Recent Submissions

  • Linking pangenomes and metagenomes : the Prochlorococcus metapangenome 

    Delmont, Tom O.; Eren, A. Murat (PeerJ, 2018-01-25)
    Pangenomes offer detailed characterizations of core and accessory genes found in a set of closely related microbial genomes, generally by clustering genes based on sequence homology. In comparison, metagenomes facilitate ...
  • Marine isoprene production and consumption in the mixed layer of the surface ocean – a field study over two oceanic regions 

    Booge, Dennis; Schlundt, Cathleen; Bracher, Astrid; Endres, Sonja; Zäncker, Birthe; Marandino, Christa A. (Copernicus Publications on behalf of the European Geosciences Union, 2018-02-01)
    Parameterizations of surface ocean isoprene concentrations are numerous, despite the lack of source/sink process understanding. Here we present isoprene and related field measurements in the mixed layer from the Indian ...
  • Toward a consistent modeling framework to assess multi-sectoral climate impacts 

    Monier, Erwan; Paltsev, Sergey; Sokolov, Andrei P.; Chen, Y.-H. Henry; Gao, Xiang; Ejaz, Qudsia; Couzo, Evan; Schlosser, C. Adam; Dutkiewicz, Stephanie; Fant, Charles; Scott, Jeffery; Kicklighter, David W.; Morris, Jennifer; Jacoby, Henry D.; Prinn, Ronald G.; Haigh, Martin (Nature Publishing Group, 2018-02-13)
    Efforts to estimate the physical and economic impacts of future climate change face substantial challenges. To enrich the currently popular approaches to impact analysis—which involve evaluation of a damage function or ...
  • Targeted knockout of lhx1 via CRISPR/Cas9 gene editing in the Xenopus laevis kidney 

    DeLay, Bridget D.; Corkins, Mark E.; Hanania, Hannah L.; Salanga, Matthew C.; Deng, Jian Min; Sudou, Norihiro; Taira, Masanori; Horb, Marko E.; Miller, Rachel K. (2017-09-29)
    Studying genes involved in organogenesis is often difficult because many of these genes are also essential for early development. The allotetraploid frog, Xenopus laevis, is commonly used to study developmental processes, ...
  • Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into metabolism and diversity 

    Reveillaud, Julie; Anderson, Rika E.; Reves-Sohn, Sintra; Cavanaugh, Colleen M.; Huber, Julie A. (BMC, 2018-01-27)
    The microbial endosymbionts of two species of vestimentiferan tubeworms (Escarpia sp. and Lamellibrachia sp.2) collected from an area of low-temperature hydrothermal diffuse vent flow at the Mid-Cayman Rise (MCR) in the ...
  • Optimization of terrestrial ecosystem model parameters using atmospheric CO2 concentration data with the Global Carbon Assimilation System (GCAS) 

    Chen, Zhuoqi; Chen, Jing M.; Zhang, Shupeng; Zheng, Xiaogu; Ju, Weiming; Mo, Gang; Lu, Xiaoliang (John Wiley & Sons, 2017-12-23)
    The Global Carbon Assimilation System that assimilates ground-based atmospheric CO2 data is used to estimate several key parameters in a terrestrial ecosystem model for the purpose of improving carbon cycle simulation. ...
  • Cells containing aragonite crystals mediate responses to gravity in Trichoplax adhaerens (Placozoa), an animal lacking neurons and synapses 

    Mayorova, Tatiana D.; Smith, Carolyn L.; Hammar, Katherine M.; Winters, Christine A.; Pivovarova, Natalia B.; Aronova, Maria A.; Leapman, Richard D.; Reese, Thomas S. (Public Library of Science, 2018-01-17)
    Trichoplax adhaerens has only six cell types. The function as well as the structure of crystal cells, the least numerous cell type, presented an enigma. Crystal cells are arrayed around the perimeter of the animal and each ...
  • Resilience in moving water : effects of turbulence on the predatory impact of the lobate ctenophore Mnemiopsis leidyi 

    Jaspers, Cornelia; Costello, John H.; Sutherland, Kelly R.; Gemmell, Brad J.; Lucas, Kelsey N.; Tackett, Jennifer; Dodge, Kara L.; Colin, Sean P. (John Wiley & Sons, 2017-08-14)
    Despite its delicate morphology, the lobate ctenophore Mnemiopsis leidyi thrives in coastal ecosystems as an influential zooplankton predator. Coastal ecosystems are often characterized as energetic systems with high levels ...
  • Leaf-FISH : microscale imaging of bacterial taxa on phyllosphere 

    Peredo, Elena L.; Simmons, Sheri L. (Frontiers Media, 2018-01-09)
    Molecular methods for microbial community characterization have uncovered environmental and plant-associated factors shaping phyllosphere communities. Variables undetectable using bulk methods can play an important role ...
  • Cell lineage and cell cycling analyses of the 4d micromere using live imaging in the marine annelid Platynereis dumerilii 

    Ozpolat, B. Duygu; Handberg-Thorsager, Mette; Vervoort, Michel; Balavoine, Guillaume (eLife, 2017-12-12)
    Cell lineage, cell cycle, and cell fate are tightly associated in developmental processes, but in vivo studies at single-cell resolution showing the intricacies of these associations are rare due to technical limitations. ...
  • Prion protein inhibits fast axonal transport through a mechanism involving casein kinase 2 

    Zamponi, Emiliano; Buratti, Fiamma; Cataldi, Gabriel; Caicedo, Hector Hugo; Song, Yuyu; Jungbauer, Lisa M.; LaDu, Mary J.; Bisbal, Mariano; Lorenzo, Lorenzo; Ma, Jiyan; Helguera, Pablo R.; Morfini, Gerardo A.; Brady, Scott T.; Pigino, Gustavo F. (Public Library of Science, 2017-12-20)
    Prion diseases include a number of progressive neuropathies involving conformational changes in cellular prion protein (PrPc) that may be fatal sporadic, familial or infectious. Pathological evidence indicated that neurons ...
  • Highly conserved molecular pathways, including Wnt signaling, promote functional recovery from spinal cord injury in lampreys 

    Herman, Paige E.; Papatheodorou, Angelos; Bryant, Stephanie A.; Waterbury, Courtney K. M.; Herdy, Joseph R.; Arcese, Anthony A.; Buxbaum, Joseph D.; Smith, Jeramiah J.; Morgan, Jennifer R.; Bloom, Ona E. (Nature Publishing Group, 2018-01-15)
    In mammals, spinal cord injury (SCI) leads to dramatic losses in neurons and synaptic connections, and consequently function. Unlike mammals, lampreys are vertebrates that undergo spontaneous regeneration and achieve ...
  • Subtle microbiome manipulation using probiotics reduces antibiotic-associated mortality in fish 

    Schmidt, Victor T.; Gomez-Chiarri, Marta; Roy, Chelsea; Smith, Katherine F.; Amaral-Zettler, Linda A. (American Society for Microbiology, 2017-11-07)
    Prophylactic antibiotics in the aquaculture and ornamental fish industry are intended to prevent the negative impacts of disease outbreaks. Research in mice and humans suggests that antibiotics may disturb microbiome ...
  • Northern Eurasia Future Initiative (NEFI) : facing the challenges and pathways of global change in the twenty-first century 

    Groisman, Pavel Ya; Shugart, Herman; Kicklighter, David W.; Henebry, Geoffrey; Tchebakova, Nadezhda; Maksyutov, Shamil; Monier, Erwan; Gutman, Garik; Gulev, Sergey; Qi, Jiaguo; Prishchepov, Alexander; Kukavskaya, Elena; Porfiriev, Boris; Shiklomanov, Alexander; Loboda, Tatiana; Shiklomanov, Nikolay; Nghiem, Son; Bergen, Kathleen; Albrechtová, Jana; Chen, Jiquan; Shahgedanova, Maria; Shvidenko, Anatoly; Speranskaya, Nina; Soja, Amber; de Beurs, Kirsten; Bulygina, Olga N; McCarty, Jessica; Zhuang, Qianlai; Zolina, Olga (Springer, 2017-12-27)
    During the past several decades, the Earth system has changed significantly, especially across Northern Eurasia. Changes in the socio-economic conditions of the larger countries in the region have also resulted in a variety ...
  • Widespread utilization of passive energy recapture in swimming medusae 

    Gemmell, Brad J.; Colin, Sean P.; Costello, John H. (The Company of Biologists, 2017-11-27)
    Recently, it has been shown that some medusae are capable of swimming very efficiently, i.e. with a low cost of transport, and that this is in part due to passive energy recapture (PER) which occurs during bell relaxation. ...
  • Density imaging of heterochromatin in live cells using orientation-independent-DIC microscopy 

    Imai, Ryosuke; Nozaki, Tadasu; Tani, Tomomi; Kaizu, Kazunari; Hibino, Kayo; Ide, Satoru; Tamura, Sachiko; Takahashi, Koichi; Shribak, Michael; Maeshima, Kazuhiro (American Society for Cell Biology, 2017-08-23)
    In eukaryotic cells, highly condensed inactive/silenced chromatin has long been called “heterochromatin.” However, recent research suggests that such regions are in fact not fully transcriptionally silent and that there ...
  • A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer 

    Tully, Benjamin J.; Wheat, C. Geoffrey; Glazer, Brian T.; Huber, Julie A. (Nature Publishing Group, 2017-11-03)
    The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, ...
  • Recurrent patterns of microdiversity in a temperate coastal marine environment 

    Chafee, Meghan E.; Fernàndez-Guerra, Antonio; Buttigieg, Pier Luigi; Gerdts, Gunnar; Eren, A. Murat; Teeling, Hanno; Amann, Rudolf I. (Nature Publishing Group, 2017-10-24)
    Temperate coastal marine environments are replete with complex biotic and abiotic interactions that are amplified during spring and summer phytoplankton blooms. During these events, heterotrophic bacterioplankton respond ...
  • α-Synuclein dimers impair vesicle fission during clathrin-mediated synaptic vesicle recycling 

    Medeiros, Audrey T.; Soll, Lindsey G.; Tessari, Isabella; Bubacco, Luigi; Morgan, Jennifer R. (Frontiers Media, 2017-12-11)
    α-Synuclein is a presynaptic protein that regulates synaptic vesicle (SV) trafficking. In Parkinson’s disease (PD) and several other neurodegenerative disorders, aberrant oligomerization and aggregation of α-synuclein lead ...
  • Preservation of three-dimensional spatial structure in the gut microbiome 

    Hasegawa, Yuko; Mark Welch, Jessica L.; Rossetti, Blair J.; Borisy, Gary G. (Public Library of Science, 2017-11-27)
    Preservation of three-dimensional structure in the gut is necessary in order to analyze the spatial organization of the gut microbiota and gut luminal contents. In this study, we evaluated preparation methods for mouse gut ...

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