Scanning Labyrinthulomycete Genomes For Yeast Transcription Factor Binding Site Motifs, 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
Discovery And Characterization Of Bile Acid And Steroid Metabolism Pathways In Gut-Associated Microbes, 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 ...
Measuring Bacterial Growth Using A 3d-Printable Spectrometer, 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 ...
The Roles Of Biotin In Candida Albicans Physiology, 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, 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 ...
Biosynthesis And Roles Of Virulence Conferring Cell Wall Associated Dimycocerosate Esters In Mycobacterium Marinum, 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, 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, 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 ...
Environmentally Driven Orchestration Of Metabolisms By Prochlorococcus Spp., 2016 University of Tennessee - Knoxville
Environmentally Driven Orchestration Of Metabolisms By Prochlorococcus Spp., Martin James Szul
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, 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- ...
Microbial Community And Chemical Characteristics Of Swine Manure During Maturation, 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 ...
Conversion Of Cellulose To Ethanol By The Biofuels Microbe Clostridium Phytofermentans: Quantification Of Growth And Role Of An Rnf-Complex In Energy Conservation, 2016 University of Massachusetts Amherst
Conversion Of Cellulose To Ethanol By The Biofuels Microbe Clostridium Phytofermentans: Quantification Of Growth And Role Of An Rnf-Complex In Energy Conservation, Jesús G. Alvelo-Maurosa
Doctoral Dissertations May 2014 - current
The anaerobic mesophilic bacterium Clostridium phytofermentans grows and ferments multiple plant-based substrates into ethanol as the main product of fermentation. The capacity of C. phytofermentans to convert plant biomass into ethanol, propanol, and short-chain fatty acids is strongly attractive for industry. Specific physiological capabilities of C. phytofermentans allow the microbe to generate high amounts of ethanol compared to acetate. However, little is known about membrane energetics in C. phytofermentans, or its role in energy conservation and production of high levels of ethanol during fermentation of plant biomass substrates.
In the first research project presented in this dissertation, we examined C ...
Expansion Of And Reclassification Within The Family Lachnospiraceae, 2016 University of Massachusetts - Amherst
Expansion Of And Reclassification Within The Family Lachnospiraceae, Kelly N. Haas
Doctoral Dissertations May 2014 - current
Many of the taxa in the family Lachnospiraceae are currently misclassified as Clostridium spp. Here attempt to rectify many of these issues, beginning with an in-depth genomic and physiologic analysis of Clostridium methoxybenzovorans, culminating in the assertion that is a heterotype of Clostridium indolis, followed by reclassification of the broader group in which this organism resides. We propose two novel genera, Lacriformis and Enterocloster, to reclassify this clade, this includes reclassification of Clostridium sphenoides, Clostridium indolis, Clostridium saccharolyticum, Clostridium celerecrescens, Clostridium xylanolyticum, Clostridium algidixylanolyticum, Clostridium aerotolerans, Clostridium amygdalinum, and Desulfotomaculum guttoideum as Lacriformis sphenoides, comb. nov., Lacriformis indolis, comb. nov ...
Toxicity Of Engineered Nanomaterials To Plant Growth Promoting Rhizobacteria, 2016 University of Kentucky
Toxicity Of Engineered Nanomaterials To Plant Growth Promoting Rhizobacteria, Ricky W. Lewis
Theses and Dissertations--Plant and Soil Sciences
Engineered nanomaterials (ENMs) have become ubiquitous in consumer products and industrial applications, and consequently the environment. Much of the environmentally released ENMs are expected to enter terrestrial ecosystems via land application of nano-enriched biosolids to agricultural fields. Among the organisms most likely to encounter nano-enriched biosolids are the key soil bacteria known as plant growth promoting rhizobacteria (PGPR). I reviewed what is known concerning the toxicological effects of ENMs to PGPR and observed the need for high-throughput methods to evaluate lethal and sublethal toxic responses of aerobic microbes. I addressed this issue by developing high-throughput microplate assays which allowed me ...
Physiological Characterization Of Prochlorococcus Under Abiotic Stressors Temperature And Hydrogen Peroxide, 2015 University of Tennessee - Knoxville
Physiological Characterization Of Prochlorococcus Under Abiotic Stressors Temperature And Hydrogen Peroxide, Lanying Ma
Cyanobacteria of the genus Prochlorococcus are the smallest and most abundant phytoplankters in the ocean. Temperature is a major influence on Prochlorococcus abundance and distribution in the ocean, but the physiological basis for this relationship is not well understood. In other microbes, lipid and fatty acid composition have been shown to be influenced by temperature, and temperature has also been proposed as a relevant factor for setting the elemental allocation in marine phytoplankton. In this study, we found that percentage of fatty acids unsaturation was negatively related with temperature in some Prochlorococcus strains, but this was not universal. Temperature had ...
Direct Visualization Of Hiv-1 Replication Intermediates Shows That Capsid And Cpsf6 Modulate Hiv-1 Intra-Nuclear Invasion And Integration, 2015 University of Massachusetts Medical School
Direct Visualization Of Hiv-1 Replication Intermediates Shows That Capsid And Cpsf6 Modulate Hiv-1 Intra-Nuclear Invasion And Integration, Christopher R. Chin, Jill Perreira, George Savidis, Jocelyn M. Portmann, Aaron M. Aker, Eric M. Feeley, Miles C. Smith, Abraham L. Brass
Microbiology and Physiological Systems Publications and Presentations
Direct visualization of HIV-1 replication would improve our understanding of the viral life cycle. We adapted established technology and reagents to develop an imaging approach, ViewHIV, which allows evaluation of early HIV-1 replication intermediates, from reverse transcription to integration. These methods permit the simultaneous evaluation of both the capsid protein (CA) and viral DNA genome (vDNA) components of HIV-1 in both the cytosol and nuclei of single cells. ViewHIV is relatively rapid, uses readily available reagents in combination with standard confocal microscopy, and can be done with virtually any HIV-1 strain and permissive cell lines or primary cells. Using ViewHIV ...
Rnasek Is A V-Atpase-Associated Factor Required For Endocytosis And The Replication Of Rhinovirus, Influenza A Virus, And Dengue Virus, 2015 University of Massachusetts Medical School
Rnasek Is A V-Atpase-Associated Factor Required For Endocytosis And The Replication Of Rhinovirus, Influenza A Virus, And Dengue Virus, Jill Perreira, Aaron Aker, George Savidis, Christopher R. Chin, William M. Mcdougall, Jocelyn M. Portmann, Paul Meraner, Miles Smith, Motiur Rahman, Richard E. Baker, Annick Gauthier, Michael Franti, Abraham L. Brass
Open Access Articles
Human rhinovirus (HRV) causes upper respiratory infections and asthma exacerbations. We screened multiple orthologous RNAi reagents and identified host proteins that modulate HRV replication. Here, we show that RNASEK, a transmembrane protein, was needed for the replication of HRV, influenza A virus, and dengue virus. RNASEK localizes to the cell surface and endosomal pathway and closely associates with the vacuolar ATPase (V-ATPase) proton pump. RNASEK is required for endocytosis, and its depletion produces enlarged clathrin-coated pits (CCPs) at the cell surface. These enlarged CCPs contain endocytic cargo and are bound by the scissioning GTPase, DNM2. Loss of RNASEK alters the ...
The Role Of Phosphatidylserine And Phosphatidylethanolamine In Candida Albicans Virulence, 2015 University of Tennessee - Knoxville
The Role Of Phosphatidylserine And Phosphatidylethanolamine In Candida Albicans Virulence, Sarah Elizabeth Davis
In hospitalized patients with neutropenia, Candida albicans is the fourth leading cause of systemic bloodstream infections, which have a mortality rate of approximately 30 %. The phosphatidylserine synthase enzyme of C. albicans, Cho1p, appears to be a good drug target as a mutant lacking this enzyme (the cho1Δ/Δ [null mutant]) is avirulent in animal models of Candida infections and this enzyme is not conserved in humans. We discovered that the loss of phosphatidylserine (PS) synthesis affects C. albicans' expression of the Als3p adhesin, a virulence protein, and loss of PS synthesis also compromises the cell wall, causing increased exposure ...
Secretion Of Heat-Labile Enterotoxin By Porcine-Origin Enterotoxigenic Escherichia Coli And Relation To Virulence, 2015 University of Nebraska-Lincoln
Secretion Of Heat-Labile Enterotoxin By Porcine-Origin Enterotoxigenic Escherichia Coli And Relation To Virulence, Prageeth R. Wijemanne
Dissertations & Theses in Veterinary and Biomedical Science
Heat-labile enterotoxin (LT) is an important virulence factor secreted by some strains of porcine-origin enterotoxigenic Escherichia coli (pETEC). The prototypic human-origin strain H10407 secretes LT via a type II secretion system (T2SS), but its presence or importance in pETEC has not been established. Exposure of pETEC to glucose has been shown to result in different secretion levels of LT. Furthermore, the relationship between the level of LT secreted and the virulence potential of the respective pETEC strain has not been established. To determine the relationship between the capacity to secrete LT and virulence in wild-type (WT) pETEC, 16 strains isolated ...
Influence Of Current Land Use And Edaphic Factors On Arbuscular Mycorrhizal (Am) Hyphal Abundance And Soil Organic Matter In And Near Serengeti National Park, Geofrey Soka
Arbuscular mycorrhizal fungi (AMF) are important microbial symbionts for plants especially when soil phosphorus (P) and nitrogen (N) are limited. Little is known about the distribution of AM hyphae in natural systems of tropical soils across landscapes and their association with different land uses. We studied mycorrhizal hyphal abundance in a wildlife grazed system, a livestock grazed system and under cultivated soils in and near Serengeti National Park, Tanzania. Samples of the upper 15 cm of soil beneath locally dominant plant species were collected. Hyphae were preserved on permanent slides and the length of hyphae per cubic centimeter of soil ...