Microbiology Commons^™

Conserved Glycines Control Disorder And Function In The Cold-Regulated Protein, Cor15a, Oluwakemi T. Sowemimo, Patrick Knox-Brown, Wade M. Borcherds, Tobias Rindfleisch, Anja Thalhammer, Gary W. Daughdrill

Molecular Biosciences Faculty Publications

Cold-regulated (COR) 15A is an intrinsically disordered protein (IDP) from Arabidopsis thaliana important for freezing tolerance. During freezing-induced cellular dehydration, COR15A transitions from a disordered to mostly α-helical structure. We tested whether mutations that increase the helicity of COR15A also increase its protective function. Conserved glycine residues were identified and mutated to alanine. Nuclear magnetic resonance (NMR) spectroscopy was used to identify residue-specific changes in helicity for wildtype (WT) COR15A and the mutants. Circular dichroism (CD) spectroscopy was used to monitor the coil–helix transition in response to increasing concentrations of trifluoroethanol (TFE) and ethylene glycol. The impact of the COR15A …

Host Restriction Factors In The Replication Of Tombusviruses: From Rna Helicases To Nucleocytoplasmic Shuttling, Cheng-Yu Wu

Theses and Dissertations--Plant Pathology

Positive-stranded (+)RNA viruses replicate inside cells and depend on many cellular factors to complete their infection cycle. In the meanwhile, (+)RNA viruses face the host innate immunity, such as cell-intrinsic restriction factors that could block virus replication.

Firstly, I have established that the plant DDX17-like RH30 DEAD-box helicase conducts strong inhibitory function on tombusvirus replication when expressed in plants and yeast surrogate host. This study demonstrates that RH30 blocks the assembly of viral replicase complex, the activation of RNA-dependent RNA polymerase function of p92pol and viral RNA template recruitment.

In addition, the features rendering the abundant plant DEAD-box helicases either …

Staphylococcus Aureus Evasion Of The Innate Immune System, James Paul Grayczyk

Dissertations

Upon entry into the host, pathogens must overcome innate immunity in order to cause disease. The innate immune system represents a fast-acting initial line of defense to prevent infection. In order to withstand innate defenses, bacterial pathogens like the Gram-positive bacterium Staphylococcus aureus, produce a wide array of virulence factors that can inhibit innate immune cell recruitment and antimicrobial activity, or directly target and kill phagocytic leukocytes thereby facilitating pathogenesis. Infection with S. aureus can cause disease in virtually any tissue site and is a significant burden to human health. In this dissertation, we sought to understand how S. aureus …

Generating Biologic And Genetic Research Tools To Investigate Serotype I Feline Coronaviruses, Robert Christian Mettelman

Dissertations

Serotype I feline infectious peritonitis virus (FIPV) is an alphacoronavirus of high veterinary importance due to the 99% mortality rate observed in cats. Since the 1980s, robust experimentation on these viruses has been limited by availability of culturable pathogenic strains, few permissive cell lines, and a lack of standardized methods to study their basic virology. These complications have resulted in variable and conflicting literature reports, have slowed study of clinical strains and hindered effective vaccine design. The goal of this dissertation was to develop a laboratory "toolbox" containing standardized methods, permissive cell lines and genetic techniques to alleviate some of …

Strain-Specific Protein Interaction And Localization Of Two Strains Of Potato Yellow Dwarf Virus And Functional Domains Of Their Matrix Protein, Chanyong Jang

Theses and Dissertations--Plant Pathology

Potato yellow dwarf virus (PYDV) is the type species of the genus nucleorhabdovirus which is typified by its nucleotropic characters of the members. The virus accomplishes its replication and morphogenesis in the nuclei of infected cells. Two strains, Constricta strain (CYDV) and Sanguinolenta strain (SYDV) have been described at the level of vector-specificity. CYDV is vectored by Agallia constricta and SYDV is transmitted by Aceratagllia sanguinolenta. The full-length genome of CYDV was sequenced. The 12,792 nt antisense genome encodes seven open reading frames in the order of, nucleocapsid protein (N), unknown protein (X), phosphoprotein (P), movement protein (Y), matrix …

Functional Inhibition Of Acid Sphingomyelinase Disrupts Infection By Intracellular Bacterial Pathogens, Chelsea L. Cockburn, Ryan S. Green, Sheela R. Damle, Rebecca K. Martin, Naomi N. Ghahrai, Punsiri M. Colonne, Marissa S. Fullerton, Daniel H. Conrad, Charles E. Chalfant, Daniel E. Voth, Elizabeth A. Rucks, Stacey D. Gilk, Jason A. Carlyon

Molecular Biosciences Faculty Publications

Intracellular bacteria that live in host cell–derived vacuoles are significant causes of human disease. Parasitism of low-density lipoprotein (LDL) cholesterol is essential for many vacuole-adapted bacteria. Acid sphingomyelinase (ASM) influences LDL cholesterol egress from the lysosome. Using functional inhibitors of ASM (FIASMAs), we show that ASM activity is key for infection cycles of vacuole-adapted bacteria that target cholesterol trafficking—Anaplasma phagocytophilum, Coxiella burnetii, Chlamydia trachomatis, and Chlamydia pneumoniae. Vacuole maturation, replication, and infectious progeny generation by A. phagocytophilum, which exclusively hijacks LDL cholesterol, are halted and C. burnetii, for which lysosomal cholesterol accumulation is bactericidal, …

Functional Analysis Of The Replication Fork Proteome Identifies Bet Proteins As Pcna Regulators, Sarah R. Wessel, Kareem N. Mohni, Jessica W. Luzwick, Huzefa Dungrawala, David Cortez

Molecular Biosciences Faculty Publications

Identifying proteins that function at replication forks is essential to understanding DNA replication, chromatin assembly, and replication-coupled DNA repair mechanisms. Combining quantitative mass spectrometry in multiple cell types with stringent statistical cutoffs, we generated a high-confidence catalog of 593 proteins that are enriched at replication forks and nascent chromatin. Loss-of-function genetic analyses indicate that 85% yield phenotypes that are consistent with activities in DNA and chromatin replication or already have described functions in these processes. We illustrate the value of this resource by identifying activities of the BET family proteins BRD2, BRD3, and BRD4 in controlling DNA replication. These proteins …

P53 Phosphomimetics Preserve Transient Secondary Structure But Reduce Binding To Mdm2 And Mdmx, Robin Levy, Emily Gregory, Wade Borcherds, Gary W. Daughdrill

Molecular Biosciences Faculty Publications

The disordered p53 transactivation domain (p53TAD) contains specific levels of transient helical secondary structure that are necessary for its binding to the negative regulators, mouse double minute 2 (Mdm2) and MdmX. The interactions of p53 with Mdm2 and MdmX are also modulated by posttranslational modifications (PTMs) of p53TAD including phosphorylation at S15, T18 and S20 that inhibits p53-Mdm2 binding. It is unclear whether the levels of transient secondary structure in p53TAD are changed by phosphorylation or other PTMs. We used phosphomimetic mutants to determine if adding a negative charge at positions 15 and 18 has any effect on the transient …

The Otud5–Ubr5 Complex Regulates Fact-Mediated Transcription At Damaged Chromatin, Angelo De Vivo, University Of South Florida, Jose Yegres, Jeonghyeon Kim, Sylvia Emly, Younghoon Kee

Molecular Biosciences Faculty Publications

Timely stalling and resumption of RNA polymerases at damaged chromatin are actively regulated processes. Prior work showed an importance of FACT histone chaperone in such process. Here we provide a new role of OTUD5 deubiquitinase in the FACT-dependent process. Through a DUB RNAi screen, we found OTUD5 as a specific stabilizer of the UBR5 E3 ligase. OTUD5 localizes to DNA double strand breaks (DSBs), interacts with UBR5 and represses the RNA Pol II elongation and RNA synthesis. OTUD5 co-localizes and interacts with the FACT component SPT16 and antagonizes the histone H2A deposition at DSB lesions. OTUD5 interacts with UBR5 and …

Six-Nine Months Long Term Culture Of Mouse Bone Marrow Cells Differentiated To Macrophages And Eosinophils, Olena B. Svitlova

Browse all Theses and Dissertations

Mouse models of eosinophil-associated diseases have been used to study the mechanisms of disease pathogenesis. In this study, mouse-derived bone marrow cells were used in long-term (6 and 9 months) cell cultures of differentiated eosinophils and macrophages. IL-5 was used to differentiate the stem cells to eosinophils and GM-CSF was used to propagate macrophages from the bone marrow stem cells. The maximum time period for observing the eosinophil cultures was 252 days which is censurably longer than the 18 days culture period observed by others. The results were assessed by describing the microscopic cell morphology by Wright staining, modified Giemsa …

Best Practices In Patellar Tendinopathy Management: An Evidence To Practice Review, Christopher J. Burcal, Adam B. Rosen, Tony Taylor, Mike Nicola

Clinical Practice in Athletic Training

Patellar tendinopathy (PT) is a degenerative condition that is common in sporting populations due to the loads placed on the tendon during dynamic activity. PT often occurs in overtraining situations; however, it may also occur in conjunction with and/or worsen through poor biomechanics, persistent inflammation, and altered movement patterns. Although sports medicine practitioners have evidence to support the prevalence of this injury, we do not have a strong base of evidence surrounding the contributing factors and pathophysiology that lead the pain and disability reported in patients with PT. The purpose of this evidence to practice review was to summarize a …

Development And Evaluation Of Vaccine Candidates For Senecavirus A, Bishwas Sharma

Electronic Theses and Dissertations

Senecavirus A (SVA) has been associated with several outbreaks of vesicular disease (VD) since 2014 in major swine-producing countries around the world. The virus causes VD that is clinically indistinguishable from foot-and-mouth disease (FMD) in pigs. Currently there are no commercial vaccines available for SVA. Here, we developed a live attenuated SVA strain by mutating a wild type SVA strain SD15-26 (wt SVA). The live attenuated virus, rSVA mSacII, replicated less efficiently in cell cultures in vitro and expressed lower amounts of VP1 and VP2 capsid proteins than wt SVA. Most importantly, the rSVA mSacII virus failed to induce clinical …

Shrimp Production Environment And The Gut Microbiome: Effects Of Aquaculture Practices And Selective Breeding On The Gut Microbiome Of Pacific Whiteleg Shrimp, Litopenaeus Vannamei, Angela Landsman

Electronic Theses and Dissertations

Knowledge of the functional role of the gut microbiome in animal health and nutrition may provide solutions to shrimp aquaculture challenges, such as improving disease resistance and optimizing growth particularly with low cost feeds. Successful manipulation of bacteria found in the gut requires a deeper understanding of shrimp microbial communities and how their compositional structure is influenced by environmental conditions, and inherent host factors such as genetics. The initial research investigated the intestinal bacterial communities of the Pacific whiteleg shrimp (Litopenaeus vannamei) reared in pond systems compared to indoor aquaculture facilities as an exploration of the effects of aquaculture practices …

Isolation And Identification Of Potential Bioinoculants Based On Phosphate Solubilizing And Plant Growth Promoting Benefits, Rachel Raths

Electronic Theses and Dissertations

Conservative models have shown that as populations rise, food production needs to double by 2050. Population increase and the green revolution have caused fertilizer inputs to increase since the 1960’s, increasing environmental issues and production costs. These intensive practices have led to degraded arable land and there has been an increase in urbanization meaning we need to make best use of the farming land that is available and ensure it is sustainable for future food production. Due to this, there has been a higher demand for research on more environmentally and economically friendly approaches to food production. Plant growth promoting …

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 …

Comparing Gut Microbiome And Virome In The Breast Milk- And Formula-Fed Late Preterm Infants, Zyi Wang

Electronic Theses and Dissertations

The neonatal intestinal microbiome consists of all microorganisms in the gut. Although the microbiome is critical to human health and disease, its colonization remains incompletely understood, particularly in the preterm infant. We aimed to characterize the intestinal bacteria microbiome and virome in moderate-to-late preterm infants. We hypothesized that the bacteria microbiome and virome differs between breast milk and formula-fed infants. We collected stool samples from twenty infants born between 32 0/7 and 36 6/7 weeks gestation. Samples were collected after infants reached full volume enteral feedings. Ten infants were breast milk fed and ten received infant formula. DNA and RNA …

Assessing Listeria Risk During Different Stages Of Ice Cream Manufacturing And Storage, Neha Singh

Electronic Theses and Dissertations

Listeriosis is a life-threatening infection caused by foods contaminated with Listeria monocytogenes. Some of the major ice cream recalls in recent years reaffirm the ability of this food-borne pathogen to survive in diverse dairy processing environments and cause cross contamination. Inspection reports revealed certain lapses in implementing adequate hygienic practices for Listeria persistence in the processing environment, leading to cross contamination of ice cream. The higher levels of cross contamination of raw ice cream mix might result in random heat-injured cells when exposed to minimum heat treatment (69°C for 30 min). Evidence about the presence of injured cells in ice …

Stability Of Temperate Coral Astrangia Poculata Microbiome Is Reflected Across Different Sequencing Methodologies, Dawn B. Goldsmith, Zoe A. Pratte, Koty H. Sharp

Arts & Sciences Faculty Publications

The microbiome of the temperate coral Astrangia poculata was first described in 2017 using next-generation Illumina sequencing to examine the coral’s bacterial and archaeal associates across seasons and among hosts of differing symbiotic status. To assess the impact of methodology on the detectable diversity of the coral’s microbiome, we obtained near full-length Sanger sequences from clone libraries constructed from a subset of the same A. poculata samples. Eight samples were analyzed: two sets of paired symbiotic (brown) and aposymbiotic (white) colonies collected in the fall (September) and two sets collected in the spring (April). Analysis of the Sanger sequences revealed …

Linking Microbial Community Structure And Ecosystem Functions In Acidic Soil From Pennsylvania, Usa, Madison T. James, Sophia T. Farrisi, Shreya Shah, Vishal Shah

Sustainability Research & Creative Activities Grants Reports

Microorganisms play a critical role in the structure and functioning of soil ecosystems. Within acidic soil across the northeastern United States and Canada, we have little understanding of the microbial diversity present and its relationship to the biochemical cycles. The current study is aimed at understanding the taxonomical and functional diversities in the acidic soil obtained from near various types of trees, how the diversities change as a function of depth, and the linkage between taxonomical and functional diversities. From eight sampling locations, soil samples were collected from three horizons (depths). The three depths were 0-10 cm (A), 11-25 cm …

A Bioinfomatic Analysis Of Luminal And Mucosal Ileal Bacteria Colonizing Nursery Pigs Fed Different Protein Sources, Jamie L. Ortman

Electronic Theses and Dissertations

Weaning is a critical time in a young pig’s life that will greatly impact its adult growth and development. The objective of this research was to evaluate the effects of various protein sources on the bacterial composition within luminal and mucosal populations in simple and complex diets to gain a better understanding of factors influencing gut health. Weaned pigs were fed 1 of 3 simple experimental diets: 1) basic diet containing corn and soybean meal (Negative Control - NEG), 2) basic diet + fishmeal (FM; Positive Control - POS), and 3) basic diet + microbially-enhanced soybean meal (MSBM). Phase I …