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Anaerobic Oxidation Of Ethane, Propane, And Butane By Marine Microbes: A Mini Review, Rajesh Singh, Michael S. Guzman, Arpita Bose 2017 Washington University in St. Louis

Anaerobic Oxidation Of Ethane, Propane, And Butane By Marine Microbes: A Mini Review, Rajesh Singh, Michael S. Guzman, Arpita Bose

Biology Faculty Publications & Presentations

The deep ocean and its sediments are a continuous source of non-methane short-chain alkanes (SCAs) including ethane, propane, and butane. Their high global warming potential, and contribution to local carbon and sulfur budgets has drawn significant scientific attention. Importantly, microbes can use gaseous alkanes and oxidize them to CO2, thus acting as effective biofilters. A relative decrease of these gases with a concomitant 13C enrichment of propane and n-butane in interstitial waters vs. the source suggests microbial anaerobic oxidation. The reported uncoupling of sulfate-reduction (SR) from anaerobic methane oxidation supports their microbial consumption. To date, strain BuS5 ...


Intestinal Organoids Model Human Responses To Infection By Commensal And Shiga Toxin Producing Escherichia Coli, Sayali S. Karve, Suman Pradhan, Doyle V. Ward, Alison A. Weiss 2017 University of Cincinnati

Intestinal Organoids Model Human Responses To Infection By Commensal And Shiga Toxin Producing Escherichia Coli, Sayali S. Karve, Suman Pradhan, Doyle V. Ward, Alison A. Weiss

Open Access Articles

Infection with Shiga toxin (Stx) producing Escherichia coli O157:H7 can cause the potentially fatal complication hemolytic uremic syndrome, and currently only supportive therapy is available. Lack of suitable animal models has hindered study of this disease. Induced human intestinal organoids (iHIOs), generated by in vitro differentiation of pluripotent stem cells, represent differentiated human intestinal tissue. We show that iHIOs with addition of human neutrophils can model E. coli intestinal infection and innate cellular responses. Commensal and O157:H7 introduced into the iHIO lumen replicated rapidly achieving high numbers. Commensal E. coli did not cause damage, and were completely contained ...


Scanning Labyrinthulomycete Genomes For Yeast Transcription Factor Binding Site Motifs, Jackie L. Collier, Joshua Rest 2017 SUNY Stony Brook

Scanning Labyrinthulomycete Genomes For Yeast Transcription Factor Binding Site Motifs, Jackie L. Collier, Joshua Rest

Interdisciplinary Research Data

To develop broadly useful methods for the genetic manipulation of Labyrinthulomycetes (a diverse group of ubiquitous osmoheterotrophic marine protists), it is essential to understand the similarities and differences in regulation of gene expression among them. Toward this end we have used FIMO from the MEME suite (http://meme-suite.org/doc/fimo.html) to identify potential transcription factor binding sites in each of the three available genome sequences: Aplanochytrium kerguelense PBS07, Schizochytrium aggregatum ATCC 28209, and Aurantiochytrium limacinum ATCC MYA-1381


Measuring Bacterial Growth Using A 3d-Printable Spectrometer, Samuel R. Bunting 2017 The University of Akron

Measuring Bacterial Growth Using A 3d-Printable Spectrometer, Samuel R. Bunting

Honors Research Projects

Visible light spectroscopy is a commonly used technique for measuring the growth of bacterial cultures, and growth curves provide broadly important data. However, the equipment and resources required for these experiments has been restricted to higher education and industry due to high cost and sophistication. We have previously reported on an inexpensive, 3D-printable photospectrometer called the SpecPhone. This device utilizes an iPhone as the camera, along with several other, inexpensive additions to make a fully functional spectrometer. Here, the application of the SpecPhone is expanded to the quantification of actively dividing E. coli cultures. Two protocols have been developed; one ...


Discovery And Characterization Of Bile Acid And Steroid Metabolism Pathways In Gut-Associated Microbes, Spencer Harris 2017 Virginia Commonwealth University

Discovery And Characterization Of Bile Acid And Steroid Metabolism Pathways In Gut-Associated Microbes, Spencer Harris

Theses and Dissertations

The human gut microbiome is a complex microbial ecosystem residing in the lumen of our gastrointestinal tract. The type and amounts of microbes present in this ecosystem varies based on numerous factors, including host genetics, diet, and environmental factors. The human gut microbiome plays an important role in normal host physiological functions, including providing energy to colonocytes in the form of short-chain fatty acids. However, gut microbial metabolites have also been associated with numerous disease states. Current tools for analyzing the gut microbiome, such as high-throughput sequencing techniques, are limited in their predictive ability. Additionally, “-omic” approaches of studying the ...


Proteomic Approach For Extracting Cytoplasmic Proteins From Streptococcus Sanguinis Using Mass Spectrometry, Fadi Elrami, Kristina Nelson, Ping Xu 2017 Virginia Commonwealth University

Proteomic Approach For Extracting Cytoplasmic Proteins From Streptococcus Sanguinis Using Mass Spectrometry, Fadi Elrami, Kristina Nelson, Ping Xu

Philips Institute for Oral Health Research Publications

Streptococcus sanguinis is a commensal and early colonizer of oral cavity as well as an opportunistic pathogen of infectious endocarditis. Extracting the soluble proteome of this bacterium provides deep insights about the physiological dynamic changes under different growth and stress conditions, thus defining “proteomic signatures” as targets for therapeutic intervention. In this protocol, we describe an experimentally verified approach to extract maximal cytoplasmic proteins from Streptococcus sanguinis SK36 strain. A combination of procedures was adopted that broke the thick cell wall barrier and minimized denaturation of the intracellular proteome, using optimized buffers and a sonication step. Extracted proteome was quantitated ...


Loss Of Outer Membrane Porins In Clonally Related Clinical Isolates Of Klebsiella Pneumoniae Modifies The Bacteria; Resulting In Altered Resistance To Phagocytosis By Macrophages, Debra Nickole Brunson 2017 University of North Florida

Loss Of Outer Membrane Porins In Clonally Related Clinical Isolates Of Klebsiella Pneumoniae Modifies The Bacteria; Resulting In Altered Resistance To Phagocytosis By Macrophages, Debra Nickole Brunson

UNF Theses and Dissertations

Klebsiella pneumoniae is an opportunistic pathogen responsible for lobar pneumoniae, liver abscess, and septicemia. Clinical isolates are found to be extended spectrum beta lactamase positive with differential expression of the two classical porins, OmpK35 and OmpK36. Porin loss is associated with increased minimum inhibitory concentrations of beta lactam, cephalosporin, and carbapenem antibiotics that target the peptidoglycan. However, little is known about how porin loss affects other aspects of the cell envelope. The focus of this study was to characterize clinical isolates exhibiting differential porin expression and determine if the cumulative changes altered the resistance to phagocytosis by macrophages. The results ...


Jmh Dissertation 2016.Pdf, Jennifer Hayashi 2016 University of Massachusetts - Amherst

Jmh Dissertation 2016.Pdf, Jennifer Hayashi

Jennifer Hayashi

Mycobacterium is a diverse genus of actinobacteria that includes the causative agents of human tuberculosis and leprosy. Mycobacteria are protected by their unique, multilaminar cell envelope, which grants them intrinsic resistance to environmental challenges such as antibiotics. This essential cellular structure is elongated at the polar ends of cells, but the regulation of cytosolic precursor synthesis and localized envelope synthesis remains unclear. Here, we present the PMf (plasma membrane free of cell wall components), a membrane domain distinct from the bulk plasma membrane of Mycobacterium smegmatis. Proteomic and lipidomic characterization demonstrate that the PMf contains lipidic substrates ...


Spot 42 Srna Regulates Arabinose-Inducible Arabad Promoter Activity By Repressing Synthesis Of The High-Affinity Low-Capacity Arabinose Transporter., Jiandong Chen, Susan Gottesman 2016 National Cancer Institute

Spot 42 Srna Regulates Arabinose-Inducible Arabad Promoter Activity By Repressing Synthesis Of The High-Affinity Low-Capacity Arabinose Transporter., Jiandong Chen, Susan Gottesman

Jiandong Chen

The L-arabinose-inducible araBAD promoter (PBAD) allows tightly controlled and tunable expression of genes of interest in a broad range of bacterial species. It has been successfully used to study bacterial sRNA regulation, where PBAD drives expression of target mRNA translational fusions. Here we report that in Escherichia coli, Spot 42 sRNA can regulate PBAD promoter activity by affecting arabinose uptake. We demonstrate that Spot 42 sRNA represses araF, a gene encoding the AraF subunit of the high-affinity low-capacity arabinose transporter AraFGH, through direct base pairing interactions. We further show that endogenous Spot 42 sRNA is sufficient to ...


The Roles Of Biotin In Candida Albicans Physiology, Nur Ras Aini Ahmad Hussin 2016 University of Nebraska-Lincoln

The Roles Of Biotin In Candida Albicans Physiology, Nur Ras Aini Ahmad Hussin

Dissertations and Theses in Biological Sciences

Due to the increased number of immunocompromised patients, infections by Candida albicans have significantly increased in recent years. C. albicans transition from yeast to germ tubes is an essential factor for virulence. In this study we noted that Lee's medium, commonly used to induce filamentation, contained 500-fold more biotin than needed for growth. Thus, we investigated the effects of excess biotin on growth rate and filamentation by C. albicans in different media. At 37 °C, excess biotin (4 µM) enhanced germ tube formation (GTF) ca. 10-fold in both Lee's medium and a defined glucose proline medium, and ca ...


Characterization Of Antimicrobial Activity Of Culturable Bacteria Isolated From Krubera-Voronja Cave, Aiste Klusaite, Vida Vickackaite, Birute Vaitkeviciene, Rasa Karnickaite, Dominykas Bukelskis, Ieva Kieraite-Aleksandrova, Nomeda Kuisiene 2016 Vilnius University

Characterization Of Antimicrobial Activity Of Culturable Bacteria Isolated From Krubera-Voronja Cave, Aiste Klusaite, Vida Vickackaite, Birute Vaitkeviciene, Rasa Karnickaite, Dominykas Bukelskis, Ieva Kieraite-Aleksandrova, Nomeda Kuisiene

International Journal of Speleology

In the present study we aimed to perform the first analysis of antimicrobial activity of bacteria isolated from Krubera-Voronja Cave, with the main focus on their activity against Grampositive bacteria, including Gram-positive pathogens. Using five different media, in total 874 heterotrophic cultures were isolated from water and sediment samples collected in Krubera-Voronja Cave at a depth from 220 m to 1640 m. 14.0% of all isolates demonstrated antibacterial activity against Gram-positive and Gram-negative test microorganisms. Our results show that this percentage was not uniform; it increased with the sampling depth and was the highest in the lower part of ...


The Effects Of Exogenous Fatty Acids On Enterococcus Faecalis Og1rf, Holly Elizabeth Johnson Saito 2016 University of Tennessee, Knoxville

The Effects Of Exogenous Fatty Acids On Enterococcus Faecalis Og1rf, Holly Elizabeth Johnson Saito

Doctoral Dissertations

Enterococcus faecalis is a commensal of the mammalian intestine and an opportunistic pathogen that infects various locations in the human host. Specifically, the organism can infect surgical wounds, the urinary tract, and is an agent of endocarditis. Regardless of niche, this organism has access to fatty acid sources in the host, which may influence its ability to survive and cause infection; yet, the effects of exogenous fatty acids were unknown in E. faecalis. We have shown that complex sources of fatty acids such as bile or serum can significantly alter the membrane content and protect E. faecalis from acute membrane ...


Biosynthesis And Roles Of Virulence Conferring Cell Wall Associated Dimycocerosate Esters In Mycobacterium Marinum, Poornima Mohandas 2016 Graduate Center, City University of New York

Biosynthesis And Roles Of Virulence Conferring Cell Wall Associated Dimycocerosate Esters In Mycobacterium Marinum, Poornima Mohandas

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

Mycobacterial species include a variety of obligate and opportunistic pathogens that cause several important diseases affecting mankind such as tuberculosis and leprosy. The most unique feature of these bacteria is their intricate cell wall that poses a permeability barrier to antibiotics and contributes to their pathogenicity and persistence within the host. The cell wall hosts several complex lipids such as dimycocerosate esters (DIMs), which are found in many clinically relevant pathogenic species of mycobacteria. DIMs have been implicated in the virulence of mycobacteria and play a major role in helping the bacteria evade host immune responses. It is therefore crucial ...


The Effects Of Quorum Sensing And Temperature On The Soluble Proteome Of Vibrio Salmonicida, Christopher L. Massey 2016 California Polytechnic State University, San Luis Obispo

The Effects Of Quorum Sensing And Temperature On The Soluble Proteome Of Vibrio Salmonicida, Christopher L. Massey

Master's Theses and Project Reports

Vibrio salmonicida causes cold-water vibriosis in salmon populations around the world and causes financial damage to fisheries designed to farm these salmon. Very little is known about the physiology of how V. salmonicida causes disease and measures to contain vibriosis are restricted to either vaccinating individual fish against disease or administering antibiotics when an outbreak is detected. These procedures are costly and increase the risk for selection of antibiotic-resistant V. salmonicida strains. A recent reoccurrence of outbreaks in Norwegian fisheries provided incentive to better understand the virulence mechanisms of V. salmonicida. In this thesis, a proteomic approach was used to ...


Handwashing: A Study Of The History, Methods, And Psychology Surrounding Hand Hygiene, Daniel J. Remillard 2016 Liberty University

Handwashing: A Study Of The History, Methods, And Psychology Surrounding Hand Hygiene, Daniel J. Remillard

Senior Honors Theses

This paper covers three different areas concerning handwashing. First a review of the history of handwashing is done, going from ancient times to its introduction into modern medicine via Dr. Ignaz Semmelweis. This section gives a sobering reminder not to instantly reject data that comes in conflict with prevalent thought.

Then current medical knowledge about handwashing is examined, and the conclusion reached states that handwashing is best done with non-antibacterial soap.

Finally, a review of the psychology of handwashing shows that medical professionals often tend toward neglect if unwatched and unmotivated by an outside source. However, those suffering from obsessive ...


Biophysical Studies Of Cell Division Protein Localization Mechanisms In Escherichia Coli, Matthew Wayne Bailey 2016 University of Tennessee - Knoxville

Biophysical Studies Of Cell Division Protein Localization Mechanisms In Escherichia Coli, Matthew Wayne Bailey

Doctoral Dissertations

How nanometer-scale proteins position accurately within micron-scale bacteria has intrigued both biologists and physicists alike. A critical process requiring precise protein localization is cell division. In most bacteria, cell division starts with the self-assembly of the FtsZ proteins into filaments that form a ring-like structure encircling the cell at its middle, the Z-ring. The Z-ring is a scaffold for additional proteins that synthesize the lateral cell wall which separates the two daughter cells. If division planes are misplaced relative to bacterial chromosomes, also called nucleoids, daughter cells with incomplete genetic material can be produced. In Escherichia coli, research carried out ...


Environmentally Driven Orchestration Of Metabolisms By Prochlorococcus Spp., Martin James Szul 2016 University of Tennessee - Knoxville

Environmentally Driven Orchestration Of Metabolisms By Prochlorococcus Spp., Martin James Szul

Doctoral Dissertations

In the oligotrophic waters of the world’s open oceans physical factors such as pH, salinity, and temperature are generally stable. The nutrient limited conditions as well as the low environmental variability endemic to these ecosystems select for specialists that gain fitness advantages through minimalism, efficiency, and thrift. These physical characteristics are thought to reduce nutrient demand while allowing for constant metabolic activity and growth, but the mechanisms that promote these fitness advantages are currently unknown. To better understand how these physiologies improve selective fitness for the dominant phytoplankton, we observed metabolic parameters under environmental conditions typical to these waters ...


Xct Increases Tuberculosis Susceptibility By Regulating Antimicrobial Function And Inflammation, Yi Cai, Subhalaxmi Nambi, Christopher M. Sassetti, Fudi Wang, Xinchun Chen 2016 Guangdong Medical College

Xct Increases Tuberculosis Susceptibility By Regulating Antimicrobial Function And Inflammation, Yi Cai, Subhalaxmi Nambi, Christopher M. Sassetti, Fudi Wang, Xinchun Chen

Open Access Articles

The physiological functions of macrophage, which plays a central role in the pathogenesis of tuberculosis, depend on its redox state. System xc-, a cystine-glutamate transporter, which consists of xCT and CD98, influences many ROS-dependent pathways by regulating the production of the antioxidant glutathione. xCT's ability to alter this critical host redox balance by increasing the glutathione synthesis aspect of phagocyte physiology suggested that it might influence tuberculosis pathogenesis. In this study, we found that the xCT expression was increased in peripheral blood monocyte of active tuberculosis. xCT expression in macrophage was induced by Mycobacterium tuberculosis (Mtb) through TLR2/Akt- ...


Defining Environmental Stresses That Activate The Rna Repair Operon In Salmonella Typhimurium, Caleb M. Gulledge 2016 Olivet Nazarene University

Defining Environmental Stresses That Activate The Rna Repair Operon In Salmonella Typhimurium, Caleb M. Gulledge

Honors Program Projects

Background

RNA polymerase holoenzyme (Eσ) mediates transcription in eubacteria, and is composed of five constant subunits (α2ββ’ω) and a variable sigma (σ) subunit that is responsible for promoter recognition and initiation of transcription. An alternative sigma factor in Salmonella Typhimurium, σ54 (also called RpoN), is mechanistically different than classical σ70-type sigmas, requiring a different promoter consensus sequence, an activator, and ATP hydrolysis. The Rtc RNA repair operon lies within the regulon of RpoN in S. Typhimurium, but has no known physiological function. Previous work characterized similar systems in archaea and humans, which were determined ...


Microbial Community And Chemical Characteristics Of Swine Manure During Maturation, Steven L. Trabue, Brian J. Kerr, Bradley L. Bearson, Manhoi Hur, Timothy Parkin, Eve S. Wurtele, Cherrie J. Ziemer 2016 United States Department of Agriculture

Microbial Community And Chemical Characteristics Of Swine Manure During Maturation, Steven L. Trabue, Brian J. Kerr, Bradley L. Bearson, Manhoi Hur, Timothy Parkin, Eve S. Wurtele, Cherrie J. Ziemer

Genetics, Development and Cell Biology Publications

Swine diet formulations have the potential to lower animal emissions, including odor and ammonia (NH3). The purpose of this study was to determine the impact of manure storage duration on manure chemical and microbial properties in swine feeding trials. Three groups of 12 pigs were fed a standard corn–soybean meal diet over a 13-wk period. Urine and feces were collected at each feeding and transferred to 12 manure storage tanks. Manure chemical characteristics and headspace gas concentrations were monitored for NH3, hydrogen sulfide (H2S), volatile fatty acids, phenols, and indoles. Microbial analysis of the stored ...


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