Microbiology Commons^™

What Drives Gut Microbial Diversity And Community Structure Among Closely-Related Host Species?, Rylee Jensen

All NMU Master's Theses

The gut microbiome (GMB) of mammals hosts an important community of microbes that perform countless micro-ecosystem services for the host and are influenced by numerous factors including host physiology, environment, and phylogeny. Phylogeny may have a unique effect on GMB diversity and community structure (i.e., a GMB profile) via phylosymbiosis, a theory in which the evolution of hosts matches the evolution of their associated microbiota. Elucidating phylosymbiosis in mammals is difficult because multiple intrinsic and extrinsic factors collectively drive individual GMB variation. Thus, there is a need to simultaneously analyze the role of physiology, environment, and phylogeny on shaping host …

The Implementation And Effect Of An Guided Inquiry Based Lab Within An Introductory Lab, Gwendelyn Tran

2024 Spring Honors Capstone Projects - Archive

Microbiology lab is a foundational course within microbiology, biology, and nursing students’ education at many colleges. Overall, while microbiology lab pedagogy within upper level courses has shifted from a cookbook style lab to favor more inquiry based labs, there is a lack of introductory level microbiology inquiry based labs. This study aims to both introduce an easily adaptable one week guided inquiry based lab to an introductory microbiology lab curriculum and assess the effects of this pedagogy change on the students. To analyze the impact of this shift, student attitude and success within UT Arlington’s undergraduate microbiology labs were assessed …

Characterization Of Ato Family Transporters In The Fungal Pathogen Cryptococcus Neoformans, Will Betsill

All Theses

Fungal pathogens are a significant threat to public health as they are becoming increasingly common and more resistant to treatment. Cryptococcus neoformans contributes greatly to this threat annually by causing an estimated 278,000 cases of cryptococcal meningitis resulting in approximately 181,000 deaths globally according to the CDC. C. neoformans is ubiquitous across most of the globe and can be found in such places as in trees or soil. Exposure to this fungus is especially dangerous to individuals who are immunocompromised or immunosuppressed. In these cases, inhalation of spores can lead to infection in the lungs. Once in the lungs, C. …

Analysis Of Antibiotic Sensitivity Patterns In Pasteurellaceae Family Isolates: A Microbial And Molecular Investigation, Jillian Barron

Honors Scholar Theses

Bacteria in the Pasteurellaceae family are known to cause disease in both human and animal species. Like all species of bacteria, the pathogens in the Pasteurellaceae family evolve and acquire antimicrobial-resistant traits. Antimicrobial resistance of bacteria is a significant public health concern, as treatment of resistant pathogens becomes more difficult, if not impossible, with current medical capabilities. In this project, phenotypic and genotypic analyses were performed on Pasteurellaceae family isolates sourced from the Connecticut Veterinary Medical Diagnostic Laboratory. Phenotypic antibiotic sensitivity patterns of each isolate were assessed against a panel of antibiotics through a Kirby-Bauer disk diffusion test. Disk diffusion …

Determining The Impacts Of Corn Silage Mixing Ratios On Hydrogen Production From Beef Cattle Manure, Katya Faber-Quimby

Honors Program: Senior Projects (Public)

With global warming becoming an increasingly serious threat and a growing population requiring additional energy resources, interest in the production of clean energy from the agricultural sector has surged in popularity. Biohydrogen, also known as green hydrogen, is H₂ that has been produced using renewable energy, such as from agricultural byproducts or waste materials. It presents a promising alternative to nonrenewable resources due to its high potential for energy storage and lack of carbon emissions when used. Cattle manure has been explored as a resource for the production of biohydrogen. Selecting for hydrogen-producing microbes in the manure serves the …

Life Line Spring 2024, Otterbein Biology And Earth Science Department

Life Line - The Biology Department Newsletter

In this Issue:

The Department Welcomes Dr. Grooms; Otterbein's New Pollinator/Rain Garden; Alumni Return to Share Research; Svitana Serves on Ohio EPA VAP Rules Review Advisory Committee; Field Geology Students Explore Death Valley and the Grand Canyon; Students Volunteer at Remote Area Medical Clinic; The Mussels of the Stillwater River and Greenville Creek; More Than "Just" a Chickadee; An Enriching Time at the Zoo; Human Reaction Times; Using Computer Models to Inform Real World Control Methods in Street Dogs; Svitana Continues Work with NGWA; DIY Microbial Fuel Cell Challenge; Birds of a Feather...; Students Research Impact of Sunscreens on Corals; …

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 …

Novel Microbiological Medium Developed For The Isolation Of Bacteria Associated With Estuarine Anemones, Parker K. Lund, Catalina Cuellar-Gempeler

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

Out of the nearly one trillion species of microbiota estimated to inhabit Earth only ten thousand have been cultured in the laboratory. Culturing continues to play a vital role in determining the physiology and ecologic function of individual bacteria in microbial communities and for microbes associated with host organisms one of the major challenges is developing microbiological media that mimics the bacteria’s natural environment enough to promote growth. Here, we target bacteria associated with the estuary anemones Diadumene lineata and Metridium senile by developing a novel medium that uses anemone tissue as the sole source of nutrients. We further measured …

Using Single Cell Genomics To Explore The Impact Of Marine Viruses On Microbial Respiration., Paxton Tomko

MCB Articles

Viral metabolic reprograming of marine prokaryotes, through the use of virally encoded auxiliary metabolic genes (AMGs), plays a critical role in marine ecosystem function by influencing biochemical cycles and genetic diversity in these environments. Despite the fundamental role viruses play in global environmental ecosystems, they remain an understudied aspect of microbial ecology and evolution, in part due to the methods available for studying virus host interactions in natural systems. Thus far, metagenomic analyses have been used to study the interactions of virus host pairs, but these types of analyses have their limitations in accurately linking viruses to hosts, or culture-based …

Characterization Of Serx: A Putative Periplasmic Binding Protein In A Selenate Respiring Bacteria, Henry Jacques, Susan E. Childers

Honors Theses

A selenate respiring bacterium, Dechloromonas sp. A34, was isolated from a seleniferous mining site in southeastern Idaho. A34 was of interest due to its ability to respire up to 20 mM selenate, the highest concentration tested. The strain has been proposed to represent a new species of bacteria within the Dechloromonas genera, with the prospective name Dechloromonas selenatirespirans (manuscript in preparation). Our research presents characterization of a putative periplasmic binding protein found within an operon that contains genes encoding a putative selenate reductase. The gene, named serX (selenate reductase gene X), is 855 base pairs and encodes a putative …

Bloom: A Microbial Self-Portrait, Emily Lauren Mulvaney

Graduate Student Theses, Dissertations, & Professional Papers

No abstract provided.

Role Of Interleukin 2 Receptor Alpha In The Cellular Response To Dna Damage, Shristi Khanal

Browse all Theses and Dissertations

The interleukin 2 receptor alpha (IL-2Rα), which is integral to the functioning of the cytokine interleukin 2, has recently been found to be present in different cell types besides just lymphocytes. Previous studies done by our laboratory showed that several other non-lymphoid cells including smooth muscle cells express IL-2Rα. Vascular smooth muscle cell (VSMC) deficient in IL-2Rα exhibited increased proliferation, decreased size, and hypodiploid DNA content when compared to wild type (WT) cells. Previous studies also suggested that VSMC proliferate in response to IL-2 and that IL-2 increases following interventions to stimulate intimal hyperplasia in vivo. These findings, in total, …

Studies Of Selective And Reversible Inhibitors Of Calcium Entry In Immune Cells, Naga Lakshmi Gandi

Browse all Theses and Dissertations

Calcium signaling is a crucial regulator in many cellular processes, from immune response modulation to gene expression and apoptosis. Here, I have investigated the dynamics of calcium entry pathways, namely, store-operated calcium entry and store-independent calcium entry using a variety of cell types such as Jurkat T cells, HEK-293 cells and murine macrophages. Using fluorescence calcium imaging and selective inhibitor compounds, I have investigated the contributions of Orai and related calcium channels to calcium entry in both immune and non-immune cell types. The results demonstrate the pharmacological modulation of store-operated and store-independent calcium entry, showing the ability of compounds such …

Ribosome Hibernation Factor Induces Antibiotic Persisters Of Mycobacterium Tuberculosis In Neutrophil-Rich Lung Lesions, Jamie Corro

Electronic Theses & Dissertations (2024 - present)

Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, is a prescient global health threat and the leading cause of death by an infectious agent. Treatment of Mtb infection involves administering 2-4 antibiotics for a minimum of 6 months. This extended drug regimen is required to target a subpopulation of persistent bacilli. As their name implies, these bacteria can “persist” by acquiring nonhereditary and transient antibiotic tolerance. Although the precise mechanism is unknown, it’s often attributed to slowing cellular growth and metabolic processes. During zinc deprivation, bacteria can remodel their ribosomes by replacing their zinc-binding paralogues containing the CXXC motif (C+) …

Genetic Engineering Of Escherichia Coli For The Production Of Riboflavin, Adeyemi Adesanwo

Graduate Research Theses & Dissertations

Riboflavin, a water-soluble vitamin B2, is essential for the growth and reproduction of living organisms. However, humans and animals lack a riboflavin synthesis pathway and must rely on diets derived from plants and microbes for this essential vitamin. To meet our needs for vitamin B2, industrial riboflavin production is currently being pursued using strains of Bacillus subtilis. The fermentation process is successful, but improvements are needed for better substrate-to-product conversion yield. To this end, it is imperative to develop alternative microbial strains for cost-effective riboflavin production.

Due to its simple growth requirement, well-understood genetic background, and widely available genetic tools, …

Exploring Representation In Microbiology Introductory Courses Can Encourage A More Inclusive And Inspiring Environment For Students And Instructors, Jill A. Mikucki, Elizabeth Fozo

Feminist Pedagogy

Microbiology has a relatively brief history where significant discoveries are often linked with major events in human history - from disease outbreak to industrialization to climate change. The founders of key microbiological principles span across continents, genders, ethnicities, and socioeconomic status. However, the portrait described in many introductory textbooks center around a lone, typically white male scientist. Such narratives not only are misleading regarding the development of key principles in microbiology but can also reinforce inappropriate stereotypes as to whom belongs in microbiology. In our introductory microbiology course, we designed group work for Zoom break-out rooms to help engage students …

Allergic Bronchopulmonary Aspergillosis: Radiological And Microbiological Profile Of Patients Presented In An Outpatient Pulmonary Clinic In A Developing Country, Nousheen Iqbal, Muhammad Irfan, Mustafa Bin Ali Zubairi, Maaha Ayub, Safia Awan, Kauser Jabeen, Ali Bin Sarwar Zubairi

Section of Pulmonary & Critical Care

There is limited data available about allergic bronchopulmonary aspergillosis (ABPA) in Pakistan. The aim of the study was to describe the radiological and microbiological profile of ABPA patients presenting to the outpatient pulmonary clinic of a tertiary care hospital in Karachi, Pakistan. A retrospective study was conducted on ABPA patients who presented to the pulmonary outpatient clinic at Aga Khan University Hospital, Karachi, Pakistan, from January 2017 to December 2019. Data was collected on microbiology and radiology features on predesigned proforma. A total of 7759 asthmatic patients presented at the outpatient pulmonology clinic during the study period. Of the 245 …

Investigating The Ability Of Saltwater Isolates To Inhibit Biofilm Formation By Clinically Significant Pathogens, Monica Murphy

ORBioM (Open Research BioSciences Meeting)

Background

Nosocomial pathogens are responsible for chronic and persistent infections partly due to their ability to form protective biofilms which enhance their antibiotic tolerance. Biofilm disruption combats antimicrobial resistance as dispersed cells regain antibiotic susceptibility. The goal of this study was to evaluate the antibiofilm potential of isolates from marine environments against a pathogen panel consisting of MRSA and clinical Staphylococcus aureus strains, Acinetobacter baumannii and Escherichia coli pathogens.

Method

A large bank of saltwater bacterial isolates was cultured in glucose-supplemented trypticase soy broth (TSBg) and resulting colonies were screened against the pathogen panel. Isolates of interest were further examined …

Examining The Absorbance Maximum, Protein Concentration And Antimicrobial Activity Of Seaweed Extracts, Claudia Kenneally

ORBioM (Open Research BioSciences Meeting)

Background

The emergence of antimicrobial resistance (AMR) has highlighted the need for novel antimicrobials. Antimicrobial compounds can be isolated from various marine sources, including seaweed, which contain pigments and proteins. This study focuses on screening seaweeds for potential antimicrobial compounds.

Methods

Four seaweed types (A, B, C, D) were collected from beaches in Cork, Ireland, and extracts of each were prepared using both methanol (-M) and water (-H₂O). The absorbance maximum (λ_max)of seaweed extracts was determined from 220 – 800 nm to investigate potential pigment interference at 600 nm. The bicinchoninic acid (BCA) assay was preformed …

Dynamics And Inhibition Of Abc And Rnd Transporters Associated With Multidrug Resistances In Cancer And Pathogenic Bacteria, Hang Zhao

Biological Sciences Theses and Dissertations

The overexpression of efflux transporters is deemed to be one of the important mechanisms that contribute to Multidrug Resistance (MDR). In this dissertation, three transporters of significance were studied, the Breast Cancer Resistance Protein (BCRP/ABCG2) in a variety of cancer cells, the mtrCDE transporter from Neisseria gonorrhoeae, and the acrAB-tolC transporter from Escherichia coli. It is well known that the overexpression of BCRP in cancer cells results in these cells being resistant to the effects of many chemotherapeutics. This results in multidrug resistance for this cancer because of the fact that BCRP can transport many different types of …

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 …

Biofilms And Their Role On Diseases, Vijay Singh Gondil, Bindu Subhadra

Faculty Publications - Biological Sciences

Biofilms are complex, three-dimensional structures that provide a long-established survival mechanism for microorganisms. Biofilms play a substantial role in pathogenesis as they can evade the immune response and be highly resistant to conventional antimicrobials, thus impacting the human health and healthcare system. To address this issue, BMC Microbiology invites submissions to the collection ‘Biofilms and its impact on disease’.

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 …

Antimicrobial Resistance In Eskape Pathogens And Its Effect On Modern Medicine And Treatment, Cameran Runge

Honors Program: Senior Projects (Public)

Abstract

ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella

pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter

spp.) are seeing a growing resistance to multiple classes of antibiotics. Misuse and overuse of antibiotics have played directly into the resistance observed, and the problem is growing exponentially. Antibiotic resistance is partially due to several intrinsic factors limiting the drug's uptake. These include efflux pumps, increased biofilm production, and reduced cell wall permeability in the resistant bacteria. ESKAPE pathogens also acquire resistance through horizontal gene transfer and plasmids. As antibiotics have become less effective, the bacteria can continue to thrive, leading to a detrimental …

Investigating The Impact Of Edaphobacter Aggregans (Wbg-1) On Arabidopsis Thaliana Development, Julia Talbert

Undergraduate Research Symposium

Acidobacteria is a phylum of bacteria that make up 50% of soil microbes. While making up a large proportion of bacteria found in soil, this phylum is largely unexplored with limited information about the bacteria and their impact on plant growth. The selected target of this study is Edaphobacter aggregans, WBG-1, which is a part of a subdivision of acidobacteria. Examining the bacteria’s effects on the development of the model plant Arabidopsis thaliana will provide insight into understanding this unknown phylum of soil-dwelling bacteria. Acidobacteria are an important realm to investigate as they affect agriculture practices. With Missouri being such …

Life Line Spring 2023, Otterbein Biology And Earth Science Department

Life Line - The Biology Department Newsletter

In this Issue:

Feathered Friends Living on Campus; The Hidden Mussels of the Olentangy River; Early Assurance Program Students Graduate from HCOM; Students Present at American Society for Microbiology Microbe 2022 Meeting; Environmental Science Upgrades Its Remote Monitoring Capabilities; Speed!; UK Students Visit Local Attractions; That's a Lottl Axolotls.

Protocol To Identify The Core Gene Supported By An Essential Gene In E. Coli Bacteria Using A Genome-Wide Suppressor Screen, Isao Masuda, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

We describe here a genome-wide screening approach to identify the most critical core reaction among a network of many that are supported by an essential gene to establish cell viability. We describe steps for maintenance plasmid construction, knockout cell construction, and phenotype validation. We then detail isolation of suppressors, whole-genome sequencing analysis, and reconstruction of CRISPR mutants. We focus on E. coli trmD, which encodes an essential methyl transferase that synthesizes m1G37 on the 3'-side of the tRNA anticodon. For complete details on the use and execution of this protocol, please refer to Masuda et al. (2022).

A Novel Therapeutic Approach To Regulate Carex8 Protein Expression Through E6-Conjugated Cell Penetrating Peptides, Jared D. Compaleo

Browse all Theses and Dissertations

Adenovirus is a human pathogen that causes cold like symptoms in healthy individuals, which could be lethal in pediatrics and the immunocompromised. In polarized epithelia, adenovirus uses the eight-exon isoform of the Coxsackievirus and Adenovirus Receptor (CAREx8) on the apical surface, to facilitate infection. CAREx8 protein expression level is regulated by the scaffolding protein MAGI-1, using two of its PSD95/Dlg-1/ZO-1 (PDZ) domains: PDZ2 and PDZ4. We previously showed that CAREx8 is degraded after interaction with PDZ4 and rescued following interaction with PDZ2. We then developed a PDZ2 binding decoy molecule (E6) that blocks the interaction between CAREx8 and PDZ2, which …

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 …

Environmental Toxicants And Human B Cells: Insights From Crispr Editing And Genomic Sequencing, Clayton Allex-Buckner

Browse all Theses and Dissertations

The human immunoglobulin heavy chain gene locus (IGH) has two 3 prime regulatory regions (3’IGHRR), each containing three enhancers (hs3, hs1.2, hs4). In animal models, the 3’IghRR regulates IgH expression and class switch recombination (CSR) to different Ig isotypes. The 3’IGHRR hs1.2 enhancer in humans is polymorphic in that an invariant sequence (IS) can be repeated one to four times in tandem. The hs1.2 polymorphism is of interest due to its association with several human autoimmune disorders and its potential sensitivity to exogenous substances such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD or dioxin). In mouse models, TCDD inhibits the hs1.2 enhancer and 3’IghRR …