Recent Submissions

  • Identifying contamination with advanced visualization and analysis practices : metagenomic approaches for eukaryotic genome assemblies 

    Delmont, Tom O.; Eren, A. Murat (PeerJ, 2016-03-29)
    High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target ...
  • Synaptic activity regulates AMPA receptor trafficking through different recycling pathways 

    Zheng, Ning; Jeyifous, Okunola; Munro, Charlotte; Montgomery, Johanna M.; Green, William N. (eLife Sciences Publications, 2015-05-13)
    Changes in glutamatergic synaptic strength in brain are dependent on AMPA-type glutamate receptor (AMPAR) recycling, which is assumed to occur through a single local pathway. In this study, we present evidence that AMPAR ...
  • Satisfaction, water and fertilizer use in the American residential macrosystem 

    Groffman, Peter M.; Grove, J. Morgan; Polsky, Colin; Bettez, Neil D.; Morse, Jennifer L.; Cavender-Bares, Jeannine; Hall, Sharon J.; Heffernan, James B.; Hobbie, Sarah E.; Larson, Kelli L.; Neill, Christopher; Nelson, Kristen; Ogden, Laura; O'Neil-Dunne, Jarlath; Pataki, Diane; Roy Chowdhury, Rinku; Locke, Dexter H. (IOPScience, 2016-02-29)
    Residential yards across the US look remarkably similar despite marked variation in climate and soil, yet the drivers of this homogenization are unknown. Telephone surveys of fertilizer and irrigation use and satisfaction ...
  • Association of cesarean delivery and formula supplementation with the intestinal microbiome of 6-week-old infants 

    Madan, Juliette C.; Hoen, Anne G.; Lundgren, Sara N.; Farzan, Shohreh F.; Cottingham, Kathryn L.; Morrison, Hilary G.; Sogin, Mitchell L.; Li, Hongzhe; Moore, Jason H.; Karagas, Margaret R. (American Medical Association, 2016-01-11)
    The intestinal microbiome plays a critical role in infant development, and delivery mode and feeding method (breast milk vs formula) are determinants of its composition. However, the importance of delivery mode beyond the ...
  • A shared role for sonic hedgehog signalling in patterning chondrichthyan gill arch appendages and tetrapod limbs 

    Gillis, J. Andrew; Hall, Brian K. (Company of Biologists, 2016-04-19)
    Chondrichthyans (sharks, skates, rays and holocephalans) possess paired appendages that project laterally from their gill arches, known as branchial rays. This led Carl Gegenbaur to propose that paired fins (and hence ...
  • Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis 

    Zozaya, Marcela; Ferris, Michael J.; Siren, Julia D.; Lillis, Rebecca; Myers, Leann; Nsuami, M. Jacques; Eren, A. Murat; Brown, Jonathan; Taylor, Christopher M.; Martin, David H. (BioMed Central, 2016-04-19)
    The epidemiology of bacterial vaginosis (BV) suggests it is sexually transmissible, yet no transmissible agent has been identified. It is probable that BV-associated bacterial communities are transferred from male to female ...
  • Bacterial diversity and community composition from seasurface to subseafloor 

    Walsh, Emily A.; Kirkpatrick, John B.; Rutherford, Scott D.; Smith, David; Sogin, Mitchell L.; D'Hondt, Steven (Nature Publishing Group, 2015-10-02)
    We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the ...
  • DNA damage induces nuclear actin filament assembly by Formin-2 and Spire-1/2 that promotes efficient DNA repair 

    Belin, Brittany J.; Lee, Terri; Mullins, R. Dyche (eLife Sciences Publications, 2015-08-19)
    Actin filaments assemble inside the nucleus in response to multiple cellular perturbations, including heat shock, protein misfolding, integrin engagement, and serum stimulation. We find that DNA damage also generates ...
  • 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 ...
  • A framework to assess biogeochemical response to ecosystem disturbance using nutrient partitioning ratios 

    Kranabetter, J. Marty; McLauchlan, Kendra K.; Enders, Sara K.; Fraterrigo, Jennifer M.; Higuera, Philip E.; Morris, Jesse L.; Rastetter, Edward B.; Barnes, Rebecca T.; Buma, Brian; Gavin, Daniel; Gerhart, Laci M.; Gillson, Lindsey; Hietz, Peter; Mack, Michelle C.; McNeil, Brenden; Perakis, Steven S. (2015-11)
    Disturbances affect almost all terrestrial ecosystems, but it has been difficult to identify general principles regarding these influences. To improve our understanding of the long-term consequences of disturbance on ...
  • 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. ...

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