Microbiology Commons^™

Antibiotic-Induced Changes In Efflux Transporter Expression: A Key Factor In Pseudomonas Aeruginosa Biofilm Resistance, Zara Imtiaz, Avinash Chatoo, Will Wang, Weiqi Li, Paramita Basu

Touro College of Pharmacy (New York) Publications and Research

Listed by WHO as an antibiotic-resistant priority pathogen, Pseudomonas aeruginosa(P.A.) is a serious threat in nosocomial infections. Its high antibiotic resistance is attributed to major mechanisms that can be categorized into intrinsic, acquired, and adaptive resistance. This study tests the ability of three commonly used antibiotics to inhibit new biofilm formation and eradicate mature biofilm growth, as well as investigate changes in the expression levels of selected genes coding for multidrug efflux pumps in P.A. planktonic cells and biofilms before and after treatment with antibiotics to provide a conceptual estimate of the activity of the efflux transporters that work to …

Delivering Crispr To The Hiv-1 Reservoirs, Theodore Gurrola, Samuel Effah, Ilker Sariyer, Will Dampier, Michael Nonnemacher, Brian Wigdahl

Kimmel Cancer Center Faculty Papers

Human immunodeficiency virus type 1 (HIV-1) infection is well known as one of the most complex and difficult viral infections to cure. The difficulty in developing curative strategies arises in large part from the development of latent viral reservoirs (LVRs) within anatomical and cellular compartments of a host. The clustered regularly interspaced short palindromic repeats/ CRISPR-associated protein 9 (CRISPR/Cas9) system shows remarkable potential for the inactivation and/or elimination of integrated proviral DNA within host cells, however, delivery of the CRISPR/Cas9 system to infected cells is still a challenge. In this review, the main factors impacting delivery, the challenges for delivery …

Biogeographic Patterns In Phyllosphere Bacterial Communities On Southern Magnolia Trees In A Small Town, Elizabeth M. Eckard, Venkat K. Kota, Kurre T. Luber

Honors Theses

The phyllosphere, consisting of aerial plant surfaces colonized by microorganisms, remains a relatively understudied ecosystem in terms of bacterial biogeography, particularly at intermediate spatial scales. This study characterized the bacterial community on the leaves of 89 Magnolia grandiflora trees throughout a small town, encompassing an area of approximately 60 km². Sequencing of the 16S ribosomal RNA gene revealed the dominant bacterial phyla to be Alphaproteobacteria, Bacteroidetes, and Acidobacteria, consistent with other studies of the phyllosphere. Unlike other studies over smaller spatial scales, there was no significant relationship between phyllosphere community similarity and distance between trees (i.e., trees further …

Characterization Of A Novel Metalloid Reductase Outer Membrane Porin Rara From Sulfurospirillum Barnesii Ses-3, Narthana Jeganathar Kanmanii

Electronic Theses and Dissertations

Sulfurospirillum barnesii SES-3 is a gram-negative epsilon proteobacterium that grows anaerobically by coupling the oxidation of lactate to the reduction of arsenate. Previous work on metal and metalloid metabolism in S. barnesii had identified a redox active protein, designated RarA that when provided an artificial electron donor (i.e., reduced methyl viologen, FMN, or NADH), could reduce a variety of substrates, including arsenate, selenate, selenite, nitrite, and even phosphate. The enzyme’s inferred amino acid sequence showed weak similarity (30%) to outer membrane porins with homologs found in only certain species of Sulfurospirillum. Further, the enzyme did not contain cysteine residues …

Greening The Edge: Investigating Riparian Buffer Restorations In A Pastoral Setting And Their Effects On Soil Carbon And Microbial Community Composition., Seth Mccullough

Masters Theses, 2020-current

Riparian buffer restoration represents a critical strategy for enhancing ecosystem health and resilience in agricultural landscapes. This study investigates the effects of riparian buffer restoration on soil properties, microbial communities, and carbon dynamics in Rockingham County, VA. Through a comprehensive field study, we assessed the physicochemical properties of soil, microbial biomass, community composition, and soil carbon storage in restored and unrestored riparian buffers. Our findings reveal significant improvements in soil physical properties in restored buffers, including increased soil moisture (p < 0.05) and decreased bulk density (p < 0.01), indicating enhanced soil structure and water retention capacity. While no significant differences were detected in soil pH or cation exchange capacity, restored buffers exhibited higher soil carbon stocks (p < 0.05) and carbon-to-nitrogen ratios, suggesting potential differences in nutrient cycling processes and organic matter decomposition rates. Moreover, restored buffers showed increased microbial biomass (p < 0.01), potentially driven by improved habitat conditions and shifts towards a fungal-dominated microbial community.

Although no significant differences were found in overall microbial community composition between restored and unrestored sites, specific shifts in bacterial …

The Influence Of A Ubiquitous Filter Feeder On Coastal Microbial Communities., Melissa Steinman, Moritz S. Schmid, Robert K. Cowen, Su Sponaugle, Kelly R. Sutherland, Anne W. Thompson

Student Research Symposium

Doliolids have a unique ability to impact the marine microbial community through bloom events and high filtration rates. Their predation on large eukaryotic microorganisms is established and evidence of predation on smaller prokaryotic microorganisms is beginning to emerge. We studied the retention of both eukaryotic and prokaryotic microbial taxa by wild-caught doliolids in the northern California Current system. We use qPCR to quantify the impact of doliolids on three important and globally abundant taxa: Synechococcus, SAR11 and diatoms. Doliolids were collected during bloom events identified at three different shelf locations with variable upwelling intensities. We discovered that in addition …

Role Of Integrase-Pp2a Interaction In Human T-Cell Leukemia Virus Type-1 Replication And Pathogenesis, Shayna Turbin

Senior Honors Papers / Undergraduate Theses

Human T-cell leukemia virus type-1 (HTLV-1) is an oncogenic retrovirus that causes multiple disorders, including adult T-cell leukemia and HTLV-1-associated myelopathy/tropical spastic paraparesis. HTLV-1 retroviral integrase binds to the regulatory B’56γ subunit of the host cell Protein Phosphatase 2A (PP2A). Integrase contains a highly conserved LxxIxE motif that is essential for binding, which increases integration efficiency and facilitates HTLV-1 hijack of host cell machinery. We aim to understand how mutations introduced in the highly conserved binding site can affect viral particle production and infectivity. We transfected 729B human lymphoblastoid cells and 293T cells with mutant and wildtype virus. Mutations L213A, …

Lmpact Of Salmonella Enterica Effector Proteins On Plant Physiology And Immunity, Sara Qader

Honors Theses

Salmonella enterica serovar Typhimurium are primarily recognized as pathogens associated with foodborne illnesses in humans. Salmonella also can colonize plant tissue effectively. The pathogen relies on type III secretion systems (T3SS) to infect mammals and plants successfully and counteract the immune response. Understanding the molecular mechanisms underlying Salmonella’s interactions with plants is essential for developing effective strategies to reduce its impact on human health and agriculture. Effector proteins, known for their role in modulating host-pathogen interactions, have been implicated in the virulence and pathogenicity of Salmonella. However, their specific functions and contributions to Salmonella’s interactions with plants remain largely unknown. …

Impact Of Salmonella Enterica On Plant Physiology And Immunity, Sara Qader

Poster Presentations

Salmonella can colonize plant tissue effectively. Understanding the molecular mechanisms underlying Salmonella’s interactions with plants is essential for developing effective strategies to reduce its impact on human health and agriculture. Effector proteins, known for their role in modulating host-pathogen interactions, have been implicated in the virulence and pathogenicity of Salmonella. However, their specific functions and contributions to Salmonella’s interactions with plants remain largely unknown. Here, we aim to investigate the functions of Salmonella effector proteins during the colonization of plants.

The Physiological Significance Of Nitric Oxide Synthase In Staphylococci, Ryan M. Singh

Theses & Dissertations

Staphylococci, particularly Staphylococcus epidermidis, are common causes of implant-associated infections that may result in notable morbidity and mortality. One of the ways the innate immune system attempts to combat these invading pathogens is via the respiratory burst, in which free radical species such as nitric oxide (NO^•), toxic to bacterial respiration, are released in large quantities. Despite the toxicity of NO^•, some bacteria, including staphylococci, encode an endogenous bacterial nitric oxide synthase (bNOS), whose physiological role has been unclear until now. In this dissertation, we demonstrate that S. epidermidis is able to overcome the toxicity …

Understanding The Non-Canonical Regulation Of Srebp In Aspergillus Fumigatus, Muhammad Abubakar Khan

Dartmouth College Ph.D Dissertations

Aspergillus fumigatus is an opportunistic fungal pathogen causing invasive pulmonary aspergillosis (IPA), with high mortality rates in immunocompromised individuals. Adaptation to the hypoxic microenvironment of IPA is crucial for fungal virulence. The transcription factor SrbA, a Sterol Regulatory Element-Binding Protein (SREBP) homolog, plays a key role in this hypoxic response and regulates genes involved in hypoxic growth, sterol biosynthesis, and azole resistance, making it an attractive therapeutic target.

However, SrbA activation in A. fumigatus lacks critical components of the canonical SREBP pathway, such as SCAP, Site-1 protease (S1P), and Site-2 protease (S2P). Instead, the rhomboid protease RbdB, signal peptide peptidase …

Fiddler Crab Gut Microbiomes As An Indicator For Eutrophication Due To Waste-Water Contamination In Estuaries, Madison L. Geraci

Honors Theses

Estuaries are unique biogeochemical zones in coastal systems that provide a myriad of ecological functions: providing habitat for critically important fishery species, diverse species of plants and animals, and contributing to nutrient cycling. Estuaries are vulnerable to anthropogenic stressors as they are intersections between marine and terrestrial communities and are often the hotspot of coastal development and activity. Estuarine sediments act as repositories for anthropogenic contaminants, including excess nutrient runoffs and waste-water pollution that can cause states of eutrophication. Microorganisms are sensitive to these environmental changes, presenting a unique opportunity of being useful bioindicators of environmental stress. Isolating microorganisms from …

Efficacy Of Mcl-1 Inhibitors In Multiple Myeloma Cells Resistant To Bortezomib, Emily Nelson, Omar S. Al-Odat, Sabrina M. Paparo, Daniel A. Guirguis, Gabriella Yao, Manoj Pandey, Subash Jonnalagadda, Tulin Budak-Alpdogan

Rowan-Virtua Research Day

Multiple myeloma (MM) is a type of cancer that affects plasma B cells. Patients with MM often experience frequent relapses and can develop resistance to drugs. As a medical researcher, it is important to understand the role of Mcl-1 in preventing intrinsic apoptosis and drug resistance. Mcl-1 belongs to the anti-apoptotic subgroup of Bcl-2 family proteins and plays a crucial role in these processes. Mcl-1 plays a crucial role in driving disease progression and contributing to drug resistance in MM. It has been observed that there is an increased expression of Mcl-1 in 52% of patients with MM during diagnosis, …

From Cells To Clinics- The Role Of College Biology Education In Shaping Future Physician Assistants, Monica Manley

Honors Theses

This thesis provides a personal reflection on translating concepts and techniques learned in multiple biology courses (i.e. microbiology, neuroscience, comparative physiology, and genetics) in to clinical practice as an intern in the emergency room of a hospital. Each selected concept contains a description followed by an example of how this knowledge relates to a specified duty of a physician assistant with in an emergency medical setting.

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 …

Implicating North American Lizards In The Borrelia Burgdorferi Sensu Stricto Sylvatic Cycle, Tristan Anthony Nowak

Legacy Theses & Dissertations (2009 - 2024)

Borrelia burgdorferi sensu lato (B. burgdorferi s.l.) spirochetes are the causative agents of Lyme disease (LD, Lyme borreliosis), the leading cause of tick-borne illness in North America (NA), Europe, and throughout temperate zones of the Holarctic region. Ixodes ticks are the only competent genus that permit acquisition, maintenance, and successful transmission of LD bacteria to subsequent hosts. LD spirochetes are unable to effectively pass through transovarial barriers, from adults to eggs, and therefore, next generation larvae are Lyme borreliae-free. Instead, B. burgdorferi s.l. are reliant on maintenance in both vertebrate and arthropod hosts to perpetuate high prevalence in nature. Of …

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 …

Archaeal Diversity In The Anna's Hummingbird Microbiome, Lauren E. Chance

Honors Scholar Theses

The microbial communities that are present in and on vertebrates are collectively called the microbiome. The composition of a microbiome is dependent upon the host, the environment, and evolution. There has been extensive research on the bacterial composition of host-associated microbiomes, however, there has been much less work on the archaeal composition of host-associated microbiomes. Archaea have previously been assumed to primarily exist in extreme environments, but this may not be true and has been influenced by their generally low abundance and methodological difficulties in detection. It is possible they are consistent members of diverse host-associated microbiomes.

Archaea-specific PCR primers …

Investigating Effects Of Co-Culturing With Vibrio Fischeri On Secondary Metabolite Production Of Hawaiian Bobtail Squid Symbionts, Mariam A. Zedan

Honors Scholar Theses

Microbes are a fruitful source of natural product drug discovery since many of their secondary metabolites show defensive activity and have unique structures. However, extracting and elucidating the structure of those compounds can be challenging in vitro due to particular environmental and nutritional requirements of some bacteria. Those requirements may include proximity to other organisms that the microbes have symbiotic relationships with. Under those conditions, the organism may activate silent biosynthetic gene clusters (BGCs) responsible for production of certain secondary metabolites not typically expressed otherwise. One method of BGC induction is co-culturing with other microbes since this mimics the natural …

Genome-Scale Metabolic Modeling Of Chitin-Degrading Microbial Systems, Aimee Kristin Kessell

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

As a major component of fungal cell walls and exoskeletons of invertebrates, chitin is widespread in soils, constituting the second most abundant biopolymer in nature. Composed of N-acetyl-D-glucosamine chains, it serves as a vital source of nutrients, including both carbon and nitrogen, for the growth of microorganisms. A solid understanding of the microbial degradation of chitin is critical for predicting their impacts on biogeochemical cycling in soil ecosystems. Organisms that degrade biopolymers (degraders) produce energetically expensive extracellular enzymes to break down complex organic carbons into simpler labile forms that are sharable with other species, including those that do not contribute …

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 …

Biosorption Of Lithium Using Microbes, Adebola Daisy Olade

Theses (2016-Present)

Lithium (Li) is a very valuable metal that is used across several industries including ceramics, glass, batteries, pharmaceuticals, and polymers. However, in recent years, the global demand for Li and its market price have increased considerably, due to its application as a critical component in the production of rechargeable Li-ion batteries and energy storage systems that are used in electric vehicles and a variety of electronic devices. Although Li occurs as a mineral in hard rocks and salt brines, substantial amounts are found in our environment as part of industrial wastes and oil-field wastewaters. Despite its importance, Li is also …

A Meta-Analysis For Laboratory Diagnostics For Coccidioidomycosis, Mary C. Cowen

Biological Sciences Undergraduate Honors Theses

Coccidioidomycosis, commonly referred to as Valley Fever, is a fungal infection found in arid regions of the southwestern United States and Mexico. Infection occurs through inhalation of airborne spores from Coccidioides species, Coccidioides immitis and/or Coccidioides posadasii, and proceeds in both pulmonary and disseminated fashions. Approximately 60% of patients with coccidioidomycosis remain asymptomatic, while 40% will experience symptoms. Within the literature, there are no papers that summarize sensitivity and specificity values between different tests; therefore, this paper presents sensitivity and specificity results across different tests and companies (Meridian, IMMY, and MiraVista).

Pipecolic Acid And Novel Insights Into Cerebral Malaria, Akua E. Mensah

Theses and Dissertations

Cerebral malaria (CM), a severe manifestation of Plasmodium infection, prompts our investigation into the nuanced role of pipecolic acid in its pathophysiology. To unravel the molecular intricacies, we conducted in vitro lysine labeling techniques of mice infected with P. berghei ANKA parasites, and human P. falciparum grown in vitro, aiming to discern the impact of Plasmodium on pipecolic acid production. Previous observations indicated an elevation in pipecolic acid levels correlating with neurological decline in children with CM. In our study, confirming elevated pipecolic acid presence in the plasma and brain tissues of CM patients and the animal model of CM, …

Characterizing The Role Of Pa5189 Of Pseudomonas Aeruginosa In Deletion And Overexpression Mutants, Seh Na Mellick

Theses/Capstones/Creative Projects

In the context of rising multidrug resistance in biofilm-forming pathogens like Pseudomonas aeruginosa, this study investigates the role of the understudied transcription factor PA5189 in antibiotic resistance and biofilm formation. PA5189 deletion and overexpression mutants were created in a parent P. aeruginosa strain using pEX18Tc-based recombinant suicide vectors, with genotypic verification of putative triparental conjugants achieved through restriction digestion and PCR. The study revealed that PA5189 overexpression significantly increases resistance to commonly used broad spectrum antibiotics such as ciprofloxacin and imipenem. Additionally, differential expression of PA5189 was found to notably affect biofilm formation, with variations contingent on the nutrient …

College Of Natural Sciences Newsletter, Spring 2024, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 1 Dean's Message
Page 2 New Faculty and New Club on Campus
Page 3 2024 URSCAD Awards
Page 4 Day of Scholars 2024
Page 5 SDSU's First Representation at the Association for Anatomy's 2024
Annual Conference
Page 6-7 2024 Honor's College Convocation
Page 8 Other Student Activities
Page 9 Faculty Awards
Page 10-11 Other News
Page 12 2024 Drone Day and American Association of Geographers Convention - Hawaii
Page 13 55th Annual Geography Convention
Page 14 2024 Stethoscope Ceremony
Page 15 Open PRAIRIE Data

The Effect Of Microbial Bile Acid Metabolism On Clostridium Perfringens Virulence, Tahrir Jatli Alenezi

Graduate Theses and Dissertations

Clostridium perfringens is a predominant intestinal pathogen affecting both humans and animals, including chickens resulting in significant economic losses. In chapter I, I have overviewed the dynamics of the intestinal immune system, the composition of the intestinal microbiome, and how the microbiome influences inflammation in the development of Clostridium infection. The intricate interplay between immunity, microbiota, and their metabolites is likely critical in the pathogenesis of C. perfringens and uncovering these interactions may unveil new avenues for prevention and treatment. The objective of this chapter is to provide updated insights into the role of host-microbe interactions and their potential therapeutic …

Associations Between Gut Microbiome Metabolomics And Endometriosis Risk, Progression, And Non-Invasive Diagnosis: A Review, Marlee Sanders

Honors Theses

Endometriosis is a gynecological condition that affects 1 in 10 women of reproductive age, is characterized by growth of endometrial tissue outside of the uterus, and encompasses metabolic, immunologic, and endocrine dysfunction. Despite its significant impact, endometriosis remains inadequately studied within the realm of women's health, emphasizing the crucial need for innovative approaches in the analysis and diagnosis of this complex condition. The cause of endometriosis is unknown however it could be influenced by genetics, environmental factors, diet, lifestyle, and notably composition of the gut microbiome. Recent scholarly interest has sparked inquiries into the correlations between endometriosis and the gut …

Determining The Antimicrobial Activity And Permeabilizing Effects Of Polyunsaturated Fatty Acids And Piscidins On Vibrio Parahaemolyticus And Vibrio Vulnificus, Christina Harris

Honors Theses

Antimicrobial peptides (AMPs) are found in all organisms and have gained attention for their effectiveness against a variety of pathogens. Piscidins are AMPs that were discovered in mast cells of vertebrates, mostly within marine animals, and are an important part of the innate immune system due to their potent antimicrobial properties. Piscidin 1 (P1) and piscidin 3 (P3) are found within sea bass and have different antimicrobial activities. P1 exhibits strong membrane disruptive properties, while P3 goes through the membrane to the targeted DNA. These piscidins can experience metalation with copper (Cu2+) which enhances their antimicrobial activity in vitro (P1-Cu2+ …