Recent Submissions

  • Multiplexed spectral imaging of 120 different fluorescent labels 

    Valm, Alex M.; Oldenbourg, Rudolf; Borisy, Gary G. (Public Library of Science, 2016-07-08)
    The number of fluorescent labels that can unambiguously be distinguished in a single image when acquired through band pass filters is severely limited by the spectral overlap of available fluorophores. The recent development ...
  • Genome-wide identification of enhancer elements 

    Tulin, Sarah; Barsi, Julius C.; Bocconcelli, Carlo; Smith, Joel (UPV/EHU Press, 2016-06)
    We present a prospective genome-wide regulatory element database for the sea urchin embryo and the modified chromosome capture-related methodology used to create it. The method we developed is termed GRIP-seq for genome-wide ...
  • Particulate organic carbon and nitrogen export from major Arctic rivers 

    McClelland, James W.; Holmes, Robert M.; Peterson, Bruce J.; Raymond, Peter A.; Striegl, Robert; Zhulidov, Alexander V.; Zimov, Sergey; Zimov, Nikita; Tank, Suzanne E.; Spencer, Robert G. M.; Staples, Robin; Gurtovaya, Tatiana Y.; Griffin, Claire G. (John Wiley & Sons, 2016-05-11)
    Northern rivers connect a land area of approximately 20.5 million km2 to the Arctic Ocean and surrounding seas. These rivers account for ~10% of global river discharge and transport massive quantities of dissolved and ...
  • A large-scale methane model by incorporating the surface water transport 

    Lu, Xiaoliang; Zhuang, Qianlai; Liu, Yaling; Zhou, Yuyu; AghaKouchak, Amir (John Wiley & Sons, 2016-06-28)
    The effect of surface water movement on methane emissions is not explicitly considered in most of the current methane models. In this study, a surface water routing was coupled into our previously developed large-scale ...
  • Evaluation of laser-based spectrometers for greenhouse gas flux measurements in coastal marshes 

    Brannon, Elizabeth; Moseman-Valtierra, Serena M.; Rella, Chris W.; Martin, Rose M.; Chen, Xuechu; Tang, Jianwu (John Wiley & Sons, 2016-04-18)
    Precise and rapid analyses of greenhouse gases (GHGs) will advance understanding of the net climatic forcing of coastal marsh ecosystems. We examined the ability of a cavity ring down spectroscopy (CRDS) analyzer (Model ...
  • Relationship of bacterial richness to organic degradation rate and sediment age in subseafloor sediment 

    Walsh, Emily A.; Kirkpatrick, John B.; Pockalny, Robert; Sauvage, Justine; Spivack, Arthur J.; Murray, Richard W.; Sogin, Mitchell L.; D'Hondt, Steven (American Society for Microbiology, 2016-06-10)
    Subseafloor sediment hosts a large, taxonomically rich and metabolically diverse microbial ecosystem. However, the factors that control microbial diversity in subseafloor sediment have rarely been explored. Here we show ...
  • The influence of fishmeal-free diets on microbial communities in Atlantic salmon Salmo salar recirculation aquaculture systems 

    Schmidt, Victor T.; Amaral-Zettler, Linda A.; Davidson, John; Summerfelt, Steven; Good, Christopher (American Society for Microbiology, 2016-04-29)
    Reliance on fishmeal as a primary protein source is among the chief economic and environmental concerns in aquaculture today. Fishmeal-based feeds often require harvest from wild fish stocks, placing pressure on natural ...
  • Importance of soil thermal regime in terrestrial ecosystem carbon dynamics in the circumpolar north 

    Jiang, Yueyang; Zhuang, Qianlai; Sitch, Stephen; O'Donnell, Jonathan A.; Kicklighter, David W.; Sokolov, Andrei P.; Melillo, Jerry M. (2016-04-19)
    In the circumpolar north (45-90°N), permafrost plays an important role in vegetation and carbon (C) dynamics. Permafrost thawing has been accelerated by the warming climate and exerts a positive feedback to climate through ...
  • Biomass offsets little or none of permafrost carbon release from soils, streams, and wildfire : an expert assessment 

    Abbott, Benjamin W.; Jones, Jeremy B.; Schuur, Edward A. G.; Chapin, F. Stuart; Bowden, William B.; Bret-Harte, M. Syndonia; Epstein, Howard E.; Flannigan, Michael; Harms, Tamara K.; Hollingsworth, Teresa N.; Mack, Michelle C.; McGuire, A. David; Natali, Susan M.; Rocha, Adrian V.; Tank, Suzanne E.; Turetsky, Merritt R.; Vonk, Jorien E.; Wickland, Kimberly; Aiken, George R.; Alexander, Heather D.; Amon, Rainer M. W.; Benscoter, Brian; Bergeron, Yves; Bishop, Kevin; Blarquez, Olivier; Bond-Lamberty, Benjamin; Breen, Amy L.; Buffam, Ishi; Cai, Yihua; Carcaillet, Christopher; Carey, Sean K.; Chen, Jing M.; Chen, Han Y. H.; Christensen, Torben R.; Cooper, Lee W.; Cornelissen, J. Hans C.; de Groot, William J.; DeLuca, Thomas Henry; Dorrepaal, Ellen; Fetcher, Ned; Finlay, Jacques C.; Forbes, Bruce C.; French, Nancy H. F.; Gauthier, Sylvie; Girardin, Martin; Goetz, Scott J.; Goldammer, Johann G.; Gough, Laura; Grogan, Paul; Guo, Laodong; Higuera, Philip E.; Hinzman, Larry; Hu, Feng Sheng; Hugelius, Gustaf; JAFAROV, ELCHIN; Jandt, Randi; Johnstone, Jill F.; Karlsson, Jan; Kasischke, Eric S.; Kattner, Gerhard; Kelly, Ryan; Keuper, Frida; Kling, George W.; Kortelainen, Pirkko; Kouki, Jari; Kuhry, Peter; Laudon, Hjalmar; Laurion, Isabelle; Macdonald, Robie W.; Mann, Paul J.; Martikainen, Pertti; McClelland, James W.; Molau, Ulf; Oberbauer, Steven F; Olefeldt, David; Paré, David; Parisien, Marc-André; Payette, Serge; Peng, Changhui; Pokrovsky, Oleg; Rastetter, Edward B.; Raymond, Peter A.; Raynolds, Martha K.; Rein, Guillermo; Reynolds, James F.; Robards, Martin; Rogers, Brendan; Schädel, Christina; Schaefer, Kevin; Schmidt, Inger K.; Shvidenko, Anatoly; Sky, Jasper; Spencer, Robert G. M.; Starr, Gregory; Striegl, Robert; Teisserenc, Roman; Tranvik, Lars J.; Virtanen, Tarmo; Welker, Jeffrey M.; Zimov, Sergey (IOPScience, 2016-03-07)
    As the permafrost region warms, its large organic carbon pool will be increasingly vulnerable to decomposition, combustion, and hydrologic export. Models predict that some portion of this release will be offset by increased ...
  • Phase separation of signaling molecules promotes T cell receptor signal transduction 

    Su, Xiaolei; Ditlev, Jonathon; Hui, Enfu; Xing, Wenmin; Banjade, Sudeep; Okrut, Julia; King, David S.; Taunton, Jack; Rosen, Michael K.; Vale, Ronald D. (2016-03)
    Activation of various cell surface receptors triggers the reorganization of downstream signaling molecules into micron- or submicron-sized clusters. However, the functional consequences of such clustering has been unclear. ...
  • Identification of specialists and abundance-occupancy relationships among intestinal bacteria of Aves, Mammalia, and Actinopterygii 

    Green, Hyatt C.; Fisher, Jenny C.; McLellan, Sandra L.; Sogin, Mitchell L.; Shanks, Orin C. (2015-12-16)
    The coalescence of next generation DNA sequencing methods, ecological perspectives, and bioinformatics analysis tools is rapidly advancing our understanding of the evolution and function of vertebrate-associated bacterial ...
  • Time, impact, and the need for digital history and philosophy of science 

    Maienschein, Jane (University of Chicago, 2016-06)
  • A brief review of cephalopod behavioral responses to sound 

    Samson, Julia E.; Mooney, T. Aran; Gussekloo, Sander W. S.; Hanlon, Roger T. (2016)
    Sound is a widely available cue in aquatic environments and is used by many marine animals for vital behaviors. Most research has focused on marine vertebrates. Relatively little is known about sound detection in marine ...
  • Combined measurement and modeling of the hydrological impact of hydraulic redistribution using CLM4.5 at eight AmeriFlux sites 

    Fu, Congsheng; Wang, Guiling; Goulden, Michael L.; Scott, Russell L.; Bible, Kenneth; Cardon, Zoe (Copernicus Publications on behalf of the European Geosciences Union, 2016-05-17)
    Effects of hydraulic redistribution (HR) on hydrological, biogeochemical, and ecological processes have been demonstrated in the field, but the current generation of standard earth system models does not include a ...
  • Insights into the pathogenesis of ulcerative colitis from a murine model of stasis-induced dysbiosis, colonic metaplasia, and genetic susceptibility 

    Ward, Marc A.; Pierre, Joseph F.; Leal, Raquel F.; Huang, Yong; Shogan, Benjamin; Dalal, Sushila R.; Weber, Christopher R.; Leone, Vanessa A.; Musch, Mark W.; An, Gary C.; Rao, Mrinalini C.; Rubin, David; Raffals, Laura E.; Antonopoulos, Dionysios A.; Sogin, Mitchell L.; Hyman, Neil H.; Alverdy, John C.; Chang, Eugene B. (2016-04)
    Gut dysbiosis, host genetics, and environmental triggers are implicated as causative factors in inflammatory bowel disease (IBD), yet mechanistic insights are lacking. Longitudinal analysis of ulcerative colitis patients ...
  • Embryos, microscopes, and society 

    Maienschein, Jane (Elsevier, 2016-03-17)
    Embryos have different meanings for different people and in different contexts. Seen under the microscope, the biological embryo starts out as one cell and then becomes a bunch of cells. Gradually these divide and differentiate ...
  • Microbial associations with macrobiota in coastal ecosystems : patterns and implications for nitrogen cycling 

    Moulton, Orissa M.; Altabet, Mark; Beman, J. Michael; Deegan, Linda A.; Lloret, Javier; Lyons, Meaghan K.; Nelson, James A.; Pfister, Catherine (John Wiley & Sons, 2016-05-02)
    In addition to their important effects on nitrogen (N) cycling via excretion and assimilation (by macrofauna and macroflora, respectively), many macrobiota also host or facilitate microbial taxa responsible for N ...
  • Individuality, stability, and variability of the plaque microbiome 

    Utter, Daniel R.; Mark Welch, Jessica L.; Borisy, Gary G. (Frontiers Media, 2016-04-22)
    Dental plaque is a bacterial biofilm composed of a characteristic set of organisms. Relatively little information from cultivation-independent, high-throughput analyses has been published on the temporal dynamics of the ...
  • RCC1-dependent activation of Ran accelerates cell cycle and DNA repair, inhibiting DNA damage–induced cell senescence 

    Cekan, Pavol; Hasegawa, Keisuke; Pan, Yu; Tubman, Emily; Odde, David; Chen, Jin-Qiu; Herrmann, Michelle A.; Kumar, Sheetal; Kalab, Petr (American Society for Cell Biology, 2016-02-10)
    The coordination of cell cycle progression with the repair of DNA damage supports the genomic integrity of dividing cells. The function of many factors involved in DNA damage response (DDR) and the cell cycle depends on ...
  • Discontinuities concentrate mobile predators : quantifying organism–environment interactions at a seascape scale 

    Kennedy, Cristina G.; Mather, Martha E.; Smith, Joseph M.; Finn, John T.; Deegan, Linda A. (John Wiley & Sons, 2016-02-26)
    Understanding environmental drivers of spatial patterns is an enduring ecological problem that is critical for effective biological conservation. Discontinuities (ecologically meaningful habitat breaks), both naturally ...

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