Other Microbiology Commons^™

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 …

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, 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, 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 …

Mechanism Of Incorporation And Repair Of Uracil At Highly Transcribed Genes In Saccharomyces Cerevisiae, Norah Auma Owiti

Dissertations and 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, 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, 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. …

Factors Affecting The Parasitism Of Gregarine Species In Grasshoppers In Western Nebraska, Alexandra Creigh, Kristin Mclarty, Scott Lyell Gardner

Honors Program: Senior Projects (Public)

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, 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 …

About Logan Weihe And Beloved Microcosm, Logan M. Weihe

Steeplechase: An ORCA Student Journal

No abstract provided.

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, Jaeil Han

Dissertations and 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, Rrp44^ch (channel) and Rrp44^da (direct-access). The Rrp44^ch appears to recruit RNA substrates from the central channel formed by the core subunits, while the substrate is directly recruited to Rrp44^da bypassing the central channel. Although in vivo function of the Rrp44^ch-exosome is extensively studied, the function or even the presence of the Rrp44^da-exosome in …

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 …

Bioethics In The Work Of Ernest Everett Just: + Missing - Some 400 Pages, Theodore Walker

Perkins Faculty Research and Special Events

Biology + ethics = bioethics. Here we see that Howard University biologist Ernest Everett Just (born 1883, died 1941) connected biology to ethics.

According to Just, various forms of specific biology (including especially cell biology) plus “general biology” are necessary for explaining adequately the origin of ethical behaviors. Social ethical behaviors, especially mutual aid and cooperative interactions with others and the environment, are essential to evolutionary advances among living creatures, ranging from humans to cells. Accordingly, theory of ethics (moral theory) should have roots in biology.

Also, Just wrote an unpublished book-length manuscript—“some 400 typed pages” (Just 1940)—on seeking the …

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

The Elasmobranch-Microbe Relationship: Trimethylamine N-Oxide Synthesis, Urea Hydrolysis, And Microbe-Osmolyte Interactions In The Atlantic Stingray, Dasyatis Sabina, Kaitlin Kelly Doucette

Master's Theses

The elasmobranch osmoregulatory strategy is predicated on the accumulation of nitrogenous compounds, primarily urea and trimethylamine n¬-oxide (TMAO). Despite the abundance of these plasma osmolytes, it is notable that elasmobranchs appear to lack urease and TMA oxidase (Tmase), enzymes that scavenge urea-nitrogen and synthesize TMAO, respectively. However, urease and Tmase are found in many species of bacteria. Therefore, I hypothesized that intestinal bacteria are responsible for urease and Tmase activity in elasmobranchs. Absent dietary nitrogen sources, I evaluated the effects of reduced intestinal microbiota on osmoregulation in Atlantic stingray (Dasyatis sabina) in vivo. D. sabina were given …

Fecal Bacterial Communities As An Indicator Of Trophic Interactions Among Anuran Larvae, Steven Jacob Everman

Master's Theses

Anurans are mass spawners, often with multiple females spawning together, resulting in thousands of tadpoles sharing a habitat. Such large numbers of tadpoles with limited dispersal can lead to intense competition for resources. Inter and intra-specific competition for food could have negative impacts on the growth and survival of smaller tadpoles. Fecal bacterial communities have the potential to be used as indicators of changes in diet making it possible to determine if tadpoles in the wild are eating the same food or not. After feeding on two prepared diets that differed in the percentage of complex carbohydrates, the fecal bacterial …

Identification Of Microorganisms Isolated From Mars-Bound Spacecraft Using Maldi-Tof, Melanie K. Phillips

STAR Program Research Presentations

The primary goal of the Biotechnology and Planetary Protection Group (BPPG) at the Jet Propulsion Laboratory (JPL) is to prevent microbial contamination between Earth and other planetary bodies. This helps preserve the ability to study other worlds as they exist in their natural states and protects our biosphere from extraterrestrial life. The process for identifying microbes located on space-bound hardware in JPL can be more efficient and precise by using the technique called matrix-assisted laser desorption and ionization time of flight (MALDI-TOF). Once this identification technique is fully implemented, the process time will be reduced from two weeks to one …

Identification, Characterization, And Life Cycle Of Intein-Associated Homing Endonucleases, Joshua J. Skydel

Honors Scholar Theses

Inteins are molecular parasites that have been identified in unicellular organisms from the three domains of life. The intein self-excises following translation of the host gene, and therefore incurs a fitness cost for its carrier. The symbiotic state of the intein to its host is dependent on the presence or absence of a homing endonuclease domain, which facilitates horizontal transfer of the molecule. Identification of this domain provides information on the evolutionary history of the intein, as well as patterns of horizontal gene transfer in microbial communities. I have therefore developed Hidden Markov Models (HMMs) to identify homing endonuclease domains …

Engineering A Mutation In The Heparin Binding Pocket Of The Human Fibroblast Growth Factor, Roshni Patel

Chemistry & Biochemistry Undergraduate Honors Theses

Fibroblast growth factors (FGFs) are family of proteins that belong to a group of growth factors that are found in mammals and play an important role in angiogenesis, differentiation, organogenesis, and tissue repair. In summary, their main functionality is involved in cell division and proliferation. Because FGFs plays such a vital role in cell proliferation, they are mainly involved in the process of wound healing and injuries. FGF binds to its ligand, heparin—a heavily sulfated glycosaminoglycan. The binding of heparin to FGF occurs through electrostatic interactions, specifically between the negatively charged sulfate groups on heparin and positively charged residues such …

Oxidative Stress Response In Archaea: Elucidation Of Oxidant Sensing And Tolerance Mechanisms In Methanosarcina Acetivorans, Matthew Edward Jennings

Graduate Theses and Dissertations

Methanogens are archaea possessing a conserved metabolic pathway which produces methane. Many of the enzymes in the methanogenesis pathway are Fe-S proteins, meaning methanogens are sensitive to conditions which disrupt Fe-S clusters. Molecular oxygen is capable of disrupting Fe-S clusters through oxidation of the iron atoms. Furthermore, reduced iron can facilitate the production of reactive oxygen species (ROS), meaning methanogens must possess antioxidant mechanisms. Detection and eradication of ROS is important for all cells, due to the potentially fatal consequences of unchecked oxidation. This dissertation presents two separate projects investigating mechanisms the model methanogen Methanosarcina acetivorans possess for dealing with …

Effects Of Lactobacillus Rhamnosus Milk Isolate On The Production Of Inflammatory Cytokines In Enterocytes, Beverly C. Ngeny

Electronic Theses and Dissertations

In the gastrointestinal tract, probiotics have been shown to promote host immunity and to regulate immune signaling pathways. This study used Caco-2 cell line to examine the effects of a Lactobacillus rhamnosus isolate from “amabere amaruranu” a Kenyan traditional cultured milk, on the production inflammatory cytokines in enterocytes. Live Lactobacillus rhamnosus (MRS6AN), its cytoplasmic fraction (CF), filtered spent broth (FSB) or heat inactivated FSB (HIB) were used as treatments on differentiated Caco-2 cell monolayer in transwells. Cytokine content in the cell lysates, apical and basolateral supernatants were determined using ELISA. Caco-2 cell lysate treatments showed significantly increased anti-inflammatory TGF-β (ng/ml) …

The Prevalence Of Escherichia Coli And Fecal Coliforms On Backpacks Of College Students In Central Kentucky, Samantha Mcmichael

Butler Journal of Undergraduate Research

Abstract

Escherichia coli (E. coli) is a gram negative, rod-shaped, facultative anaerobic bacterium, it is normally found in the lower intestines of warm-blooded animals and humans. E. coli and/or fecal coliforms have been used as fecal indicators in water, food, and contact surfaces. The purpose of this experiment is to identify the prevalence of E. coli and fecal coliforms on the bottom of backpacks belonging to college students in central Kentucky. Forty samples were taken from bottoms of college students’ backpacks in central Kentucky. Sterile swabs were used to collect the samples from the backpacks. The swabs …

Aeromonas Hydrophila In Amphibians: Harmless Bystander Or Opportunistic Pathogen, Zachary P. Rivas

Honors Undergraduate Theses

For several decades amphibian populations have been declining. Historically, the bacterium A. hydrophila (Ah) was hypothesized to be the causal factor in amphibian disease and population declines. However, with the discovery of a chytrid fungus, Batrachochytrium dendrobatidis (Bd) in 1998, which was identified on the skin of amphibians during documented mortality events, Ah research became of minor interest as focus shifted to Bd. Recent studies into the immunocompromising abilities of Bd, however, have opened new questions about its relationship with Ah and their combined effects on a host.

In this study, I explore the …

Interactomics-Based Functional Analysis: Using Interaction Conservation To Probe Bacterial Protein Functions, J. Harry Caufield

Theses and Dissertations

The emergence of genomics as a discrete field of biology has changed humanity’s understanding of our relationship with bacteria. Sequencing the genome of each newly-discovered bacterial species can reveal novel gene sequences, though the genome may contain genes coding for hundreds or thousands of proteins of unknown function (PUFs). In some cases, these coding sequences appear to be conserved across nearly all bacteria. Exploring the functional roles of these cases ideally requires an integrative, cross-species approach involving not only gene sequences but knowledge of interactions among their products. Protein interactions, studied at genome scale, extend genomics into the field of …

Production And Harvest Of Microalgae In Wastewater Raceways With Resource Recycling, Alexander Colin Roberts

Master's Theses

Microalgae can be grown on municipal wastewater media to both treat the wastewater and produce feedstock for algae biofuel production. However the reliability of treatment must be demonstrated, as well as high areal algae productivity on recycled wastewater media and efficient sedimentation harvesting. This processes was studied at pilot scale in the present research.

A pilot facility was operated with nine CO₂-supplemented raceway ponds, each with a 33-m² surface area and a 0.3-m depth, continuously from March 6, 2013 through September 24, 2014. The ponds were operated as three sets of triplicates with two sets continuously fed …

Method Assessment For Microalgae Quantification In Wastewater Treatment And Biofuel Production, Kristen S. Harrison

Crop, Soil and Environmental Sciences Undergraduate Honors Theses

There is growing interest in the use of microalgae for wastewater treatment and biofuel production. However, there is not yet a reliable, user-friendly method of quantifying the biomass and lipid production of a large sample of algae. This study aims to establish and validate new methods for green microalgae quantification using the Microplate reader and the Coulter Counter. Chlorella vulgaris was chosen as the ‘ideal’ algal species for wastewater treatment and biofuel production due to its structure, lipid production, and pollution removal ability. Three traditional quantification methods -- microscope cell count, lipid separation, and chlorophyll extraction -- were compared to …

Influence Of Lactobacillus Rhamnosus Isolated From “Amabere Amaruranu” Cultured Milk On Adipogenesis, Justin E. Kotala

Electronic Theses and Dissertations

This study was performed to test the in vitro effects of a Lactobacillus rhamnosus isolate from “amabere amaruranu”, a traditional Kenyan cultured milk, on 3T3-L1 and Caco-2 cell lines. Cultures of fully mature 3T3-L1 adipocytes were treated with bacterial isolate cell extract (CE), filtered spent broth (FSB) from overnight bacterial culture, or with a PBS control. Expression levels of PPAR³1 and 2, C/EBP±, and ATGL proteins in 3T3-L1 cells were upregulated by FSB treatment. CE treatment did not affect protein expression levels. Expression of MTTP and SREBP-1c proteins in Caco-2 cells showed no change with either treatment. Optical density measurements …

A Tail Of Two Phages: Genomic And Functional Analysis Of Listeria Monocytogenes Phages Vb_Lmos_188 And Vb_Lmos_293 Reveal The Receptor-Binding Proteins Involved In Host Specificity, Aidan Casey, Kieran Jordan, Horst Neve, Aidan Coffey, Olivia Mcauliffe

Department of Biological Sciences Publications

The physical characteristics of bacteriophages establish them as viable candidates for downstream development of pathogen detection assays and biocontrol measures. To utilize phages for such purposes, a detailed knowledge of their host interaction mechanisms is a prerequisite. There is currently a wealth of knowledge available concerning Gram-negative phage-host interaction, but little by comparison for Gram-positive phages and Listeria phages in particular. In this research, the lytic spectrum of two recently isolated Listeria monocytogenes phages (vB_LmoS_188 and vB_LmoS_293) was determined, and the genomic basis for their observed serotype 4b/4e host-specificity was investigated using comparative genomics. The late tail genes of these …

Variation In Microbiome Composition And Stability For A Vancomycin Treated Primary Sclerosing Cholangitis Patient With Ulcerative Colitis Compared With Controls, Alanna Dubrovsky

Symposium

The bacterial composition of the human intestines contributes to much more than just digestion. In the inflammatory, autoimmune conditions primary sclerosing cholangitis (PSC) and ulcerative colitis (UC), the microbiome may be, in some cases, a factor. To gain a better understanding of the composition and stability of the microbiome in a patient treated with vancomycin for PSC, terminal restriction fragment (TRF) analysis was performed on 13 controls and 1 patient, and 16s rRNA microbiome composition analysis was performed on 1 patient and 3 controls. Results showed similar levels of stability, with surprising differences in composition.