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Adherent-Invasive Escherichia Coli (Aiec) Promotes Mild Colitis In The C57bl/6 Il-10 Ko Mouse Model Of Crohn's Disease, Sarah Sm Zaw

Senior Theses

Crohn's disease (CD) is a chronic inflammatory bowel disease. Interleukin-10 knockout (IL-10 KO) mice are crucial in CD research. Adherent-invasive Escherichia coli (AIEC) is a subgroup of E. coli. In one study, IL-10 KO mice colonized with AIEC developed colitis in the distal colon compared to wild-type (WT) mice. I investigated how AIEC NC101 WT affects colitis severity in IL-10 KO mice of the C57BL/6 genetic background. Similar results in both genotypes would enhance mouse strain accessibility. Germ-free C57BL6 IL-10 KO mice were divided into groups: colonized with AIEC NC101 for 12, 15, or 18 weeks, or kept germ-free. Histopathological …

Investigating Potential Indicators Of Soil Health Through Microbiome Response To Environmental And Anthropogenic Stressors, Austin Cook

Theses and Dissertations

Traditionally, the analysis of soil health has overlooked the biological component of soil due to poor understanding of connections between the microbiome and empirically measured soil health indicators. The purpose of this study was to assess the effects of environmental and anthropogenic stressors on the soil microbiome, with the aim of identifying measurable soil biological indicators. Chosen soils were examined under distinct conditions to evaluate the effect of selected environmental and anthropogenic stressors on the microbiome. Soil biological responses were analyzed via enzymatic response, microbial functional genes, and microbial community. Environmental factors such as soil moisture and organic matter showed …

The Effect Of Algal Wastewater Treatment Systems On Microbial Communities, Alexis Leach

University Honors Program Senior Projects

In collaboration with the Metropolitan Water Reclamation District of Greater Chicago and Gross-Wen Technologies, I examined the microbial communities in experimental tertiary wastewater treatment systems employing algal phytoremediation. Three algal phytoremediation systems were examined: two vertical conveyor belt systems, known as the 10-foot belt system and the series 4 system, and a third system lacking a converter belt in which planktonic algae grew in a control pond. I used EcoPlates to measure carbon substrate utilization by microorganisms in each system. EcoPlates contain thirty-one different carbon substrates, with a dye that indicates microbial use of each substrate. I conducted a Principal …

The Antibacterial Efficacy Of Silver (I) Cyanoximates Against Streptococcus Mutans Ua159 Biofilm Growth And Infection In Galleria Mellonella Larvae, Jill Hughes

Honors Program Theses

Streptococcus mutans is the known etiological agent of dental caries. S. mutans’ virulence factors, namely biofilm formation and lactic acid fermentation, contribute to its pathogenic behavior within the oral cavity. Biofilms are thick, antibiotically resistant communities of bacteria that are much more difficult to treat than planktonic or free-floating bacteria. Continued misuse of antibiotics against dynamic communities, like biofilms, has led to increased research on non-antibiotic alternatives. Amongst these alternatives, there are silver and silver-based compounds. Silver is commonly incorporated into medicine due to its inhibitory and bactericidal effects and antibacterial properties. Silver (I) cyanoximates have demonstrated promising antibacterial activity …

Application Of Nitrate To An Anaerobic Subsurface Bioremediation, Cassie Marie Roberts

Masters Theses

"The highly contaminated subsurface matrix of the Baird and McGuire Superfund site is currently threatening the health and safety of the surrounding environment of Holbrook, MA. Contaminants of significant concern due to high concentration are inorganic arsenite and petroleum hydrocarbons, such as naphthalene. Parsons Corporation and the Massachusetts Department of Environmental Protection have implemented a bioremediation pilot to attempt to degrade the hydrocarbons and arsenic with the application of nitrate. The nitrate would act as an electron acceptor for biodegradation of the hydrocarbon contaminants, produce nitrite that would oxidize reduced iron, and iron oxides would sequester arsenic. Preliminary data showed …

Effects Of Mass Death On Community Structure And Ecosystem Function, Abby Kimpton Jones

Theses and Dissertations

Death and decomposition are natural processes that are generally well-understood. However, large events of death, such as mass mortality events (MMEs) are increasing in frequency and their impacts on the ecosystem are largely unknown. These events may have both bottom-up effects from increased nutrient input as well as top-down effects from loss of an ecological functional group by the affected population. Different functional MMEs may result in different top-down effects, creating cascading effects. In Chapter 1, I test the hypothesis that scavenger and herbivore simulated MMEs generate novel bottom-up and top-down effects. Results indicate that MMEs have a significant effect …

Implications Of Antibiotic And Bacteriophage Resistance In Environmentally Isolated E. Coli, Michael Connolly

Honors Theses

The increasing prevalence of antibiotic-resistant bacteria is an emerging problem for humans. Clinical misuse, overuse in agricultural and food settings, and limited numbers of new antibiotics have accelerated the proliferation of antibiotic-resistant bacteria. To confront this threat, scientists must develop new therapeutics that kill these antibiotic-resistant bacteria. In this study, we used Escherichia coli to analyze antibiotic and bacteriophage susceptibility. E. coli is a common, mostly benign, enteric, gram-negative bacteria. We isolated three E. coli strains from the Hans Groot Kill, a stream that runs through Union College’s campus. We sought to assess various E. coli strains’ antibiotic resistance, susceptibility …

Assembly Of The Peripheral Arm Subunits Of Escherichia Coli Complex I And Analysis Of Clinical Mutations, Hind Alkhaldi

Biological Sciences Theses and Dissertations

Respiratory Complex I from E. coli is a proto-type of the mitochondrial enzyme, consisting of a 6-subunit peripheral arm (B-CD-E-F-G-I) and a 7-subunit membrane arm. When subunits E-F-G (N-module), were expressed alone they formed an active complex as determined by co-immunoprecipitation and native gel electrophoresis. When co-expressed with subunits B and CD, only a complex of E-F-G was found. When these five subunits were co-expressed with subunit I and two membrane subunits, A and H, a complex of B-CD-E-F-G-I was membrane-bound, constituting the N- and Q-modules. Assembly of Complex I was also followed by splitting the genes between two plasmids, …

Antibiotic-Resistant Bacteria In Freshwater Crayfish, Colby Finch

Honors Theses

The presence of antibiotic-resistant bacteria is increasing in natural aquatic environments. Alongside this, organisms that live in these ecosystems are increasingly harboring antibiotic-resistant bacteria. In this study, I analyzed the capacity for the crayfish species Procambarus vioscai paynei to harbor antibiotic-resistant bacteria. Crayfish, as well as water and sediment, were sampled from a pond at the University of Mississippi Field Station. The guts of crayfish were plated on TSA agar, as well as agar containing vancomycin, erythromycin, penicillin, tetracycline, or ciprofloxacin. Following incubation, counts of bacteria were determined. Selected bacterial isolates were tested for multiple antibiotic-resistance. Bacterial isolates were also …

A Comparison Of Heterotroph Isolation And Sequencing Methods From Various Cyanobacterial And Algal Microbiomes, Victoria Starks

Honors Theses

Cyanobacteria have provided a vast, new source of natural products to be utilized in drug development. Because of their non-axenic nature, cyanobacteria typically have an abundance of symbiotic heterotrophs living in association with them. These bacteria can play significant roles in the survival of its cyanobacterial host as well as provide the potential production of unique compounds. The possibility of unknown natural products is only increased by the flexible nature of these bacteria, as altering its environmental state can change the activity of biosynthetic pathways and even activate novel production. Our research team’s intent is to isolate cyanobacterial strains from …

Analysis And Identification Of Lipolytic Bacterial Species For The Degradation Of Wastewater Lipids, Lindsay C. Smoak

Honors College Theses

The aim of this study was to isolate native bacterial strains from the wastewater treatment facilities of Statesboro, GA to identify their lipolytic activities. Obtained bacterial strains were further assessed via morphological and biochemical methods to determine their enzymatic capabilities. Use of the detergent Tween-20 in growth mediums was the first criteria to assess lipase activity, and these isolates were further investigated to quantitatively measure lipase presence and activity. Lipase protein was precipitated and dialyzed to perform a lipase activity assay, followed by Sodium Dodecyl Sulphate–Polyacrylamide Gel Electrophoresis (SDS-PAGE) to confirm the presence of the lipolytic enzymes. Sanger sequencing was …

Links Between Electrophilic Stress And Antifungal Resistance In Pathogenic Candida Species, Amy R. Biermann

Dartmouth College Ph.D Dissertations

Collectively, Candida species are the most prevalent cause of both superficial and invasive fungal infections worldwide. Invasive Candida infections have a high mortality rate and predominantly affect individuals with underlying diseases, such as diabetes, HIV, or cancer. Unfortunately, many invasive Candida infections are recalcitrant to antifungal treatment, while intrinsically multidrug-resistant pathogens, like Candida auris, are increasing in prevalence. Although the canonical mechanisms of antifungal resistance in Candida species are well established, i.e., overexpression of efflux pumps and overexpression of or mutations in genes encoding drug targets, factors affecting the natural evolution and regulation of resistance mechanisms remain poorly understood. …

Microbial Community And Soil Responses To Land Management Practices In Remnant And Restored Tallgrass Prairies, Desirae Marie Klimek

Graduate Research Theses & Dissertations

Critical ecosystem functions, such as decomposition and nutrient cycling, are driven by microbial communities within soil. As such, it is important to examine the effect of restoration practices, such as the presence of native grazers and prescribed burning, on these microbes and the soil they inhabit. The Nachusa Grasslands provides a chronosequence of restored tallgrass prairies ranging in restoration age from 5 to 33 years, as well as remnant prairies, and agricultural fields. These sites were sampled seasonally from 2013-2020 and microbial ribosomal RNA genes were surveyed to characterize soil microbial communities and assess how common restoration practices affect these …

Inhibition Of Staphylococcus Aureus Biofilm By Variovorax Paradoxus, Esther Gomez

University of the Pacific Theses and Dissertations

Staphylococcus aureus is one of the leading causes of fatal nosocomial infections. Often, S. aureus can grow as a biofilm which protects the population from the surrounding environment. Strains of S. aureus are resistant to virtually all known antibiotics on the market. Variovorax paradoxus is a soil microbe with many unusual metabolic activities. It has been previously observed that, V. paradoxus can inhibit the growth of S. aureus when in co-culture. In this work we report on inhibition of S. aureus biofilm formation by V. paradoxus due to a suspected inhibitory soluble factor.

The Bgs 13 Mutant Of Pichia Pastoris And Its Effect On Structural Changes Of The Reporter Protein B-Lactogolbulin, Bushra Irshad

University of the Pacific Theses and Dissertations

Pichia pastoris, a methylotrophic yeast, is an ideal host for recombinant protein expression. It has the capability of performing many eukaryotic post-translational modifications and grows to high cell densities. However, P. pastoris’s secretion properties are not always efficient, and its secretory pathway mechanisms have not been thoroughly elucidated. A previously identified mutant strain, bgs13, was found to efficiently secrete most recombinant proteins tested, raising the possibility that this bgs13 mutant is a universal super secreter and understanding its secretion process is needed. In this study, we used a reporter protein, ?-lactoglobulin (b-LG), to perform structural analysis and comparisons of protein …

Microbial Community Analysis: Biofilm Inhibition & Algae Associated Community Structure, Michelle V. Fong

University of the Pacific Theses and Dissertations

Natural products chemistry is the pursuit of bioactive small molecules from living organisms. These can be classified as primary metabolites if they are essential to survival, and secondary metabolites if they are accessory, playing a role in communication, defense, recruitment, etc.. Natural products have made a significant contribution to society – of 1,881 FDA-approved drugs from 1981 to 2019, 4% were pure natural products, 19% were natural products derived, and 3% were synthetic drugs with a natural products pharmacophore targeting a wide range of diseases and infections (Newman & Cragg, 2020). Pharmacophores are structural components of drugs that are responsible …

Factors Influencing Primate Hair Microbiome Diversity, Catherine Kitrinos

Masters Theses

Primate hair is both a substrate upon which essential social interactions occur and an important host-pathogen interface. As commensal microbes provide important immune functions for their hosts, understanding the microbial diversity in primate hair could provide insight into primate immunity and disease transmission. While studies of human hair and skin microbiomes show differences in microbial communities across body regions, little is known about the nonhuman primate hair microbiome. In this study, we collected hair samples (n=159) from 8 body regions across 12 nonhuman primate species housed at 3 US institutions to examine 1) the diversity and composition of the primate …

Investigating Streptococcus Pneumoniae And Adenovirus Co-Infections Of Lung Epithelial Cells, Mark Nicholas Calabro

Browse all Theses and Dissertations

Co-infection is common among viruses and bacteria in the human respiratory system. Adenovirus (AdV) and Streptococcus pneumoniae are clinically relevant respiratory pathogens that cause morbidity and mortality in a variety of patient populations with the highest morbidity occurring among immunocompromised individuals, but also prevalent in infants and the elderly. Acute respiratory distress syndrome may become severe in healthy individuals when co-infection with S. pneumoniae and AdV occurs due to synergistic effects of the pathogens on the host. I hypothesized that S. pneumoniae infection decreases AdV transduction of airway epithelia. To test this hypothesis, we utilized the polarized immortalized airway epithelial …

Il-10 And Tgf-Beta Increase Connexin-43 Expression And Membrane Potential Of Hl-1 Cardiomyocytes Coupled With Raw 264.7 Macrophages, Cora B. Cox

Browse all Theses and Dissertations

Cardiomyocytes and macrophages have been found to interact via connexin-43 hemichannels. The role of connexin-43, however, is not fully understood. This study shows that these interactions aid in increasing the membrane potential of cardiomyocytes allowing contraction of the cells. HL-1 cardiomyocytes and RAW 264.7 macrophages in coculture increased expression of connexin-43 compared to cardiomyocytes alone. Co-cultures also increased the fluorescence of Di-8-ANEPPS potentiometric dye indicating an increase in cardiomyocyte membrane potential. Treatment with IL-10 and TGF-beta further increased connexin-43 expression and membrane potential. Treatment with SOCS3 inhibited the effects of TGF-beta and IL-10 while having no effect on its own. …

Investigating Streptococcus Pneumoniae And Adenovirus Co-Infections Of Lung Epithelial Cells, Mark Nicholas Calabro

Browse all Theses and Dissertations

Co-infection is common among viruses and bacteria in the human respiratory system. Adenovirus (AdV) and Streptococcus pneumoniae are clinically relevant respiratory pathogens that cause morbidity and mortality in a variety of patient populations with the highest morbidity occurring among immunocompromised individuals, but also prevalent in infants and the elderly. Acute respiratory distress syndrome may become severe in healthy individuals when co-infection with S. pneumoniae and AdV occurs due to synergistic effects of the pathogens on the host. I hypothesized that S. pneumoniae infection decreases AdV transduction of airway epithelia. To test this hypothesis, we utilized the polarized immortalized airway epithelial …

Network And Ecological Methods To Study Enteric Pathogen Co-Infections, Connor L. Klopfer

Graduate College Dissertations and Theses

Diarrhea remains a leading cause of childhood morbidity and mortality, especially inchildren under 5 years of age. Enteric pathogen co-infection has been found to cause increased diarrheal severity and some pathogens may work in tandem to enhance infection. It is important to identify patterns of pathogen co-infection and their impact on diarrhea to inform intervention strategies for improving child health. In this thesis, I use data from the MAL-ED and PROVIDE birth cohort studies in Bangladesh to generate bipartite networks that represent the relationship between stool samples and pathogens. I randomly rewire the network while preserving connectivity to randomize the …

More Than The Sum Of Their Parts: Building A Framework For Understanding Host-Microbe Interactions In Medicago Sativa, Katherine Mackenzie Moccia

Doctoral Dissertations

This dissertation seeks to understand plant-microbe interactions in the agriculturally relevant plant Medicago sativa from three distinct vantage points within microbiology. Within the plant microbiome, we examine how primer usage and the application of peptide nucleic acids impacts 16S and 18S rRNA gene sequencing. In doing so, we design a novel peptide nucleic acid, PNA, and test its impact using multiple primers and sequencing protocols. Once microbial sequencing methodology is established, we generate a synthetic consortium of bacterial isolates from M. sativa leaves and modulate nitrogen levels to better understand microbial structure. Drop out communities, where we remove one member …

Extracting Detailed Metabolic Information And Connections From Mammalian Gut Microbiomes Via Metaproteomics, Jose A. Blakeley-Ruiz

Doctoral Dissertations

A diverse community of bacteria populates the mammalian gastrointestinal tract. These populations exist in a balance with the host assisting with key functions, particularly metabolism of intractable fibers and immune modulation. Disruption of this balance can lead to diseases such as infection, inflammatory bowel syndrome, and obesity. Common symptoms include chronic pain, chronic inflammation, and altered metabolism. Several taxonomic classifications of bacteria have been associated with these diseases, but Recent studies have indicated that these finding are not always statistically valid. An explanation for this is that microbial communities between individuals and even across time can vary substantially even when …

Diverse Community Of Arsenic Resistant Bacteria Display Arsenate Reducing Capabilities, Stephanie Maeda

Undergraduate Honors Theses

Naturally found in soil and water environments arsenic is toxic to many organisms, carcinogenic to humans, and poses a significant public health risk. Yet communities of bacteria found thriving in arsenic ridden environments have evolved mechanisms to tolerate and exploit both oxidation states of this heavy metal (arsenite and arsenate). As the site of an old arsenic mine, Black Mountain Open Space Park in San Diego, California has yielded concentrations of arsenic in the soil between 111-14,800 ppm. Exceeding average arsenic soil concentrations and levels considered safe in the environment by the World Health Organization, we sought to characterize the …

Innovative Approaches In The Discovery Of Aquatic Mycobacteriophages, Janis H. Doss

Biomedical Sciences Theses & Dissertations

Bacteriophages (phages), viruses that infect bacteria, have many applications in medicine, agriculture, molecular biology, and other fields. As antibiotic resistance becomes an increasing problem, interest in phages has grown. The traditional techniques of phage discovery are successful for some phages, but others require modified procedures to achieve detectable host infection.

Mycobacterium is a diverse bacterial genus characterized by a unique cell wall containing mycolic acids, which aids in survival and pathogenesis. The aims of the present research were to isolate mycobacteriophages, use bioinformatics techniques to analyze mycobacterial prophages, and combine genetic analysis with multi-well plate host range studies to identify …

Whole Genome Sequence Analysis Of A Transmissible Multidrug-Resistance Plasmid Captured Without Cultivation From Poultry Litter, Emma C. Eisemann

Senior Honors Projects, 2020-current

Use of antibiotics in the agricultural industry introduces selective pressure and, consequently, could increase the presence of antibiotic resistant organisms in surrounding environments. One such environment is litter (manure and bedding) produced during large-scale poultry production in the Shenandoah Valley. Litter, with its microorganisms, is commonly applied to fields within the Shenandoah River watershed. Antibiotic resistance (AR) and virulence genes are potentially transmissible between organisms through horizontal gene transfer of genetic mobile elements, for which poultry litter could be a reservoir. The typical, culture-based approach to detecting and analyzing AR plasmids and other mobile genetic elements is limited due to …

Lysogeny And Use Of Mycobacteriophage Pita2, Eleanor Behling, Neocles B. Leontis, Jill Zeilstra-Ryalls

Honors Projects

The CDC has classified antibiotic resistance as the biggest health challenge of our era; every year 2 million lives are impacted and even lost due to resistant bacteria. Bacteriophages provide an alternative route to fighting infections that does not further the development of antibiotic resistance among bacterial species. A bacteriophage replicates inside a bacterial cell and then causes that cell to lyse, an event that kills the bacterial host. However, some phage can integrate their genomes into the host chromosome without causing lysis. The HHMI SEA-PHAGES program has generated a collection of bacteriophage that infect Actinobacteria species. Over 13,000 phages …

Evaluation Of Microbiome On Chicken Necrotic Enteritis And Growth Performance, Mussie Abraha

Graduate Theses and Dissertations

Necrotic enteritis (NE) has re-emerged following restriction of antimicrobial usage and costs $6 billion every year worldwide. The primary objective of the studies was to evaluate prevention and treatment of NE using a microbiota metabolic product, secondary bile acid deoxycholic acid (DCA), in drinking water. Day-old birds were tagged and placed in floor pens. In experiments 1 and 2, the birds were infected with Eimeria maxima (Em) at d 18 and C. perfringens at d 23 and 24 and the birds were euthanized at d 26. In experiment 3, birds were infected with Eimeria at d 20 and C. perfringens …

Characterization Of The Broad-Spectrum Inhibitory Capability Of Alcaligenes Faecalis And A. Viscolactis Against Potential Pathogenic Microorganisms, Andrew Fuqua

Undergraduate Honors Theses

The recent rise of multidrug resistant microorganisms has grown from an isolated concern to a massive public health crisis. It has become imperative that scientists look for new ways to combat this issue. Due to the selective pressures of competition, bacteria and other microbes possess a host of defenses and weapons designed to exploit vulnerabilities in other microorganisms. Consequently, the study of these systems and microbial interactions has much to reveal in the search for novel antimicrobial treatments. Previous research from our laboratory has discovered that both Alcaligenes faecalis and Alcaligenes viscolactis, two rarely studied and generally non-virulent bacteria, …

Development Of In Vitro Models To Study The Rapid Extraintestinal Dissemination Of Salmonella., Adarsh Gopinath

Electronic Theses and Dissertations

Salmonella appears in the bloodstream of mice in as little as 15 minutes after oral inoculation and establishes persistent colonies in the spleen and liver. While its pathway to blood is undetermined, this phenomenon is dependent on the activity of Salmonella pathogenicity island 2 (SPI-2) coded type III secretion system (T3SS) and CD18+ phagocytes. We hypothesize that dendritic cells associated with the basal face of the gut epithelium, that are naturally migratory and known to sample for luminal antigens directly transport Salmonella to the bloodstream. This process comprises of at least two phases, dissociation and reverse transmigration. We define dissociation …