Now showing items 1-20 of 216

    • Accuracy and quality of massively parallel DNA pyrosequencing 

      Huse, Susan M.; Huber, Julie A.; Morrison, Hilary G.; Sogin, Mitchell L.; Mark Welch, David B. (BioMed Central, 2007-07-20)
      Massively parallel pyrosequencing systems have increased the efficiency of DNA sequencing, although the published per-base accuracy of a Roche GS20 is only 96%. In genome projects, highly redundant consensus assemblies can ...
    • Adaptive evolution of voltage-gated sodium channels : the first 800 million years 

      Zakon, Harold H. (2012-04)
      Voltage-gated Na+-permeable (Nav) channels form the basis for electrical excitability in animals. Nav channels evolved from Ca2+ channels and were present in the common ancestor of choanoflagellates and animals although ...
    • Alkenone producers inferred from well-preserved 18S rDNA in Greenland lake sediments 

      D'Andrea, William J.; Lage, Melissa; Martiny, Jennifer B. H.; Laatsch, Abby D.; Amaral-Zettler, Linda A.; Sogin, Mitchell L.; Huang, Yongsong (American Geophysical Union, 2006-09-19)
      The 18S ribosomal DNA (rDNA) sequences of haptophyte algae were successfully amplified using the polymerase chain reaction (PCR) from water filtrate, surface sediments, and a late-Holocene sediment sample (∼1000 years old) ...
    • Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis 

      Suga, Koushirou; Mark Welch, David B.; Tanaka, Yukari; Sakakura, Yoshitaka; Hagiwara, Atsushi (Public Library of Science, 2007-08-01)
      Rotifers are among the most common non-arthropod animals and are the most experimentally tractable members of the basal assemblage of metazoan phyla known as Gnathifera. The monogonont rotifer Brachionus plicatilis is a ...
    • 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 ...
    • Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys 

      Nelson, Michael C.; Morrison, Hilary G.; Benjamino, Jacquelynn; Grim, Sharon L.; Graf, Joerg (Public Library of Science, 2014-04-10)
      The exploration of microbial communities by sequencing 16S rRNA genes has expanded with low-cost, high-throughput sequencing instruments. Illumina-based 16S rRNA gene sequencing has recently gained popularity over 454 ...
    • Anvi’o : an advanced analysis and visualization platform for ‘omics data 

      Eren, A. Murat; Esen, Ozcan C.; Quince, Christopher; Vineis, Joseph H.; Morrison, Hilary G.; Sogin, Mitchell L.; Delmont, Tom O. (PeerJ, 2015-10-08)
      Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively ...
    • Aquarium microbiome response to ninety-percent system water change : clues to microbiome management 

      Van Bonn, William; LaPointe, Allen; Gibbons, Sean M.; Frazier, Angel; Hampton-Marcell, Jarrad T.; Gilbert, Jack A. (2015-04)
      The bacterial community composition and structure of water from an established teleost fish system was examined before, during and after a major water change to explore the impact of such a water-change disturbance on the ...
    • Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys 

      Brazelton, William J.; Ludwig, Kristin A.; Sogin, Mitchell L.; Andreishcheva, Ekaterina N.; Kelley, Deborah S.; Shen, Chuan-Chou; Edwards, R. Lawrence; Baross, John A. (2009-12-06)
      The Lost City Hydrothermal Field, an ultramafic-hosted system located 15 km west of the Mid-Atlantic Ridge, has experienced at least 30,000 years of hydrothermal activity. Previous studies have shown that its carbonate ...
    • ASPIRE : the Amundsen Sea Polynya International Research Expedition 

      Yager, Patricia L.; Sherrell, Robert M.; Stammerjohn, Sharon E.; Alderkamp, Anne-Carlijn; Schofield, Oscar M. E.; Abrahamsen, E. Povl; Arrigo, Kevin R.; Bertilsson, Stefan; Garay, D. Lollie; Guerrero, Raul; Lowry, Kate E.; Moksnes, Per-Olav; Ndungu, Kuria; Post, Anton F.; Randall-Goodwin, Evan; Riemann, Lasse; Severmann, Silke; Thatje, Sven; van Dijken, Gert L.; Wilson, Stephanie (The Oceanography Society, 2012-09)
      In search of an explanation for some of the greenest waters ever seen in coastal Antarctica and their possible link to some of the fastest melting glaciers and declining summer sea ice, the Amundsen Sea Polynya International ...
    • 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 ...
    • Axial Seamount 

      Chadwick, William W.; Butterfield, David A.; Embley, Robert W.; Tunnicliffe, Verena; Huber, Julie A.; Nooner, Scott L.; Clague, David A. (Oceanography Society, 2010-03)
      Axial Seamount is a hotspot volcano superimposed on the Juan de Fuca Ridge (JdFR) in the Northeast Pacific Ocean. Due to its robust magma supply, it rises ~ 800 m above the rest of JdFR and has a large elongate summit ...
    • 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 ...
    • Bacterial group II introns in a deep-sea hydrothermal vent environment 

      Podar, Mircea; Mullineaux, Lauren S.; Huang, Hon-Ren; Perlman, Philip S.; Sogin, Mitchell L. (American Society for Microbiology, 2002-12)
      Group II introns are catalytic RNAs and mobile retrotransposable elements known to be present in the genomes of some nonmarine bacteria and eukaryotic organelles. Here we report the discovery of group II introns in a ...
    • Bidirectional incompatibility among divergent Wolbachia and incompatibility level differences among closely related Wolbachia in Nasonia 

      Bordenstein, Seth R.; Werren, John H. (2007-03-07)
      Most insect groups harbor obligate bacterial symbionts from the alphaproteobacterial genus Wolbachia. These bacteria alter insect reproduction in ways that enhance their cytoplasmic transmission. One of the most common ...
    • A bifunctional DNA binding region in Tn5 transposase 

      Gradman, Richard J.; Ptacin, Jerod L.; Bhasin, Archna; Reznikoff, William S.; Goryshin, Igor Y. (Blackwell, 2007-12-16)
      Tn5 transposition is a complicated process that requires the formation of a highly ordered protein–DNA structure, a synaptic complex, to catalyse the movement of a sequence of DNA (transposon) into a target DNA. Much is ...
    • Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents 

      Anderson, Rika E.; Sogin, Mitchell L.; Baross, John A. (2014-11)
      Environmental gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in ...
    • The biogeography of the Plastisphere : implications for policy 

      Amaral-Zettler, Linda A.; Zettler, Erik R.; Slikas, Beth; Boyd, Gregory D.; Melvin, Donald W.; Morrall, Clare E.; Proskurowski, Giora; Mincer, Tracy J. (Ecological Society of America, 2015-12)
      Microplastics (particles less than 5 mm) numerically dominate marine debris and occur from coastal waters to mid-ocean gyres, where surface circulation concentrates them. Given the prevalence of plastic marine debris (PMD) ...
    • Broadly sampled multigene trees of eukaryotes 

      Yoon, Hwan Su; Grant, Jessica; Tekle, Yonas I.; Wu, Min; Chaon, Benjamin C.; Cole, Jeffrey C.; Logsdon, John M.; Patterson, David J.; Bhattacharya, Debashish; Katz, Laura A. (BioMed Central, 2008-01-18)
      Our understanding of the eukaryotic tree of life and the tremendous diversity of microbial eukaryotes is in flux as additional genes and diverse taxa are sampled for molecular analyses. Despite instability in many analyses, ...