Microbiology Commons^™

Transcription Factor Binding And Discovery Of Novel Gene In The Opportunistic Human Pathogen, Pseudomonas Aeruginosa, Alaina Westee

Symposium of Student Scholars

Pseudomonas aeruginosa (PA) is a gram-negative, ubiquitously-found bacterium that primarily causes nosocomial, or hospital-borne, infections within immunocompromised patients. Therefore, it has been deemed a critical priority pathogen by the World Health Organization (WHO) and the Center for Disease Control (CDC), generating a need for research on its fundamental biology. The Van Dyke laboratory focuses on proteins called transcription factors, which promote or repress gene expression to regulate an organism’s functioning. We are specifically studying the cadmium-responsive transcription factor, CadR, due to the importance of metals in virulence and the lack of information on PA’s response to metal fluctuations. We intend …

Immuno-Bioinformatics Study Of Secondary Metabolites From Watercress Nasturtium Officinale As Immunostimulant In Whiteleg Shrimp Litopenaeus Vannamei By Targeting Peroxinectin And Scavenger Receptor Class B, Qurrota A’Yunin, Muhaimin Rifa’I, Maftuch Maftuch, Yoga Dwi Jatmiko, Muhammad Hermawan Widyananda, Triyanto Triyanto, Muhammad Tegar Handrianto

Karbala International Journal of Modern Science

The viral disease affects the whiteleg shrimp (Litopenaeus vannamei) and causes losses. Immunostimulants are recognized as a more environmentally friendly approach to disease management and antimicrobial properties of aquatic organisms. Watercress (Nasturtium officinale) is an aquatic plant species that contains antioxidant properties that can protect the organism from disease and boost the immune system. Shrimp rely heavily on innate immunity to combat infectious agents due to their absence of adaptive immunity. Peroxinectin and scavenger receptor class B (SRB) play essential roles in the shrimp defense system. This research employs a bioinformatic to assess the immunostimulatory potential …

Clonal Variation In Effector Gene Expression As A Mechanism For Pathogenic Adaptation In Magnaporthe Oryzae, Rebekah J. Ellsworth

Theses and Dissertations--Plant Pathology

Magnaporthe oryzae is a filamentous fungal pathogen that causes destructive diseases in cereals, including rice blast, wheat blast, and gray leaf spot. It is responsible for 10–30% annual yield losses in rice (Nalley et al., 2016) and up to 100% loss in wheat under favorable conditions (Kohli et al., 2011). Disease management typically relies on the use of resistant cultivars, but M. oryzae rapidly overcomes host resistance by mutating or deleting avirulence (AVR) genes recognized by host immune receptors. This rapid adaptation, often occurring within one to two growing seasons, presents a major challenge to breeding for durable resistance.

The …

Genetic Analysis Of Methionine Restriction-Associated Mitochondrial Unfolded Protein Response Signaling., Josh D. Dodge

Biology Dissertations - Archive

The lifespan of an organism is dictated by various genetic and environmental factors. One such determinant is the health of mitochondria which are organelles that mediate various critical cell functions including a significant role in generating the vast supply of cellular energy. Indeed, the gradual decline of mitochondrial function is believed to be a hallmark and possible cause of aging. Paradoxically, mild mitochondrial dysfunction early in life extends lifespan in various model organisms. Cells use diverse approaches to promote mitochondrial homeostasis, including the transcriptional reprogramming of cells by mitochondrial unfolded protein response (UPRmt) to mitigate mitochondrial stress. Consistently, UPRmt activation …

Multisociety Guidance For Infection Prevention And Control In Nursing Homes, Lona Mody, Sonali D. Advani, Muhammad Salman Ashraf, Allison H. Bartlett, Suzanne F. Bradley, Deborah P. Burdsall, Jennifer A. Hanrahan, Susan S. Huang, Robert L.P. Jump, Lindsay Nicolle, Mary-Claire Roghmann, Patricia Stone, Rekha K. Murthy

Department of Medicine Faculty Publications

This multisociety guidance was endorsed by SHEA, APIC, IDSA, PALTmed, and AGS. It provides recommendations for infection prevention and control (IPC) in the context of the complexity of nursing home care in the United States: increased medical acuity of residents, the spread of multidrug-resistant organisms, and the threat of emerging pathogens. Recommendations and implementation suggestions address IPC leadership, staffing, and resources, healthcare personnel and residents‘ adherence to precautions and effective hand hygiene, outbreak preparedness, training, occupational health, cleaning and disinfection in the care environment, and the involvement of IPC in the facility. The guidance also addresses the challenges of maintaining …

The Impact Staphylococcus Aureus Has On Conventional And Organic Dairy Herds In New Hampshire And New York, Jacqueline Rose Holmes

Honors Theses and Capstones

Staphylococcus aureus is a potentially virulent bacterium that causes mastitis in dairy cattle. The toxins produced from S. aureus impact host immunity, damage the mammary gland, and can adapt to cause antimicrobial resistance. It is important to manage both organic and conventional farms correctly by practicing proper hygiene while milking and providing a clean environment. There is a significant increase of S. aureus cases on organic farms compared to conventional, so there may be ways in which organic management and treatment options could be altered to reduce economic loss and animal suffering. The thesis focuses on the involvement S. aureus …

The Role Of Horizontal Gene Transfer In Antibiotic Resistance Amidst Prevalent Community And Healthcare-Associated Mrsa Rates, Gabrielle Nascimento

Honors College Theses

In recent decades, cases of community-acquired MRSA (CA-MRSA) and healthcare-associated MRSA (HA-MRSA) have been on the rise. The ability of antibiotic resistance to transfer between microorganisms greatly expands its threat to the effective treatment and containment of bacterial infections. The mecA gene is found on a mobile cassette within the Staphylococcal cell and encodes for PBP2a, an alternate version of penicillin-binding protein (PBP) with less binding affinity for β-lactam antibiotics, increasing resistance to the effects of antibiotics. The goal of this research is to investigate the horizontal transfer of the mecA gene between various Staphylococcus species as well as to …

Wasting Disease Of A Marine Foundation Species Links Community Interactions To Disease Dynamics, Lillian R. Aoki, Olivia J. Graham, Reyn M. Yoshioka, Rebecca Maher, Lindsay Alma, Eileen E. Hofmann, Colleen A. Burge, Drew Harvell, Maya L. Groner

CCPO Publications

Infectious disease plays a key role in shaping marine communities, including in seagrass meadows, which form biodiverse coastal habitats. Eelgrass (Zostera marina) is the most widespread seagrass species and is susceptible to seagrass wasting disease, caused by the protist Labyrinthula zosterae. As a foundation species, eelgrass strongly influences ecosystem structure, function and services; recent work has begun to explore the links between critical community interactions and seagrass wasting disease. Here, we highlight recent advances about how the eelgrass community regulates and responds to seagrass wasting disease, from the microbiome to herbivores and filter feeders. We further show …

Nucleotide-Derived Bacterial Alarmones Attenuate The Induction Of Type-I Interferon Responses In A Murine Macrophage Reporter Cell Line, Ryan P. Kilduff, Erin B. Purcell, Lisa M. Shollenberger

Chemistry & Biochemistry Faculty Publications

The stringent response is a well-studied phenomenon in many bacterial systems and regulates resource-consuming activities such as transcription, translation, and replication. The stringent response is a well-conserved signaling framework, as are the nucleotide-derived signaling mediators, collectively referred to as (p)ppGpp or as alarmones. There is a wealth of research evaluating nucleotide-derived alarmone signaling in bacterial models, however, their potential to modulate innate immune signaling has not yet been evaluated. Several common pathogen-synthesized molecules, such as lipopolysaccharide (LPS) and cyclic-di-AMP (c-di-AMP), act as pathogen-associated molecular patterns (PAMPs), which are common patterns that alert the innate immune system of bacterial infection. The …

Caveolin-Mediated Endocytosis: Bacterial Pathogen Exploitation And Host-Pathogen Interaction, Dibyasri Barman, Rishi Drolia

Biological Sciences Faculty Publications

Within mammalian cells, diverse endocytic mechanisms, including phagocytosis, pinocytosis, and receptor-mediated endocytosis, serve as gateways exploited by many bacterial pathogens and toxins. Among these, caveolae-mediated endocytosis is characterized by lipid-rich caveolae and dimeric caveolin proteins. Caveolae are specialized microdomains on cell surfaces that impact cell signaling. Caveolin proteins facilitate the creation of caveolae and have three members in vertebrates: caveolin-1, caveolin-2, and caveolin-3. Many bacterial pathogens hijack caveolin machinery to invade host cells. For example, the Gram-positive facultative model intracellular bacterial pathogen Listeria monocytogenes exploits caveolin-mediated endocytosis for efficient cellular entry, translocation across the intestinal barrier, and cell–cell spread. Caveolin …

Impacts Of Tick Parasitism On The Rodent Gut Microbiome, Robert J. Brinkerhoff, Joshua Pandian, Meghan Leber, Isabella D. Hauser, Holly D. Gaff

Biological Sciences Faculty Publications

Host microbiota may impact disease vector behavior and pathogen transmission, but little is known about associations between ectoparasites and microbial communities in wildlife reservoir species. We used Illumina metagenomic sequencing to explore the impacts of tick parasitism on the rodent fecal microbiome in both a field and laboratory setting. We found that tick parasitism on wild hosts was associated with variation in the fecal microbiota of both the white-footed deermouse, Peromyscus leucopus, and the southern cotton rat, Sigmodon hispidus. In a lab experiment, we detected significant changes to the fecal microbiome after experimental exposure to immature ticks in …

Novel Infection By Mucor Hiemalis Kills Caenorhabditis Hosts Through Intestinal Perforation, Jay Ni

West Chester University Graduate Theses, Dissertations, and Final Projects

The nematode Caenorhabditis elegans has emerged as a popular model system to investigate cell biology and host-pathogen interactions. Presently, C. elegans is studied as a natural host of intracellular pathogens such as microsporidia and Orsay virus along with extracellular bacterial and fungal pathogens. The use of C. elegans as a model in host-pathogen research is limited by the number of naturally occurring pathogens to the organism. Through a sampling project to identify new pathogens of C. elegans, we identified the fungus Mucor hiemalis as a pathogen of Caenorhabditis species. We observed the fungus in the intestinal lumen of wild-caught …

Watershed-Level Survey Of Antimicrobial Resistance From Onsite Wastewater Systems, Trey Franklin Clark

Graduate Theses, Dissertations, and Problem Reports (ETD)

The emergence of antimicrobial resistance (AMR) has quickly become one of the largest global health and development threats. Research related to environmental modes of transmission of AMR has accelerated in recent years, and the US Environmental Protection Agency is particularly interested in this emerging contaminant. Knowledge of how onsite (decentralized) wastewater treatment systems contribute to this issue is lacking, so this research serves to analyze and quantify the environmental dissemination of AMR and fecal contamination from these sources at a watershed level while using statistical analysis to assess relationships between physiochemical, spatial, and sampling parameters. This research surveyed four watersheds …

The Effects Of Salinity On The Cutaneous Microbiome And Pathogen Infection On The Pacific Tree Frog (Pseudacris Regilla) In Monterey Bay, California, Usa, Hannah Eunhae Kim

EWU Masters Thesis Collection

Global climate change and infectious diseases are considered a leading cause of amphibian population declines worldwide. Changes in precipitation and salinity have altered watershed systems and microbial communities, reducing habitat availability and physiological performances for amphibian survival. The salt refuge hypothesis, however, is a proposed explanation that higher saline environments may reduce susceptibility to pathogens such as Batrachochytrium dendrobatidis (Bd). The Moro Cojo Slough State Marine Reserve (MCSSMR) (California, USA) is known as an abundant breeding ground for endangered/threatened amphibian species. To test and expand the salt refuge hypothesis, I evaluated Bd prevalence and intensity and the cutaneous microbiome of …

Biochemical And Molecular Analysis Of Anr-Dependent Microoxic Fitness Factors In Pseudomonas Aeruginosa, Stacie E. Balsam

Dartmouth College Ph.D Dissertations

Pseudomonas aeruginosa is a prominent opportunistic pathogen that is often found in microoxic environments like sites of infection and colony biofilms. P. aeruginosa can grow at oxygen (O2) at concentrations as little as 3 μM and also grows anaerobically by generating energy using nitrate as an alternate electron acceptor. An important way P. aeruginosa adapts to low O2 is through Anr, a transcription factor that upregulates many genes important for microoxic and anoxic fitness.

Specifically, Anr regulates mhr which encodes a hemerythrin protein (Mhr) that binds O2 with affinities relevant to microoxia and is also necessary for full fitness of …

Interactions Between Lipopolysaccharide And Capsule Retention In Klebsiella Pneumoniae And The Resultant Effects On Macrophages, Juliane Leigh Nguy

UNF Graduate Theses and Dissertations

Klebsiella pneumoniae is the third most common cause of nosocomial infections in the United States. The capsular polysaccharides (CPS) are virulence factors allowing K. pneumoniae to evade host immune systems. The current model of capsule structure indicates that CPS fibrils interact with the external O-antigen of lipopolysaccharide molecules to enhance retention to the bacterial outer membrane. These interactions may influence pathogenicity in clinically relevant strains. This study characterized alterations to LPS and CPS structure, the impact of these changes on capsule retention, membrane permeability, biofilm formation, and macrophage interactions. LPS and CPS were quantified and visualized in four strains of …

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 …

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 …

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 …

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 …

Analysis Of Microbiome In Various Human Medical Conditions Using Next-Generation Sequencing Of The 16s Rrna Gene, Pallavi Sharma

Electronic Theses and Dissertations

Studies of human microbiomics, spanning diverse anatomical sites, offer a unique perspective into the complex microbial communities within the body. Influenced by age, gender, and disease, it mirrors broader microbial ecosystems. This study specifically delves into the ocular and gastrointestinal tract microbiome, comparing its composition in 43 healthy and diseased patients using 16S rRNA gene sequencing. We identified a rich microbial landscape, identifying over 338 bacterial taxa. Notably, Acinetobacter, Cutibacterium, Acidovorax and Herbaspirillum were prevalent in the ocular samples and Akkermansia, Faecalibacterium, and Anaerostipes were mostly prevalent in gut samples. Moreover, dry eye disease conditions were characterized by …

Induced Systemic Resistance Against Nematodes By Plant Growth-Promoting Microbes In Potatoes, Cole Grannan

Master's Theses

Biofertilizers consist of plant growth-promoting microorganisms that establish symbiotic relationships with plant roots and stems. These beneficial microbes play a crucial role in enhancing plant defenses against various threats including insects, nematodes, and microbial pathogens. The purpose of this study was to investigate the effectiveness of two fungal biofertilizers (an endophytic strain of Beauveria bassiana (BA) and a mixture of arbuscular mycorrhizal (AM) fungi), specifically their ability to induce systemic resistance against plant- parasitic nematodes (PPNs) in potatoes (Solanum tuberosum cv. Masquerade) under controlled greenhouse conditions. The study utilized soil collected from Colorado State University’s San Luis Valley (SLV) Research …

Ophidiomyces Ophidiicola And Texas Snakes: A Field To Bench Study Of Ophidiomycosis, Kenlynn L. Volz

Biology Theses

Ophidiomyces ophidiicola (Oo), the primary cause of Ophidiomycosis, is a fungal pathogen recently detected in Texas snakes. Prior to this study, there were major knowledge gaps regarding Oo growth, spread, and suitable environmental conditions. This study filled those gaps using a field to bench approach involving sampling snakes across Texas, in vitro fungal growth, and ecological niche modeling. 103 snakes were sampled across Texas in 2023 and 2024 and six cases of Oo infection were detected. Results of the growth experiment suggest that Oo prefers more stable temperatures and high humidity to a point and that there is a …

Antibiotic Susceptibility Pattern And Esbl Prevalence In Nosocomial Escherichia Coli From Urinary Tract Infection In Kpk, Peshawar, Muhammad Fawad, Noha E Abdel-Razik, Zain Alhindi, Muhammad Usman Amin, Eman Adnan Abu-Seer, Mashael S.Alfaifi, Murad Ali, Farkad Bantun, Sheraz Dawar, Suleman Khan, Saad Alghamdi

Journal of Bioresource Management

The study aimed to evaluate antibiotic susceptibility patterns and extended-spectrum beta-lactamase prevalence in Escherichia coli isolated from urinary tract infections. Total fifty (50) samples of E. coli were obtained from urinary tract infection specimens in Hayatabad Medical Complex and private clinics in Peshawar, Pakistan. The present study obtained 50 E. coli isolates from 100 UTI specimens. The plates were incubated at 35 to 37°C for 24 to 48 hours. Different biochemical tests were carried out to identify the isolates. Antibiotic susceptibility testing and ESBL screening were done per the CLSI (2023) guidelines. The disc diffusion method was used to determine …

Molecular Detection Of Mycoplasma Spp. And Its Associated Risk Factors In Domestic Cats In The City Of Ibagué, Tolima, Karen D. Osorio Muñoz Dr., Iang S. Rondon Barragan Prof.

The Thai Journal of Veterinary Medicine

Feline hemoplasmosis is a disease with worldwide distribution, mainly in tropical countries, where its transmission is favored by the presence of vectors such as fleas and ticks. In Colombia, the diagnosis of the disease in small animals has been limited to the identification of the pathogen in blood smears, which have low sensitivity and specificity, demanding methods of higher diagnostic value, such as those based on molecular techniques. The objective of the present study was to investigate the prevalence of Mycoplasma spp. in felines from the city of Ibagué using the PCR and the associated risk factors. Briefly, blood samples …

Avicennia Marina Mangrove Plant Mediated Selenium Nanoparticles And Their Therapeutic Activity Against Oral Pathogens And Other Biological Properties, Kannan Kamala, Pitchiah Sivaperumal, Dhanraj Ganapathy

Journal of Dentistry Indonesia

In the last few decades nanoparticles are widely used in the control of many pathogenic bacteria, fungi, viruses, and cancer growth both in-vitro and in-vivo. A marine plant of Avicennia marina is widely used in traditional medicine for diabetes, inflammation and skin diseases. Objective: In general Avicennia marina has been used as a traditional medicine to treat various diseases and it has shown significant inhibition against various pathogen and the formation of free radicals. Also, the plant A.marina mediated selenium nanoparticles has therapeutic activity has promising to develop biocompatible new cost effective treatment for various oral diseases. Methods: …

The Molecular Detection Of Hemotropic Mycoplasma Species In Dogs, Hafize Tuğba Yüksel Dolgun, Şükrü Kirkan

The Thai Journal of Veterinary Medicine

Hemotropic mycoplasmas are uncultured bacteria that cause different degrees of hemolytic anemia in infected hosts. Molecular approaches are used to diagnose hemotropic mycoplasmas since they are difficult to identify using conventional methods. The aim of this study was to use molecular approaches to determine hemotropic mycoplasmas in dogs. Blood samples were collected in tubes (with EDTA) from 100 dogs. After DNA extraction, 100 DNA samples were investigated by PCR. Hemotropic mycoplasma was detected in 12 (12%) samples and positive samples were subjected to Sanger sequencing. Mycoplasma haemocanis was detected in 6 (50.0%) of the samples, Candidatus Mycoplasma hematoparvum in 5 …

Targeting Aspergillus Fumigatus Hypoxia Response Pathways For Novel Antifungal Drug Development., Cecilia Gutierrez Perez

Dartmouth College Ph.D Dissertations

Invasive fungal disease present are difficult to diagnose and treat and present a high mortality rate across the world with approximately 1.5 million people a year succumbing to fungal infections worldwide. Currently, there are limited antifungal classes used therapeutically, and antifungal drug resistance on the rise further exacerbates the dire need for novel therapeutics with innovative mode of actions. The filamentous fungi, Aspergillus fumigatus is the causative agent of invasive pulmonary aspergillosis (IPA). It is estimated that contemporary antifungals fail in about 50% of patients with invasive filamentous fungal infections, likely due to the biofilm mode of growth exhibited in …

Exploring The Interaction Between Klebsiella Pneumoniae And Clostridioides Difficile At The Mucosal Interface, Taylor D. Ticer

MUSC Theses and Dissertations

The gut microbiota plays a major role in human diseases. The impact of these microbes on human health comes not only from individual microbes but also from their interactions with each other. A prime example of this is Clostridioides difficile, an intestinal pathobiont that causes severe gastrointestinal illness. C. difficile works cooperatively with other gut bacteria, including Klebsiella pneumoniae. We hypothesized that K. pneumoniae would work synergistically with C. difficile and promote its pathogenesis. We screened over 40 K. pneumoniae strains to assess their interaction with the intestinal mucus layer, a key colonization site for C. difficile. …