A Comparative Study Of Equine Gut Microbiomes Using 16s And 18s Rrna Sequencing,
2019
Otterbein University
A Comparative Study Of Equine Gut Microbiomes Using 16s And 18s Rrna Sequencing, Jillian Jorgenson
Undergraduate Honors Thesis Projects
The gut microbiome of domestic horses (Equus ferus caballus) can be broken down into two primary divisions of interest: (1) prokaryotic composition, consisting of bacteria and archaea and (2) fungal composition. Within the gut, there are also eukaryotic parasite communities that may interact with the microbiome. While each has been the subject of various scientific explorations, in this study we analyze the potential interconnectedness of these categories. To determine the extent to which each component of the gut microbiome/parasitic communities influences the other, DNA was extracted and amplified from the fecal samples of eight horses. A combination of …
The Gut Microbiome: Is Fecal Matter Microbial Composition A Proxy For Intestinal Microbial Composition In Studies Of The Microbiome,
2019
Central Washington University
The Gut Microbiome: Is Fecal Matter Microbial Composition A Proxy For Intestinal Microbial Composition In Studies Of The Microbiome, Enique Reyes
All Master's Theses
As many health phenomena seem to be affected directly and indirectly by the microbiome, gut microbiome research has increased in the last decade. Issues such as allergies, cancer, obesity, and other health complications have been shown to be influenced by the microbiome. Most of gut microbiome research is done by collecting and sequencing the DNA of the microbiome of the fecal matter from model organisms or human subjects. Studies that use this method of sample collection and analysis assume that fecal matter microbiomes are similar to intestinal microbiomes, and that it can be used as a proxy. At present, no …
Phenotypic And Transcriptomic Characterization Of Colonial Phase Variation In The Cholera Pathogen Reveals A Novel Smooth Biofilm-Defective Form,
2018
Louisiana State University and Agricultural and Mechanical College
Phenotypic And Transcriptomic Characterization Of Colonial Phase Variation In The Cholera Pathogen Reveals A Novel Smooth Biofilm-Defective Form, Bliss Nicole Lambert
LSU Doctoral Dissertations
Biofilm formation, through the production of Vibrio polysaccharide (VPS), greatly enhances the environmental fitness and pathogenic success of Vibrio cholerae. As a result of phase variation, V. cholerae can switch from a smooth form to rugose, whose cells produce excess VPS, resulting in highly structured biofilms and greater resistance to stress. To further characterize the reversible process of phase variation, we isolated three colonial lineages. Each lineage began with a smooth parent, N16961, and contained a rugose variant derived from the parent, N16961R, as well as a smooth revertant of the rugose, N16961SD. We found clear phenotypic and transcriptomic …
Methanogens, Plausible Extraterrestrial Life Forms On Mars, And Their Tolerance To Increasing Concentrations Of Illite Clay,
2018
University of Arkansas, Fayetteville
Methanogens, Plausible Extraterrestrial Life Forms On Mars, And Their Tolerance To Increasing Concentrations Of Illite Clay, Chandler Kern
Biological Sciences Undergraduate Honors Theses
Methanogens, some of Earth’s most primitive prokaryotic organisms, are candidates for possible life forms capable of inhabiting Mars. Specifically, four different species (Methanobacterium formicicum, Methanococcus maripaludis, Methanosarcina barkeri, Methanothermobacter wolfeii) were analyzed for their tolerance to the presence of illite clay. Illite is a crystalline mineral that has been identified from regions of Mars’s surface. Results indicated that all four species grew with some success in the illite at different concentrations. This experimentation with methanogens’ abilities to survive and reproduce in the presence of illite allows for a more accurate understanding of the potential capability of microbial …
Engineering Yeast To Evaluate Human Proteins Involved In Selective Rna Packaging During Hiv Particle Production,
2018
California Polytechnic State University, San Luis Obispo
Engineering Yeast To Evaluate Human Proteins Involved In Selective Rna Packaging During Hiv Particle Production, Ryan M. Bitter
Master's Theses
Despite recent advances in antiretroviral therapy, nearly 37 million people continue to live with human immunodeficiency virus (HIV). Basic and applied research on the assembly of HIV could be enhanced by using a genetically tractable organism, such as yeast, rather than mammalian cells. While previous studies showed that expression of the HIV Gag polyprotein in Saccharomyces cerevisiae spheroplasts resulted in the production of virus-like particles (VLPs), many questions regarding the utility of yeast in HIV assembly remain uninvestigated. Here, we report use of S. cerevisiae for both the production of VLPs with selectively packaged RNA and to evaluate the human …
Clpxp-Regulated Proteins Suppress Requirement For Reca In Dam Mutants Of Escherichia Coli K-12,
2018
University of Massachusetts Amherst
Clpxp-Regulated Proteins Suppress Requirement For Reca In Dam Mutants Of Escherichia Coli K-12, Amie Savakis
Masters Theses
Double strand breaks (DSB) are a common source of DNA damage in both prokaryotes and eukaryotes. If they are not repaired or are repaired incorrectly, they can lead to cell death (bacteria) or cancer (humans). In Escherichia coli, repair of DSB are typically accomplished via homologous recombination and mediated by RecA. This repair pathway, among others, is associated with activation of the SOS response. DNA adenine methyltransferase (dam) mutants have an increased number of DSB and, therefore, are notorious for being RecA-dependent for viability. Here, we show that the synthetic lethality of Δdam/ΔrecA is suppressed when clpP is removed, suggesting …
Mechanism Of Incorporation And Repair Of Uracil At Highly Transcribed Genes In Saccharomyces Cerevisiae,
2018
The University of Texas M D Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
Mechanism Of Incorporation And Repair Of Uracil At Highly Transcribed Genes In Saccharomyces Cerevisiae, Norah Auma Owiti
Dissertations & Theses (Open Access)
Recombination and mutagenesis are elevated by high levels of transcription. The correlation between transcription and genome instability is largely explained by the topological and structural changes in DNA and the associated physical obstacles generated by the transcription machinery. However, such explanation does not directly account for the unique types of mutations originating from the non-canonical residues such as uracil, which are also elevated at highly transcribed regions. Apurinic/Apyrimic or Abasic (AP) sites derived from uracil excision, accumulate at a higher rate in actively transcribed regions of the genome in S. cerevisiae and are primarily repaired by base excision repair (BER) …
Exploring The Microbiome: Diversity Of The Microbial Community Of Three Foam Nesting Frogs, Genus: Polypedates, Across A Developmental Gradient,
2018
James Madison University
Exploring The Microbiome: Diversity Of The Microbial Community Of Three Foam Nesting Frogs, Genus: Polypedates, Across A Developmental Gradient, Sarah Mcgrath
Masters Theses, 2010-2019
Characterization of microbial biodiversity, including that of the amphibian skin-associated microbiome, is a frontier of research recently made accessible through advances in sequencing technology. Microbial interaction with a host has been determined to have profound influences on host health across a wide range of macroscopic organisms. For amphibians, the influence of the skin-associated microbiome has been found to have particular importance, as amphibians are currently one of the fastest disappearing vertebrate groups on the planet, largely in part to skin-associated diseases caused by pathogenic microbes. Therefore, it is important to characterize the amphibian skin-associated microbiome, particularly for species with no …
Identification Of “Fhua” Like Genes In Rhizobium Leguminosarum Atcc 14479 And Its Role In Vicibactin Transport And Investigation Of Heme Bound Iron Uptake System,
2018
East Tennessee State University
Identification Of “Fhua” Like Genes In Rhizobium Leguminosarum Atcc 14479 And Its Role In Vicibactin Transport And Investigation Of Heme Bound Iron Uptake System, Sushant Khanal
Electronic Theses and Dissertations
Siderophores are low molecular weight, iron chelating compounds produced by many bacteria for uptake of iron in case of iron scarcity. Vicibactin is a trihydroxamate type siderophore produced by Rhizobium leguminosarum bv. trifolii ATCC 14479. This work focuses on identifying an outer membrane receptor involved in the transport of vicibactin. We have confirmed the presence of the putative fhuA gene in R. leguminosarum bv. trifolii ATCC 14479. This bacteria shows mutualistic symbiosis with the red clover plant Trifoliium prantense. Leghemoglobin, with its cofactor heme is present in the plant root nodules that surrounds the infecting organism present in the nodules. …
The Effects Of Inulin And Galactooligosaccharides On The Production Of Reuterin By Lactobacillus Reuteri,
2018
Olivet Nazarene University
The Effects Of Inulin And Galactooligosaccharides On The Production Of Reuterin By Lactobacillus Reuteri, Micah Forshee
Honors Program Projects
The microbiome is a dynamic community that can positively and negatively influence host health. Lactobacillus reuteri is a probiotic that has received much attention for its ability to inhibit pathogens such as Salmonella Typhimurium, Escherichia coli, and Clostridium difficile. It does so by its unique ability to metabolize glycerol into the antimicrobial compound 3-HPA, which is commonly referred to as reuterin. The ability to secrete reuterin is dependent not only on glycerol availability but also the concentration of glucose. In fact, there appears to be a “goldilocks” ratio between glucose and glycerol as either too much or too …
Impacts Of Genome And Nuclear Architecture On Molecular Evolution In Eukaryotes,
2018
University of Massachusetts Amherst
Impacts Of Genome And Nuclear Architecture On Molecular Evolution In Eukaryotes, Xyrus Maurer-Alcalá
Doctoral Dissertations
The traditional view of genomes suggests that they are static entities changing slowly in sequence and structure through time (e.g. evolving over geological time-scales). This outdated view has been challenged as our understanding of the dynamic nature of genomes has increased. Changes in DNA content (i.e. polyploidy) are common to specific life-cycle stages in a variety of eukaryotes, as are changes in genome content itself. These dramatic genomic changes include chromosomal deletions (i.e. paternal chromosome deletion in insects; Goday and Esteban 2001; Ross, et al. 2010), developmentally regulated genome rearrangements (e.g. the V(D)J system in adaptive immunity in mammals; Schatz …
Factors Affecting The Parasitism Of Gregarine Species In Grasshoppers In Western Nebraska,
2018
University of Nebraska-Lincoln
Factors Affecting The Parasitism Of Gregarine Species In Grasshoppers In Western Nebraska, Alexandra Creigh, Kristin Mclarty, Scott Lyell Gardner
Honors Theses
We conducted a survey of the species of parasites found in grasshoppers around the area of Dunwoody’s Pond to investigate whether there were any species specific parasitic relationships occurring there. We collected grasshoppers from several areas around Dunwoody’s Pond totaling 15 species including Melanoplus bivittatus (Say 1825) , Melanoplus sanguinipes (Fabricius, 1798) , Melanoplus differentialis (Thomas 1865), and Melanoplus femurrubrum (De Geer 1773), along with others (Seymour et al., 2009) and compared the parasites found in them. This study is similar to one conducted in South America by Lloyd in 1951, and we hoped to find connections between species to …
Evolution And Niche Specialization Of Microbial Taxa In Vaginal Infection And Pregnancy,
2018
Virginia Commonwealth University
Evolution And Niche Specialization Of Microbial Taxa In Vaginal Infection And Pregnancy, Abigail L. Glascock
Theses and Dissertations
The vaginal microbiome plays an important role in reproductive health and pregnancy. It has coevolved with humans and has direct effects on reproductive success, rendering selective pressure more pronounced at this site. Herein, we probe coevolution of the vaginal microbiome using a systems-level approach. In Chapter 2, we examine the evolutionary trajectory of two vaginal Veillonellaceae phylotypes evolved from an ancestral gastrointestinal lineage to inhabit the vaginal niche. We present evidence of their divergence and subniche specification and describe their differential associations with vaginal infection and pregnancy. In Chapter 3, we identify ten bacterial taxa, predicted to contribute to the …
Evidence For The Priming Effect In Single Strain And Simplified Communities Of Estuarine Bacteria,
2017
University of Tennessee, Knoxville
Evidence For The Priming Effect In Single Strain And Simplified Communities Of Estuarine Bacteria, Abigail Amina Edwards
EURēCA: Exhibition of Undergraduate Research and Creative Achievement
Through their transformation of naturally occurring organic matter, coastal marine bacteria play an essential role in carbon cycling. A phenomenon termed the priming effect (PE) occurs when microbial communities remineralize recalcitrant organic matter faster in the presence of labile organic matter and may be prevalent in coastal systems. To understand how microbial community members interact to induce PE, it is essential to first understand the mechanisms underlying PE in single strains and simplified bacterial communities. The effect to which different concentrations and sources of labile carbon stimulated the production of bacterial biomass from riverine organic matter by two marine bacteria …
Systematics And Biogeography Of The Cortinarius Violaceus Group And Sequestrate Evolution In Cortinarius (Agaricales),
2017
University of Tennessee, Knoxville
Systematics And Biogeography Of The Cortinarius Violaceus Group And Sequestrate Evolution In Cortinarius (Agaricales), Emma Harrower
Doctoral Dissertations
Phylogenetics is a powerful tool used for illuminating the diversity of life on Earth, their evolution and their ecology. I created a multi-gene phylogenetic tree of Cortinarius section Cortinarius and uncovered five previously overlooked species, increasing the number of species in the section from seven to twelve. All members of the clade possess both cheilocystidia and pleurocystidia and possess a pigment known as (R)-39,49-dihydroxybphenylalanine. Ancestral state reconstruction estimated that the ancestral host was most likely an angiosperm, switching hosts when encountering novel host species in new lands, and only C. violaceus associating with the Pinaceae in North America. Biogeographic analysis …
About Logan Weihe And Beloved Microcosm,
2017
University of Illinois at Chicago
About Logan Weihe And Beloved Microcosm, Logan M. Weihe
Steeplechase: An ORCA Student Journal
No abstract provided.
Anti-Staphylococcal Activity Of Variovorax Paradoxus Eps,
2017
California State University, San Bernardino
Anti-Staphylococcal Activity Of Variovorax Paradoxus Eps, Patricia Holt-Torres
Electronic Theses, Projects, and Dissertations
Variovorax paradoxus EPS is a gram-negative rod isolated from the sunflower rhizosphere at CSUSB. Preliminary research has shown that Variovorax paradoxus EPS has anti-staphylococcal activity in liquid and solid co-culture. Anti-staphylococcal activity of Wild type and V. paradoxus EPS 𝚫4519 on 0.5% YE agar with embedded S. aureus AH1710 supports the idea that a soluble molecule is responsible for this activity, as the agar acted as a physical barrier between V. paradoxus EPS and S. aureus colonies. Preliminary genetic analysis of V. paradoxus EPS identified three loci that suitable candidates for the synthesis of a potential anti-staphylococcal small molecule. …
Functional Consequences Of Rna Exosome Complex Alteration By Conformational Changes And Cofactor Binding,
2017
The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
Functional Consequences Of Rna Exosome Complex Alteration By Conformational Changes And Cofactor Binding, Jaeil Han
Dissertations & Theses (Open Access)
The RNA exosome is an essential 3’-5 ribonuclease that processes or degrades a variety of RNA species in eukaryotes. It is composed of nine structural cores and one catalytic subunit, Rrp44. Structural studies captured two different conformations of Rrp44, Rrp44ch (channel) and Rrp44da (direct-access). The Rrp44ch appears to recruit RNA substrates from the central channel formed by the core subunits, while the substrate is directly recruited to Rrp44da bypassing the central channel. Although in vivo function of the Rrp44ch-exosome is extensively studied, the function or even the presence of the Rrp44da-exosome in …
An Integrated Bioinformatic/Experimental Approach For Discovering Novel Type Ii Polyketides Encoded In Actinobacterial Genomes,
2017
University of New Mexico
An Integrated Bioinformatic/Experimental Approach For Discovering Novel Type Ii Polyketides Encoded In Actinobacterial Genomes, Wubin Gao
Chemistry and Chemical Biology ETDs
Discovery of new natural products (NPs) is critical both for diseases treatment and crops protection. Numerous NP biosynthetic gene clusters (BGCs) in sequenced microbial genomes allow identification of new NPs through genome mining. Developing an integrated bioinformatic/experimental approach for discovering novel type II polyketides (PK-IIs) facilitates investigation of this family of NPs in an efficient, systematic way. Here, we developed an approach to analyze ketosynthase α/β (KSα/β) gene sequences to predict PK-II core structures, allowing us to target novel PK-II BGCs either from isolated genomic DNA or genomes from the NCBI databank, and to isolate novel PK-IIs produced by these …
Candida And Pseudomonas Interact To Enhance Mucosal Infection In Transparent Zebrafish,
2017
The University of Maine
Candida And Pseudomonas Interact To Enhance Mucosal Infection In Transparent Zebrafish, Audrey C. Bergeron
Electronic Theses and Dissertations
Polymicrobial communities exist throughout the human body and include both fungi and bacteria. During disease, cross-kingdom interactions among bacteria, fungi, and/or the immune system can alter virulence and lead to complex polymicrobial infections. The fungus C. albicans is among the most commonly isolated fungi in the context of fungal-bacterial co-infections and is often accompanied by the bacterium P. aeruginosa at a variety of sites throughout the body including mucosal tissues such as the lung. In vitro, C. albicans and P. aeruginosa have a cyclic, bi-directional, and largely antagonistic relationship, but these interactions do not account for the role of the …
