Microbiology Commons^™

Evaluation Of The Symbiotic Relation Between Endophyte And Poplar Trees Exposed To Landfill Leachate, Catalina Vega Hurtado

Masters Theses

“The contamination of soil and groundwater from leachate leakage from landfill has turned, nowadays, into a global public issue. One of the main concerns about this pollutant is the potential threat to human and ecosystem health. The current research studied endophyte bacteria in association with poplar trees (Populus sp.), as a method of bioremediation of landfill leachates. The objective of the project was to identify treatment strategies that may improve plant performance (survival rates, plant fitness, and degradation efficacy) with the purpose of being implemented in phytoremediation plots, aimed to intercept and treat landfill leachate, before the contamination of watershed. …

Draft Genome Sequence Of Verrucosispora Sp. Strain Cwr15, Isolated From A Gulf Of Mexico Sponge, Sarah J. Kennedy, Eleonora Cella, Mohammad Jubair, Taj Azarian, Bill J. Baker, Lindsey N. Shaw

Molecular Biosciences Faculty Publications

Here, we present the draft genome sequence of Verrucosispora sp. strain CWR15, a bacterial symbiont of a Gulf of Mexico sponge. The genome consists of 35 contigs encoding 5,840 genes. The genome is the basis for future study and presents an underexplored taxonomy and biosynthetic potential.

Mir146a-Mediated Targeting Of Fancm During Inflammation Compromises Genome Integrity, Devakumar Sundaravinayagam, Hye Rim Kim, Tingting Wu, Hyun Hee Kim, Semo Jun, Jeong-Heon Cha, Younghoon Kee, Ho Jin You, Jung-Hee Lee

Molecular Biosciences Faculty Publications

Inflammation is a potent inducer of tumorigenesis. Increased DNA damage or loss of genome integrity is thought to be one of the mechanisms linking inflammation and cancer development. It has been suggested that NF-κB-induced microRNA-146 (miR146a) may be a mediator of the inflammatory response. Based on our initial observation that miR146a overexpression strongly increases DNA damage, we investigated its potential role as a modulator of DNA repair. Here, we demonstrate that FANCM, a component in the Fanconi Anemia pathway, is a novel target of miR146a. miR146a suppressed FANCM expression by directly binding to the 3’ untranslated region of the gene. …

Virus-Induced Changes In Nuclear Proteins And Membranes In Nicotiana Benthamiana Cells, Caleb Mathias

Theses and Dissertations--Plant Pathology

Viruses rely on host proteins to complete their life cycles. This results in alterations to normal cell physiology to processes which benefit viral processes such as replication and movement to other cells. This may involve the relocalization of host proteins away from their original subcellular targets to sites which may benefit the virus, a process that is not as well understood as it relates to the nucleus. To identify nuclear proteins that may be involved in such processes, a library of random Nicotiana benthamiana cDNAs were expressed as GFP fusions in a transgenic marker lines expressing a histone 2B:RFP nuclear …

Investigating The Mechanism Of The Coronavirus Endoribonuclease In Antagonizing Innate Immune Signaling, Matthew Hackbart

Dissertations

Coronaviruses (CoVs) are positive-sense RNa viruses that can emerge from endemic reservoirs and infect zoonotically, causing significant morbidity and mortality. CoVs encode an endoribonuclease (EndoU) that cleaves RNa in biochemical assays, but the target and function of EndoU activity during viral replication was not known. My work focused on characterizing the functions of EndoU during infection. I report that EndoU is an innate immune antagonist. to function as an immune antagonist, EndoU cleaves the 5'-Poly-Uridines from Negative-sense viral RNA, termed PUN RNA, which is the product of polyA-templated RNa synthesis. Using a virus containing an EndoU catalytic-inactive mutation, I detected …

The Effects Of The Estrus Cycle On Microbiota Composition And The Opportunistic Pathogen Listeria Monocytogenes Infection Process In Murine Models, Ryan William-Thomas Donkin

Online Theses and Dissertations

In the U.S., Listeria monocytogenes accounts for less than one percent of foodborne illnesses but has a 28% mortality rate. Infection in healthy individuals causes colonization of the intestinal lumen and subclinical noninvasive listeriosis. However, translocation of L. monocytogenes across the intestinal epithelium produces invasive systemic listeriosis with central nervous system involvement. Little is known of the gastrointestinal stages of L. monocytogenes pathogenesis. Enteric pathogens such as L. monocytogenes interact directly with the host-microbiota during the gastrointestinal phase of pathogenesis. Recent research has recognized that microbiota plays a role in activating immune response and protecting against invasive pathogens. Individual host …

Analysis Of Student Perceptions Of Just-In-Time Teaching Pedagogy In Pharmd Microbiology And Immunology Courses, Charitha Madiraju, Eglis Tellez-Corrales, Henry Hua, Jozef Stec, Andromeda M. Nauli, Deborah M. Brown

Nebraska Center for Virology: Faculty Publications

Just-In-Time Teaching (JiTT) active learning pedagogy is utilized by various disciplines, but its value in a professional pharmacy curriculum has not yet been demonstrated. The purpose of our research study is to implement and evaluate JiTT in a Doctor of Pharmacy (PharmD) program. The impetus in implementing JiTT into a PharmD curriculum was to provide students with an out-of-classroom learning opportunity to enhance knowledge-based skills. The current study summarizes the implementation of JiTT in four distinct instances: two iterations of the required courses “Integrated Microbiology and Virology” (Fall 2016 and Fall 2017) and “Integrated Immunology” (Winter 2016–2017 and Winter 2017–2018). …

Lack Of Cd8+ T-Cell Co-Localization With Kaposi’S Sarcoma- Associated Herpesvirus Infected Cells In Kaposi’S Sarcoma Tumors, Salum J. Lidenge, For Yue Tso, Owen Ngalamika, Jaydeep Kolape, John R. Ngowi, Julius Mwaiselage, Charles Wood, John T. West

Nebraska Center for Virology: Faculty Publications

Despite the close association between Kaposi’s sarcoma (KS) and immune dysfunction, it remains unclear whether tumor infiltrating immune cells (TIIC), by their absence, presence, or dysfunction, are mechanistically correlated with KS pathogenesis. Therefore, their potential capacity to serve as prognostic biomarkers of KS disease progression or control is unclear. Because epidemic-KS (EpKS) occurs with HIV-1 co-infection, it is particularly important to compare TIIC between EpKS and HIV-negative African endemic-KS (EnKS) to dissect the roles of HIV-1 and Kaposi Sarcoma-associated herpesvirus (KSHV) in KS pathogenesis. This cross-sectional study of 13 advanced KS (4 EnKS, 9 EpKS) patients and 3 healthy controls …

Prevalence Of Kaposi's Sarcoma-Associated Herpesvirus And Transfusion-Transmissible Infections In Tanzanian Blood Donors, Salum J. Lidenge, Tara Tran, For Yue Tso, John R. Ngowi, Danielle M. Shea, Julius Mwaiselage, Charles Wood, John T. West

Nebraska Center for Virology: Faculty Publications

Objective: Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent for Kaposi's sarcoma (KS), one of the most common cancers in Tanzania. We have investigated KSHV prevalence and factors associated with KSHV infection in Tanzania.

Methods: This is a cross-sectional study of voluntary blood-donors from Dar es Salaam, Tanzania. Plasma was screened for KSHV, HIV-1, HBV, HCV and Treponema pallidum (syphilis). Associations between KSHV sero-status and risk factors were analyzed. Odds ratios (OR) and 95% confidence intervals (CI) are reported to evaluate risk factors of KSHV infection. All tests were 2-tailed, and P-values <0.05 were considered statistically significant.

Results: The overall KSHV seroprevalence was 56.9%. Significantly …

Incidence Of The Covid-19 In Iraq – Implications For Travellers, Maysaa Kadhim Al-Malkey, Maitham Ahmed Al-Sammak

Nebraska Center for Virology: Faculty Publications

The first emerged Coronavirus Disease 2019 (COVID-19) was in Wuhan, Hubei Province, China at the end of 2019, then spread to the rest of China [1], followed by the spread of the COVID-19 epidemics into the world caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) [2]. Many epidemiological assessments in different countries from Asia, Europe, and North America have been published [3]. Nevertheless, there are countries in the Middle East like Iraq, with a rapid increase in cases and a high number of deaths, with a lack of studies. It is worth noting that the Iraqi Foreign Ministry was …

Cervico-Vaginal Inflammatory Cytokine And Chemokine Responses To Two Different Siv Immunogens, Nikki P.L. Toledo, Hongzhao Li, Robert W. Omange, Tamara G. Dacoba, Jose Crecente-Campo, Dane Schalk, Mohammad A. Kashem, Eva Rakasz, Nancy Schultz-Darken, Qingsheng Li, James B. Whitney, Maria J. Alonso, Francis A. Plummer, Ma Luo

Nebraska Center for Virology: Faculty Publications

Studies have shown that vaccine vectors and route of immunization can differentially activate different arms of the immune system. However, the effects of different HIV vaccine immunogens on mucosal inflammation have not yet been studied. Because mucosal sites are the primary route of HIV infection, we evaluated the cervico-vaginal inflammatory cytokine and chemokine levels of Mauritian cynomolgus macaques following immunization and boost using two different SIV vaccine immunogens. The PCS vaccine delivers 12 20-amino acid peptides overlapping the 12 protease cleavage sites, and the Gag/Env vaccine delivers the full Gag and full Env proteins of simian immunodeficiency virus. We showed …

Genetic Diversity Of Potassium Ion Channel Proteins Encoded By Chloroviruses That Infect Chlorella Heliozoae, Carter Murry, Irina V. Agarkova, Jayadri S. Ghosh, Fiona C. Fitzgerald, Roger M. Carlson, Brigitte Hertel, Kerri Kukovetz, Oliver Rauh, Gerhard Thiel, James L. Van Etten

Nebraska Center for Virology: Faculty Publications

Chloroviruses are large, plaque-forming, dsDNA viruses that infect chlorella-like green algae that live in a symbiotic relationship with protists. Chloroviruses have genomes from 290 to 370 kb, and they encode as many as 400 proteins. One interesting feature of chloroviruses is that they encode a potassium ion (K+) channel protein named Kcv. The Kcv protein encoded by SAG chlorovirus ATCV-1 is one of the smallest known functional K+ channel proteins consisting of 82 amino acids. The KcvATCV-1 protein has similarities to the family of two transmembrane domain K+ channel proteins; it consists of two transmembrane -helixes with a pore region …

Viral And Immunological Analytes Are Poor Predictors Of The Clinical Treatment Response In Kaposi’S Sarcoma Patients, Salum J. Lidenge, For Yue Tso, Yasaman Mortazavi, John R. Ngowi, Danielle M. Shea, Julius Mwaiselage, Charles Wood, John T. West

Nebraska Center for Virology: Faculty Publications

Kaposi’s sarcoma-associated herpes virus (KSHV) is the etiologic agent for Kaposi’s sarcoma (KS). The prognostic utility of KSHV and HIV-1 (human immunodeficiency virus) viremia as well as immunological parameters in clinical management of participants with KS is unclear. The objective of this study was to investigate viral and immunological parameters as predictors of KS treatment responses in participants with KS from sub-Saharan Africa (SSA). Plasma KSHV-DNA, HIV-1 viral load, total anti-KSHV antibody, KSHV-neutralizing antibody (nAb), cytokine/chemokine levels, and T-cell differentiation subsets were quantified before and after KS treatment in 13 participants with KS and in 13 KSHV-infected asymptomatic control individuals. …

Non-Naturally Occurring Porcine Reproduction And Respiratory Syndrome Virus (Prrsv) And Methods Of Using, Hiep Lai Xuan Vu, Fernando Osorio, William W. Laegreid, Asit K. Pattnaik, Fangrui Ma

Nebraska Center for Virology: Faculty Publications

A non-naturally occuring porcine reproductive and respiratory syndrome virus (PRRSV) is provided herein, and methods of making and using the non-naturally occurring PRRSV also are provided.

Diversity Of Trna Clusters In The Chloroviruses, Garry A. Duncan, David D. Dunigan Ph. D., James L. Van Etten

Nebraska Center for Virology: Faculty Publications

Viruses rely on their host’s translation machinery for the synthesis of their own proteins. Problems belie viral translation when the host has a codon usage bias (CUB) that is different from an infecting virus due to differences in the GC content between the host and virus genomes. Here, we examine the hypothesis that chloroviruses adapted to host CUB by acquisition and selection of tRNAs that at least partially favor their own CUB. The genomes of 41 chloroviruses comprising three clades, each infecting a different algal host, have been sequenced, assembled and annotated. All 41 viruses not only encode tRNAs, but …

Cornus Officinalis Promotes Igfbp2 And Autophagy In Human 1.1b4 Pancreatic Cell Line As Revealed By Employing A Global Proteomic Approach Via Mass Spectrometry, Arielle Elizabeth Tawfik, Jennifer Guergues, Stanley M. Stevens Jr, Brant Roger Burkhardt

Molecular Biosciences Faculty Publications

Type 1 diabetes (T1D) results in the loss of pancreatic beta cells and subsequent loss of insulin production. Exogenous insulin is the only effective treatment, but there is still no cure or interventional therapy available to inhibit progression of T1D. Successful T1D interventional therapy must protect pancreatic beta cells from autoimmunity while enhancing beta cell survival and function. Our data suggests Cornus officinalis (CO) may be a candidate for interventional therapy to protect pancreatic beta cells from autoimmune attack and increase their function. CO has been used in traditional Chinese medicine (TCM) for over 2,000 years and has shown characteristics …

Analysis Of Bacterial Dna And Water Quality: Surface Water Sampling At Gardner-Webb University, Celsea Reeder

Undergraduate Honors Theses

Part 1 of this experiment was to explore the bacterial types within the surface water on the campus of Gardner-Webb University, located in Boiling Springs, NC. Two water samples were collected from four locations on campus, including the boiling spring, Lake Hollifield, and an adjacent creek. Using the Zymo Research “Quick-DNA^™ Fungal/Bacterial Miniprep Kit,” the bacterial DNA within these samples was isolated and sent to Psomagen, Inc. for analysis. The resulting DNA sequences were analyzed through BLAST, and subsequently interpreted. For the second part of this experiment, one surface water sample was taken from the boiling spring, and another …

Massard Prairie Restoration And Soil Microbiome Succession, Jeffrey M. Shaver, Emily S. Bellis, Chizuko Iwaki, Jake Qualls, Jay Randolph, Jeremiah Smith

Journal of the Arkansas Academy of Science

We have initially sequenced soil microbial DNA from 4 restored and 4 virgin tallgrass prairie soil samples from Ben Geren Park and Massard Prairie (Fort Smith, AR), respectively. As expected, the soil microbiomes are distinct, with several lineages of nitrogen-fixing bacteria more common in virgin tall grass prairie. However, we predict that as restoration of tallgrass prairie in Ben Geren Park progresses, the soil microbiome of restored prairie will more closely mirror those of the virgin prairie.

Group B Streptococcus: Molecular Epidemiology, Pathogenic Profiling And Control Strategies, Katherine Mary Hayes

Theses

Group B Streptococcus (GBS) are frequent colonisers of the gastrointestinal tract of healthy adults with worldwide rates of 18% colonisation; however, they are also opportunistic pathogens capable of causing invasive disease, particularly in neonates and adults with underlying conditions. Indeed, GBS is the leading cause of invasive neonatal disease worldwide with a global incidence of 0.49 per 1000 live births and GBS disease in adults is increasing globally, with estimated rates of 10.9 cases per 100,000 people. While GBS remain largely susceptible to penicillin, there have been reports of reduced beta-lactam susceptibility in certain countries and resistance to other antibiotic …

In Situ Analysis Of Line-1 Promoter Activity Using Lacz Transgenic Mice, Partha Sarathi Saha

Electronic Theses and Dissertations

Apart from an evolutionary role, transposable elements have been implicated in animal development and also in pathophysiology. Non-LTR retrotransposons– LINE-1, Alu and SVA - are responsible for over 120 cases of human genetic diseases as heritable insertions, and are emerging as an important etiological factor for cancer and neurological disorders as somatic mutations. It is estimated that among the total number of 500,000 LINE-1s presents in the human genome, 80-100 LINE-1s remain competent for retrotransposition. Retrotransposition is only possible when LINE-1 is expressed. Because LINE-1 transcription is regulated by its 5’UTR promoter, it is essential to understand the spatiotemporal control …

Mechanistic Studies To Understand The Role Of Human Gut Microbiota In Colonization Resistance And Gut Health, Sudeep Ghimire

Electronic Theses and Dissertations

Human gut microbiota is comprised of thousands of species which fall into two major categories or “enterotypes” based on dominating bacteria: “Bacteroides” and “Prevotella”. Bacteroides enterotype dominates the microbiota of the western population because of a high protein and fat diet, whereas Prevotella enterotype is dominate in the gut of the eastern population because of a high carbohydrate diet. While most of the microbiota studies focused on the Bacteroides enterotype using both metagenomics and culturomics, Prevotella enterotype is understudied, especially in the field of culturomics. The structure of the Prevotella dominated gut microbiome is revealed by …

Genomic And Culturomic Analysis Of Gut Microbiota Function And Salmonella Enterica Expansion, Gavin Fenske

Electronic Theses and Dissertations

Enteric bacteria that are resident in the hindgut of mammals are critical in immune development, digestion, and colonization resistance against pathogens. One of the major pathogens that gut commensals provide resistance against is Salmonella enterica, a major foodborne pathogen capable of infecting almost every warm-blooded animal. Given the interplay between pathogens and commensals in the gut lumen, the gut microbiota of pigs was studied by combining two disparate techniques: shotgun metagenomics and high throughput culturomics. Metagenomics readily identifies major taxa present in samples and can give an estimation to total genetic catalogue from an environment. However, many rare or …

A Natural Antimicrobial From Bacillus Subtilis As A Biosanitizer For Resilient Membrane Biofilms, Pratishtha Verma

Electronic Theses and Dissertations

The microbial attachment and colonization on separation membranes lead to biofilm formation. Some selective isolates within the biofilm constitutive microflora acquire resistance and emerge predominant over prolonged use of the membrane. Thus, proving the cleaning and sanitization protocols to be ineffective in adequately removing resilient biofilms. This subsequently leads to selecting microbial resistance within the constitutive microflora to almost all antimicrobial treatments and hence, creates a need to develop novel alternative strategies to control biofilm formation on membrane surfaces. The first research project under this study was designed to understand the microbial interactions and emergence of predominance within biofilm constitutive …

The Role And Molecular Mechanisms Of Wss1 In Preserving Genomic Stability, Daniel Kwesi Sam

Electronic Theses and Dissertations

Cells are constantly under threat from both exogenous and endogenous sources of DNA damage. Eukaryotic organisms, however, possess conserved mechanisms that accurately and faithfully respond to DNA damage. The inability to effectively remove DNA lesions can lead to an accumulation of mutations which can compromise cellular viability. The DNA damage response is conserved from bacteria to eukaryotic organisms and have been well characterized, however, how covalently crosslinked proteins are removed from DNA remains enigmatic This thesis provides genetic and biochemical evidence implicating Wss1, a yeast metalloprotease in genome maintenance. We have identified SUMOylation to be an important signal that mediates …

Interaction Of Streptomyces Closely Associated With Bacillus In Nitrogen-Limiting Conditions, Aminya Baniya

Electronic Theses and Dissertations

Biological Nitrogen Fixation is the process of conversion of atmospheric dinitrogen into ammonia which is performed by symbiotic as well as free-living diazotrophic bacteria. A previous project to isolate free-living nitrogen fixing bacteria from a natural prairie yielded Streptomyces which grew on nitrogen free medium. Genome sequencing of three isolates revealed the presence of a second 16S rRNA gene sequence aligning with Bacillus, however repeated streaking only yielded Streptomyces colonies. The aim of this research was to characterize the interaction of three Streptomyces isolates that grow under nitrogen-free conditions, and appeared to be associated with Bacillus. The separation of Bacillus …

Exploring Heterogeneous Phenotypes In Response To Stress, Heather S. Deter

Electronic Theses and Dissertations

This work combines traditional microbiology with bioinformatic and synthetic biology approaches to study antibiotic tolerance. Antibiotic tolerance is a widespread phenomenon that facilitates antibiotic resistance and decreases the effectiveness of antibiotic treatment. Tolerance is distinct from antibiotic resistance, because tolerance is short term survival and typically results from phenotypic variations rather than genetic variation. The molecular mechanisms underlying tolerance are varied and debated in the literature. I have explored two intracellular processes related to tolerance, toxin-antitoxin (TA) systems (Chapter 2) and proteases (Chapter 4). Specifically, I focus on the ratio of antitoxin-to-toxin in type II TA systems, because type II …

Investigating Links Between Soil Microbial Structure And Function In Three Major Plant Communities Across Temporal Scales Of Arctic Alaska, Kaj Lynoe

Electronic Theses and Dissertations

Arctic microbial systems continue to get attention today as our understanding regarding their structure and function in a changing system is paramount to C feedbacks with warming and changes in precipitation. Plant communities and microbial community processes across the Arctic landscape are central to understanding tundra ecosystem processes because environmental conditions and plant community structure drive microbial cycling of soil organic matter. Here, we want to understand how soil microbial respiration, mineralization, biomass, and community composition are linked to three Alaskan tundra plant communities, namely Shrub, Tussock, and Sedge tundra and the seasonal variability in this system. A total of …

Developing Microbial Based Process To Produce High Value Natural Antimicrobial (Glyceollin) In Soybeans And Pullulan From Sucrose, Andrea Zavadil

Electronic Theses and Dissertations

Glyceollin is a secondary metabolite produced under stress conditions by soybean to act as a plant defender to pathogen attack. The antimicrobial nature of glyceollin makes it a promising natural alternative to antibiotics if incorporated into livestock feed. However, production of glyceollin is highly variable, dependent on soybean variety, and fungal elicitor used as inoculum. Our study compares two fungal spore elicitors, Trichoderma reesei and Aspergillus sojae on soybeans of diverse maturity level, and fungal susceptibility to determine highest glyceollin titer. Spore inoculation with T. reesei elicited highest glyceollin titers of 2.42±0.20 mg/g at 120 h, while A. sojae elicited …

Characterization Of The Influences Of Human Cytomegalovirus Glycoprotein O (Go) Expression On Gh/Gl Complexes Assembly And Its Polymorphisms On Cell-Free And Cell-To-Cell Spread, And Antibody Neutralization., Le Z. Day

Graduate Student Theses, Dissertations, & Professional Papers

Human cytomegalovirus (HCMV) is widely spread throughout the world and immunocompromised individuals can suffer severe diseases from HCMV infection. Once the infection is established, HCMV can spread through the body and infect many major somatic cell types. The glycoproteins H and L (gH/gL) on HCMV envelope can be bound by either gO or the UL128-131 proteins to form complexes gH/gL/gO and gH/gL/UL128-131 that are critical for viral entry and spread, and these two complexes are important targets of neutralizing antibodies. Strains of HCMV vary considerably in the levels of gH/gL/gO and gH/gL/UL128-131. gO is one of the most diverse loci …

Mass Spectrometry Based Lipidomic Investigation Of Staphylococcus Aureus Lipid Metabolism And Characterization Of Lipase A, Naren Gajenthra Kumar

Theses and Dissertations

Staphylococcus aureus produces an arsenal of virulence factors and is adept at colonizing multiple hosts by employing specific processes to persist at different sites of infection. Infections caused by this pathogen range from self-limiting infections of the skin like folliculitis to life threatening and chronic conditions like infective endocarditis, non-healing diabetic foot ulcers and atopic dermatitis. As the field continues to expand its understanding of the mechanisms by which this pathogen rapidly develops resistance to new antibiotics, the underlying mechanisms that facilitates niche adaptation and host colonization among healthy individuals remain elusive.

Bacterial and host lipid metabolism presents and area …