Life Sciences Commons^™

Influenza A Virus Genomic Reassortment And Packaging, Graham Devin Williams

Arts & Sciences Electronic Theses and Dissertations

Influenza A viruses (IAV) are a major human and environmental pathogen. IAV successfully infects a diverse host range and adaptation of new viral strains to humans may cause pandemic events with high morbidity and mortality. As a member of the Orthomyxoviridae family, IAV inherently possesses a segmented genome, which enables a process of segment transmission between viruses following cellular co-infection, a process termed reassortment. The high rate of IAV mutation and continued co-circulation of diverse viral strains in divergent host species leads to the persistent prospect for emergence of new IAV with pandemic potential. Therefore, it is of great importance …

Understanding The Paradox Of Genetic Diversity In Uropathogenic E. Coli: The Uncommon Evolution Of A Common Pathogen, Henry Louis Schreiber

Arts & Sciences Electronic Theses and Dissertations

Urinary tract infections (UTIs) are the second most common bacterial infection of people in the U.S.A and are frequently recurrent, as an initial UTI is quickly followed by a second episode in 30-35% of cases despite appropriate antibiotic treatment and clearance of the bacteria from the urine. The vast majority, >80%, of UTIs are caused by uropathogenic Escherichia coli (UPEC). UPEC that colonize the bladder are thought to originate in the gut, where they live as commensal organisms. UPEC can be shed in feces to colonize the vagina and/or periurethral area, and then can ascend into the bladder to start …

Anaerobic Oxidation Of Ethane, Propane, And Butane By Marine Microbes: A Mini Review, Rajesh Singh, Michael S. Guzman, Arpita Bose

Biology Faculty Publications & Presentations

The deep ocean and its sediments are a continuous source of non-methane short-chain alkanes (SCAs) including ethane, propane, and butane. Their high global warming potential, and contribution to local carbon and sulfur budgets has drawn significant scientific attention. Importantly, microbes can use gaseous alkanes and oxidize them to CO₂, thus acting as effective biofilters. A relative decrease of these gases with a concomitant ¹³C enrichment of propane and n-butane in interstitial waters vs. the source suggests microbial anaerobic oxidation. The reported uncoupling of sulfate-reduction (SR) from anaerobic methane oxidation supports their microbial consumption. To date, strain …

Expansion Of Microbial Virology By Impetus Of The Reduction Of Viral Dark Matter, Siddharth Ravindran Krishnamurthy

Arts & Sciences Electronic Theses and Dissertations

Modern metagenomic methods have rapidly accelerated the rate of viral discovery. Currently, to discover a novel virus, deep sequencing reads must align to a known reference virus. While alignment is effective at identifying closely related viruses, highly divergent viruses can often share no discernable sequence alignment with known viruses. Therefore, the accurate classification of viral dark matter – metagenomic sequences that originate from viruses but do not align to any reference virus sequences – is one of the major obstacles in not only discovering novel viruses, but also by extension, comprehensively defining the virome. As viral dark matter results fundamentally …

Type 1 And F17-Like Pili Promote The Establishment Of The Uropathogenic E. Coli Intestinal Reservoir, Caitlin Nicole Spaulding

Arts & Sciences Electronic Theses and Dissertations

Urinary tract infections (UTI) affect over 150 million individuals worldwide every year. These infections are associated with significant morbidity and have a sizeable economic impact, with $5 billion being spent on UTI treatment in the USA annually. Uropathogenic E. coli (UPEC) are responsible for 80% of community acquired UTIs and 65% of nosocomial UTI. The current standard of care for UTI is antibiotic therapy. However, 30-50% of women experience recurrent UTI (rUTI) despite receiving antibiotic therapy. The prevalence of single and multi-drug resistant UPEC strains has led to increased reliance on carbepenems, which are primarily reserved for multi-drug resistant infections, …

Exploring Host-Virus Interactions In Caenorhabditis Nematodes, Kevin Chen

Arts & Sciences Electronic Theses and Dissertations

Caenorhabditis elegans is a powerful model organism that has elucidated many biological questions in the fields of genetics, development, and neurobiology. In addition, C. elegans has been used in the past decade to investigate host-pathogen interactions with bacteria and fungi. The recent identification of nematode viruses that naturally infect C. elegans and Caenorhabditis briggsae provides a unique opportunity to define host-virus interactions in these model hosts.

This dissertation first explored the transcriptional response of C. elegans and C. briggsae to virus infection by RNA-seq. I identified a total of 320 differentially expressed genes (DEGs) in C. elegans following Orsay virus …

Understanding The Relationship Between Hosts And Their Microbiome, Boahemaa Adu-Oppong

Arts & Sciences Electronic Theses and Dissertations

Microbes are bountiful and associated with every animal and plant kingdom. Furthermore, microbes can alter host phenotype, development, health and functioning. However, this is not a one-way interaction, hosts can structure microbial communities by changing the environment to be suitable for certain microbial species. Several studies have characterized microbial communities associated with hosts to answer two2 main questions in ecology: who’s there, and what are they doing? However, two questions from the field of community ecology are often ignored (1) what forces are structuring the microbial communities (how was the community formed) and (2) how stable are these communities. Vellend …

Investigation Of The Contribution Of Type 1 Pili In Enterotoxigenic Escherichia Coli (Etec) Pathogen-Host Interactions, Alaullah Sheikh

Arts & Sciences Electronic Theses and Dissertations

Enterotoxigenic Escherichia coli (ETEC) are one of the leading causes of death due to diarrhea in children living in developing countries. ETEC are also the leading cause of diarrhea in travelers to developing countries lacking sanitation and safe drinking water. Unfortunately, there is no broadly protective vaccine available against these important pathogens. In order to cause infection, ETEC colonize the intestinal epithelium and secrete toxins, including heat-labile toxin (LT) and/or heat-stable toxin (ST). Efficient delivery of these toxins to the cognate receptors on target intestinal cells requires direct ETEC-host interactions. Earlier studies demonstrated that ETEC facilitate interactions with host by …

Identification And Characterization Of An Interferon Stimulated Gene That Restricts Alphavirus Infection And Pathogenesis, Subhajit Poddar

Arts & Sciences Electronic Theses and Dissertations

Viral infection of host cells induces the Type I interferon (IFN) response, which is

characterized by the production of hundreds of IFN-stimulated genes (ISGs). Altogether, these

ISGs function to induce an antiviral state, hindering or blocking various steps of the viral

lifecycle. Many individual ISGs have potent and broad antiviral functions. However elimination

of a single ISG does not completely abrogate protection, suggesting that other ISGs, although

moderate or moderate when considered alone, must work cooperatively to provide optimal

antiviral activity.

In order to identify and characterize novel ISGs, an attenuated strain of the alphavirus

chikungunya (CHIKV-181/25) was tested against …

Antiviral Nucleoside Inhibitors Of Leishmania Rna Virus 1: Discovery And Mechanism, John Isaac Robinson

Arts & Sciences Electronic Theses and Dissertations

Some Leishmania parasites in the Viannia sub-genus are persistently infected with Leishmania RNA virus 1 (LRV1), a single-segmented double-stranded RNA virus belonging to the family Totiviridae. Infected parasites cause greater pathology and reach higher populations in mouse models of Leishmania infection. In human disease, LRV1+ parasites are correlated with increased frequency of treatment failure and relapse. Efficient methods to detect LRV1 and eliminate it from parasites are required to better understand the role of LRV1 in Leishmania infection. We optimized multiple techniques to measure LRV1 levels in parasites, most notably using flow cytometry to measure the amount of viral capsid …

The Role Of Bhlhe40 In Autoimmune Neuroinflammation And Mycobacterial Infection, Chih-Chung Lin

Arts & Sciences Electronic Theses and Dissertations

The mammalian immune system is composed of innate and adaptive compartments, which cooperate with each other to maintain homeostasis and protect the host from the invasion by a variety of pathogens. The tight control of immune responses is extremely important for all individuals. Here, we discovered that the transcription factor basic helix-loop-helix family, member e40 (Bhlhe40) is a critical protein that regulates the autoimmune ("against self") and anti-microbial ("against non-self") responses of myeloid cells and T lymphocytes. Multiple sclerosis (MS) is a human neuroinflammatory disease in the central nervous system with an autoimmune etiology. We have reported that Bhlhe40 positively …

The Role Of Histidine Rich Protein Ii In Cerebral Malaria, Priya Pal

Arts & Sciences Electronic Theses and Dissertations

Human malaria is caused by five species of Plasmodium. Of these, P. falciparum is the deadliest and is the only species that causes cerebral malaria (CM). CM is a disease of the vascular endothelium characterized by parasite sequestration, increased inflammatory cytokine production, vascular leakage and leukocyte infiltration. A distinguishing feature of P. falciparum infection is the parasite’s production and secretion of histidine-rich protein II (HRPII). HRPII accumulates to high concentrations (up to 100 µg/ml) in serum, which correlates with disease severity. Due to high serum levels of this protein, HRPII has classically been considered a biomarker for P. falciparum infection. …

The Role Of Rna Interference In The Control Of Leishmania Rna Virus 1 Infection, Erin Acino Brettmann

Arts & Sciences Electronic Theses and Dissertations

The presence of Leishmania RNA virus 1 (LRV1) in parasites of the Leishmania (Viannia) subgenus increases the virulence of the parasite in mouse models of leishmaniasis and is correlated with treatment failure, relapse, and the development of mucocutaneous disease in humans. LRV1 is not shed or infectious; rather, the infection is persistent, and as yet it is unknown how the parasite controls virus levels. Many eukaryotic organisms use RNA interference (RNAi) to limit virus replication, and Leishmania (Viannia) parasites have an active RNAi pathway. To determine whether Leishmania are capable of using RNAi to control LRV1, we sequenced sRNAs from …

Ancient Bacteria–Amoeba Relationships And Pathogenic Animal Bacteria, Joan E. Strassmann, Longfei Shu

Biology Faculty Publications & Presentations

Long before bacteria infected humans, they infected amoebas, which remain a potentially important reservoir for human disease. Diverse soil amoebas including Dictyostelium and Acanthamoeba can host intracellular bacteria. Though the internal environment of free-living amoebas is similar in many ways to that of mammalian macrophages, they differ in a number of important ways, including temperature. A new study in PLOS Biology by Taylor-Mulneix et al. demonstrates that Bordetella bronchiseptica has two different gene suites that are activated depending on whether the bacterium finds itself in a hot mammalian or cool amoeba host environment. This study specifically shows that B. …

Does High Relatedness Promote Cheater-Free Multicellularity In Synthetic Lifecycles?, R F. Inglis, E Ryu, O Asikhia, Joan E. Strassmann, David C. Queller

Biology Faculty Publications & Presentations

The evolution of multicellularity is one of the key transitions in evolution and requires extreme levels of cooperation between cells. However, even when cells are genetically identical, noncooperative cheating mutants can arise that cause a breakdown in cooperation. How then, do multicellular organisms maintain cooperation between cells? A number of mechanisms that increase relatedness amongst cooperative cells have been implicated in the maintenance of cooperative multicellularity including single-cell bottlenecks and kin recognition. In this study, we explore how relatively simple biological processes such as growth and dispersal can act to increase relatedness and promote multicellular cooperation. Using experimental populations of …

Draft Genome Sequences Of Three Closely Related Isolates Of The Purple Nonsulfur Bacterium Rhodovulum Sulfidophilum, Michael S. Guzman, Beau Mcginley, Natalia Santiago-Merced, Dinesh Gupta, Arpita Bose

Biology Faculty Publications & Presentations

We report here the draft genome sequences of three isolates of Rhodovulum sulfidophilum from a single population that will serve as a model system for understanding genomic traits that underlie metabolic variation within closely related marine purple nonsulfur bacteria in natural microbial communities.

Bioelectrohydrogenesis And Inhibition Of Methanogenic Activity In Microbial Electrolysis Cells - A Review, Rengasamy Karthikeyan, Ka Yu Cheng, Ammaiyappan Selvam, Arpita Bose, Jonathan W.C. Wong

Biology Faculty Publications & Presentations

Microbial electrolysis cells (MECs) are a promising technology for biological hydrogen production. Compared to abiotic water electrolysis, a much lower electrical voltage (~0.2V) is required for hydrogen production in MECs. It is also an attractive waste treatment technology as a variety of biodegradable substances can be used as the process feedstock. Underpinning this technology is a recently discovered bioelectrochemical pathway known as "bioelectrohydrogenesis". However, little is known about the mechanism of this pathway, and numerous hurdles are yet to be addressed to maximize hydrogen yield and purity. Here, we review various aspects including reactor configurations, microorganisms, substrates, electrode materials, and …

Antifungal Genome Mining And Genetics In Filamentous Actinomycete Bacteria Isolated From Local Soils, Jacob Alex, Kevin Lou, Bilal Makhdoom

Undergraduate Research Symposium Posters

Actinomycetes are gram positive, filamentous bacteria that produce useful antibiotics, antitumor agents, and agricultural products. A series of enrichments were undertaken to isolate actinomycetes from local soils, varying enrichment media, antibacterials, and soil treatments (including heat and CaCO3). Isolates were characterized by 16S rDNA sequencing, phenotypic and morphological observations, and antibiotic production. The genetic tractability of select isolates was analyzed using a panel of integrating vectors derived from ɸC31, ɸBT1, and OzzyJ phage using intergeneric conjugation. Further, a semi-degenerate multiplex PCR assay to detect ɸBT1 genomic integrants was designed and tested for the first time. Finally, PCR screens were used …