Recent Submissions

  • Introducing the JMBE themed issue on scientific citizenship 

    Gilbert, Jack A.; Klyczek, Karen K.; Elliott, Samantha L. (American Society for Microbiology, 2016-03)
    In this Editorial, the three Guest Editors for JMBE's first standalone themed issue introduce the topic of scientific citizenship and provide an overview of the current ideas and best practices contained within the issue.© ...
  • Micron-scale plasma membrane curvature is recognized by the septin cytoskeleton 

    Bridges, Andrew A.; Jentzsch, Maximilian S.; Oakes, Patrick W.; Occhipinti, Patricia; Gladfelter, Amy S. (Rockefeller University Press, 2016-04-04)
    Cells change shape in response to diverse environmental and developmental conditions, creating topologies with micron-scale features. Although individual proteins can sense nanometer-scale membrane curvature, it is unclear ...
  • Analysis of lung microbiota in bronchoalveolar lavage, protected brush and sputum samples from subjects with mild-to-moderate cystic fibrosis Lung Disease 

    Hogan, Deborah A.; Willger, Sven D.; Dolben, Emily L.; Hampton, Thomas H.; Stanton, Bruce A.; Morrison, Hilary G.; Sogin, Mitchell L.; Czum, Julianna; Ashare, Alix (Public Library of Science, 2016-03-04)
    Individuals with cystic fibrosis (CF) often acquire chronic lung infections that lead to irreversible damage. We sought to examine regional variation in the microbial communities in the lungs of individuals with mild-to-moderate ...
  • Seasonal variability of multiple leaf traits captured by leaf spectroscopy at two temperate deciduous forests 

    Yang, Xi; Tang, Jianwu; Mustard, John F.; Wu, Jin; Zhao, Kaiguang; Serbin, Shawn; Lee, Jung-Eun (2015-08)
    Understanding the temporal patterns of leaf traits is critical in determining the seasonality and magnitude of terrestrial carbon and water fluxes. However, robust and efficient ways to monitor the temporal dynamics of ...
  • Nutrient limitation of woody debris decomposition in a tropical forest : contrasting effects of N and P addition 

    Chen, Yao; Sayer, Emma J.; Li, Zhian; Mo, Qifeng; Li, Yingwen; Ding, Yongzhen; Wang, Jun; Lu, Xiankai; Tang, Jianwu; Wang, Faming (2015-04)
    Tropical forests represent a major terrestrial store of carbon (C), a large proportion of which is contained in the soil and decaying organic matter. Woody debris plays a key role in forest C dynamics because it contains ...
  • Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins 

    Nguyen, Phuong A.; Field, Christine M.; Groen, Aaron C.; Mitchison, Timothy J.; Loose, Martin (2015-01)
    Cell division in prokaryotes and eukaryotes is commonly initiated by the well-controlled binding of proteins to the cytoplasmic side of the cell membrane. However, a precise characterization of the spatiotemporal dynamics ...
  • Simulating social-ecological systems : the Island Digital Ecosystem Avatars (IDEA) consortium 

    Davies, Neil; Field, Dawn; Gavaghan, David; Holbrook, Sally J.; Planes, Serge; Troyer, Matthias; Bonsall, Michael; Claudet, Joachim; Roderick, George; Schmitt, Russell J.; Amaral-Zettler, Linda A.; Berteaux, Veronique; Bossin, Hervé C.; Cabasse, Charlotte; Collin, Antoine; Deck, John; Dell, Tony; Dunne, Jennifer A.; Gates, Ruth D.; Harfoot, Mike; Hench, James L.; Hopuare, Marania; Kirch, Patrick; Kotoulas, Georgios; Kosenkov, Alex; Kusenko, Alex; Leichter, James J.; Lenihan, Hunter; Magoulas, Antonios; Martinez, Neo; Meyer, Chris; Stoll, Benoit; Swalla, Billie; Tartakovsky, Daniel M.; Teavai Murphy, Hinano; Turyshev, Slava; Valdvinos, Fernanda; Williams, Rich; Wood, Spencer; IDEA Consortium (BioMed Central, 2016-03-17)
    Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to ...
  • Cisplatin resistant spheroids model clinically relevant survival mechanisms in ovarian tumors 

    Chowanadisai, Winyoo; Messerli, Shanta M.; Miller, Daniel H.; Medina, Jamie E.; Hamilton, Joshua W.; Messerli, Mark A.; Brodsky, Alexander S. (Public Library of Science, 2016-03-17)
    The majority of ovarian tumors eventually recur in a drug resistant form. Using cisplatin sensitive and resistant cell lines assembled into 3D spheroids we profiled gene expression and identified candidate mechanisms and ...
  • Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate 

    De Filippis, Francesca; Genovese, Alessandro; Ferranti, Pasquale; Gilbert, Jack A.; Ercolini, Danilo (Nature Publishing Group, 2016-02-25)
    Traditional cheeses harbour complex microbial consortia that play an important role in shaping typical sensorial properties. However, the microbial metabolism is considered difficult to control. Microbial community succession ...
  • Recovering complete and draft population genomes from metagenome datasets 

    Sangwan, Naseer; Xia, Fangfang; Gilbert, Jack A. (BioMed Central, 2016-03-08)
    Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. ...
  • Najas flexilis (Hydrocharitaceae) in Alaska : a reassessment 

    Les, Donald H.; Les, Angela M.; King, Ursula M.; Peredo, Elena L. (New England Botanical Club, 2015-09-23)
    Fifteen Najas flexilis collections were made in Alaska during the summer of 2012, with 13 of the stations representing either new or formerly undocumented localities for this imperiled Alaskan species. These field collections ...
  • The terrestrial biosphere as a net source of greenhouse gases to the atmosphere 

    Tian, Hanqin; Lu, Chaoqun; Ciais, Philippe; Michalak, Anna M.; Canadell, Josep G.; Saikawa, Eri; Huntzinger, Deborah N.; Gurney, Kevin R.; Sitch, Stephen; Zhang, Bowen; Yang, Jia; Bousquet, Philippe; Bruhwiler, Lori; Chen, Guangsheng; Dlugokencky, Edward J.; Friedlingstein, Pierre; Melillo, Jerry M.; Pan, Shufen; Poulter, Benjamin; Prinn, Ronald G.; Saunois, Marielle; Schwalm, Christopher R.; Wofsy, Steven C. (2015-12-21)
    The terrestrial biosphere can release or absorb the greenhouse gases, carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) and therefore plays an important role in regulating atmospheric composition and climate1. ...
  • A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge 

    Meyer, Julie L.; Jaekel, Ulrike; Tully, Benjamin J.; Glazer, Brian T.; Wheat, C. Geoffrey; Lin, Huei-Ting; Hsieh, Chih-Chiang; Cowen, James P.; Hulme, Samuel M.; Girguis, Peter R.; Huber, Julie A. (Nature Publishing Group, 2016-03-03)
    The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active ...
  • Spatial and temporal trends in summertime climate and water quality indicators in the coastal embayments of Buzzards Bay, Massachusetts 

    Rheuban, Jennie E.; Williamson, Shanna; Costa, Joe E.; Glover, David M.; Jakuba, Rachel W.; McCorkle, Daniel C.; Neill, Christopher; Williams, Tony; Doney, Scott C. (Copernicus Publications on behalf of the European Geosciences Union, 2016-01-15)
    Degradation of coastal ecosystems by eutrophication is largely defined by nitrogen loading from land via surface water and groundwater flows. However, indicators of water quality are highly variable due to a myriad of other ...
  • The amyloid precursor protein of Alzheimer’s disease clusters at the organelle/microtubule interface on organelles that bind microtubules in an ATP dependent manner 

    Stevenson, James W.; Conaty, Eliza A.; Walsh, Rylie B.; Poidomani, Paul J.; Samoriski, Colin M.; Scollins, Brianne J.; DeGiorgis, Joseph A. (Public Library of Science, 2016-01-27)
    The amyloid precursor protein (APP) is a causal agent in the pathogenesis of Alzheimer’s disease and is a transmembrane protein that associates with membrane-limited organelles. APP has been shown to co-purify through ...
  • Extensive modulation of the fecal metagenome in children With Crohn’s disease during exclusive enteral nutrition 

    Quince, Christopher; Ijaz, Umer Zeeshan; Loman, Nick; Eren, A. Murat; Saulnier, Delphine; Russell, Julie; Haig, Sarah J.; Calus, Szymon T.; Quick, Joshua; Barclay, Andrew H.; Bertz, Martin; Blaut, Michael; Hansen, Richard; McGrogan, Paraic; Russell, Richard K.; Edwards, Christine A.; Gerasimidis, Konstantinos (Nature Publishing Group, 2015-11-03)
    Exploring associations between the gut microbiota and colonic inflammation and assessing sequential changes during exclusive enteral nutrition (EEN) may offer clues into the microbial origins of Crohn’s disease (CD). Fecal ...
  • The use and limits of scientific names in biological informatics 

    Remsen, David P. (Pensoft Publishers, 2016-01-07)
    Scientific names serve to label biodiversity information: information related to species. Names, and their underlying taxonomic definitions, however, are unstable and ambiguous. This negatively impacts the utility of names ...
  • Mobile genetic elements : in silico, in vitro, in vivo 

    Arkhipova, Irina R.; Rice, Phoebe A. (2015-11-30)
    Mobile genetic elements (MGEs), also called transposable elements (TEs), represent universal components of most genomes and are intimately involved in nearly all aspects of genome organization, function, and evolution. ...
  • Tools for the microbiome : nano and beyond 

    Biteen, Julie S.; Blainey, Paul C.; Cardon, Zoe G.; Chun, Miyoung; Church, George M.; Dorrestein, Pieter C.; Fraser, Scott E.; Gilbert, Jack A.; Jansson, Janet K.; Knight, Rob; Miller, Jeff F.; Ozcan, Aydogan; Prather, Kimberly A.; Quake, Stephen R.; Ruby, Edward G.; Silver, Pamela A.; Taha, Sharif; van den Engh, Ger; Weiss, Paul S.; Wong, Gerard C. L.; Wright, Aaron T.; Young, Thomas D. (American Chemical Society, 2015-12-22)
    The microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating ...
  • Relationship between leaf physiologic traits and canopy color indices during the leaf expansion period in an oak forest 

    Liu, Zhunqiao; Hu, Haibo; Yu, Hua; Yang, Xi; Yang, Hualei; Ruan, Cunxin; Wang, Yan; Tang, Jianwu (John Wiley & Sons, 2015-12-11)
    Plant phenology has a significant impact on the forest ecosystem carbon balance. Detecting plant phenology by capturing the time-series canopy images through digital camera has become popular in recent years. However, the ...

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