Microbiology Commons^™

Evaluation Of The Virulence Potential Of Avian Pathogenic Escherichia Coli Isolated From Broiler Breeders With Colibacillosis In Mississippi, Jiddu Joseph

Theses and Dissertations

Avian pathogenic Escherichia coli (APEC) is a bacterium that is responsible for colibacillosis in birds. However, information about broiler breeder APEC isolates is limited, but the data is critical due to the transfer of this bacteria down the production pyramid to progenies resulting in high mortality. Therefore, we evaluated the phenotypic virulence characteristics of 28 isolates using embryo lethality and day-old chick challenge assays. Also, the in vitro adhesion and invasion potential of selected nine isolates were identified. Results showed more than 1/3^rd of the isolates were highly virulent and the virulence increased as the number of virulence-associated genes …

Evaluating The Role Of The Bovine Vaginal Microbiome In Neonatal And Maternal Health Outcomes, Riley D. Messman

Theses and Dissertations

The dam vaginal microbiota is the first major microbial inoculating community within the neonate. The composition of the dam vaginal microbiota has implications in calf commensal microbiota development. Alterations of the dam microbial community prior to parturition could alter inoculating communities and immune responses in both the dam and calf. Thus, authors aimed to elucidate the microbial community composition of the bovine dam vaginal and calf nasal microbiota post-partum after utilizing betadine lavages (BL). The dam vaginal and calf nasal microbial communities and immune responses were evaluated at 0-, 15-, 30- and 60-day post-partum. Microbiota composition of the dam haircoat, …

Investigating Potential Indicators Of Soil Health Through Microbiome Response To Environmental And Anthropogenic Stressors, Austin Cook

Theses and Dissertations

Traditionally, the analysis of soil health has overlooked the biological component of soil due to poor understanding of connections between the microbiome and empirically measured soil health indicators. The purpose of this study was to assess the effects of environmental and anthropogenic stressors on the soil microbiome, with the aim of identifying measurable soil biological indicators. Chosen soils were examined under distinct conditions to evaluate the effect of selected environmental and anthropogenic stressors on the microbiome. Soil biological responses were analyzed via enzymatic response, microbial functional genes, and microbial community. Environmental factors such as soil moisture and organic matter showed …

Vertical Transmission Of Zika Virus In Monodelphis Domestica, Mohini Moulick

Theses and Dissertations

Zika Viral infection in pregnant women may lead to infants born with microcephaly and other neurological complications, making Zika viral research imperative. Prior research demonstrated Monodelphis domestica to be a unique animal model for Zika virus studies, and viral proteins were detected in brain tissue of juveniles after intracerebral inoculation of infants. We wanted to determine if we can detect a viral protein, non-structural protein 1 (NS1), in brain tissue after intraperitoneal inoculation and we found it to be possible through immunohistochemistry (IHC) analysis. We also investigated if inoculated dams (mothers) would give rise to Zika positive pups (natural inoculation), …

Treponema Denticola Synthesizes C-Di-Amp And Encodes The Cdaa-Type Diadenylate Cyclase Cdaa, Claire R. O'Brien

Theses and Dissertations

Periodontitis is a form of oral disease characterized by dysbiosis of the oral microbiome, leading to inflammation, bone resorption, and in severe cases, entire tooth loss, affecting 42% of adults in the US. One of the bacteria most associated with periodontal disease progression is Treponema denticola (Td), an oral spirochete which inhabits the mouth in small quantities during health but which can dominate the biofilms that form during periodontal disease. The ability of Td to survive in a disease environment and contribute to the progression of disease requires the use of robust signaling networks. Analysis of Td cultures …

The Type Iv Pilus Secretin Bfpb: Structural Analysis And Binding Interactions, Janay I. Little

Theses and Dissertations

Enteropathogenic Escherichia coli (EPEC) causes severe diarrhea in young children. The type IV pilus (T4P) of EPEC, known as the bundle-forming pilus (BFP), plays an important role in EPEC pathogenesis. T4Ps are a family of surface appendages that are important for adhesion, colonization, biofilm formation, virulence, twitching motility and many other functions. One essential component of the BFP system is the secretin, BfpB. Secretins are a large family of integral outer membrane proteins found in T4Ps as well as type II and type III secretion systems, and filamentous phages. Details of the secretin structure have been limited to the overall …

Development Of Whole-Cell Biosensors For Early Detection Of Oral Squamous Cell Carcinoma, Sharona Adina Priyev

Theses and Dissertations

Accurate and timely diagnosis is crucial in preventing progression to advanced disease stages and in improving survival rates of oral squamous cell carcinoma (OSCC). Using synthetic biology tools, we aim to integrate synthetic biological circuits into the construction of a novel, whole-cell biosensor (WCB) that will detect salivary biomarkers of OSCC. In treating biological parts and genetic circuits as modular pieces, we can intentionally rearrange selected domains of interest to create new transcription factors that will enable the detection of molecules of interest. Our end-goal is the creation of portable devices carrying living cells that express our synthetic genetic circuits …

Metagenomic Analysis Of Root-Associated Microbiome Of Healthy And Taproot Decline-Affected Soybeans And Identification Of Healthy Soybean Root Endophytes With Protective Activity Against The Causal Agent, Xylaria Necrophora, Uyen Wesser

Theses and Dissertations

Plant roots are associated with a diverse microbial community of bacteria and fungi. The root microbiome communities associate with the root surface or penetrate the superficial layers of root tissues. It is of high agronomic interest to characterize root microbiomes and identify microbes with beneficial effects on plant defense against pathogens. Soybean taproot decline (TRD) is an emerging soil-borne disease caused by a fungus classified as Xylaria necrophora, challenging to control and with devastating effects on yield. Our group has initiated a study of the soybean root microbiome with three primary experiments: (I) perform a comparative study of root …

Effects Of Microcystin-Lr On Channel Catfish (Ictalurus Punctatus) Susceptibility To Microbial Pathogens (Aeromonas Hydrophila And Edwardsiella Piscicida), Alison Marchant

Theses and Dissertations

Microcystin-LR is a hepatotoxin produced by cyanobacteria. Aeromonas hydrophila and Edwardsiella piscicida infections are leading causes of losses in market-sized channel catfish (Ictalurus punctatus). These older fish should have natural immunity in place and a predisposing factor is likely a prerequisite for these disease outbreaks. While microcystin-LR rarely causes mortality in warm-water aquaculture, we believe it may be a predisposing factor that leads to bacterial disease outbreaks during the summer months due to its ability to damage the liver. Our study investigated microcystin-LR’s effects on channel catfish susceptibility to these pathogens. We found that a sublethal dose of microcystin-LR induced …

Evaluation Of Novel Litter Amendments For Use In The Commercial Broiler Industry, Jorge A. Urrutia

Theses and Dissertations

Poultry litter amendments (LA) are commonly used to maintain good litter quality; the most common ones; are acidifiers. However, concern over the lifespan of LA acidifiers (d) and corrosive nature revealed a need for alternative LA. Products of interest include biochar (BC), superabsorbent polymers (SAPs), and alum mud (AM). Experiment 1 was a screening study (n=17 treatments, no birds) conducted to determine the optimal application rate/method of BC, SAPs, and AM vs.commercial LA and a control. Most SAPs treatments measured metrics may be similar (i.e., bacteria, water activity) or better (pH) vs. commercial LA (PLT). High inclusions of novel LA …

Microbial Ecology Of Urban Sewers, Emily Lou Lamartina

Theses and Dissertations

Municipal sewage provides a glimpse into the health and activities of a human society. For more than a century, sewage exploration has helped expose the sources of disease outbreaks and track disease progression over time. Recent advancements in wastewater surveillance born from the COVID-19 pandemic have potential to enhance mitigation efforts against the decades-long global health crisis of microbial antibiotic resistance. However, critical knowledge gaps exist in wastewater surveillance, stemming from a lack of understanding in sewer microbial ecology. Ecology reveals trends in how communities respond and adapt to change, which has far-reaching implications for identifying effective strategies for disease …

Effects Of Mass Death On Community Structure And Ecosystem Function, Abby Kimpton Jones

Theses and Dissertations

Death and decomposition are natural processes that are generally well-understood. However, large events of death, such as mass mortality events (MMEs) are increasing in frequency and their impacts on the ecosystem are largely unknown. These events may have both bottom-up effects from increased nutrient input as well as top-down effects from loss of an ecological functional group by the affected population. Different functional MMEs may result in different top-down effects, creating cascading effects. In Chapter 1, I test the hypothesis that scavenger and herbivore simulated MMEs generate novel bottom-up and top-down effects. Results indicate that MMEs have a significant effect …

Characterization Of Antimicrobial Activity Of The Symbiotic Bacterium Xenorhabdus Szentirmaii, Miliya Ansad

Theses and Dissertations

Xenorhabdus species belonging to the Enterobacteriaceae family are gram negative bacteria that engage in symbiotic associations with the entomopathogenic soil dwelling nematodes of the family Steinernematidae. In this bacterium–nematode mutualistic interaction, both partners benefit from the association. By entering and perforating the insect gut and translocating to the body cavity of hemocoel, the nematodes gain access to the nutrient resource of the insect hemolymph. Xenorhabdus spp are released in the hemolymph in which they produce toxins and immunosuppressive compounds that kill the insect. During the infection Xenorhabdus spp grow to high cell density in the hemolymph. As the nematode invades …

Complex Regulatory Pathways Connect Vfm Quorum-Sensing And Cyclic-Di-Gmp Signaling To Bacterial Virulence In The Phytopathogen Dickeya Dadantii 3937, Biswarup Banerjee

Theses and Dissertations

The bacterial second messenger Bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP) regulates multiple cellular behaviors in most bacteria. Bacterial c-di-GMP signaling involves enzymes that synthesize and degrade c-di-GMP, c-di-GMP binding effectors, and targets that are acted upon by the effectors. So far, the c-di-GMP signaling pathways have been understudied. In this work, we explore the c-di-GMP signaling network further in the phytopathogen Dickeya dadantii 3937. In Chapter 2, we identified VfmE as a c-di-GMP binding transcriptional activator that represses pectate lyase production under a high c-di-GMP condition. VfmE was found to bind c-di-GMP in vitro via the RxxxR motif, similar to PilZ …

Evaluating Soil Health Changes Following Cover Crop And No-Till Integration Into A Soybean (Glycine Max) Cropping System In The Mississippi Alluvial Valley, Alexandra Gwin Firth

Theses and Dissertations

The transition of natural landscapes to intensive agricultural uses has resulted in severe loss of soil organic carbon (SOC), increased CO₂ emissions, river depletion, and groundwater overdraft. Despite negative documented effects of agricultural land use (i.e., soil erosion, nutrient runoff) on critical natural resources (i.e., water, soil), food production must increase to meet the demands of a rising human population. Given the environmental and agricultural productivity concerns of intensely managed soils, it is critical to implement conservation practices that mitigate the negative effects of crop production and enhance environmental integrity. In the Mississippi Alluvial Valley (MAV) region of Mississippi, USA, …

Identification Of Pneumococcal Membrane Proteins Involved In Colonization/Biofilm Formation And Cognate Host Cellular Receptors, Yoonsung Hu

Theses and Dissertations

Colonization is prerequisite for infection and transmission of Streptococcus pneumoniae, or pneumococcus. Currently available pneumococcal conjugate and pneumococcal polysaccharide vaccines can provide protection against a limited number of capsular serotypes. Implementation of vaccines has decreased the frequency of invasive pneumococcal disease and their colonization rates, but only in a serotype-dependent manner. This has led to serotype replacement in pneumococcal ecology and increased invasive disease caused by non-vaccine serotypes. Development of conserved protein-based vaccine that can provide protection against all pneumococcal serotypes is needed. Numerous surface proteins are conserved in all serotypes, and some are known to be involved in …

Influence Of Nutrients And The Native On E. Coli Survival In The Beach Environment, Brigid Meyers

Theses and Dissertations

E. coli is used as an indicator for water quality to determine if water poses a health risk for pathogens. Past research has shown that E. coli is present in high numbers in freshwater beach sands distinct from fecal pollution events, yet the precise mechanism for their persistence in not well understood. Persistent E. coli populations in sand can resuspend into adjacent water and lead to increased beach closures when no threat is present. This work identifies factors that influence the survival of E. coli in sand using laboratory microcosms to replicate beach conditions. Microcosms were deployed to examine the …

Pili And Chpc The Two Adaptor Proteins In Pseudomonas Aeruginosa Chp Chemosensory System, Samuel Engel

Theses and Dissertations

Pseudomonas aeruginosa’s Chp system is an important signal transduction system for its virulence and controls many cellular processes through adenosine 3’,5’ cyclic monophosphate (cAMP) and its interactions with virulence factor regulator (Vfr). Twitching motility, the other output of the Chp system also plays a large role in virulence. This study was completed to better understand the roles the adaptor proteins, PilI and ChpC, fill in the Chp system. The function of the adaptor proteins was investigated through deletion strains via fluorescence microscopy, β-galactosidase assays, twitching motility assays, and surface piliation assays. By viewing these outputs PilI’s status as the dominant …

Development Of A Methodology For The Quantification Of Reaerosolization Of A Biological Contaminant Surrogate Particle From Military Uniform Fabric, George D. Cooksey

Theses and Dissertations

During a mass casualty medical evacuation after a bioaerosol attack, a decontamination method is needed that is effective at both decontamination and preventing the secondary hazard of biological particles reaerosolizing from contaminated clothing. However, neither the efficacy of current decontamination methods nor the risk of biological particle reaerosolization is significantly explored in existing literature. The goals of this thesis were to develop a repeatable methodology to quantify the reaerosolization of a biological contaminate off Airman Battle Uniform (ABU) fabric swatches, and to test the efficacy of one decontamination method (high-volume, low-pressure water) using 1 mpolystyrene latex (PSL) spheres as a …

Design Of A Synthetic Temperature-Activated Epigenetic Biocontainment System, Owen Rivers Page

Theses and Dissertations

The need for an internal control to govern engineered strain survival is becoming apparent when considering the biosafety and ethics within biotechnological research. Using understudied regulatory elements known as RNA thermometers (RNATs) that can modulate protein translation based on temperature changes and a Type II restriction modification system, we posit the creation of a synthetic temperature-activated epigenetic biocontainment system, termed the ‘sentinel switch’. We have mined a wide variety of bacteria from Yersinia pestis to Synechocystis sp. looking for novel RNATs. A complementary synthetic biology approach based on library generation and screening of chimeric RNATs (ChRNATs) was also conducted. RNATs …

Bioinformatic Pipeline For Determining Terminal Repeats In The Human Cytomegalovirus Genome Assembled With Pacbio Long Read Sequences, Ahmed Al Qaffas

Theses and Dissertations

Human Cytomegalovirus (HCMV) is a member of the betaherpesvirinae subfamily of the Herpesvirus family. HCMV infection is common among adults worldwide, with an estimated seroprevalence of 66 to 95%, depending on the geographic region (Zuhair et al., 2019). Although most of the virus genomic content has been studied extensively, the terminal repeating region sequences remain understudied. Two main challenges hindered the study of the region: a) limitations of sequencing technologies; and b) misassembly of the repeats due to its complex nature. Here I show a novel bioinformatics pipeline that takes advantage of PacBio's long reads to resolve the challenges mentioned …

The Influence Of Salinity On The Structure And Function Of Soil Prokaryotic Communities In Coastal Freshwater Wetlands, Joseph C. Morina Ii

Theses and Dissertations

Microbial communities are critical biological components of the world’s ecosystems, and their respiratory pathways are directly involved in the biogeochemical cycling of essential nutrients. As genomic technologies advance, allowing for more detailed profiling of microbial communities, efforts have successfully linked microbial community composition to ecosystem-level functions and have shown microbial communities are susceptible and resistant to disturbance events. The goal of this dissertation is to address the temporal scales in which microbial communities respond to the disturbance of salinization, and the repercussions this has on microbially-meditated carbon and nitrogen cycling. Coastal freshwater wetlands are an excellent study system to investigate …

Antiviral Effects Of Metalloshielding: Differential Antiviral Activity Of Polynuclear Platinum And Cobalt Compounds, Mary Zoepfl

Theses and Dissertations

The majority of antiviral drug development has focused on virus-specific discovery targeting discrete steps in the individual life cycles. Although great strides have been made for a number of clinically relevant diseases such as human immunodeficiency virus, influenza virus, and hepatitis B, broad spectrum antivirals do not exist. Broad spectrum antivirals would offer (1) treatment for viruses without specifically-targeted antivirals, (2) treatment for viruses which have developed resistance to their available treatments, and (3) a rapidly deployable treatment option in viral epidemics. Many viruses including human cytomegalovirus (HCMV), HIV, and SARS-CoV-2. rely on heparan sulfate (HS), a highly sulfated glycosaminoglycan …

Human Papillomavirus 16 E2 Regulates Host Cell Pathways Important For Cancer Progression And Treatment Sensitivity Which May Contribute To Cancer Outcomes, Christian Fontan

Theses and Dissertations

Human papillomaviruses (HPVs) are causative agents in around 5% of all cancers, including cervical and oropharyngeal. A feature of HPV cancers is their better clinical outcome compared with non-HPV anatomical counterparts. In turn, the presence of E2 predicts a better clinical outcome in HPV-positive cancers; the reason(s) for the better outcome of E2-positive patients is not fully understood.

Previously, we demonstrated that HPV16 E2 regulates host gene transcription that is relevant to the HPV16 lifecycle in N/Tert-1 cells. One of the genes repressed by E2 and the entire HPV16 genome in N/Tert-1 cells is TWIST1. In these studies, we demonstrate …

Modification Of Culture Medium And Identification Of Microbial Contaminants For Improved In Vitro Propagation Of Freshwater Mussels, Raquel M. Wetzell

Theses and Dissertations

In vitro propagation efforts play an essential role in conserving and restoring threatened freshwater mussel populations by circumventing the need for a fish host. Across a broad range of taxa, transformation is induced with an artificial M199 medium and rabbit serum. However, such formulation may not be sufficient in culturing critical species with more specific physiological requirements. In this study, multiple serum mixtures were tested to improve in vitro transformation of two freshwater mussel species: yellow lampmussel (Lampsilis cariosa) and tidewater mucket (Atlantaconcha ochracea). These species were selected because they parasitize similar fish host species but …

Genetic Characterization Of Antimicrobial Activities Of Endophytic Bacteria Burkholderia Strains Ms455 And Ms389, Jiayuan Jia

Theses and Dissertations

Strains MS455 and MS389, endophytic bacteria, were isolated from healthy soybean plant growing adjacent to a patch of plants affected by charcoal rot disease, caused by the fungal pathogen Macrophomina phaseolina. The complete genomes of both strains were sequenced and identified as Burkholderia species Strain MS455 exhibits broad-spectrum antifungal activities against economically important pathogens, including Aspergillus flavus. Random and site-specific mutations were employed in discovery of the genes that share high homology to the ocf gene cluster of Burkholderia contaminans strain MS14, which is responsible for production of the antifungal compound occidiofungin. RNA-seq analysis demonstrated ORF1, a …

Evaluating The Effects Of Pine And Miscanthus Biochar On Water Activity And Escherichia Coli Populations In Commercial Broiler Litter, Christopher Austin Marty

Theses and Dissertations

The decrease in subtherapeutic antibiotic administration in poultry has increased the need to address production challenges caused by pathogens, such as E. coli. One potential way to improve bird health and reduce bacterial infection is through the addition of litter amendments that absorb moisture. Biochar (BC) has previously been shown to increase water holding capacity in poultry litter, but its effects on E. coli mitigation are unknown. The objectives of this research were to 1) evaluate water activity of poultry litter amended with pine and miscanthus BC, and 2) determine the effects of different BC inclusion rates on litter …

Microbial Communities Hosted By Carnivorous Pitcher Plants: Diversity, Recruitment, Functions And Succession In Sarracenia Purpurea Microbiomes, Jacob Jeffrey Grothjan

Theses and Dissertations

The pitcher plant Sarracenia purpurea supplements nutrient acquisition through carnivory, capturing insect prey which are digested by a food web community of eukaryotes and bacteria. Analysis of both bacterial and eukaryotic diversity, and an understanding of bacterial recruitment into pitchers and succession of bacterial and eukaryotic communities over time have not been well explored. This thesis presents three studies designed to address these gaps using field sampling and manipulative greenhouse experiments. Study I compared bacterial and eukaryotic composition and diversity of pitcher communities within and between populations of plants in two distinct wetland habitats. Genetic sequence analysis revealed an underappreciated …

Prospecting For And Isolation Of Microalgae In South Texas, Mauricio Alejandro Peña

Theses and Dissertations

Microalgae is a very important microorganism that can be used for beneficial purposes for humans. One way to show the importance of algae in this planet is the contribution of Oxygen it provides to the atmosphere, which many organisms rely on (Medeiros et al., 2015). Carbon footprint has been one of the greatest causes for global warming and it is due to the use of fossils to create diesel. One of the ways to avoid contamination is to replace those fuels that are used on daily basis, such as for transportation. The microalgae are able to produce lipids that can …

The Study Of The Phytopathogen Dickeya Dadantii 3937 Cpx Signaling On The Regulation Of Virulence And Antimicrobial Resistance, Daqing Jiang

Theses and Dissertations

Bacteria respond to environmental cues through a variety of mechanisms. Two-component systems (TCSs) are a conserved mechanism used by bacteria to accurately respond and sense environmental changes. The monitoring of envelope perturbance is linked to TCS CpxA/CpxR in animal-infecting pathogens. The study of the TCS response regulator (RR) CpxR is largely unexplored in phytopathogens. This work focuses on the genetic linkage between cpxR and T3SS expression regulation. We identified the multiple roles of CpxR on several T3SS regulators and its participation in the bacterial second messenger (c-di-GMP) signaling cascade. Moreover, a compound library screening revealed a novel Cpx inducer CHIR-090, …