heterotrophic or mixotrophic nutritional modes. Members of the Mesodinium major/rubrum species complex photosynthesize by sequestering and maintaining organelles from cryptophyte prey, and under certain conditions form periodic or recurrent blooms (= red tides). Here, we present an analysis of the genetic diversity of Mesodinium and cryptophyte populations from 10 environmental samples (eight globally dispersed habitats including five Mesodinium blooms), using group-specific primers for Mesodinium partial 18S, ITS, and partial 28S rRNA genes as well as cryptophyte large subunit RuBisCO genes (rbcL). In addition, 22 new cryptophyte and four new M. rubrum cultures were used to extract DNA and sequence rbcL and 18S-ITS-28S genes, respectively, in order to provide a stronger phylogenetic context for our environmental sequences. Bloom samples were analyzed from coastal Brazil, Chile, two Northeastern locations in the United States, and the Pribilof Islands within the Bering Sea. Additionally, samples were also analyzed from the Baltic and Barents Seas and coastal California under non-bloom conditions. Most blooms were dominated by a single Mesodinium genotype, with coastal Brazil and Chile blooms composed of M. major and the Eastern USA blooms dominated by M. rubrum variant B. Sequences from all four blooms were dominated by Teleaulax amphioxeia-like cryptophytes. Non-bloom communities revealed more diverse assemblages of Mesodinium spp., including heterotrophic species and the mixotrophic Mesodinium chamaeleon. Similarly, cryptophyte diversity was also higher in non-bloom samples. Our results confirm that Mesodinium blooms may be caused by M. major, as well as multiple variants of M. rubrum, and further implicate T. amphioxeia as the key cryptophyte species linked to these phenomena in temperate and subtropical regions.
  • Article
    Genetic tool development in marine protists: emerging model organisms for experimental cell biology
    (Nature Research, 2020-04-06) Faktorová, Drahomíra ; Nisbet, R. Ellen R. ; Fernández Robledo, José A. ; Casacuberta, Elena ; Sudek, Lisa ; Allen, Andrew E. ; Ares, Manuel, Jr. ; Aresté, Cristina ; Balestreri, Cecilia ; Barbrook, Adrian C. ; Beardslee, Patrick ; Bender, Sara J. ; 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 J. ; Docampo, Roberto ; Dupont, Christopher L. ; Edgcomb, Virginia P. ; Einarsso, 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 A. T. ; 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 M. G. ; 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. ; Smith, G. Jason ; Sprecher, Brittany N. ; Stern, Rowena ; Swart, Estienne C. ; Tsaousis, Anastasios D. ; Tsypin, Lev ; Turkewitz, Aaron ; Turnšek, Jernej ; Valach, Matus ; Vergé, Valérie ; von Dassow, Peter ; von der Haar, Tobias ; Waller, Ross F. ; Wang, Lu ; Wen, Xiaoxue ; Wheeler, Glen L. ; Woods, April ; Zhang, Huan ; Mock, Thomas ; Worden, Alexandra Z. ; Lukes, Julius
    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.