Bacteriology Commons^™

Co-Occurrence Of Manganese Oxidase Genes Indicates Lateral Transfer Between Classes Of Proteobacteria, Jacob Olichney

Student Scholar Showcase

Pseudomonas putida GB-1 is a model organism for the study of manganese oxidation in bacteria, however, the frequency of co-localization of multiple known and suspected manganese oxidizing proteins, as well as their occurrence between species, is unknown. Eight different genes isolated from known manganese oxidizing bacteria (MnxG, MopA, McoA, PputGB1_2552, PputGB1_2553, MoxA, MofA, and Bacillus MnxG) were tested individually using BioPython and BLAST (Basic Local Alignment Search Tool) on multiple genomic databases. BLAST searches had an expect value cutoff of 1e-50, limiting gene homologs to those with high sequence similarity. The abundance of homologous genes across classes of proteobacteria point …

Symbiosis In Archaea: Functional And Phylogenetic Diversity Of Marine And Terrestrial Nanoarchaeota And Their Hosts, Emily Joyce St. John

Dissertations and Theses

The Nanoarchaeota are an enigmatic lineage of Archaea found in deep-sea hydrothermal vents and geothermal springs across the globe. These small (~100-400 nm) hyperthermophiles live ectosymbiotically with diverse hosts from the Crenarchaeota. Despite their broad distribution in high-temperature environments, very few Nanoarchaeota have been successfully isolated in co-culture with their hosts and nanoarchaeote genomes are poorly represented in public databases. However, the Nanoarchaeota provide unique insights into the structure and function of symbiosis in the archaeal domain. This study describes novel nanoarchaeotes from multiple geothermal habitats, using a combination of direct cultivation techniques and genomic analysis. A new nanoarchaeote …

Establishment Of Listeria Monocytogenes In The Gastrointestinal Tract, Morgan L. Davis, Steven C. Ricke, Janet R. Donaldson

Faculty Publications

Listeria monocytogenes is a Gram positive foodborne pathogen that can colonize the gastrointestinal tract of a number of hosts, including humans. These environments contain numerous stressors such as bile, low oxygen and acidic pH, which may impact the level of colonization and persistence of this organism within the GI tract. The ability of L. monocytogenes to establish infections and colonize the gastrointestinal tract is directly related to its ability to overcome these stressors, which is mediated by the efficient expression of several stress response mechanisms during its passage. This review will focus upon how and when this occurs and how …

Diversity And Shifts Of The Bacterial Community Associated With Baikal Sponge Mass Mortalities, Sergei Belikov, Natalia Belkova, Tatiana Butina, Lubov Chernogor, Alexandra Martynova-Van Kley, Armen Nalian, Colin Rorex, Igor Khanaev, Olga Maikova, Sergey Feranchuk

Faculty Publications

The disease of freshwater sponges was first discovered in 2011, when pink samples were found in the Central Basin of Lake Baikal. Subsequently, the visible signs of the disease have changed, and now sponges appear with various symptoms of damage to the body, such as discoloration, tissue necrosis, the formation of brown patches and dirty-purple biofilms on some branches. These signs of the disease are accompanied by the mass death of sponges. We identified differences in microbiomes by sequencing 16S rRNA genes and found changes in the consortium of microorganisms of freshwater Baikal sponges. We found that the observed imbalance …

Assessing The Prevalence Of Multidrug Resistant Salmonella Enterica From Stream Sediment And Poultry Litter In The Shenandoah Valley Of Virginia, Noah Greenman

Masters Theses, 2010-2019

Multidrug resistant Salmonella enterica present in stream sediment and poultry litter represent a critical health concern. A small number of S. enterica serotypes are responsible for most lab-confirmed infections in the US each year. To assess the prevalence of these significant strains, we isolated 88 S. enterica from stream sediment and poultry litter. Sequence data for all isolates were generated using an Illumina® sequencing platform, with long-reads for some isolates from the Oxford Nanopore MinION™ used in a hybrid genome assembly approach. Isolates were typed according to their serotype and multi-locus sequence type using SeqSero/SISTR and Enterobase respectively. Antibiotic resistance …

Structure/Function Analysis Of Fega And Fhua In Bradyrhizobium Sp., Alexander James Herd

Senior Honors Projects, 2010-2019

Bradyrhizobium japonicum is a Gram-negative soil bacterium commonly known for its agriculturally significant mutualistic relationship with soybean. In this symbiosis, the bacteria and plant undergo complex molecular signaling characterized by sent and received signals resulting in the formation of infection threads and root nodules. This research aimed to compare two related bacterial outer membrane proteins, FegA and FhuA, associated with the molecular signaling between the bacteria and plant. Previous work has led to the hypothesis that the N-terminal domain (NTD) of FegA in B. japonicum is needed for a functional symbiosis to occur. Recombinant bacterial strains expressing altered FegA proteins …

The Anaplasma Phagocytophilum Adhesin Asp14 Directs Pdi-Mediated Disulfide Reduction To Promote Infection, Ryan S. Green

Theses and Dissertations

Obligate intracellular pathogens must invade host cells to survive and pose a global health risk. As such, internalization is a critical life stage and represents an excellent therapeutic target. Oxidoreductase exploitation is a thematic invasion strategy among obligate intracellular pathogens. Delineating the mechanisms and proteins mediating this exploitation could identify novel therapeutic targets for many important pathogens. Anaplasma phagocytophilum infects neutrophils by an incompletely defined mechanism, resulting in the emerging potentially fatal disease, human granulocytic anaplasmosis. The bacterial adhesin, Asp14, contributes to invasion by virtue of its C-terminus engaging an unknown receptor. Yeast two-hybrid analysis identified protein disulfide isomerase (PDI) …

Hydrodynamic Cavitation As In-Line Process To Control Common Dairy Sporeformers, Pratibha Chaudhary

Electronic Theses and Dissertations

Sporeforming bacteria and their endospores have the ability to survive thermal treatments and proliferate in the milk and dairy products to cause spoilages. We applied the effect of hydrodynamic cavitation in controlling these bacteria and their spores at pilot scale level. Our aim was to investigate a technology that would improve the microbial quality of milk and dairy products, and is capable of being scaled up to be adapted at industrial level. Cavitation damages the cell walls of the bacteria and their endospores (releasing dipicolinic acid, responsible for endospore resistance to extreme conditions), thereby making them susceptible to thermal treatments …

Interactions Of Arbuscular Mychorrhizal Fungi And Bacterial Endophytes On Disease Resistance Of Common Root Pathogens In Wheat, Janice L. Eibensteiner

Electronic Theses and Dissertations

Arbuscular mycorrhiza, a symbiosis between plants and fungi, help plants to capture nutrients such as phosphorus (P), nitrogen (N) and other micronutrients from the aggre in exchange for up to 20% of the fixed carbon (C) from the plant. In addition, arbuscular mycorrhizal (AM) fungi can improve the resistance against abiotic (drought, salinity), and also biotic (pathogen) stresses. Bacterial endophytes promote plant growth and yield by fixing N2 from the atmosphere, assimilating N and transfer it to the plant. Bacterial endophytes can also solubilize phosphate and stimulate plant defense responses, suppressing pathogens. The host plant provides sucrose and a favorable …

High Resolution Modeling Of Tick Density And Detection Of Rickettsia Spp. In Dermacentor Spp. Ticks At Turnbull National Wildlife Refuge, Wa, Justin L. Donahue

EWU Masters Thesis Collection

The tick species Dermacentor andersoni and Dermacentor variabilis are known vectors of pathogens. One such pathogen is the bacteria Rickettsia rickettsii, which causes Rocky Mountain spotted fever. The detection of this bacterium in ticks at Turnbull National Wildlife Refuge (TNWR) indicates a potential risk to human health. In order to follow up on this discovery, we had two separate objectives. First we developed a high resolution predictive map for Dermacentor spp. distribution across the public use area of TNWR. To do so, 50m transects (27 in total) were established across the public use area. Ticks were collected weekly within the …

Adaptation Of The Streptococcal Collagen-Like Protein 1, Scl1, Of Group A Streptococcus To Recognize Fibronectin Type Iii Repeats, Dudley H. Mcnitt

Graduate Theses, Dissertations, and Problem Reports (ETD)

Background: Group A Streptococcus (GAS) is responsible more than 700 million infections worldwide each year. Most of these infections start with initial colonization of the throat and skin, which is augmented by surface adhesins. The streptococcal collagen-like protein 1 (Scl1) is a major adhesin expressed by GAS that contains an N-terminal sequence-variable (V) domain, protruded away from the cell surface by the collagen domain. The Scl-V domain is comprised of three pairs of anti-parallel α-helices interconnected by surface-exposed loops. For attachment, GAS adhesins require a portal of entry, such as a wound or breach in the epithelium, to enter …

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 …

Effects Of 5��-Dihydrotestosterone (Dht) On Mouse Gut Microbiome– A Study Of Sex Differences And Hormonal Effects On Gut Microbiome Composition, Bikesh Shrestha

All Master's Theses

Type 1 Diabetes (T1D) is a polygenic and multifactorial disease, traditionally attributed to genetic susceptibility and diet. Over the past decade, novel studies have placed a higher significance on the role of gut microbiome in T1D pathogenesis. Furthermore, diabetic mouse models have shown higher incidence of T1D in females compared to males, attributed to the differences in gut microbial community structure. Interestingly, female mouse models elicit male-like protection from T1D when transplanted with the male gut microbiome. In a previous study, we observed that female Non-obese diabetic (NOD) mice implanted with slow release 5��-Dihydrotestosterone(DHT) for 90 days showed improved glucose …

Impact Of Seasonal And Host-Related Factors On The Intestinal Microbiome And Cestode Community Of Sorex Cinereus And Sorex Monticola, Katelyn D. Cranmer

College of Graduate Studies: Theses & Dissertations

The intestinal microbiome of mammals plays a significant role in host health and response to environmental stimuli and can include both beneficial native bacteria as well as parasitic worms. In this study, I examined the intestinal cestode and bacterial communities of two closely related species of shrew, Sorex monticola and Sorex cinereus, over a six month period in 2016. Specimens were collected approximately every three weeks from May to October from the Sangre de Cristo Mountains in Cowles, New Mexico. A total of 79 shrews were prepared with the gastrointestinal tracts removed and flash-frozen in liquid nitrogen. An additional …

Evaluation Of Intra-Species Diversity Of Oxalobacter Formigenes Strains Using Pulsed-Field Gel Electrophoresis (Pfge) And Multiplex Pcr, Nivedita Pareek

Masters Theses

Oxalobacter formigenes is a beneficial, strict anaerobic gut bacterium that plays an important role in the prevention of kidney stone disease with a unique characteristic of using only oxalate as a carbon and energy source. To date, twenty-one strains of O. formigenes have been isolated which are further divided into two groups based on differences in the patterns of cell membrane lipids, cellular proteins, and nucleic acid fragments. The objective of the study was to evaluate intra-species diversity of O. formigenes strains using pulsed-field gel electrophoresis (PFGE) and multiplex PCR.

Nine pure cultures of O. formigenes strains (5 strains group …

Xylan Metabolism By Caulobacter Crescentus, Viet Bui

Masters Theses

Bacteria present unique opportunities to explore the molecular mechanisms of nutrient acquisition processes at single cell level under various experimental conditions. Caulobacter crescentus is a gram-negative oligotrophic environmental bacterium with adaptive physiological responses, such as slow growth or complete arrest of cell cycle, presence of sessile and motile progenies with the sessile cells growing stalk to enhance nutrient uptake for growth in low-nutrient conditions. Details of plant polysaccharide-derived carbon compound, such as cellobiose, maltose, and xylose utilization by C. crescentus can be found but molecular details or mechanisms of polysaccharide utilization, such as xylan, has not been reported. Database analyses …

Preconditioning Of The Tumor Microenvironment By Means Of Low Dose Chemotherapies For An Effective Immunotherapy Of Breast Cancer, Hussein F. Aqbi

Theses and Dissertations

Breast cancer mortality is mainly due to distant recurrence of the disease arising from dormant tumor cells established by cancer therapies. Patients who initially respond to cancer therapies often succumb to distant recurrence of the disease. It is not clear why people with the same type of breast cancer respond to treatments differently; some escape from dormancy and relapse earlier than others. In addition, some tumor clones respond to immunotherapy while others do not. We investigated how autophagy plays a role in accelerating or delaying recurrence of neu overexpressing mouse mammary carcinoma (MMC) following adriamycin (ADR) treatment, and in affecting …

Nitrogen Assimilation In Picocyanobacteria Inhabiting The Oxygen-Deficient Waters Of The Eastern Tropical North And South Pacific, Montserrat Aldunate, Carlos Henriquez-Castillo, Qixing Ji, Jessica Lueders-Dumont, Margaret R. Mulholland, Bess B. Ward, Peter Von Dassow, Osvaldo Ulloa

OES Faculty Publications

Prochlorococcus and Synechococcus are the most abundant free-living photosynthetic microorganisms in the ocean. Uncultivated lineages of these picocyanobacteria also thrive in the dimly illuminated upper part of oxygen-deficient zones (ODZs), where an important portion of ocean nitrogen (N) loss takes place via denitrification and anaerobic ammonium oxidation. Recent metagenomic studies revealed that ODZ Prochlorococcus have the genetic potential for using different N forms, including nitrate and nitrite, uncommon N sources for Prochlorococcus, but common for Synechococcus. To determine which N sources ODZ picocyanobacteria are actually using in nature, the cellular 15N natural abundance (δ15N) and assimilation rates 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 …

Harnessing The Anopheles Microbiome To Conditionally Express Anti-Plasmodial Effectors During The Blood Meal, Jackie Shane

Electronic Theses and Dissertations

The control of vector-borne diseases such as malaria has been an extremely important research subject for hundreds of years. Because of the complex lifecycles of the pathogens that cause these diseases, finding a comprehensive treatment or preventative strategy has proven extremely difficult. Malaria alone is responsible for almost half a million deaths annually, most of them children under 5 years old. This disease is caused by parasitic protists in the genus Plasmodium that are transmitted to humans from Anopheles sp. mosquitoes. Most preventative strategies that are in use today revolve around controlling the vectors, including bed nets, insecticides, and larval …

Stress Response Mechanisms Of Listeria Monocytogenes, Oindrila Paul

Dissertations

Listeria monocytogenes is a Gram-positive, facultative intracellular food-borne pathogen that causes the disease listeriosis. In order to establish an infection, L. monocytogenes must survive multiple stressors encountered within the gastrointestinal tract, including alterations in pH, bile, salt, and oxygen availability. This dissertation focused on understanding the stress response of L. monocytogenes to bile. Bile acts as a bactericidal agent by disrupting the membrane integrity and causing instability to macromolecules like DNA. Thus, a bacterium must be able to maintain its membrane architecture, composition and integrity.

Often times, bacteria will modulate their fatty acid composition in the membrane to cope with …

Dna Methylation By Restriction Modification Systems Affects The Global Transcriptome Profile In Borrelia Burgdorferi, Timothey Casselli, Yvonne Tourand, Adam Scheidegger, William K. Arnold, Anna Proulx, Brian Stevenson, Catherine A. Brissette

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Prokaryote restriction modification (RM) systems serve to protect bacteria from potentially detrimental foreign DNA. Recent evidence suggests that DNA methylation by the methyltransferase (MTase) components of RM systems can also have effects on transcriptome profiles. The type strain of the causative agent of Lyme disease, Borrelia burgdorferi B31, possesses two RM systems with N6-methyladenosine (m6A) MTase activity, which are encoded by the bbe02 gene located on linear plasmid lp25 and bbq67 on lp56. The specific recognition and/or methylation sequences had not been identified for either of these B. burgdorferi MTases, and it was not previously known whether these RM …

Floxed-Cassette Allelic Exchange Mutagenesis Enables Markerless Gene Deletion In Chlamydia Trachomatis And Can Reverse Cassette-Induced Polar Effects, Gabrielle Keb, Robert Hayman, Kenneth A. Fields

Microbiology, Immunology, and Molecular Genetics Faculty Publications

As obligate intracellular bacteria, Chlamydia spp. have evolved numerous, likely intricate, mechanisms to create and maintain a privileged intracellular niche. Recent progress in elucidating and characterizing these processes has been bolstered by the development of techniques enabling basic genetic tractability. Florescence-reported allelic exchange mutagenesis (FRAEM) couples chromosomal gene deletion with the insertion of a selection cassette encoding antibiotic resistance and green fluorescent protein (GFP). Similar to other bacteria, many chlamydial genes exist within polycistronic operons, raising the possibility of polar effects mediated by insertion cassettes. Indeed, FRAEM-mediated deletion of Chlamydia trachomatis tmeA negatively impacts the expression of tmeB. We …

Insights Into The Reactivation, Regulation And Essentiality Of Oxidative Protein Folding Pathways In Actinobacteria, Belkys Sanchez

Dissertations and Theses (Open Access)

Accurate disulfide bond formation is important for proper folding, stability and function of exported proteins. The process of disulfide bond formation, termed oxidative protein folding, is catalyzed by thiol-disulfide oxidoreductase enzymes. Oxidative protein folding pathways influence processes essential for bacterial physiology and pathogenicity. In the Gram-positive actinobacterial pathogens Actinomyces oris and Corynebacterium diphtheriae oxidative protein folding is catalyzed by the primary thiol-disulfide oxidoreductase MdbA. MdbA is required for assembly of adhesive pilus, which mediate receptor-dependent bacterial interactions, or coaggregation, in A. oris. In the first part of this dissertation, I identify components of the electron transport chain (ETC) required for …

Assembly And Display Of Surface Proteins In Actinomyces Oris, Sara Siegel

Dissertations and Theses (Open Access)

Bacteria are an integral part of human health and disease. In the human host, dental plaques form as a result of up to 700 individual bacterial species colonizing oral surfaces and forming a multispecies biofilm. These biofilms are the cause of prevalent human diseases such as dental caries, gingivitis, and periodontitis. The microbes present in the oral biofilm are highly spatially and temporally structured and require a primary colonizing species to adhere to host tissue. As an important primary colonizer of the oral biofilm, the actinobacterium Actinomyces oris utilizes cell wall anchored proteins and glycoconjugates to initiate adherence to host …

Biofilm Producing Clinical Staphylococcus Aureus Isolates Augmented Prevalence Of Antibiotic Resistant Cases In Tertiary Care Hospitals Of Nepal, Sarita Manandhar, Anjana Singh, Ajit Varma, Shanti Pandey, Neeraj Shrivastava

Student Publications

Staphylococcus aureus, a notorious human pathogen, is a major cause of the community as well as healthcare associated infections. It can cause a diversity of recalcitrant infections mainly due to the acquisition of resistance to multiple drugs, its diverse range of virulence factors, and the ability to produce biofilm in indwelling medical devices. Such biofilm associated chronic infections often lead to increase in morbidity and mortality posing a high socio-economic burden, especially in developing countries. Since biofilm formation and antibiotic resistance function dependent on each other, detection of biofilm expression in clinical isolates would be advantageous in treatment decision. …

Triatomines: Trypanosomatids, Bacteria, And Viruses Potential Vectors?, Caroline Barreto Viera, Yanna Reis Praça, Kaio Luis Da Silva Bentes, Paula Beatriz Santiago, Sofia Marcelino Martins Silva, Gabriel Dos Santos Silva, Flávia Nader Motta, Izabela Marques Dourado Bastos, Jaime Martins De Santana, Carla Nunes De Araújo

Harold W. Manter Laboratory of Parasitology: Library Materials

Triatominae bugs are the vectors of Chagas disease, a major concern to public health especially in Latin America, where vector-borne Chagas disease has undergone resurgence due mainly to diminished triatomine control in many endemic municipalities. Although the majority of Triatominae species occurs in the Americas, species belonging to the genus Linshcosteus occur in India, and species belonging to the Triatoma rubrofasciata complex have been also identified in Africa, the Middle East, South-East Asia, and in the Western Pacific. Not all of Triatominae species have been found to be infected with Trypanosoma cruzi, but the possibility of establishing vector transmission …

Triatomines: Trypanosomatids, Bacteria, And Viruses Potential Vectors? [Review], Caroline Barreto Vieira, Yanna Reis Praça, Kaio Luís Da Silva Bentes, Paula Beatriz Santiago, Sofia Marcelino Martins Silva, Gabriel Dos Santos Silva, Flávia Nader Motta, Izabela Marques Dorado Bastos, Jaime Martins De Santana, Carla Nunes De Araújo

Harold W. Manter Laboratory of Parasitology: Library Materials

Triatominae bugs are the vectors of Chagas disease, a major concern to public health especially in Latin America, where vector-borne Chagas disease has undergone resurgence due mainly to diminished triatomine control in many endemic municipalities. Although the majority of Triatominae species occurs in the Americas, species belonging to the genus Linshcosteus occur in India, and species belonging to the Triatoma rubrofasciata complex have been also identified in Africa, the Middle East, South-East Asia, and in the Western Pacific. Not all of Triatominae species have been found to be infected with Trypanosoma cruzi, but the possibility of establishing vector transmission …

Identification And Heterologous Reconstitution Of A 5-Alk(En)Ylresorcinol Synthase From Endophytic Fungus Shiraia Sp. Slf14, Huiwen Yan, Lei Sun, Jinge Huang, Yixing Qiu, Fuchao Xu, Riming Yan, Du Zhu, Wei Wang, Jixun Zhan

Biological Engineering Faculty Publications

A new type III polyketide synthase gene (Ssars) was discovered from the genome of Shiraia sp. Slf14, an endophytic fungal strain from Huperzia serrata. The intron-free gene was cloned from the cDNA and ligated to two expression vectors pET28a and YEpADH2p-URA3 for expression in Escherichia coli BL21(DE3) and Saccharomyces cerevisiae BJ5464, respectively. SsARS was efficiently expressed in E. coli BL21(DE3), leading to the synthesis of a series of polyketide products. Six major products were isolated from the engineered E. coli and characterized as 1,3-dihydroxyphenyl-5-undecane, 1,3-dihydroxyphenyl-5-cis-6'-tridecene,1,3-dihydroxyphenyl-5-tridecane, 1,3-dihydroxyphenyl-5-cis-8'-pentadecene, 1,3-dihydroxyphenyl-5-pentadecane and 1,3-dihydroxyphenyl-5-cis-10'-heptadecene, respectively, …

Simulating Antibiotic Resistance In The Computer Lab And Biology Lab: Ideas For Undergraduate Projects, Anne E. Yust

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.