Microbiology Commons^™

Optimizing Crispri Gene Silencing Of Putative Drug Targets In Mycobacterium Abscessus, Max Ivanov

Honors Undergraduate Theses

Among nontuberculous mycobacteria (NTM), Mycobacterium abscessus (Mab) poses a particular threat to patients with cystic fibrosis and chronic obstructive pulmonary disease due to the lung damage and higher mortality rate it causes. Current treatments involve prolonged multi-antibiotic regimens that are often ineffective, highlighting the need for new drug targets.

The CRISPR Interference (CRISPRi) system uses a deactivated Cas9 protein (dCas9) to enable inducible gene silencing, offering a potential approach to identifying new targets. Genes that lead to a loss of Mab viability when silenced are considered essential, an important attribute of potential drug targets. While CRISPRi has shown …

Development Of A Proposed Selective Medium For The Isolation And Differentiation Of P. Sordellii, Dimyana Bottros

Honors Undergraduate Theses

Clostridium, a genus of anaerobic, spore-forming bacteria, includes clinically and ecologically significant species like Clostridium difficile and Paeniclostridium sordellii. C. difficile causes antibiotic-associated colitis, while P. sordellii is linked to fatal infections and spontaneous abortions. Recent studies found both species in marine sediments, suggesting their role in environmental and wildlife health disturbances, including the 2013 mass mortality of over 300 manatees in the Indian River Lagoon. However, isolating and differentiating P. sordellii is challenging due to the lack of selective media optimized for its growth. This thesis proposes a novel selective medium tailored to P. sordellii’s physiological …

Investigation Of Hydrogen Gas Production And Motility In Δselab And Δfdhf Mutants Of Clostridioides Difficile, Ria D. Gupta

Honors Undergraduate Theses

Clostridioides difficile is a Gram-positive, spore-forming, anaerobic bacterium and the leading cause of antibiotic-associated diarrhea worldwide. During infection, antibiotic-induced disruption of the gut microbiota allows C. difficile to colonize and proliferate. Motility, enabled by flagella, is an important factor in colonization and may be influenced by metabolic activity. Recent experiments have observed gas production during C. difficile motility assays, but the biochemical basis of this phenomenon remains unknown. Because gas formation in other bacteria such as E. coli involves the formate hydrogenlyase complex and the enzyme formate dehydrogenase (FDH), we hypothesize that C. difficile gas production under motility conditions is …

Role Of Coronavirus Envelope Protein On Infectivity, Garrett E. Zaagman

Dissertations

Coronaviruses infect a wide range of hosts and have caused recent human pandemics. While much has been learned, gaps remain in understanding viral assembly and egress, particularly the role of the envelope (E) protein in specific infectivity. To study this, recombinant MHV viruses were created with E gene deletions and HiBiT-tagged spike (S) proteins to monitor virion release. In mouse cells, MHV∆E S-HiBiT secreted less spike and fewer infectious particles, indicating reduced specific infectivity. Comparisons between human HeLa-CEACAM and mouse DBT cells showed species-specific support for virus production. TMED10, a host membrane protein, was tested as a potential E-interacting partner …

Cultures For Acid-Fast Bacilli: Are We Being Good Stewards?, Jennifer Hanrahan, Julie D. Sill, Patricia Ver Schneider, Jessica F. Copeland, Elsie Frimpongmaa Amoako-Kissi, Ogochukwu O. Ilobi, Angela J. Toepp

Department of Medicine Faculty Publications

Objective: To describe the use of cultures for acid-fast bacilli (AFB) and situations in which AFB cultures are unlikely to be of clinical benefit.

Design: Retrospective descriptive study of AFB cultures submitted to Sentara Health microbiology laboratory from December 1, 2021, to December 1, 2023. Data were collected from the electronic medical record and included patient demographics, the service line that ordered the culture, specimen source, and culture results.

Setting: Sentara Healthcare System.

Patients: All patients who had specimens submitted to the microbiology laboratory during the study period were included.

Results: A total of 13,944 AFB cultures from 8,243 …

Investigation Of Multiple Factors Influencing The Vector-Borne Transmission Of Salmonella Typhimurium Via Blattella Germanica, Landen Sean Van Hulzen

Dissertations and Theses

The German cockroach (Blattella germanica) is a common urban pest that lives ubiquitously in human structures around the world. German cockroaches are a severe public health threat as they are known carriers and vectors of human pathogens including Salmonella enterica, Escherichia coli, Shigella spp, and more. German cockroach infestations have been associated with Salmonellosis outbreaks. While mechanical transmission by the German cockroach vector is well known, new research suggests that more nuanced biological transmission has a role in maintaining and transmitting Salmonella enterica serovar Typhimurium (S. Typhimurium). Despite this recent finding, many biological variables influencing vector-borne transmission of S. Typhimurium …

Oral Microbiome And Inflammatory Bowel Disease: New Understanding And Call To Action, Michael Saadeh, Sydney Donohue, Shaina Ailawadi, Gordon Hong, David A. Johnson

Department of Medicine Faculty Publications

The oral microbiome is the second largest microbial community in the human body after the gut microbiome. It includes an array of fungi, bacteria, amoebae, flagellates, archaea, and viruses, all of which are potential pathogens. This microbiome can act as a facilitator not only for protection but also for aggravation when dysbiosis occurs. Although conventional thought is this is primarily in terms of oral health issues, such as dental caries and gingival disease. The systemic effects of the oral microbiome however, are relevant to both gastrointestinal (GI) disease and non-GI disease. These systemic risks occur for several reasons, including upregulation …

Characterization Of Adaptive Quorum Sensing In Pseudomonas Aeruginosa, Kayla Simanek

Electronic Theses & Dissertations (2024 - present)

Pseudomonas aeruginosa is an opportunistic pathogen that is highly antibiotic resistant and causes tens of thousands of infections each year. It persists in hospitals by forming biofilms on medical equipment like ventilators and catheters, making it difficult to eradicate. Biofilm formation, among other virulence factors of P. aeruginosa, is regulated through quorum sensing, a mechanism of bacterial communication. Quorum sensing is primarily coordinated through LuxI-R type systems comprised of an autoinducer synthase and receptor, respectively. Canonically, the first system to be expressed is LasI-R, and LasR upregulates the second arm of the quorum sensing network, the RhlI-R system. Research …

Exploring The Role Of Host Immune Responses And Bacterial Sensory Pathways In The Development Of Treponema Denticola-Mediated Periodontal Disease, Annie N. Hinson

Theses and Dissertations

Periodontitis is a chronic inflammatory disease driven by dysbiotic microbial communities and maladaptive host responses. Treponema denticola, a spirochete pathobiont, is strongly associated with disease severity. However, the molecular mechanisms underlying its interaction with host tissues and regulation of virulence remain incompletely understood. This work examines both the epithelial immune responses and bacterial transduction systems that shape T. denticola pathogenesis. Transcriptomic analysis of gingival keratinocytes revealed IL-36γ as the most highly induced cytokine following infection with T. denticola. Functional studies demonstrated that IL-36γ induction occurs in a dose- and time-dependent manner through TLR2/6 signaling, requiring the NF-κB, PI3K/Akt, and …

Molecular Mechanisms Of Kynurenine-Mediated Lifespan Regulation In Yeast, Ryan E. Counterman Jobb

Theses and Dissertations

The kynurenine pathway is a highly conserved pathway that acts as the primary pathway for tryptophan catabolism and has been found to be involved in lifespan regulation across many diverse organisms. Caloric restriction (CR) is the only known dietary intervention to date that both increases the mean lifespan and the health span of multiple organisms, although the molecular mechanisms of these effects are not fully understood. There are known and sometimes contradictory relationships between the kynurenine pathway activity and the life- extending effect of CR but the crosstalk between the two is not well characterized. Understanding these relationships could lead …

Reversible Degradation Of Peptidoglycan By Lytic Transglycosylases, Aaron Devereaux

Theses and Dissertations (Comprehensive)

Antimicrobial resistance continues to be a burden on the global healthcare system with an estimated cost of billions of dollars and millions of deaths each year. Recently, there has been little to no development on new antibiotics to treat bacterial infection, and any that are developed become resisted to within a few years. Both Gram-positive and Gram-negative bacteria contain a mesh-like layer called peptidoglycan (PG) that surrounds their cells providing strength, cell shape, and protection from their environments. This layer is a polymer of N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) connected via a b-1,4-glycosidic bond, with each strand being cross-linked …

Practical Experimental Microbiology: Laboratory Manual, Rivka Levron

Open Touro Created

2025

Microbiology, especially the laboratory component, is a highly practical and useful course for students pursuing many career options. While a number of excellent microbiology laboratory manuals are available, many are more suitable for a full-year course in microbiology or for more advanced studies.

Microbiology Experimental Laboratory Manual is comprehensive in teaching students basic microbiological techniques, i.e., how to grow and stain bacteria, how to identify bacteria and fungi, and means of identifying different species of bacteria microscopically. Further experiments enable students to identify the most effective soap/detergent from those readily available; to discover which spices have the most anti-bacterial …

Cath-Ddg: Towards Robust Mutation Effect Prediction On Protein-Protein Interactions Out Of Cath Homologous Superfamily, Guanglei Yu, Xuehua Bi, Teng Ma, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Protein-protein interactions (PPIs) are fundamental aspects in understanding biological processes. Accurately predicting the effects of mutations on PPIs remains a critical requirement for drug design and disease mechanistic studies. Recently, deep learning models using protein 3D structures have become predominant for predicting mutation effects. However, significant challenges remain in practical applications, in part due to the considerable disparity in generalization capabilities between easy and hard mutations. Specifically, a hard mutation is defined as one with its maximum TM-score < 0.6 when compared to the training set. Additionally, compared to physics-based approaches, deep learning models may overestimate performance due to potential data leakage.

Results: We propose new training/test splits that mitigate data leakage according to the CATH homologous superfamily. Under the constraints of physical …

Evaluation Of Microbial Contamination In Tube Well And Filter Water Of Lahore And Treatment With Copper Nanoparticles, Khadeeja Moazzam, Sumaira Mazhar

Journal of Bioresource Management

Water contamination is a global issue and different techniques are being devised to reduce water contamination. Among these techniques, use of nanoparticles for water purification is an efficient and cost-effective method with minimum or no side effect. Metal nanoparticles are known for their antibacterial activity against various pathogens. Synthesis of these nanoparticles using green synthesis methods minimizes the harmful effects while ensuring their antibacterial activity. Therefore, in the present work, it was aimed to evaluate the microbial contamination in water samples collected from different tube wells and filter plants located in different areas of Lahore, Pakistan for the isolation of …

Degradation Of Cyanobacteria And Microalgae Using Ultraviolet Radiation At 222 Nm And Its Application In The Bleaching Of Lampenflora On Cave Rock Surfaces, Keisuke Naito, Shuji Watanabe, Masuo Komukai, Takehiro Kazama, Masayuki Itoh, Masahiro Kawasaki

International Journal of Speleology

Cyanobacterial and microalgae blooms negatively affect ecological environments. One of the emerging problems of these blooms occurs in calcareous caves, where visible lighting systems in tourist caves induce the formation of photosynthetic biofilms known as lampenflora on rock surfaces. In this study, we evaluated the inactivation effect of ultraviolet (UV) light irradiation at 222 nm (rare gas halide lamp) and 254 nm (mercury lamp) on cyanobacteria and microalgae in a laboratory and on lampenflora in Ryusenshindo Cave in Japan. Based on the laboratory experiments, irradiation at 222-nm was more effective than that at 254-nm for degrading plants. The photosensitivity of …

Interactions Of The Sars-Cov-2 Viral Genome 3’-Untranslated Region With Viral And Host Rnas, Caleb Frye, Mihaela Rita Mihailescu

Electronic Theses and Dissertations

This dissertation focuses on the characterization of RNA-RNA interactions within the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and with host microRNAs. As the causative agent of coronavirus disease 2019 (COVID-19), SARS-CoV-2 has evolved rapidly since its appearance. This has warranted prompt characterization of the virus particularly of its single stranded RNA (ssRNA) genome. By using a combination of bioinformatics, biophysics, and/or biological assays, we analyzed the SARS-CoV-2 viral genomic RNA and uncovered interactions of genomic RNA with host RNAs, highlighting an underutilized method of targeting RNA viruses. We showed here that the conserved elements in the viral genomic …

Characterizing The Francisella Tularensis Universal Stress Protein, Benjamin Girardo

Theses & Dissertations

Francisella tularensis is an extremely virulent pathogen responsible for the zoonotic disease tularemia. F. tularensis employs various defense mechanisms to survive and persist under diverse environmental and host-induced stress conditions. Despite its significance, the full spectrum of stress factors that enable F. tularensis persistence remain inadequately understood. In many bacterial species, universal stress proteins (Usp) play a crucial role in managing adverse conditions. The aim of this study was to elucidate the role of Usp in F. tularensis as a means of clarifying the stress response mechanisms of this pathogen. The F. tularensis Usp is encoded by a single, highly …

Evaluating The Effectiveness Of Benguet Pine (Pinus Kesiya) Xylem For Deep Well Water Filtration, Allen Conner C. Hizon, Robert Zachary M. Santos, Juan Jose B. Lacson, Jefferson Danilo G. Villarin, Juan Carlo T. Gumangan

Sinaya: A Philippine Journal for Senior High School Teachers and Students

Even today, many rural and remote communities still do not have access to safe drinking water, which is a basic right of every human. To address this problem, the effectiveness of the Benguet pine tree (Pinus kesiya) xylem as a sustainable water filtration method for well water was investigated. The physical and chemical properties of the filtered and unfiltered deep well water were tested: the total dissolved solids (TDS) and the electrical conductivity using a 5-in-1 electronic water quality tester and the pH level using pH strips. On the other hand, the microbiological metrics, such as heterotrophic plate …

Population Dynamics In Myxococcus Xanthus Developmental Biofilm, Trosporsha Tasnim Khan

Dissertations - ALL

Myxococcus xanthus, a soil-dwelling bacterium, exhibits complex multicellular behaviors through self-organization into biofilms. M. xanthus cells traverse agar surfaces, forming either predatory biofilm or vegetative swarm that expands outward in the presence of nutrients. Upon nutrient depletion, the swarm reorganizes as cells “stream” inward, coalescing into aggregates that mature into spore-filled fruiting bodies. This starvation-induced biofilm development is a complex process, governed by stringent genetic controls and coordinated population interactions. Despite extensive research into the dynamics of this development, from the onset of starvation to fruiting body maturation, a comprehensive understanding is still missing. This dissertation sheds light on the …

Using Bivalves As An Indicator For Fecal Bacteria, Kamala Chuss

Honors Scholar Theses

This project focuses on the integration of fecal bacteria from warm-blooded animals into bivalve tissue, and the utilization of bivalves as an indicator for fecal bacteria in waterways. Bivalves may give a more representative long-term average of fecal bacteria in water as compared to direct water testing. The primary objective is to create a standard operating procedure to use bacterial testing of bivalves as a proxy for bacteria concentration in the water. This method can be used in places where bivalves do not already exist by adding them to a body of water, or by collecting bivalves that already exist …

Multi-Antigen Elephant Endotheliotropic Herpesvirus (Eehv) Mrna Vaccine Induces Humoral And Cell-Mediated Responses In Mice, Jessica R Watts, Jennifer L Spencer Clinton, Jeroen Pollet, Rongsheng Peng, Jie Tan, Paul D Ling

Faculty, Staff and Students Publications

Background/Objectives: Elephant endotheliotropic herpesvirus (EEHV) causes lethal hemorrhagic disease (HD) in Asian and African elephants in human care and the wild. It is the leading cause of death for young Asian elephants in North American and European zoos despite sensitive diagnostic tests and improved treatments. Thus, there is a critical need to develop an effective vaccine to prevent severe illness and reduce mortality from EEHV-HD. We generated a multi-antigenic EEHV mRNA vaccine to address this need that encodes the EEHV1A-subtype glycoproteins gB, gH, gL, and gO. These conserved proteins are the entry machinery for several herpesviruses in the betaherpesvirus subfamily …

Large-Scale Crispr/Cas9 Deletions Within The Wfdc Gene Cluster Uncover Gene Functionality And Critical Roles In Mammalian Reproduction, Katarzyna Kent, Kaori Nozawa, Rachel Parkes, Laura Dean, Frey Daniel, Mei Leng, Antrix Jain, Anna Malovannaya, Martin M Matzuk, Thomas X Garcia

Faculty, Staff and Students Publications

Despite 96 million years of evolution separating humans and rodents, 11 closely related reproductive tract-specific genes in humans—SPINT3, WFDC6, EPPIN, WFDC8, WFDC9, WFDC10A, WFDC11, WFDC10B, WFDC13, SPINT4, and WFDC3—and the 13 reproductive tract-specific orthologous genes in mice, form highly conserved syntenic gene clusters indicative of conserved, combined critical functions. Further, despite significant progress toward a nonhormonal male contraceptive targeting the protein encoded by one of these genes, epididymal peptidase inhibitor (EPPIN), and associations found between mutations in EPPIN and an increased risk of male infertility, neither EPPIN nor …

Activities Of Cellulolytic, Amylolytic, And Secondary Metabolites From Thermophilic Actinomycetes Collected From The Heated Soil Around Cisolok Geyser, Dhian Chitra Ayu Fitria Sari, Fitria Ningsih, Mazytha Kinanti Rachmania, Akira Yokota, Wellyzar Sjamsuridzal

Makara Journal of Science

This study investigated the antimicrobial activity, cellulolytic, and amylolytic abilities of eight thermophilic Actinomy-cetes isolated from the heated soil around the Cisolok geyser, West Java, Indonesia. Cellulolytic and amylolytic abili-ties were screened for on media by adding 1% (w/v) soluble starch and carboxymethylcellulose (CMC), respectively. Antimicrobial activity was screened for using the agar-plug diffusion method by cultivating strains on various growth media. Growth at various temperatures showed that six strains could grow up to 50 °C. Seven out of eight strains showed amylolytic ability at 40 °C and 45 °C, and only four strains did so at 50 °C. Screening …

Presence Of The Ade Multidrug Systems And Response To Triclosan Exposure In Acinetobacter Baumannii From Animal Origins, Sirawit Pagdepanichkit, Rungtip Chuanchuen

The Thai Journal of Veterinary Medicine

Thirty Acinetobacter baumannii from animal origins were obtained from 210 animal carcasses submitted for post-mortem examination, including dogs (n=112), cats (n=45), rabbits (n=17), birds (n=15), pigs (n=7) and exotic animals (n=14). All the isolates were evaluated for antimicrobial susceptibility with absence and presence of efflux inhibitors i.e. reserpine and carbonyl cyanide m-chlorophenylhydrazone (CCCP) and expression profile of important six multidrug efflux systems (i.e. AdeABC, AdeDE, AdeFGH, AdeIJK, AbeM and AmvA). Fifteen isolates expressing different Ade multidrug efflux pumps were selected for determining transcription levels and regulatory mutations. A continuous in vitro exposure experiment with benzalkonium chloride, chlorhexidine and triclosan …

The Rise, Fall, And Resurgence Of Phage Therapy For Urinary Tract Infection, Jacob J Zulk, Kathryn A Patras, Anthony W Maresso

Faculty, Staff and Students Publications

In the face of rising antimicrobial resistance, bacteriophage therapy, also known as phage therapy, is seeing a resurgence as a potential treatment for bacterial infections including urinary tract infection (UTI). Primarily caused by uropathogenic Escherichia coli, the 400 million UTI cases annually are major global healthcare burdens and a primary cause of antibiotic prescriptions in the outpatient setting. Phage therapy has several potential advantages over antibiotics including the ability to disrupt bacterial biofilms and synergize with antimicrobial treatments with minimal side effects or impacts on the microbiota. Phage therapy for UTI treatment has shown generally favorable results in recent …

Current Status And The Significance Of Local Wisdom Biofertilizer In Enhancing Soil Health And Crop Productivity For Sustainable Agriculture: A Systematic Literature Review, Irwandhi, Fiqriah Hanum Khumairah, Emma Trinurani Sofyan, Nadia Nuraniya Kamaluddin, Anne Nurbaity, Diyan Herdiyantoro, Tualar Simarmata

Jurnal Kultivasi

Soil fertility is recognized as a crucial factor in supporting plant growth and productivity. The utilization of biofertilizers as environmentally friendly fertilizers is aimed at enhancing soil fertility and plant productivity. This study aims to explore the potential of local material for developing local wisdom biofertilizers (LWB) for achieving sustainable agriculture. A systematic literature review was conducted using bibliometric analysis, Preferred Reporting Items for Systematic Reviews, and Meta-Analyses (PRISMA) method, employing the Scopus search engine with the keywords "local AND wisdom AND biofertilizer" OR "biofertilizer" OR "local AND microorganism" OR "soil AND health OR crop AND productivity OR sustainable agriculture". …

Antibiotic Resistance Of Laboratory E. Coli Strains, Alexis H. Hart

Honors Projects

Antibiotic resistance is an ongoing global health crisis. The prevalence and distribution of antibiotic resistance in environmental microbial communities have become climactic areas of investigation due to their far-reaching implications for ecosystem health, human well-being, and the sustainability of antimicrobial efficacy.

An In-Depth Investigation Into Yersinia Pestis Phages: Isolating A Yersinia Pestis Phage From Soil And Constructing A Comprehensive Phylogenetic Analysis Of Known Yersinia Pestis Phages, Jacqueline Chavez

All HCAS Student Capstones, Theses, and Dissertations

Yersinia pestis, the causative agent of the plague, has become increasingly resistant to many antibiotics; therefore, alternatives such as phage therapy are necessary. Phage therapy uses combinations of bacteriophages or phages, which are viruses that only infect bacteria. However, phages—especially Y. pestis phages —are severely understudied. Thus, this research has sought to specifically isolate a phage from soil that infects Y. pestis. There were 146 samples that were collected from across the US, focusing on those with reported cases of plague. These samples were enriched with Y. pestis to maximize the amount of potential phage that target Y. pestis. …

Bioindicators Of Mercury In Riverine Systems, Kathryn Mudica

All-Inclusive List of Electronic Theses and Dissertations

This study focuses on the bioaccumulation and biomagnification of mercury in freshwater food webs, with emphasis on bioindicators, such as macroinvertebrates, crayfish, and river otters. Despite regulatory efforts and advancements in monitoring, significant gaps remain in understanding mercury dynamics in freshwater systems—especially regarding its transport, methylation, and bioavailability across different ecosystems. To address these knowledge gaps, this study adopts a biocentric approach, emphasizing the role of living organisms in their environment. By utilizing macroinvertebrates, crayfish, and river otters as bioindicators, we aim to assess mercury bioavailability and distribution. These organisms provide varying temporal and spatial scales of mercury accumulation, offering …

Elucidating The Mechanism Of Interleukin-17a Signaling In The Pathogenesis Of West Nile Virus, Farzana Nazneen

Dissertations

West Nile Virus (WNV), a neurotropic flavivirus transmitted by mosquitoes, is a leading cause of viral encephalitis in the United States and remains a significant public health concern. Unfortunately, no vaccine or therapeutic intervention is available against WNV infection. Previous studies, including ours, demonstrated that interleukin-17A (IL-17A) signaling increases the cytotoxic potential of CD8⁺ T cells to facilitate WNV and parasite clearance; however, the molecular mechanism is not understood. IL-17 receptor C (IL-17RC) is an obligatory co-receptor with IL-17 receptor A (IL-17RA) for signaling induced by IL-17A, IL-17A/F, and IL-17F. In this study, we found that IL-17RC deficient ( …