Microbiology Commons^™

Tryptophan 375 Stabilizes The Outer-Domain Core Of Gp120 For Hiv Vaccine Immunogen Design, Duoyi Hu, Dane Bowder, Wenzhong Wei, Jesse Thompson, Mark A. Wilson, Shi-Hua Xiang

Nebraska Center for Virology: Faculty Publications

The outer-domain core of gp120 may serve as a better HIV vaccine immunogen than the full-length gp120 because of its greater stability and immunogenicity. In our previous report, we introduced two disulfide bonds to the outer-domain core of gp120 to fix its conformation into a CD4-bound state, which resulted in a significant increase in its immunogenicity when compared to the wild-type outer-domain core. In this report, to further improve the immunogenicity of the outer-domain core based immunogen, we have introduced a Tryptophan residue at gp120 amino acid sequence position 375 (375S/W). Our data from immunized guinea pigs indeed shows a …

Towards The Complete Proteinaceous Regulome Of Acinetobacter Baumannii, Leila G. Casella, Andy Weiss, Ernesto Pérez-Rueda, J Antonio Ibarra, Lindsey N. Shaw

Molecular Biosciences Faculty Publications

The emergence of Acinetobacter baumannii strains, with broad multidrug-resistance phenotypes and novel virulence factors unique to hypervirulent strains, presents a major threat to human health worldwide. Although a number of studies have described virulence-affecting entities for this organism, very few have identified regulatory elements controlling their expression. Previously, our group has documented the global identification and curation of regulatory RNAs in A. baumannii. As such, in the present study, we detail an extension of this work, the performance of an extensive bioinformatic analysis to identify regulatory proteins in the recently annotated genome of the highly virulent AB5075 strain. In so …

Genomic Vs. Non-Genomic Role Of The Ahr In Human Immunoglobulin Expression, Nasser Alhamdan

Browse all Theses and Dissertations

The immunoglobulin heavy chain gene (Igh) in various animal models is regulated by numerous regulatory elements including the 3'Igh regulatory region (3'IghRR). Several transcription factors are involved in modulating the 3'R including the aryl hydrocarbon receptor (AhR). The AhR is a ligand-activated transcription factor that mediates the transcription of genes involved in the metabolism of environmental toxicants such as TCDD. TCDD binds AhR and regulates immunoglobulin (Ig) expression in B cells. This modulation appears to be directly mediated by binding of the AhR to dioxin response elements (DRE) within the 3'IghRR. In human B cells, IgG secretion inhibited by TCDD …

Phylogenetic And Associated Phenotypic Analysis Of Salmonella Enterica Serovar Mbandaka, Linto Antony

Electronic Theses and Dissertations

Food borne salmonellosis is a global public health concern caused by Salmonella, that causes enteric disease both in humans and animals. Most of the pathogenic Salmonella serovars fall under Salmonella enterica subspecies enterica, a major subspecies group that includes more than 50% of total identified Salmonella serovars. New serovars are identified each year and overall incidence of salmonellosis may mask the outbreak incidences caused by individual serovars. Infrequently reported serovar outbreaks can be a significant threat to public health. Salmonella enterica serovar Mbandaka is one of the infrequently reported causative agents of non-typhoidal salmonellosis in USA. But it …

Enhancing Cellulase Production Of Aureobasidium Pullulans For Use In Converting Dried Distillers’ Grains With Solubles Into A Higher Protein Feed, Emily L. Baldwin

Electronic Theses and Dissertations

Main limitations of dried distillers’ grains with solubles (DDGS) as meal for monogastric animals is the presence of high fiber content, reduced fat content, and poor amino acid balance. This causes a reduced economic value of DDGS for these species due to its low inclusion rates. The goal of this theses was to create new strains of a fungus, Aureobasidium pullulans, with enhanced cellulase production and use it to optimize an enzymatic saccharification, pretreatment, and fungal conversion process to enhance the nutritional value of DDGS. Various combinations of enzymatic saccharification, physical/chemical pretreatments, and mutant strains of fungi were investigated …

Intranasal Immunization Of Pigs With Porcine Reproductive And Respiratory Syndrome Virus Like Particles Plus 2’, 3’ –Cgamp Vaccigrade™ Adjuvant Exacerbates Viremia After Virus Challenge, Alexandria Marie Van Noort

Electronic Theses and Dissertations

Porcine reproductive and respiratory syndrome virus (PRRSV) is an economically devastating virus that causes a persistent infection and spreads quickly. The virus causes abortions in sows and respiratory diseases in young piglets. Current PRRSV vaccines appear to provide limited cross-protection. A virus-like particles (VLPs) vaccine is made up of key PRRSV structural proteins, which could be cross protective among the different strains. We tested PRRSV VLPs as a vaccine candidate with a 2’, 3’-cGAMP VacciGradeTM adjuvant against pigs infected with PRRSV after intranasal immunization to evaluate the immune response and protective efficacy by the VLPs and adjuvant. The VLPs contain …

Surveillance Of Emerging Livestock Viruses, Faten A. Okda

Electronic Theses and Dissertations

Accurate and rapid diagnostic tests are essential for the management and control of emerging infectious diseases. Therefore, the overall goals of studies presented in this dissertation were to provide improved diagnostic and surveillance capabilities for several emerging viral diseases impacting the livestock industry and to provide insight into appropriate control strategies. Recent, severe outbreaks of porcine epidemic diarrhea virus (PEDV) in Asia and North America highlighted the need for well-validated diagnostic tests for identification of PEDV infected animals and evaluation of their immune status. PEDV was first detected in the U.S. in May 2013 and another swine coronavirus, porcine deltacoronavirus …

Development Of A High Throughput (Ht) Raman Spectroscopy Method For Rapid Screening Of Liquid Blood Plasma From Prostate Cancer Patients, Dinesh Medipally, Adrian Maguire, Jane Bryant, John Armstrong, Mary Dunne, Marie Finn, Fiona Lyng, Aidan Meade

Articles

Extensive research has been undertaken on the examination of tissue biopsies using vibrational spectroscopic techniques. However, fewer studies have focused on less invasive and commonly acquired blood samples. Recent studies have shown the ability of Raman and Fourier transform infrared (FTIR) spectroscopy to discriminate between non-cancer controls and cancer cases using blood serum or plasma. Even though many studies have proposed Raman spectroscopy as a potential diagnostic tool in various cancers, the Raman spectroscopic technique has not been introduced as a routine clinical technology. This is due to multiple drawbacks with the application of the technique, including sample preparation, the …

Association Of Gut Luminal Metabolites And Allergic Responses, Ghaith Mohammed Fallata

Browse all Theses and Dissertations

Allergy is a global health problem, affecting more than 40% of the world population. Allergy is often associated with a dysregulation of the immune system that becomes overactive against allergens. Several genes are known to be important for the proper homeostasis of the immune system in the epithelial tissues, and the loss of function of genes such as IKKß or SOX9 impacts the interaction between external stimuli and the host. Many of the allergic responses are triggered through the regulatory cascade governed by transcriptional factor NF-κB. Regulation of NF-κB activity is complex, involves several alternative routes, and is also influenced …

The Microbiome Of Neotropical Ticks Parasitizing On Passerine Migratory Birds, Khemraj Budachetri, Jaclyn Williams, Nabanita Mukherjee, Michael Sellers, Shahid Karim

Faculty Publications

Seasonal migration of passerine birds between temperate North America and tropical Central and South America is an ecological phenomenon. Migration of birds has been associated with the introduction of ectoparasites like ticks or tick-borne pathogens across the avian migration routes. In this study, the microbial diversity was determined in the ticks and bird DNA samples using 454 pyrosequencing of bacterial 16S rRNA gene. Tick DNA samples showed the dominance of genera Lactococcus, Francisella, Raoultella, Wolbachiaand Rickettsia across all the ticks, but birds DNA did not share common microbial diversity with ticks. Furthermore, “Candidatus Rickettsia amblyommii” …

Studying Microflora Of Semi-Hard Cheese, And Sporulation Within Contact Surface Biofilms, Dalia Khan

Electronic Theses and Dissertations

The first study was conducted on commercial Italian semi-hard cheese samples that were analyzed microbiologically to understand the effect of fast and slow rate of cooling on cheese microflora during ripening process at different temperatures. A cheese plant noticed an active growth of non-starter lactic acid bacteria, especially the heterofermentative bacteria, in ripened cheese blocks, which weren’t fully cooled. For that, three cheese sample sets, each having 8 samples, were received from the cheese plant for microbiological analysis. The first set included a group of fast cooled cheese samples to 38°F, and the other group was slow cooled to 50°F. …

Effects Of Root Isoflavonoids And Hairy Root Transformation On The Soybean Rhizosphere Bacterial Community Structure, Laura White

Electronic Theses and Dissertations

Rhizodeposits play a key role in shaping rhizosphere microbial communities. In soybean, isoflavonoids are a key rhizodeposit component that aid in plant defense and enable symbiotic associations with rhizobia. However, it is uncertain if and how they influence rhizosphere microbial communities. Isoflavonoid biosynthesis was silenced via RNA interference of isoflavone synthase in soybean hairy root composite plants. Successive sonication was implemented to isolate soil fractions from 3 different rhizosphere zones at 1 and 3 weeks post planting. PCR amplicons from 16S rRNA gene variable regions V1- V3 and V3-V5 from these soil fractions were analyzed via denaturing gradient gel electrophoresis …

Senecavirus A: Epidemiology, Pathogenesis And Infection Dynamics, Lok Raj Joshi

Electronic Theses and Dissertations

Senecavirus A (SVA) is a positive sense single-stranded virus that belongs to the genus Senecavirus within the family Picornaviridae. Senecavirus has been present in US swine population since 1988. However, there have been only a few reports of SVA associated with disease in last two decades. In late 2014 early 2015, a sudden increase in the number of cases of Senecavirus A associated with vesicular disease was observed in Brazil, the US and China. Affected pigs presented vesicles on snout, coronary band, and dewclaw. Additionaly, increased neonatal mortality has been reported in the field. Many aspects of SVA epidemiology, …

The Synthetic Biology Of N2-Fixing Cyanobacteria For Photosynthetic Terpenoid Production, Charles T. Halfmann

Electronic Theses and Dissertations

In the last few decades, concerns over global climate change, energy security, and environmental pollution have been rising. To overcome these challenges, the concept of “-n^th generation” biofuels has emerged as a strategy to convert solar radiation into fuels and bulk industrial chemicals for societal use, while decreasing our consumption of nonrenewable energy sources. Nitrogen-fixing cyanobacteria hold a distinct advantage in biofuel production over plants, given their ability to convert sunlight, air (CO₂ and N₂), and mineralized water to energy-dense carbon molecules, as well as fix atmospheric nitrogen gas into ammonia for metabolism. Engineered cyanobacteria with …

Defining The Roles Of The Lipoic Acid Ligases In Promoting Staphylococcus Aureus Metabolic Homeostasis And Virulence, Irina Laczkovich

Master's Theses

Staphylococcus aureus is a major human pathogen known to cause disease in a wide range of tissues. In order to thrive in such diverse environments, S. aureus uses multiple adaptive traits such as trace metal/nutrient acquisition, shifts in metabolic activity, and expression of detoxification systems, all of which allow the bacterium to proliferate and survive in nutritionally deficient and inhospitable environments.

One essential metabolite used by S. aureus is lipoic acid, a cofactor of enzyme complexes used in aerobic metabolism, fatty acid biosynthesis, glycine detoxification, and maintenance of redox homeostasis. Prior studies in the lab used a genetic approach to …

Profiling Resistance To P450-Activated Food Carcinogens Using Toxicogenomic Approaches In Budding Yeast, Nicholas Stjohn

Legacy Theses & Dissertations (2009 - 2024)

The human response to environmental carcinogens, some of which require metabolic activation, is highly variable. Factors such as environment, lifestyle, and genetics all influence the rates of exposure to and ultimate bioactivation of these compounds. Genetic factors include mutations to cell-cycle regulation, cell proliferation, and DNA repair genes; however, epidemiological studies may lack significance due to inadequate patient numbers. We used budding yeast as a model organism to determine genetic susceptibility to food-associated carcinogens, including aflatoxin (AFB1) and heterocyclic aromatic amines (HAAs). Budding yeast does not contain P450s that activate these compounds, so expression vectors were induced that contain human …

Novel Approaches To Mitigating Bacterial Biofilm Formation And Intercellular Communication, Stephen Kasper

Legacy Theses & Dissertations (2009 - 2024)

Long thought of as solitary single-cell organisms, it is now widely accepted that bacteria can act and cooperate as social organisms. Phenomena such as biofilm formation and quorum sensing (QS) are two intimately intertwined cooperative behaviors that significantly contribute to the pathogenesis of many bacteria. Biofilms are surface associated communities of bacteria encased in a secreted extracellular matrix, which provides several advantages over an individualized lifestyle, such as increased protection from antimicrobial agents as well as enhanced opportunity for the exchange of genetic material. Bacterial QS is a system of population-based communication through the production, sensing, and response to chemical …

Structural And Functional Characterization Of An Unusual Camp Responsive Transcription Factor, Cmr, In Tb Complex Mycobacteria, Sridevi Ranganathan

Legacy Theses & Dissertations (2009 - 2024)

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis in humans, is an intracellular pathogen that infects millions of people every year. Mtb can survive inside the host for extended periods of time by sensing and adapting to the host environmental stressors. Transcriptional gene regulation plays a critical role in this adaptation. This dissertation focuses on understanding the structural and functional aspects of one such transcriptional regulatory unit, Cmr (Rv1675c), in Mtb.

Investigating The Role Of Epitranscriptomics In Viral Immunity, Kaycie S. Lawson

Legacy Theses & Dissertations (2009 - 2024)

The characterization of host-virus relationships is essential for understanding the process of viral replication and driving the development of effective viral targeting strategies. In this work, I tested the hypothesis that ribonucleic acid (RNA) post-transcriptional modifications (PTMs) may play a significant role in defining host-virus interactions. The model system consisted of a yeast strain capable of harboring the endogenous L-A virus, which allowed me to evaluate the possible involvement of PTMs in the process of cellular immunity to virus-borne toxicity. A mass spectrometry-based platform was utilized to compare the global PTM profile of wild-type yeast with those of the same …

A Tale Of Two Regulators : Characterization Of The Novel Transcription Factor Abmr And The Small Non-Coding Rna Mcr11 In Mycobacterium Tuberculosis, Roxanne Candice Girardin

Legacy Theses & Dissertations (2009 - 2024)

Genes of unknown function make up nearly one third of Mtb’s genome (Cole,