Microbiology Commons^™

Toward A Rapid Production Of Multivirus-Specific T Cells Targeting Bkv, Adenovirus, Cmv, And Ebv From Umbilical Cord Blood, Hema Dave, Min Luo, J.W. Blaney, Shabnum Patel, Cecilia Barese, Conrad Russell Cruz, Elizabeth J. Shpall, Catherine M. Bollard, Patrick J. Hanley

Pediatrics Faculty Publications

Umbilical cord blood (CB) has emerged as an effective alternative donor source for hematopoietic stem cell transplantation. Despite this success, the prolonged duration of immune suppression following CB transplantation and the naiveté of CB T cells leave patients susceptible to viral infections. Adoptive transfer of ex vivo-expanded virus-specific T cells from CB is both feasible and safe. However, the manufacturing process of these cells is complicated, lengthy, and labor-intensive. We have now developed a simplified method to manufacture a single culture of polyclonal multivirus-specific cytotoxic T cells in less than 30 days. It eliminates the need for a live virus …

The External Microbiome Of Bats: Effects Of Season, Site, Host Species, And Body Region, Kyle G. George

Master's Theses and Doctoral Dissertations

White-nose syndrome is a cutaneous fungal disease that has been detrimental to North American bats for over 10 years, but few investigators have examined the natural microbiota living on these mammals. I explored the influence of season, geographic site, host species, and body region on the external microbiome of four cave-hibernating and two migratory species. Automated ribosomal intergenic spacer analysis was used to profile bacterial communities from three cutaneous regions of 222 bats across winter and summer sites in Michigan, Illinois, and Kentucky. Season, site, host species, and body region all influenced the composition of external bacterial communities, but geographic …

Cytokine Expression, Cytoskeleton Organization, And Viability Of Sim-A9 Microglia Exposed To Staphylococcus Aureus-Derived Lipoteichoic Acid And Peptidoglycan, Erin Roberts

Browse all Theses and Dissertations

In these experiments, SIM-A9 microglia were exposed to Staphylococcus aureus cell wall components lipoteichoic acid (LTA) and peptidoglycan (PGN) at a concentration of 5 ug/mL for six, twelve, eighteen, and twenty-four hours and the cytokine expression, cytoskeleton organization, and cell viability of the cells were observed. Following LTA and PGN exposure, TNF-a; secretion increased at each time interval and was highest observed at 24 hours. No significant IL-10 secretion was detected. Over the 24 hour period, cell viability and cytotoxicity of LTA and PGN treatment groups were not significantly different from the control, indicating the observed inflammatory cytokine response was …

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’IghRR 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 …

Effects Of Socs1 And Socs3 Peptide Mimetics On Macrophage Phagocytosis Of Malignant Cells, Colt Dylan Capan

Browse all Theses and Dissertations

Macrophages play a key role in both the innate and adaptive immune system responses to foreign materials. Suppressors of cytokine signaling (SOCS) proteins are known as regulators of the immune response through various JAK/STAT pathways. This study examined the roles of SOCS1 and SOCS3 peptide mimetics on the phagocytosis of fluorescently labeled malignant target cell by RAW264.7 murine macrophages. The malignant cells used were Neuro-2a cells, a murine neuroblastoma cell line. A prominent “eat me” signal found in neuroblastoma cells is calreticulin (CRT), which permits macrophages to recognize and then phagocytize the malignant cells. When M1 (pro-inflammatory) polarized macrophages were …

A Survey Of Β-Lactam Antibiotic Resistance Genes And Culturable Ampicillin Resistant Bacteria In Minnesota Soils, Emily M. Wollmuth

Departmental Honors Projects

Since the discovery of penicillin, antibiotics have been an essential tool in the treatment of bacterial infections and diseases. It is estimated that antibiotics and antibiotic resistance genes have existed for billions of years. With the increasing appearance of resistant pathogenic bacteria, there has been growing concern. β-lactam antibiotics make up the largest portion of the global market, so resistance to these antibiotics is especially alarming. It has been theorized that frequency and type of antibiotic resistance genes vary by area. Previous studies suggest that these differences may be related to antibiotic use in agricultural and urban areas. To survey …

Carbapenem-Resistant Klebsiella Pneumoniae In Barbados: Driving Change In Practice At The National Level., Corey Forde, Bryan Stierman, Pilar Ramon-Pardo, Thais Dos Santos, Nalini Singh

Psychiatry and Behavioral Sciences Faculty Publications

Introduction

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is of growing concern globally. The risk for transmission of antimicrobial resistant organisms across several continents to the Caribbean is a real one given its tourism industry. After a cluster of cases of CRKP were detected, several studies detailed in this report were initiated to better characterize the problem.

Methods

A hospital-wide point prevalence study and active surveillance were performed at Queen Elizabeth Hospital (QEH) in Barbados in 2013 to assess the prevalence of CRKP infection/colonization. Following this, a 1-year longitudinal study measured the prevalence of CRKP isolates in the hospital and across all healthcare …

Clinical And Mucosal Immune Correlates Of Hiv-1 Semen Levels In Antiretroviral-Naive Men., Brendan J W Osborne, Angie K Marsh, Sanja Huibner, Kamnoosh Shahabi, Cindy Liu, Tania Contente, Nico J D Nagelkerke, Colin Kovacs, Erika Benko, Lance Price, Kelly S Macdonald, Rupert Kaul

Environmental and Occupational Health Faculty Publications

Background.

This study was done to characterize parameters associated with semen human immunodeficiency virus (HIV)-1 ribonucleic acid (RNA) viral load (VL) variability in HIV-infected, therapy-naive men. Methods.

Paired blood and semen samples were collected from 30 HIV-infected, therapy-naive men who have sex with men, and 13 participants were observed longitudinally for up to 1 year. Human immunodeficiency virus RNA, bacterial load by 16S RNA, herpesvirus (Epstein-Barr virus and cytomegalovirus [CMV]) shedding, and semen cytokines/chemokines were quantified, and semen T-cell subsets were assessed by multiparameter flow cytometry. Results.

Semen HIV RNA was detected at 93% of visits, with >50% of men …

Media Optimization, Scale-Up And Repeated Fed-Batch Operations For The Production Of 1,3-Propanediol From Glycerol By Halanaerobium Hydrogeniformans, Shivani Kalia

Masters Theses

"The development of renewable energy sources, such as biofuels, is of great interest in today's world due to depletion of fossil fuels and concerns about climate change. The production of the main by-product, crude glycerol, in biodiesel production presents an opportunity for the production of industrially relevant commodities. Crude glycerol in biodiesel waste is highly impure and possesses high salt concentrations and alkalinity, making it infeasible for direct industrial utilization. Moreover, current glycerol purification methods are highly cost-intensive, necessitating a search for cost-effective approaches that are feasible to employ. Genome data analysis of Halanaerobium hydrogeniformans, revealed the metabolic capability …

Review Of The Algal Biology Program Within The National Alliance For Advanced Biofuels And Bioproducts, Clifford J. Unkefer, Richard T. Sayre, Jon K. Magnuson, Daniel B. Anderson, Ivan Baxter, Ian K. Balby, Judith K. Brown, Michael Carleton, Rose Ann Cattolico, Taraka Dale, Timothy P. Devarenne, C. Meghan Downes, Susan K. Dutcher, David T. Fox, Ursula Goodenough, Jan Jaworski, Jonathan E. Holladay, David M. Kramer, Andrew T. Koppisch, Mary S. Lipton, Babetta L. Marrone, Margaret Mccormick, István Molnár, John B. Mott, Kimberly L. Ogden, Ellen A. Panisko, Matteo Pellegrini, Juergen Polle, James W. Richardson, Martin Sabarsky, Shawn R. Starkenburg, Gary D. Stormo, Munehiro Teshima, Scott N. Twary, Pat J. Unkefer, Joshua S. Yuan, José A. Olivares

Publications and Research

In 2010,when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortiumbegan, littlewas known about themolecular basis of algal biomass or oil production. Very fewalgal genome sequenceswere available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played bymetabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome …

A Family Of Genus-Specific Rnas In Tandem With Dna-Binding Proteins Control Expression Of The Bada Major Virulence Factor Gene In Bartonella Henselae, Nhan Tu, Ronan K. Carroll, Andy Weiss, Lindsey N. Shaw, Gael Nicolas, Sarah Thomas, Amorce Lima, Udoka Okaro, Burt Anderson

Molecular Biosciences Faculty Publications

Bartonella henselae is a gram-negative zoonotic bacterium that causes infections in humans including endocarditis and bacillary angiomatosis. B. henselae has been shown to grow as large aggregates and form biofilms in vitro. The aggregative growth and the angiogenic host response requires the trimeric autotransporter adhesin BadA. We examined the transcriptome of the Houston-1 strain of B. henselae using RNA-seq revealing nine novel, highly-expressed intergenic transcripts (Bartonella regulatory transcript, Brt1-9). The Brt family of RNAs is unique to the genus Bartonella and ranges from 194 to 203 nucleotides with high homology and stable predicted secondary structures. Immediately downstream of each …

The Female Urogynecological Microbiome: Determining Niche Specificity, Krystal Thomas-White

Dissertations

Contrary to dogma, urine is not sterile. Recent discoveries show that the female urinary bladder contains a unique microbiome,with differences in healthy and disease states. This female urinary microbiome (FUM) is distinguishable from vulvo-vaginal contamination; yet, only the few centimeters of the urethra separate these two niches. Recent studies show that the most common bladder organisms are Lactobacillus, Gardnerella, Streptococcus, Corynebacterium, and a diverse group of anaerobes, the same genera commonly found in the vagina. Thus, we asked if the bladder and vaginal microbiomes are interconnected.

Previous work suggests a link between these two niches. The vaginal tract of reproductive …

Investigating The Sources And Dynamics Of Escherichia Coli In A Missouri Ozarks Watershed, Kaleb Bassett

Masters Theses

"Escherichia coli, an intestinal bacterium, can serve as an indication of the presence of pathogenic microorganisms in water systems used by humans for recreation, agriculture, or drinking water. Many aquatic systems in the United States exceed the E. coli standard, set by the Environmental Protection Agency, for safe drinking water and recreational use. During 2016, a water sampling program was established in the Mill Creek watershed, a rural watershed located near the city of Newburg in Phelps County, Missouri. Water samples were collected before, during, and after storms throughout the year to examine the relationship between E. coli …

Analysis Of The Prevention Of Biocorrosion Caused By Desulfovibrio Alaskensis G20, Michael Boring

Honors Undergraduate Theses

Desulfovibrio alaskensis G20 and other sulfate-reducing bacteria cause significant damage to metal pipelines and other infrastructure through a metabolic pathway that releases toxic hydrogen sulfide into their surroundings. The biocorrosion that results from the release of hydrogen sulfide creates significant economic burden, and can pose health risks for those exposed to this chemical. They are commonly present in the form of biofilms, an extracellular matrix composed of bacterial cells, polysaccharides, proteins, nucleic acids, and other materials. These biofilms are difficult to remove, and they provide protection to the bacteria within from anti-bacterial treatments. Desulfovibrio alaskensis G20 is a strain derived …

Distinct Transcriptome Profiles Of Gag-Specific Cd8+ T Cells Temporally Correlated With The Protection Elicited By Sivδnef Live Attenuated Vaccine, Wuxun Lu, Yanmin Wu, Fangrui Ma, R. Paul Johnson, Qingsheng Li

Nebraska Center for Virology: Faculty Publications

The live attenuated vaccine (LAV) SIVmac239Δnef (SIVΔnef) confers the best protection among all the vaccine modalities tested in rhesus macaque model of HIV-1 infection. This vaccine has a unique feature of time-dependent protection: macaques are not protected at 3±5 weeks post vaccination (WPV), whereas immune protection emerges between 15 and 20 WPV. Although the exact mechanisms of the time-dependent protection remain incompletely understood, studies suggested that both cellular and humoral immunities contribute to this time-dependent protection. To further elucidate the mechanisms of protection induced by SIVΔnef, we longitudinally compared the global gene expression profiles of SIV Gag-CM9+ CD8+ (Gag-specific CD8+) …

Chloroviruses Have A Sweet Tooth, James L. Van Etten, Irina V. Agarkova, David D. Dunigan, Michela Tonetti, Cristina De Castro, Garry A. Duncan

Nebraska Center for Virology: Faculty Publications

Chloroviruses are large double-stranded DNA (dsDNA) viruses that infect certain isolates of chlorella-like green algae. They contain up to approximately 400 protein-encoding genes and 16 transfer RNA (tRNA) genes. This review summarizes the unexpected finding that many of the chlorovirus genes encode proteins involved in manipulating carbohydrates. These include enzymes involved in making extracellular polysaccharides, such as hyaluronan and chitin, enzymes that make nucleotide sugars, such as GDP-L-fucose and GDP-D-rhamnose and enzymes involved in the synthesis of glycans attached to the virus major capsid proteins. This latter process differs from that of all other glycoprotein containing viruses that traditionally use …

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 …

Quorum Sensing In Candida Albicans: Farnesol Versus Farnesoic Acid, Wayne R. Riekhof, Kenneth Nickerson

Kenneth Nickerson Papers

Candida albicans is a clinically important dimorphic fungus that exhibits either a budding yeast or a mycelial-hyphal or pseudohyphal growth, depending on environmental conditions. The yeast-to-mycelia morphologic transition, which is generally regarded as an important virulence determinant, depends on the inoculum size of liquid cultures. The yeast form is favored when cultures are inoculated at > 10⁶ cells∙mL^–1, whereas the mycelial form is favored at inoculum densities < 10⁶∙mL^–1. Farnesoic acid (FA) and farnesol (FOH) are two related sesquiterpene quorum- sensing molecules that, upon accumulation, prevent the yeast-to-mycelial conversion. Oh et al. showed that C. albicans …

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 …

The Effects Of The Hiv-1 Tat Protein And Morphine On The Structure And Function Of The Hippocampal Ca1 Subfield, William D. Marks

Theses and Dissertations

HIV is capable of causing a set of neurological diseases collectively termed the HIV Associated Neurocognitive Disorders (HAND). Worsening pathology is observed in HIV+ individuals who use opioid drugs. Memory problems are often observed in HAND, implicating HIV pathology in the hippocampus, and are also known to be exacerbated by morphine use. HIV-1 Tat was demonstrated to reduce spatial memory performance in multiple tasks, and individual subsets of CA1 interneurons were found to be selectively vulnerable to the effects of Tat, notably nNOS+/NPY- interneurons of the pyramidal layer and stratum radiatum, PV+ neurons of the pyramidal layer, and SST+ neurons …

Microbiota, Diet And Medication In Human Gut Disorders, Adam Clooney

Theses

The microbiota, a community of micro-organisms in a particular environment, have been intensely researched in the past decade and interest appears to continue to increase. The human body is richly populated with bacterial cells (3.8x10'^) and alterations in these communities are associated with disease. The work presented in this thesis explores aspects of microbiota research methodologies with regard to optimisation and concerns over a lack of reproducibility. Additionally, we investigated the effects of medication, in particular Proton Pump Inhibitors, on the human gut microbiota, along with comparisons between the microbiota of patients with active and inactive Inflammatory Bowel Disease.

Microbiota …

The Development Of New Molecular Tools To Detect Mycobacterium Avium Subspecies Paratuberculosis From A Bovine Faecal Environment By Real-Time Pcr, Marcel De Kruijf

Theses

The slow-growing intracellular pathogen Mycobacterium avium subspecies paratuberculosis (MAP) causes Johne’s disease in domesticated and wild ruminants. Johne’s disease inflicts severe annual economic losses to the dairy industry worldwide. This thesis is divided into five chapters that consist of a literature review' chapter and four experimental chapters focusing on MAP strain genotyping and the development of novel molecular MAP detection tools using real-time PCR. Chapter 1 describes published information regarding MAP characteristics, Johne’s disease, MAP genomes, available MAP detection methods, MAP epidemiology and genotyping.

To efficiently control and monitor MAP infection, molecular t>ping of MAP strains provides extensive knowledge …

A Diagnostic And Control Programme For Johne’S Disease On Irish Dairy Farms, Aideen Kennedy

Theses

Johne’s disease (JD) is an enteritis of ruminants with potential zoonotic implications. JD diagnosis and control present difficulties given JDs prolonged subclinical nature. In order to improve JD control in Ireland, PhD aims included conducting a national survey documenting high-risk husbandry practices employed on Irish farms, thereby targeting areas for improved management. Furthermore as JD has been associated with on-farm economic losses internationally, this research programme aimed to analyse production losses associated with testing JD ELISA positive on Irish dairy farms. A longitudinal study was also conducted to assess if successful JD control can be achieved using gold-standard protocols. Due …

Mycobacterium Species Identification In An Acute Hospital: Towards Rapid Identification, And Improved Epidemiology, Using Novel Mass Spectrometry Analysis, James Anthony O'Connor

Theses

Mycobacteria are a heterogeneous group of bacteria that cause a wide spectrum of disease, including Tuberculosis (TB), the single biggest killer worldwide. The genus also incorporates over 170 nontuberculosis (NTM) species, many of which are opportunistic pathogens. The aim of this project was to ascertain the burden of mycobacterial disease in the region and to determine the efficacy of Matrix-Assisted Laser Desorption/Ionisation time-of-flight (MALDI-tof) mass spectrometry (MS) for novel uses as a rapid identification method for clinical mycobacteria and as a typing tool for Mycobacterium tuberculosis complex isolates. A five-year retrospective epidemiological study of the region was conducted, the first …

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 …

Physical Activity And Sedentary Behaviors In Urban Chinese Children: Grade Level Prevalence And Academic Burden Associations, Xihe Zhu, Justin A. Haegele, Yan Tang, Xueping Wu

Human Movement Studies & Special Education Faculty Publications

The objectives of this study were (a) to report grade level prevalence in physical activity and sedentary behaviors and (b) to examine academic burden associations with these behaviors. School-aged children (n = 48,118) reported their physical activity, perception of physical activity sufficiency, factors for activity insufficiency, homework hours, and screen time in a typical week. Data were analyzed using general linear models and logistic regression models of Complex Samples. Prevalence results showed that children had lower physical activity and lower screen viewing time, but higher homework time during transition grades (6th, 9th, and 12th) and high school years. Academic burden …

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 …