Now showing items 1-20 of 1369

    • Screening of Additive Formulations Enables Off-Chip Drop Reverse Transcription Quantitative Polymerase Chain Reaction of Single Influenza A Virus Genomes 

      Loveday, Emma Kate; Zath, Geoffrey K.; Bikos, Dimitri A.; Jay, Zackary J.; Chang, Connie B. (American Chemical Society, 2021-03)
      The miniaturization of polymerase chain reaction (PCR) using drop-based microfluidics allows for amplification of single nucleic acids in aqueous picoliter-sized drops. Accurate data collection during PCR requires that ...
    • Answer Set Programming for Computing Constraints-Based Elementary Flux Modes: Application to Escherichia coli Core Metabolism 

      Mahout, Maxime; Carlson, Ross P.; Peres, Sabine (MDPI AG, 2020-12)
      Elementary Flux Modes (EFMs) provide a rigorous basis to systematically characterize the steady state, cellular phenotypes, as well as metabolic network robustness and fragility. However, the number of EFMs typically grows ...
    • An inexpensive, versatile, compact, programmable temperature controller and thermocycler for simultaneous analysis and visualization within a microscope 

      Cruz, Pablo Martínez; Wood, Mikayla A.; Abbasi, Reha; LeFevre, Thomas B.; McCalla, Stephanie E. (Springer Science and Business Media LLC, 2021-05)
      Microfluidic Lab on a Chip (LOC) devices are key enabling technologies for research and industry due to their compact size, which increases the number of integrated operations while decreasing reagent use. Common operations ...
    • Community-led, integrated, reproducible multi-omics with anvi’o 

      Eren, A. Murat; Kiefl, Evan; Shaiber, Alon; Veseli, Iva; Miller, Samuel E.; Schechter, Matthew S.; Fink, Isaac; Pan, Jessica N.; Yousef, Mahmoud; Fogarty, Emily C.; Trigodet, Florian; Watson, Andrea R.; Esen, Ozcan C.; Moore, Ryan M.; Clayssen, Quentin; Lee, Michael D.; Kivenson, Veronika; Graham, Elaina D.; Merrill, Bryan D.; Karkman, Antti; Blankenberg, Daniel; Eppley, John M.; Sjodin, Andreas; Scott, Jarrod J.; Vazquez-Campos, Xabier; McKay, Luke J.; McDaniel, Elizabeth A.; Stevens, Sarah L.R.; Anderson, Rika E.; Fuessel, Jessika; Fernandez-Guerra, Antonio; Maignien, Lois; Delmont, Tom O.; Willis, Amy D. (Springer Science and Business Media LLC, 2020-12)
      Big data abound in microbiology, but the workflows designed to enable researchers to interpret data can constrain the biological questions that can be asked. Five years after anvi’o was first published, this community-led ...
    • Role of hibernation promoting factor in ribosomal protein stability during Pseudomonas aeruginosa dormancy 

      Theng, Sokuntheary; Williamson, Kerry S.; Franklin, Michael J. (MDPI, 2020-12)
      Pseudomonas aeruginosa is an opportunistic pathogen that causes biofilm-associated infections. P. aeruginosa can survive in a dormant state with reduced metabolic activity in nutrient-limited environments, including the ...
    • Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics 

      Schweitzer, Hannah D.; Smith, Heidi J.; Barnhart, Elliott P.; McKay, Luke J.; Gerlach, Robin; Cunningham, Alfred B.; Malmstrom, Rex R.; Goudeau, Danielle; Fields, Matthew W. (Springer Science and Business Media LLC, 2022-02)
      Environmentally relevant metagenomes and BONCAT-FACS derived translationally active metagenomes from Powder River Basin coal seams were investigated to elucidate potential genes and functional groups involved in hydrocarbon ...
    • In Situ Enhancement and Isotopic Labeling of Biogenic Coalbed Methane 

      Barnhart, Elliott P.; Ruppert, Leslie; Hiebert, Randy; Smith, Heidi J.; Schweitzer, Hannah D.; Clark, Arthur C.; Weeks, Edwin P.; Orem, William H.; Varonka, Matthew S.; Platt, George; Shelton, Jenna L.; Davis, Katherine J.; Hyatt, Robert J.; McIntosh, Jennifer C.; Ashley, Kilian; Ono, Shuhei; Martini, Anna M.; Hackley, Keith C.; Gerlach, Robin; Spangler, Lee; Phillips, Adrienne J.; Barry, Mark; Cunningham, Alfred B.; Fields, Matthew W. (American Chemical Society, 2022-02)
      Subsurface microbial (biogenic) methane production is an important part of the global carbon cycle that has resulted in natural gas accumulations in many coal beds worldwide. Laboratory studies suggest that complex ...
    • Experimental Designs to Study the Aggregation and Colonization of Biofilms by Video Microscopy With Statistical Confidenc 

      Pettygrove, Brian A.; Smith, Heidi J.; Pallister, Kyler B.; Voyich, Jovanka M.; Stewart, Philip S.; Parker, Albert E. (Frontiers Media SA, 2022-01)
      The goal of this study was to quantify the variability of confocal laser scanning microscopy (CLSM) time-lapse images of early colonizing biofilms to aid in the design of future imaging experiments. To accomplish this a ...
    • Change Rippling through Our Waters and Culture 

      Martin, Christine; Doyle, John; LaFrance, JoRee; Lefthand, Myra J.; Young, Sara L.; Three Irons, Emery; Eggers, Margaret J. (Wiley, 2020-04)
      It is well established that climate change is already causing a wide variety of human health impacts in the United States and globally, and that for many reasons Native Americans are particularly vulnerable. Tribal water ...
    • The use of a CDC biofilm reactor to grow multi-strain Listeria monocytogenes biofilm 

      Mendez, Ellen; Walker, Diane K.; Vipham, Jessie; Trinetta, Valentina (Elsevier BV, 2020-12)
      Listeria monocytogenes is one of the most concerning pathogens for the food industry due to its ability to form biofilms, particularly in difficult-to-clean sites of processing facilities. There is a current industry-wide ...
    • The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases 

      Altae-Tran, Han; Kannan, Soumya; Demircioglu, F. Esra; Oshiro, Rachel; Nety, Suchita P.; McKay, Luke J.; Dlakić, Mensur; Inskeep, William P.; Makarova, Kira S.; Macrae, Rhiannon K.; Koonin, Eugene V.; Zhang, Feng (American Association for the Advancement of Science, 2021-10)
      IscB proteins are putative nucleases encoded in a distinct family of IS200/IS605 transposons and are likely ancestors of the RNA-guided endonuclease Cas9, but the functions of IscB and its interactions with any RNA remain ...
    • Next-generation physiology approaches to study microbiome function at single cell level 

      Hatzenpichler, Roland; Krukenberg, Viola; Spietz, Rachel L.; Jay, Zackary J. (Springer Science and Business Media LLC, 2020-02)
      The function of cells in their native habitat often cannot be reliably predicted from genomic data or from physiology studies of isolates. Traditional experimental approaches to study the function of taxonomically and ...
    • Streptococcus mutans and actinomyces naeslundii interaction in dual-species biofilm 

      de Oliveira, Rosa Virginia Dutra; Bonafé, Fernanda Salloume Sampaio; Spolidorio, Denise Madalena Palomari; Koga-Ito, Cristiane Yumi; de Farias, Aline Leite; Kirker, Kelly R.; James, Garth A.; Brighenti, Fernanda Lourenção (MDPI AG, 2020-01)
      The study of bacterial interaction between Streptococcus mutans and Actinomyces naeslundii may disclose important features of biofilm interspecies relationships. The aim of this study was to characterize—with an emphasis ...
    • The establishment of the CBE launched biofilms as a field of specialized research 

      Fields, Matthew W.; Sturman, Paul; Anderson, Skip (The establishment of the CBE launched biofilms as a field of specialized research, 2020-12)
      The Center for Biofilm Engineering was the first center of excellence focused on biofilms and was originally funded through the Engineering Research Center Program from the U.S. National Science Foundation. After almost ...
    • Efficacy of common antiseptic solutions against clinically relevant microorganisms in biofilm 

      O’Donnell, Jeffrey A.; Wu, Mark; Cochrane, Niall H.; Belay, Elshaday; Myntti, Matthew F.; James, Garth A.; Ryan, Sean P.; Seyler, Thorsten M. (British Editorial Society of Bone & Joint Surgery, 2021-05)
      Aims Periprosthetic joint infections (PJIs) are among the most devastating complications after joint arthroplasty. There is limited evidence on the efficacy of different antiseptic solutions on reducing biofilm burden. ...
    • Sulfenate Esters of Simple Phenols Exhibit Enhanced Activity against Biofilms 

      Walsh, Danica J.; Livinghouse, Tom; Durling, Greg M.; Chase-Bayless, Yenny; Arnold, Adrienne D.; Stewart, Philip S. (American Chemical Society, 2020-03)
      The recalcitrance exhibited by microbial biofilms to conventional disinfectants has motivated the development of new chemical strategies to control and eradicate biofilms. The activities of several small phenolic compounds ...
    • Infection Risk Reduction Program on Pathogens in High School and Collegiate Athletic Training Rooms 

      LaBelle, Mark W.; Knapik, Derrick M.; Arbogast, James W.; Zhou, Steve; Bowersock, Lisa; Parker, Albert; Voos, James E. (SAGE Publications, 2019-10)
      Background: Athletic training rooms have a high prevalence of bacteria, including multidrug-resistant organisms, increasing the risk for both local and systematic infections in athletes. There are limited data outlining ...
    • The origin of extracellular DNA in bacterial biofilm infections in vivo 

      Alhede, Maria; Alhede, Morten; Qvortrup, Klaus; Kragh, Kasper Nørskov; Jensen, Peter Østrup; Stewart, Philip Shook; Bjarnsholt, Thomas (Oxford University Press, 2020-03)
      Extracellular DNA (eDNA) plays an important role in both the aggregation of bacteria and in the interaction of the resulting biofilms with polymorphonuclear leukocytes (PMNs) during an inflammatory response. Here, transmission ...
    • Addressing wellbore integrity and thief zone permeability using microbially-induced calcium carbonate precipitation (MICP): A field demonstration 

      Kirkland, Catherine M.; Thane, Abby; Hiebert, Randy; Hyatt, Robert; Kirksey, Jim; Cunningham, Alfred B.; Gerlach, Robin; Spangler, Lee; Philips, Adrienne J. (Elsevier BV, 2020-02)
      Microbially-induced calcium carbonate precipitation (MICP) is an emerging biotechnology for wellbore integrity applications including sealing defects in wellbore cement and modifying the permeability of rock formations. ...
    • Pseudomonad reverse carbon catabolite repression, interspecies metabolite exchange, and consortial division of labor 

      Park, Heejoon; McGill, S. Lee; Arnold, Adrienne D.; Carlson, Ross P. (Springer Science and Business Media LLC, 2019-11)
      Microorganisms acquire energy and nutrients from dynamic environments, where substrates vary in both type and abundance. The regulatory system responsible for prioritizing preferred substrates is known as carbon catabolite ...

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