A Single Vertebrate Dna Virus Protein Disarms Invertebrate Immunity To Rna Virus Infection, Don B. Gammon, Sophie Duraffour, Daniel K. Rozelle, Heidi Hehnly, Rita Sharma, Michael E. Sparks, Cara C. West, Ying Chen, James J. Moresco, Graciela Andrei, John H. Connor, Darryl Conte Jr., Dawn E. Gundersen-Rindal, William L. Marshall, John R. Yates, Neal S. Silverman, Craig C. Mello

Neal Silverman

Virus-host interactions drive a remarkable diversity of immune responses and countermeasures. We found that two RNA viruses with broad host ranges, vesicular stomatitis virus (VSV) and Sindbis virus (SINV), are completely restricted in their replication after entry into Lepidopteran cells. This restriction is overcome when cells are co-infected with vaccinia virus (VACV), a vertebrate DNA virus. Using RNAi screening, we show that Lepidopteran RNAi, Nuclear Factor-kappaB, and ubiquitin-proteasome pathways restrict RNA virus infection. Surprisingly, a highly conserved, uncharacterized VACV protein, A51R, can partially overcome this virus restriction. We show that A51R is also critical for VACV replication in vertebrate cells …

In The Social Amoeba, Dictyostelium Discoideum , Density, Not Farming Status, Determines Predatory Success On Unpalatable Escherichia Coli, Susanne Disalvo, Debra A. Brock, Jeff Smith, David C. Queller, Joan E. Strassmann

Biology Faculty Publications & Presentations

Background
The social amoeba Dictyostelium discoideum interacts with bacteria in a variety of ways. It is a predator of bacteria, can be infected or harmed by bacteria, and can form symbiotic associations with bacteria. Some clones of D. discoideum function as primitive farmers because they carry bacteria through the normally sterile D. discoideum social stage, then release them after dispersal so the bacteria can proliferate and be harvested. Some farmer-associated bacteria produce small molecules that promote host farmer growth but inhibit the growth of non-farmer competitors. To test whether the farmers’ tolerance is specific or extends to other growth inhibitory …

Draft Genome Sequence Of New Bacillus Cereus Strain Tsu1, Hui Li, Suping Zhou, Terrance Johnson, Koen Vercruysse, Alexander J. Ropelewski, Theodore W. Thannhauser

Agricultural and Environmental Sciences Faculty Research

This paper reports the draft genome sequence of new Bacillus cereus strain tsu1, isolated on an agar-cellulose plate. The draft genome sequence is 5.81 Mb, revealing 5,673 coding sequences. It contains genes for cellulose-degradation and biosynthesis pathways of polyhydroxybutyrate (PHB) and 8 rRNA genes (5S, 16S, and 23S).

Role Of Peptidoglycan Modifications In Predation By Bdellovibrio Bacteriovorus 109j, Diane C. Szmiett

Electronic Thesis and Dissertation Repository

Bdellovibrio bacteriovorus is a prey dependent bacterium that traverses the outer membrane and peptidoglycan, and enters the periplasmic space of gram negative bacteria, from where it utilizes the cytoplasmic contents for growth. Soluble lytic transglycosylases could be responsible for creating the entry pore during predation. Bacteria can modify their peptidoglycan by the addition of acetate to the C-6 hydroxyl group of the N-acetylmuramic acid residues, which renders the peptidoglycan insensitive to cleavage by lytic transglycosylases. It was hypothesized that the degree of peptidoglycan O-acetylation of the prey cell affects predation efficiency. In this study it was shown that; …

Response Of Soil Nitrification To The Veterinary Pharmaceuticals Monensin, Ivermectin And Zinc Bacitracin, Magda A. Konopka

Electronic Thesis and Dissertation Repository

Pharmaceutical residues can reach agricultural land through amendment with animal or human waste. Since 2010, a series of replicated plots received annual applications of ivermectin, monensin and zinc bacitracin, either singly or in a mixture, at 0.1 mg/kg and 10 mg/kg concentrations. I collected soil samples before and after the fourth annual application of pharmaceuticals and assayed them for functional changes and amoA gene abundance, a gene needed for ammonia oxidation. In 2013, I exposed the soils to 100 mg/kg in a laboratory experiment which resulted in acceleration of nitrification. Under 10 mg/kg treatments in the field the abundance of …

Characterization Of Vibrio Vulnificus Strains Using Phenotypic And Genotypic Assays, James Conrad

Masters Theses, 2010-2019

In this study 143 V. vulnificus isolates of clinical and environmental origin, were examined for growth on differential media, identified to species and tested for antibiotic resistance. A multiplex PCR was created and optimized, and phylogenetic analysis was conducted. The first objective was to compare phenotypic methods to identify V. vulnificus. Colony colors of confirmed V. vulnificus isolates on selective media (Vibrio vulnificus agar, thiosulfate citrate bilesalts sucrose agar, CHROMAgar Vibrio (CAV), and colistin polymyxin B cellobiose agar), mostly matched those characteristic of V. vulnificus. To test the ability of these media to select for V. vulnificus, new presumptive V. …

Colloidal And Biological Properties Of Triscationic Amphiphiles With One Or Two Tails, John N. Marafino

Masters Theses, 2010-2019

The decline in the development of novel antimicrobials, combined with the misusage and over prescription of antibiotics, has contributed to the increasing prevalence of antimicrobial-resistant infections. Thus development of effective novel disinfectants could reduce the transmission of pathogens and decrease the risk of infection by antibiotic resistant organisms. The antimicrobial activity of amphiphiles, compounds with hydrophobic and hydrophilic regions, was first reported in 1935, and has influenced the synthesis of amphiphiles with variations in structure. In this study, three series of amphiphiles were synthesized by two subsequent Menshutkin reactions. Each amphiphile contains one or two hydrocarbon tails ranging from 8 …

Transcriptomic And Proteomic Dynamics In The Metabolism Of A Diazotrophic Cyanobacterium, Cyanothece Sp. Pcc 7822 During A Diurnal Light-Dark Cycle, Louis Sherman

Louis A Sherman

Background: Cyanothece sp. PCC 7822 is an excellent cyanobacterial model organism with great potential to be applied as a biocatalyst for the production of high value compounds. Like other unicellular diazotrophic cyanobacterial species, it has a tightly regulated metabolism synchronized to the light-dark cycle. Utilizing transcriptomic and proteomic methods, we were able to quantify the relationships between transcription and translation underlying central and secondary metabolism in response to nitrogen free, 12 hour light and 12 hour dark conditions.

Results: By combining mass-spectrometry based proteomics and RNA-sequencing transcriptomics, we quantitatively measured a total of 6766 mRNAs and 1322 proteins at four …

Hcpe, A Potential Immuno-Modulatory Protein From Helicobacter Pylori That Is Dependent On The Disulfide Bond Protein Dsbhp, Jeff Lester

Electronic Thesis and Dissertation Repository

H. pylori is a human gastric pathogen that colonizes ~ 50% of the world’s population. It can cause gastritis, gastric or duodenal ulcers and also gastric cancer. H. pylori produces Helicobacter cysteine rich protein HcpE, a secreted protein which may play a role in virulence. In this study we show that HcpE is secreted in the culture supernatant both as a soluble protein and in association with outer membrane vesicles, and may play a role in the modulation of H. pylori inflammatory responses. We identified that Dsb_HP is necessary for HcpE production and secretion in H. pylori, and …

Effect Of Intracellular Expression Of Antimicrobial Peptide Ll-37 On Growth Of Escherichia Coli Strain Top10 Under Aerobic And Anaerobic Conditions, Wei Liu, Shi Dong, Fei Xu, Xue Wang, T. Withers, Hongwei Yu, Xin Wang

Hongwei Yu

Antimicrobial peptides (AMPs) can cause lysis of target bacteria by directly inserting themselves into the lipid bilayer. This killing mechanism confounds the identification of the intracellular targets of AMPs. To circumvent this, we used a shuttle vector containing the inducible expression of a human cathelicidin-related AMP, LL-37, to examine its effect on Escherichia coli TOP10 under aerobic and anaerobic growth conditions. Induction of LL-37 caused growth inhibition and alteration in cell morphology to a filamentous phenotype. Further examination of the E. coli cell division protein FtsZ revealed that LL-37 did not interact with FtsZ. Moreover, intracellular expression of LL-37 results …

Melatonin And Neurogenesis: A Comparative Study Of The Efficacy Of Melatonin, Its Precursors, And L-Dopa On Neural Stem Cell Metabolism In Human Adult Neurospheres, Omar Heriba

HIM 1990-2015

Human neurosphere stem cells offer promising potential for the treatment of neurodegenerative diseases. Their well characterized multi-potency of differentiating into neurons, astrocytes, and oligodendrocytes when exposed to the optimum exogenous growth factors make them an exciting area of study (38). Finding novel endogenous methods of modulating stem cell metabolism will allow for the safer treatment of various brain disorders (34). In this experiment, melatonin, N-acetylserotonin, L-tryptophan, and L-DOPA are added in three different concentrations to neurospheres suspended in HNSC/GBM media with less than optimal concentrations of exogenous epidermal growth factor (EGF) and fibroblast growth factor (FGF). The alamarBlue assay (resazurin) …

Using The Yeast Two-Hybrid System To Determine The Function Of Parkin E3 Ubiquitin Ligase, Vanessa Nguyen

HIM 1990-2015

Parkin is a cytosolic E3 ubiquitin ligase that is recruited to the mitochondria during cellular stress and has been suggested to be involved in a variety of biological processes such as mitophagy. The recruitment of Parkin (PARK2) to the mitochondria is dependent upon the kinase activity and the accumulation of PINK1 on damaged mitochondria. Mutations in either PINK1 or Parkin genes disrupt this protective pathway and lead to the accumulation of damaged mitochondria. From a clinical standpoint, mutations in the PARK2 gene have been associated with the progression and onset of autosomal recessive juvenile parkinsonism. Without the presence of a …

Long-Term Impacts Of Tillage, Cover Crops, And Nitrogen Rates On Microbial Community Dynamics And Soil Quality Parameters Under Continuous Cotton Production In West Tennessee, Lilian Wanjiru Mbuthia

Doctoral Dissertations

Microbial communities play a central role in nutrient cycling and soil quality in agro-ecosystems. This research focused on a comparative analysis of the microbial community structure and activity of soils on long-term (31 years) continuous cotton- Gossypium hirsutum L., production in West Tennessee under conservation agricultural (CA) and conventional tillage practices that included: Nitrogen (N) fertilizer rates (N-rates) (0, 34, 67 and 101 kg N per ha); Cover crops (Hairy vetch-Vicia villosa and winter wheat- Triticum aestivum, and a No Cover control); and Tillage (Till and No-till). It was expected that microbial diversity, activity and soil quality would be …

Comparative Genomics Of Microbial Chemoreceptor Sequence, Structure, And Function, Aaron Daniel Fleetwood

Doctoral Dissertations

Microbial chemotaxis receptors (chemoreceptors) are complex proteins that sense the external environment and signal for flagella-mediated motility, serving as the GPS of the cell. In order to sense a myriad of physicochemical signals and adapt to diverse environmental niches, sensory regions of chemoreceptors are frenetically duplicated, mutated, or lost. Conversely, the chemoreceptor signaling region is a highly conserved protein domain. Extreme conservation of this domain is necessary because it determines very specific helical secondary, tertiary, and quaternary structures of the protein while simultaneously choreographing a network of interactions with the adaptor protein CheW and the histidine kinase CheA. This dichotomous …

Microbial Community Shifts Caused By Changes In The Primary Oxidant At A Drinking Water Treatment Plant, Connie Marie Moloney

Graduate Theses and Dissertations

Microbial communities resistant to common oxidants can cause concerns for water treatment plants (WTPs). If a bacterium is not fully oxidized during disinfection, these species can impede upon filtration processes or seed biofilms in the distribution system. In an effort to minimize disinfection by-products (DBP's) that result from the reaction of chlorine (Cl2) with natural organic matter, water treatment plants have the option to change their primary oxidant to chlorine dioxide (ClO2). The following study examines the change in microbial communities during the sedimentation process under differing oxidation regimes, specifically chlorine (Cl2) and ClO2 at the local water treatment plant …

The Phenotypic Effects And Transcript Response Of Salt Stress, The Impact Of Viral Infection On Salt Stress Symptoms, And The Effect Of Salt Stress On Soybean Virus Vector Activity In Soybean Varieties That Vary In Chloride Uptake, Alma Glenn Laney

Graduate Theses and Dissertations

With the increase in saline soils worldwide, understanding the mechanisms for salt tolerance in plants is important to reduce yield loss due to salt stress. Soybean, Glycine max (L.) Merr., genotypes differ in chloride uptake with genotypes that take up chloride into foliar tissues tending to be salt-sensitive whereas those that partially exclude chloride from the leaves are more salt-tolerant. Transcriptional and physiological responses were measured in two soybean cultivars, Clark and Manokin, which differ in chloride uptake in response to salt stress and in combination with Soybean mosaic virus (SMV) and its aphid vector, Aphis glycines . The interaction …

Novel Protein Secretion And Chitin Utilization Machinery Of Flavobacterium Johnsoniae, Sampada Suresh Kharade

Theses and Dissertations

Flavobacterium johnsoniae, a member of phylum Bacteroidetes, is a gliding bacterium that digests insoluble chitin. A novel protein secretion system, the Type IX secretion system (T9SS), secretes the motility adhesins SprB and RemA and is also required for chitin utilization. In order to understand F. johnsoniae chitin utilization and the role of the T9SS, Fjoh_4555 (chiA) was targeted for analysis. Disruption of chiA resulted in cells that failed to digest chitin and complementation restored this ability. Antisera raised against ChiA were used to characterize its secretion. ChiA was secreted in soluble form by wild-type cells but remained cell-associated in T9SS …

Ciliates Of Sagebrush-Steppe Soils Of Southwestern Idaho: Species Richness And Its Relationship To Changed Soil Variables After Wildfire Events, Laura G. Wendell

Boise State University Theses and Dissertations

I conducted a pilot study to examine species richness of terrestrial ciliates associated with big sagebrush habitat (Artemisia tridentata) in southwestern Idaho, USA. As wildland fires are a naturally occurring disturbance in this area, soil variables associated with these fires (% C, % N, pH, soil texture, and % clay) were measured at three sites, both in burned and unburned areas. These soil characteristics were compared to corresponding ciliate diversity and ratios of r-selected colpodeans to K-selected polyhymenophorans (C/P) in non-flooded Petri dish preparations. A total of 85 ciliate taxa were observed across the three sites, including …

Characterization Of Biofilms On Medical Device Materials With Application To Reusable Surgical Instruments, Amanda Macaluso

All Theses

Reusable medical devices or reprocessed single-use devices are original medical devices that have been used once and then are cleaned, sterilized, and remanufactured for the purpose of an additional single use on a single patient [4]. Improperly reprocessed devices are a significant contributor to hospital-associated infections [4]. Challenges that hinder reprocessing are related to the complexity of reusable medical device design, the necessary validation of cleaning protocols required by the U.S Food and Drug Administration (FDA), the impact of human factors throughout the reprocessing cycle, as well as economic factors within new business models that are centered on reprocessing. Current …

Spring Thaw Ionic Pulses Boost Nutrient Availability And Microbial Growth In Entombed Antarctic Dry Valley Cryoconite Holes, Jon Telling, Alexandre M. Anesio, Martyn Tranter, Andrew G. Fountain, Thomas H. Nylen, Jon Hawkings, Virendra B. Singh, Preeti Kaur, Michaela Musilova, Jemma L. Wadham

Geology Faculty Publications and Presentations

The seasonal melting of ice entombed cryoconite holes on McMurdo Dry Valley glaciers provides oases for life in the harsh environmental conditions of the polar desert where surface air temperatures only occasionally exceed 0°C during the Austral summer. Here we follow temporal changes in cryoconite hole biogeochemistry on Canada Glacier from fully frozen conditions through the initial stages of spring thaw toward fully melted holes. The cryoconite holes had a mean isolation age from the glacial drainage system of 3.4 years, with an increasing mass of aqueous nutrients (dissolved organic carbon, total nitrogen, total phosphorus) with longer isolation age. During …

Effects Of Water Column P-Availability And Litter Microbial Mediated Processes And Stoichiometry In Aquatic Systems, Ayla Smartt

Graduate Theses and Dissertations

Anthropogenic nutrient enrichment of aquatic ecosystems is prevalent and can have detrimental effects on biological condition. Many of these effects have been attributed directly or indirectly to changes in autotrophic processes. However, in detrital-based streams changes in course detrital stoichiometry and decomposition have been related to changes community structure and production at higher trophic levels highlighting the importance of considering the heterotrophic microbial responses to enrichment. Leaf litter stoichiometry, which is determined in part by the tree species source and the microbial communities that comprise the associated biofilm, is likely related to decomposition rates, but few studies examine these variables …

Modulation Of Host Polyubiquitination By The Ankb F-Box Protein Of Legionella Pneumophila., William M. Bruckert

Electronic Theses and Dissertations

Legionella pneumophila is a facultative intracellular pathogen that infects a wide array of protozoan hosts and human alveolar macrophages. L. pneumophila is dependent on a functional Dot/Icm type IVB secretion system that translocates bacterial effector proteins into the host cell cytosol. L. pneumophila genomes encode more than 250 effector proteins, many of which inhibit host cellular processes to form a favorable niche termed the Legionella-containing vacuole (LCV). The eukaryotic-like Dot/Icm translocated effector AnkB contains two eukaryotic-like ankyrin protein-protein interacting domains, one eukaryotic-like F- box domain and an eukaryotic C-terminal CaaX motif. Immediately following attachment of extracellular bacteria, AnkB is translocated …

A Mechanism For Trif Adaptor-Biased Signaling By Toll-Like Receptor 4., Joseph Peterson Kolb

Electronic Theses and Dissertations

Host cells respond to bacterial lipid A through Toll-like receptor 4 (TLR4). Activation of TLR4 by lipid A triggers a response that involves two main adaptor proteins, MyD88 and TRIF. MyD88-dependent gene expression is associated with proinflammatory protein production, while TRIF-dependent gene expression is essential for optimal activation of adaptive immunity by antigen-presenting cells. Detoxified, monophosphoryl lipid A agonists (MPLA or synthetic MLA) were previously suggested to elicit TRIF-biased TLR4 signaling; that is, induction of weaker MyD88-associated gene expression but relatively intact TRIF-dependent gene expression when compared to fully active diphosphoryl lipid A (lipid A). In this work, we explored …

Modulation Of The Ovarian Cancer Humoral Response By Tumor-Derived Exosomes., Carolyn Denise Roberson

Electronic Theses and Dissertations

The pathogenesis of epithelial ovarian cancer is complicated by its diagnosis during the latter stages of the disease resulting from lack of symptoms or from presence of symptoms that mimic other conditions. Because of the often fatal prognosis by the time of actual detection, efforts are being made to better understand the host immune response to ovarian cancer. In this study, the contributions of the humoral immune response were investigated by focusing on the role of tumor-derived exosomes and their ability to modulate humoral immune responses. First, ovarian cancer patient-derived free circulating antibodies were investigated for immunoreactivity to patient antigen. …

Determining The Fate Of Non-O157 Shiga Toxin-Producing Escherichia Coli In Dairy Compost During Storage Using The Optimized Detection Method, Hongye Wang

All Theses

Shiga toxin-producing Escherichia coli (STEC), a member of Enterobacteriaceae family, has been recognized as emerging pathogens. Dairy compost is commonly applied to farmland as a soil amendment. Despite the agricultural benefit of manure-based soil amendment, the inadequately treated compost can contribute to fresh produce contamination on the farm. Moreover, the epidemiological results showed that the non-O157 STEC cases have surpassed those of E. coli O157. Therefore, it is critical to evaluate the behavior of non-O157 STEC strains in the dairy manure-based compost. The objectives of this study were to: 1) optimize a culturing method for detecting non-O157 STEC from dairy …

Inhibition Of Vibrio Cholerae Biofilm Formation By Water-Soluble Cranberry Extracts, Daniel Pederson

All Theses

Vibrio cholerae, a Gram-negative bacterium found in natural aquatic environments, is the causative agent of cholera, a severe diarrheal disease most commonly spread through drinking water. An essential component to this pathogen's success and persistence in the environment is its ability to attach to both biotic and abiotic surfaces via biofilm formation. Biofilms not only aid in surface attachment, but also provide a barrier that protects and enhances survival. Water-soluble extracts from the North American cranberry (Vaccinium macrocarpon) were found to dramatically inhibit V. cholerae biofilm formation at a low concentration of 2mg/ml. This inhibition was not due to acidification …

A Portable Impedance Biosensing System Based On A Laptop With Labview For Rapid Detection Of Avian Influenza Virus, Yixiang Wang

Graduate Theses and Dissertations

Avian Influenza Virus (AIV) H5N1 is a highly pathogenic virus found not only in birds but also in human. Rapid and sensitive detection method is needed to help prevent the spread of AIV H5N1. In this study, a portable impedance biosensing system based on a laptop with LabVIEW software was developed for detection of AIV H5N1. First, a virtual instrument was programmed with LabVIEW software to form a platform for impedance measurement, data processing and control. The audio card of a laptop was used as a function generator while a data acquisition card was used with the signal channels for …

Quantitative Analysis And Imaging-Based Insights Into The Characteristics And Mechanisms Of Yeast Pattern Formation, Lin Chen

Dissertations & Theses (Open Access)

Biofilm formation is a common lifestyle adapted by bacteria and fungi in response to various environmental stresses. Bacterial and fungal biofilms adhering to medical devices convey resistance to antibiotics or biocides, causing high rates of clinical infections. Microorganisms are protected from harsh environmental conditions by reduced stress penetration through the complex biofilm architecture with distinct patterns. Although the molecular regulations of surface patterning have been well characterized in bacteria, the mechanisms underlying the complex pattern formation in eukaryotic biofilms remain unclear.

This dissertation aims to investigate the salient features of robust colony expansion in yeast biofilms and the processes driving …

Gut Bacteria And Their Influence On Metabolic Disorders, Stephanie Sorbara (Class Of 2015)

Biology Undergraduate Publications

The human gut microbial genome encodes for several metabolic processes that are not encoded for in the human genome. Through the study of metagenomics, mice, and human models, researchers have shown that changes in the gut bacterial composition can generate oxidative stress, release endotoxins, and induce lipogenesis. These pathways can disrupt normal metabolic function, resulting in obesity and other related metabolic disorders such as diabetes. Most of the health implications associated with obesity originate from the biological reactions carried out by the gut bacteria, which are strongly impacted by environmental factors. Probiotics, prebiotics and fecal transplantation are methods that can …

Antibacterial Activity Of Commercially Available Plant Extracts On Selected Campylobacter Jejuni Strains, Divya Oppath Sivasankaran

Graduate Theses and Dissertations

Campylobacter jejuni is recognized as a leading cause of foodborne illness worldwide with approximately 850,000 cases per year in the United Sates. A total of 18 species of Campylobacter have been identified worldwide to date. Foodborne transmission of C. jejuni is mainly through the consumption of unpasteurized milk, contaminated poultry meat and water. C. jejuni can survive in very diverse environments under stressful conditions in human and animals which is different from the specific conditions and media required in laboratory experiments. There has been increased research in recent years to identify naturally occurring antibacterial agents to control and eliminate C. …