Microbiology Commons^™

Glycolic Acid Utilization In Two Species Of Marine Bacteria, Erik S. Timsak

STAR Program Research Presentations

Interactions between bacteria and phytoplankton are crucial for the cycling of organic matter in marine environments. Around 50% of organic carbon taken up by marine bacteria is converted into inorganic carbon. The uptake of organic carbon by marine bacteria exuded from phytoplankton is a key factor in regulating the marine carbon cycle. One such molecule that is exuded by phytoplankton and then uptaken by marine bacteria is called glycolate - the anion of glycolic acid, a two caron molecule. Glycolate is exuded by phytoplankton during photorespiration and 10-50% of dissolved organic carbon in marine environments is comprised of glycolate. Additionally, …

Green Team: Ecological Restoration Of Plaster Creek, Yeri Kim, Benjamin Steenwyk, Rachel Warners, David P. Warners, Gail Heffner

Student Papers and Reports

No abstract provided.

Longitudinal Quantification Of Adenovirus Neutralizing Responses In Zambian Mother-Infant Pairs: Impact Of Hiv-1 Infection And Its Treatment, Sara R. Privatt, Brianna L. Bullard, Eric A. Weaver, Charles Wood, John T. West

Nebraska Center for Virology: Faculty Publications

Vaccination offers the most cost-effective approach to limiting the adverse impact of infectious and neoplastic diseases that reduce the quality of life in sub-Saharan Africa (SSA). However, it is unclear what vaccine vectors would be most readily implementable in the setting and at what age they should be applied for maximal efficacy. Adenoviruses (Ad) and Ad-based vectors have been demonstrated to induce effective humoral and cellular immune responses in animal models and in humans. However, because immunity associated with Ad infection is lifelong, there exists a debate as to whether pre-existing immunity might decrease the efficacy of Ad vectored vaccines. …

Understanding The Molecular Strategies Of Campylobacter Jejuni For Survival In Amoeba And Chicken., Deepti Pranay Samarth

Graduate Theses and Dissertations

Campylobacter jejuni endure to be major cause of gastroenteritis in humans worldwide. C. jejuni is fastidious in laboratory setup but can cause waterborne infection through contaminated water where none of these fastidious conditions are met. This dissertation presents an assortment of studies focused in reviewing three major factors which could present a helping hand to C. jejuni in its environmental survival viz. i) association with free-living amoebae (FLA) ii) horizontal gene transfer (HGT) contributing towards its genetic diversity iii). Viable but non-culturable (VBNC) state.

Acanthamoeba is a FLA linked to environmental survival of many intracellular pathogens, including C. jejuni. In …

16s Rrna Analysis And Toxin Gene Presence In Escherichia Coli Isolated From Beach Water And Sand At A Public Beach (Erie County, Ny), Jennifer D. Jackson

Biology Theses

Every year, thousands of people utilize beaches for recreation, but most are unaware of Escherichia coli (E. coli) contamination and the possibility of acquiring an infection. In this study, 173 strains of E. coli were isolated from sand and adjacent waters from a public beach in Erie County, NY and analyzed for genetic relatedness based on sequence differences in the variable regions of the 16S rRNA gene. Some of the variable regions (V1 and V6) proved useful in constructing phylogenetic trees but the discriminatory power of these regions was inadequate to resolve intraspecies differences. Therefore, whether extant populations …

The Evolutionary Diversity And Biological Function Of Phenazine Metabolite Biosynthesis In Burkholderia Spp, Samuel Hendry

Master's Theses

Burkholderia encompass a group of ubiquitous Gram-negative bacteria that include numerous saprophytes, as well as several species that cause infections in animals, immunocompromised patients, and plants. Some species of Burkholderia produce colored redox-active secondary metabolites called phenazines (Phz). In the model opportunistic pathogen Pseudomonas aeruginosa, phenazines strongly contribute to the competitiveness, formation of biofilms, and virulence in multiple models of infection. Similar depth of knowledge on the diversity, biosynthesis, and biological functions of phenazines in Burkholderiais missing. This project aimed to bridge this gap in knowledge by focusing on phenazine pathways of B. lata and closely related …

Assessing The Efficacy Of Seedling Planting As A Forest Restoration Technique In Temperate Hardwood Forests Impacted By Invasive Species, Michaela J. Woods, Meredith Cobb, Katie Hickle

Biology Faculty Publications

The emerald ash borer (Agrilus planipennis Fairmaire; EAB) is an invasive insect that causes mortality of trees in the genus Fraxinus, creating canopy gaps that may facilitate invasion by exotic plants. Planting native tree seedlings under EAB-infested Fraxinus may accelerate succession and preclude invasive plant expansion; however, the effectiveness of this approach has not been experimentally tested. We assessed understory seedling planting of Quercus rubra, Carya laciniosa, and Juglans cinerea in EAB-infested forests, where the invasive shrub Lonicera maackii (Amur honeysuckle) was removed. We tested whether the use of plastic tree shelters (“tree tubes”) or planting season (fall versus spring) …

Environmental Sampling Techniques For Herd-Level Surveillance Of Bovine Viral Diarrhea Virus, Jaden Carlson

School of Veterinary and Biomedical Sciences: Dissertations, Theses, and Student Research

Control of Bovine Viral Diarrhea Virus (BVDV) relies on resource-intensive individual animal sampling to detect and remove persistently infected (PI) cattle. Herd-level surveillance tools would be useful for herds with unknown BVDV status and for monitoring herds with BVDV-free status. The overall objective of this thesis is to explore the viability of BVDV surveillance at a herd-level using samples collected without handling individual animals. The first objective was to determine the feasibility of using stable flies as a sampling tool to detect BVDV. The second objective was to determine the feasibility of using drinking water to detect BVDV. To accomplish …

Antibiotic Drug Discovery Targeting Bacterial Metabolism, Miranda J. Wallace

Theses and Dissertations (ETD)

Over the last century, the use of antibiotics has enabled many advances in modern medicine, making life as we know it possible. In recent years, however, emerging bacterial resistance to virtually all major antibiotic classes has resulted in a worldwide increase in morbidity, mortality, and financial burden associated with drug resistant infections. The antimicrobial resistance crisis presents an urgent need for new antimicrobials with distinct mechanisms of action from existing drugs. The current pharmaceutical pipeline of new antibiotics is limited due to three obstacles: a lack of understanding of resistance mechanisms, a dearth of novel mechanisms of action among new …

Characterizing Nodule Endophyte Communities In Glycine Max And Lablab Purpureus Using Next-Generation Sequencing, Scott David Mcelveen

Graduate Theses/Dissertations

Biological nitrogen fixation by rhizobia in the root nodules of legumes is a significant source of agricultural nitrogen in global crop production systems. The influence of and interaction of factors involved in nodule endophyte selection remain poorly understood. In the present study, the influences of crop rotation (soybean-legume vs. cotton-legume) and recalcitrant soil organic matter (compost amendment) on the relative distribution of endophytic bacteria in the root nodules of greenhouse-grown soybean and lablab were investigated by extracting, amplifying, and sequencing 16S ribosomal RNA (rRNA) and nifH genes. Neither preceding crop nor compost amendment were found to have an influence on …

Elucidating Immune Signaling Of Influenza A Virus And Aspergillus Fumigatus Co-Infections Through Pioneered Model Development, Meagan Danyelle Rippee-Brooks

Graduate Theses/Dissertations

Bacterial co-infections with influenza A virus (IAV) are extremely serious and life-threatening. However, there exists limited understanding about the importance of fungal infections with IAV. Clinical case reports indicate that fungal co-infections do occur and suggest the IAV pandemic of 2009 had a propensity to predispose patients to secondary fungal infections more than previous IAV strains. IAV-fungal co-infections are marked by high mortality rates of 47 to 61% in previously healthy individuals between the ages of 20 and 60. Yet, the variables involved in this co-infection remain undetermined. I achieved effective recapitulation of this co-infection using a C57Bl/6 murine (mouse) …

The Influence Of The Pep-Pts And Other Metabolic Systems On The Master Virulence Regulator Atxa And To Xin Gene Expression In Bacillus Anthracis, Naomi Bier-Reizes

Dissertations and Theses (Open Access)

AtxA, the master virulence gene regulator in Bacillus anthracis, is a PRD-containing virulence regulator (PCVR) as indicated by the crystal structure, post-translational modifications, and activity of the protein. PCVRs are transcriptional regulators, named for the regulatory domains subject to phosphorylation by the phosphoenolpyruvate phosphotransferase system (PEP-PTS), termed PTS Regulatory Domains (PRD), and for their impact on virulence gene expression. Generally, the phosphorylation of a PCVR regulates protein activity and multimerization. AtxA is phosphorylated at two histidine residues - one in each of its two PRDs. Phosphorylation at position 199 allows for AtxA to positively affect expression of virulence genes, whereas …

Improving And Modeling Bacteria Recovery In Hollow Disk System, Clifton Anderson

Theses and Dissertations

Identifying antibiotic resistance in blood infections requires separating bacteria from whole blood. A hollow spinning disk rapidly removes suspended red blood cells by leveraging hydrodynamic differences between bacteria and whole blood components in a centrifugal field. Once the red cells are removed, the supernatant plasma which contains bacteria is collected for downstream antibiotic testing. This work improves upon previous work by modifying the disk design to maximize fractional plasma recovery and minimize fractional red cell recovery. V-shaped channels induce plasma flow and increase fractional plasma recovery. Additionally, diluting a blood sample spiked with bacteria prior to spinning it increased the …

Investigation Of Microbiota In Health And Disease Of Poultry, Bishnu Adhikari

Graduate Theses and Dissertations

The microbiotas play vital roles in health and diseases of both humans and animals. 16S rRNA genes sequence analysis is one of the most popular and commonly used methods in the analysis of microbiotas associated with hosts. In this dissertation, the microbiotas of chickens (broilers, breeders, and layers) and turkeys were evaluated by 16S rRNA gene sequencing. Characterization of the culturable subpopulations of Lactobacillus in the chicken gut can serve as a valuable resource for probiotic development. In Chapter 2, Lactobacillus subpopulations recovered on MRS from chicken gut were defined comprehensively for the first time using 16S rRNA gene profiling, …

Characterization Of The Swine Gut Microbiome Dynamics, Culturomics And Probiotics, Xiaofan Wang

Graduate Theses and Dissertations

The gastrointestinal tract is a critical place where the immune system concentrates many of its protective functions. It exerts both physical and biochemical defenses against invading foodborne pathogens and other hazards. In pigs, the gut microbiota community assembled postnatal plays a very important role in the development of multiple physiologic aspects, such as development of the gastrointestinal tract, nutrient exchange, immune defense against foreign pathogens and growth performance. Microbiome-host communication changes with age. Despite recent advances in understanding the swine gut microbiome at different growth stages, a comprehensive longitudinal study of the lifelong dynamics of the swine gut microbiome is …

Emergence Of Oxacillin Resistance In Stealth Methicillin-Resistant Staphylococcus Aureus Due To Meca Sequence Instability, Richard V. Goering, Erin A. Swartzendriber, Anne E. Obradovich, Isabella A. Tickler, Fred C. Tenover

Biology Faculty Publications

Staphylococcus aureus strains that possess a mecA gene but are phenotypically susceptible to oxacillin and cefoxitin (OS-MRSA) have been recognized for over a decade and are a challenge for diagnostic laboratories. The mechanisms underlying the discrepancy vary from isolate to isolate. We characterized seven OS-MRSA clinical isolates of six different spa types from six different states by whole-genome sequencing to identify the nucleotide sequence changes leading to the OS-MRSA phenotype. The results demonstrated that oxacillin susceptibility was associated with mutations in regions of nucleotide repeats within mecA. Subinhibitory antibiotic exposure selected for secondary mecA mutations that restored oxacillin resistance. …

The ‘Law Of Environmental Dependence’ - Biology And Ethics In The Work Of Ernest Everett Just: + Found – Some 251 Mostly Typed Pages, Theodore Walker

Perkins Faculty Research and Special Events

Abstract-

“The Origin of Man’s Ethical Behavior” (circa October 1941) by Ernest Everett Just and Hedwig A. Schnetzler Just - is an unpublished book manuscript about the biological origins and evolution of ethical behavior, and about “the law of environmental dependence.” Missing since Just’s death in October 1941, it was found and identified in May 2018 among the collected papers of Ernest Everett Just preserved at the Howard University Moorland-Spingarn Research Center in Washington, DC. In addition to the 1996 US postage with the caption “Ernest E. Just, Biologist,” we now have reason to add two new postage stamps with …

Teaching In A Competitive Science-Focused High School, Crystal Randall

Faculty Publications & Research

• What is IMSA?
What students do we serve, our role in the school system
• Teaching and Research responsibilities
Responsibilities, course load, students, teaching philosophies, resources
• Other institutional responsibilities
• Job resources

Overexpression Of Pear (Pyrus Pyrifolia) Cad2 In Tomato Affects Lignin Content, Mingtong Li, Chenxia Cheng, Xinfu Zhang, Suping Zhou, Lixia Li, Shaolan Yang

Agricultural and Environmental Sciences Faculty Research

PpCAD2 was originally isolated from the ‘Wangkumbae’ pear (Pyrus pyrifolia Nakai), and it encodes for cinnamyl alcohol dehydrogenase (CAD), which is a key enzyme in the lignin biosynthesis pathway. In order to verify the function of PpCAD2, transgenic tomato (Solanum lycopersicum) ‘Micro-Tom’ plants were generated using over-expression constructs via the agrobacterium-mediated transformation method. The results showed that the PpCAD2 over-expression transgenic tomato plant had a strong growth vigor. Furthermore, these PpCAD2 over-expression transgenic tomato plants contained a higher lignin content and CAD enzymatic activity in the stem, leaf and fruit pericarp tissues, and formed a greater number of vessel elements …

Taxonomic Features And Comparison Of The Gut Microbiome From Two Edible Fungus-Farming Termites (Macrotermes Falciger, M. Natalensis) Harvested In The Vhembe District Of Limpopo, South Africa, Stephanie L. Schnorr, Courney A. Hofman, Shandukani R. Netschifhefhe, Frances D. Duncan, Tanvi P. Honap, Julie Lesnik, Cecil M. Lewis

Anthropology Faculty Research

Background Termites are an important food resource for many human populations around the world, and are a good supply of nutrients. The fungus-farming ‘higher’ termite members of Macrotermitinae are also consumed by modern great apes and are implicated as critical dietary resources for early hominins. While the chemical nutritional composition of edible termites is well known, their microbiomes are unexplored in the context of human health. Here we sequenced the V4 region of the 16S rRNA gene of gut microbiota extracted from the whole intestinal tract of two Macrotermes sp. soldiers collected from the Limpopo region of South Africa. Results …

Intratypic Genetic Variability Of Human Adenovirus Type 4: Implication For Viral Pathogenesis, Camden Roy Bair

Biomedical Sciences ETDs

Human adenovirus type 4 (HAdV-E4) is a causative agent of acute respiratory disease and conjunctivitis worldwide. Two major lineages of HAdV-E4 genomic variants have been identified by their distinct BamHI restriction profiles: prototype-like (p-like) strains and the a-like genomic variants. Recent molecular epidemiology studies have shown a predominance of a-like genomic variants detected in association with disease which suggests a-like strains have a fitness advantage or they may be more pathogenic. The impact of HAdV-E4 intratypic genetic variability on in vitro and in vivo phenotypes relevant to pathogenesis is a major gap in knowledge. I hypothesize that HAdV-E4 comprises two …

A Method For Improving The Accuracy And Efficiency Of Bacteriophage Genome Annotation, Alicia Salisbury, Philippos K. Tsourkas

Life Sciences Faculty Research

Bacteriophages are the most numerous entities on Earth. The number of sequenced phage genomes is approximately 8000 and increasing rapidly. Sequencing of a genome is followed by annotation, where genes, start codons, and functions are putatively identified. The mainstays of phage genome annotation are auto-annotation programs such as Glimmer and GeneMark. Due to the relatively small size of phage genomes, many groups choose to manually curate auto-annotation results to increase accuracy. An additional benefit of manual curation of auto-annotated phage genomes is that the process is amenable to be performed by students, and has been shown to improve student recruitment …

Position-Specific Metabolic Probing And Metagenomics Of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities At High Temperatures, Scott C. Thomas, Kevin O. Tamadonfar, Cale O. Seymour, Dengxun Lai, Jeremy A. Dodsworth, Senthil K. Murugapiran, Emiley A. Eloe-Fadrosh, Paul Dijkstra, Brian P. Hedlund

Life Sciences Faculty Research

Temperature is a primary driver of microbial community composition and taxonomic diversity; however, it is unclear to what extent temperature affects characteristics of central carbon metabolic pathways (CCMPs) at the community level. In this study, 16S rRNA gene amplicon and metagenome sequencing were combined with 13C-labeled metabolite probing of the CCMPs to assess community carbon metabolism along a temperature gradient (60–95°C) in Great Boiling Spring, NV. 16S rRNA gene amplicon diversity was inversely proportional to temperature, and Archaea were dominant at higher temperatures. KO richness and diversity were also inversely proportional to temperature, yet CCMP genes were similarly represented across …

A Small Rna And Dna Binding Protein Contribute To Biofilm Development In Bartonella Henselae, Udoka Okaro

USF Tampa Graduate Theses and Dissertations

A biofilm, which is associated with 80% of chronic infections in humans, is formed when bacteria aggregate, attach to a substrate and secrete a matrix protecting the bacteria from host cell defenses and antibiotics. Bartonella henselae (B. henselae) is the causative agent of cat scratch disease, persistent bacteremia, and one of the most frequently reported causes of blood-culture negative endocarditis (BCNE) in patients. The ability of B. henselae to adhere to the heart valve, form a biofilm and vegetation to cause endocarditis increases the morbidity and mortality rate in infected patients. The presence of a trimeric autotransporter adhesin (TAA) called …

Infection Potential Of Rickettsia Felis Via Ingestion, Matthew M. Schexnayder

LSU Master's Theses

Rickettsia felis is the etiologic agent of flea-borne spotted fever (FBSF) in humans and a poorly described cause of fever in animals. It is transmitted by its primary arthropod vector and reservoir host, the cat flea Ctenocephalides felis. Known routes of Rickettsia felis transmission between Rickettsia felis-infected cat fleas and vertebrate hosts include cutaneous bites and contamination of cutaneous wounds with infective flea feces. The bulk of FBSF infections occur in young children in Africa, though infections of people at all ages all over the world have been confirmed. As mammals and young children frequently come into contact …

A High Throughput Assay For The Detection Of Stimulator Of Interferon Genes (Sting) Agonists, Michael J. Ingling

Graduate School of Biomedical Sciences Theses and Dissertations

The innate immune system includes a menagerie of different cell types, each with a different role in the process of monitoring the body for invaders and presenting gathered debris (antigen) to the adaptive immune system. Somatic cells have intracellular receptors for the same purpose. Cancer cells, however, have avoided these methods of detection despite, in many cases, the tumor’s immunogenic traits. Immuno-oncology is a field dedicated to the immunological traits of tumors, more recently finding ways of instigating an immune response against tumors. In this regard, STING, a receptor of cyclic dinucleotides (CDN), has come to the forefront of immuno-oncology. …

Integrated Aeration For Enhanced Nitrogen Conversion And Removal And The Effect Of Sampling Frequency On Productivity Estimates In Algae-Based Wastewater Treatment Systems, Lauren Parker

Master's Theses

Raceway ponds can be used to cultivate microalgae for purposes such as wastewater treatment and feedstock for animal feeds and biofuels. Besides nitrogen assimilation in biomass, nitrification can be a wastewater treatment mechanism but one that is hindered by the low nighttime dissolved oxygen concentrations (DO) common in wastewater treatment raceways. The large diel difference in pond conditions and changing influent wastewater quality also raises the question of the optimal frequency and timing of grab sample collection, to obtain representative water quality data. Three sets of triplicate pilot raceways (1,000-L, 0.30-m deep, fed primary clarifier effluent) were operated at an …

Development Of A Prolyl Endopeptidase Expression System In Lactobacillus Reuteri To Reduce The Clinical Manifestation Of Celiac Disease, Kara Lynn Jew

Master's Theses

Celiac Disease (CD) is an autoimmune disorder that emerges due to the ingestion of gluten, a protein found in a variety of common grains such as wheat, rye, and barley. Approximately 1 in 100 individuals in the US suffer from CD, making it the most commonly diagnosed gastrointestinal disorder (Ciclitira et. al., 2005). These proline-rich gluten peptides are resistant to proteolysis and accumulate in the duodenum of the small intestine. Once in the duodenum, these peptides illicit an autoimmune response resulting in villous atrophy. Current treatment for CD requires a rigorous adherence to a gluten-free diet. Nevertheless, gluten-containing grains are …

Bioaerosols Associated With Evaporative Cooler Use In Low-Income Homes In Semi-Arid Climates, Ashlin Elaine Cowger

Theses and Dissertations

Asthma is the leading chronic illness in children in the United States. Since children in the U.S. spend a majority of their time indoors there is an increased need to understand key sources of daily asthma triggers in the home. Bacterial endotoxin, dust mite allergens and β-D-glucan have been shown to be potent inducers of asthma attacks, and high levels of these allergens in homes can trigger attacks in those with asthma. We aim to better understand the risks to those with asthma that might be associated with evaporative cooler (EC) use in low-income homes. ECs are often promoted because …

Electrostatically Localized Proton Bioenergetics: Better Understanding Membrane Potential, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

In Mitchell's chemiosmotic theory, membrane potential Δψ was given as the electric potential difference across the membrane. However, its physical origin for membrane potential Δψ was not well explained. Using the Lee proton electrostatic localization model with a newly formulated equation for protonic motive force (pmf) that takes electrostatically localized protons into account, membrane potential has now been better understood as the voltage difference contributed by the localized surface charge density ([H-⁺_L] + ⁿΣ _i=1 [M⁽ⁱ⁺⁾_L]) at the liquid-membrane interface as in an electrostatically localized protons/cations-membrane-anions capacitor. That is, the origin of membrane …