Microbiology Commons^™

Skin Bacteriome Structure And Batrachochytrium Dendrobatidis Prevalence Differs Amongst Two Sympatric Salamanders In The San Francisco Bay Area., Aria Norwood, Jadyn Jamora, Micuel Madison, Jamiee Nguyen, Azan Yousaf, Katya Morales, Emily Vu, Obed Hernández-Gómez

Natural Sciences and Mathematics | Student Professional Publications

Microbial surveys are becoming an important component of wildlife health research, especially in cases where environmental change and infectious diseases are serious issues. Amongst amphibians, Batrachochytrium spp. have the potential to be fatal pathogens that can impact the population health of numerous species. We assessed the skin bacteriome, prevalence of Batrachochytrium dendrobatidis (Bd) and body conditions of two salamander genera with different life histories: the California slender salamander (Batrachoseps attenuatus) and members of the Pacific newt species complex (Taricha torosa and Taricha granulosa; Taricha sp.). We used 16S rRNA V4 amplicon sequencing to characterise the bacterial communities. Taricha sp. had …

Reaction Control Mechanism In Deoxyuridine 5'-Triphosphate Nucleotidohydrolase, Aaron Delay

School of Biological Sciences: Dissertations, Theses, and Student Research

Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) is an enzyme involved in the pyrimidine biosynthesis pathway, a key component of cellular DNA metabolism. It regulates intracellular uracil carrying triphosphate levels by hydrolyzing dUTP, thereby providing a substrate for thymidylate synthase (TS). The effective inhibition of dUTPase is expected to enhance TS-targeted chemotherapy by promoting thymine-less apoptosis.

Although the reaction mechanism of dUTPase has been studied, the human nuclear homotrimeric form remains complex, as all three subunits cooperatively form a single active site. As a result, the detailed molecular dynamics of its catalysis are still not fully understood. In this study, I investigated the …

Phytochemical Analysis And Antimicrobial Activity Of Micromeria Barbata Leaf And Stem Extracts Against Pseudomonas Aeruginosa: Insights From Molecular Docking And In Vitro Assays, Shiraz Rawas, Dalia El-Badan, Nawal Al Hakawati

BAU Journal - Science and Technology

The present study provides the characterization of the phytochemical content and the antibacterial activity of ethanolic extracts from the leaves (LM) and stems (SM) of Micromeria barbata (M.barbata) against Pseudomonas aeruginosa . Important functional groups were determined by analyzing the FTIR spectra of LM and SM. The phytochemical profiles were analyzed by GC-MS, and these characterized the chemicals according to retention periods and peak regions. The binding affinities of discovered compounds with the P. aeruginosa LasR and PqsD proteins were evaluated using molecular docking approach. Assays for biofilm formation, MIC, MBC, and agar well diffusion were used to assess the …

Erratum: Culture Harder: Use More Specimen To Increase Methicillin-Resistant Staphylococcus Aureus Culture Yield Relative To Pcr, Arvette E. Mitchell, Arpit P. Patel, Jennifer Dicandilo, Zachary W. Rebollido, Matthew Pettengill

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

During the copyediting stage of production an error was introduced to the title of this article. This resulted in misspelling of the word ‘specimen’ in the title of the published version of the record. The correct title is ‘Culture harder: use more specimen to increase methicillin-resistant Staphylococcus aureus culture yield relative to PCR.’

Previously the title was ‘Culture harder: use more specimens to increase methicillinresistant Staphylococcus aureus culture yield relative to PCR.’

The version of record was updated to reflect this correction.

We apologise for the inconvenience.

Knowledge Of Hiv Transmission And Prevention Among University Students In Pakistan: A Cross-Sectional Study, Muhammad Saleem, Sajid Masood, Shahid Hussain

Journal of Bioresource Management

HIV/AIDS remains a significant public health problem internationally, with young adults being especially at risk because of behavioral and knowledge deficits. In Pakistan, cultural inhibitions and suboptimal health education are the main reasons for limited awareness, particularly among university students. This study had the objectives of determining the knowledge level about HIV transmission and prevention among undergraduate students in Kohsar University Murree (KUM) and to investigate correlations with salient demographic variables. A cross-sectional survey was carried out among 510 students aged 18-27 years through a pre-validated, standardized questionnaire with 12 knowledge-based items. Descriptive statistics and Chi-square tests were utilized to …

Soil Degradation Of Solvent-Cast Pha Films Produced By Bacillus Tequilensis Pwf Using Waste Polyethylene Terephthalate (Pet), Rafeya Sohail, Rida Batool, Nazia Jamil

Journal of Bioresource Management

Polyhydroxyalkanoate (PHA) aliphatic polymers however efficiently biodegradable, still pose a contradiction with the principles of green chemistry. Use of bacterial strains capable of degrading synthetic plastics for the production of biopolymers i.e., PHAs may aid in reduction of plastic pollution. Bacterial strains PWA; Bacillus subtilis (MH142143), PWF; Bacillus tequilensis (MH142145), and PWG; Bacillus safensis (MH142146) were grown on waste shredded PET and PET flakes. Highest bioconversion of PET to PHA was observed using PET flakes. Strain PWF produced 40.47 % (0.815 g/L) and 31.80 % (0.626 g/L) PHA using PET flakes and shredded PET at 48 h, respectively. Whereas highest …

Phylogenetic Analysis Of Ftsz In Wolbachia: Implications For Host Specificity, Anwar Rovik, Ayu Rahayu

Makara Journal of Science

Wolbachia are the most prevalent and successful endosymbiont in invertebrates and are categorized into 21 supergroups based on genetic phylogeny. The filamenting temperature-sensitive Z (FtsZ) protein is essential for bacterial cell division and is hypothesized to play a role in Wolbachia's control of host reproduction. However, despite FtsZ's importance, little is known about its diversity and function within Wolbachia. This study investigated the variability of the FtsZ-encoding gene among Wolbachia strains and their hosts. FtsZ gene sequences were retrieved from the National Center for Biotechnology Information database, and representative sequences were randomly selected from each host species and analyzed …

Isolation And Selection Of Bacillus Spp. As Candidate Probiotics For Use In Chickens, Adilah Adawiah, Komang Gede Wiryawan, Anja Meryandini

Makara Journal of Science

The growth rate of chickens can be improved by using probiotics as alternatives to antibiotics. Bacillus spp. as probiotics are particularly beneficial due to ability to form spores, which remain stable as commercial products over extended periods. This study aimed to isolate and select Bacillus spp. from Jasinga soil as probiotic candidates for chickens. A total of 15 isolates obtained of these, 12 were identified as Bacillus spp based on microscopic observations and screening test including ascertaining hemolysis, protease, amylase, and cellulase activities. Only six isolates exhibited gamma hemolysis and the ability to hydrolyze proteins, starch, and cellulose. Isolates BTJ1.1, …

First Insight On The Genesis Of Iron Oxide-Hydroxide Biospeleothems In Rancho Chico Lava Tube, Mexico, Rafael López-Martínez, Elizabeth Solleiro-Rebolledo, Rocio Alcántara-Hernández, Teresa Pi Puig, Sergey Sedov, Daisy Valera Fernández, M. Nayeli Luis-Vargas, Yasmany Lima Vera, Jesús Solé, Ramon Espinasa-Pereña

International Journal of Speleology

Iron is a common element in lava tube systems, typically observed as thin crusts or inferred from the reddish coloration of secondary mineral deposits. In this study, we describe iron oxide-hydroxide biospeleothems discovered in the Rancho Chico Lava Tube, located within the Xalapa Monogenetic Volcanic Field in Mexico. We adopt an integrative approach combining petrography, soil micromorphology, scanning electron microscopy, mineralogy, and 16S rRNA gene metabarcoding. DNA sequencing reveals the presence of microorganisms such as Acidithiobacillus, Gallionella, and members of the Leptospirillaceae family, which may be involved in the oxidation of Fe²⁺ within the lava tube. The source …

Detection Of Quorum-Sensing Molecules In The Mutualistic Bacteria Vibrio Fischeri Exposed To Simulated Microgravity Using Cell-Based Biosensors., Paulina Slick, Maria C. Tobarra, Alba A. Chavez, Hugo Castillo

Beyond: Undergraduate Research Journal

Bacteria flourish in multiple environments when communicating with each other in a process known as Quorum Sensing. This process is accomplished by the production of small signaling molecules referred to as Autoinducers (AI). This communication allows the bacteria to alter their gene expression in an effort to regulate their cell number, behavior, community formation and virulence. The space environment provides stressful conditions for bacteria as they are exposed to radiation and Microgravity (µG or MG) altering synthesis and concentration of Autoinducers. The purpose of this research was to expose the model system Vibrio fischeri to simulated microgravity using the recently …

Crayfish Microhabitats Provide A Close Association With Benthic Microbiomes To Support Cleaning Symbionts., Kyle J. Harris, John Hoverson, Matthew Becker, Matthew M. Cooke Mr

NEXUS: The Liberty Journal of Interdisciplinary Studies

Stream ecosystems promote variable microhabitats along a longitudinal gradient. These microhabitats support dynamic biotic assemblages. One such microhabitat in freshwater streams involves the external surface of crayfish. We investigated the microbiome of crayfish exoskeletons and the surrounding environment (water and substrate) in association with the presence and abundance of crayfish cleaning ectosymbionts (branchiobdellidans). These ectosymbionts actively consume the biofilm on crayfish as they live and reproduce in association with crayfish microhabitats. Sequenced microbes of the environment and crayfish were compared for dominant taxa. While the sample types (water, substrate, and crayfish) had significantly different microbiomes, there was not a significant …

Identification Of Host Nuclear Factors Exploited By Kshv Lana To Maintain Latency, Anandita Ghosh

USF Tampa Graduate Theses and Dissertations

Kaposi’s Sarcoma Associated Herpes Virus (KSHV or HHV-8) is a γ-herpesvirus implicated in multiple lymphoproliferative human cancers and immune dysregulatory diseases. Like other herpesviruses, KSHV has a biphasic mode of infection primarily orchestrated by two viral proteins: the Latency-Associated Nuclear Antigen (LANA), which promotes viral persistence through latency, and the Replication and Transcription Activator (RTA), which triggers lytic reactivation. During latency, the KSHV genome exists as a highly heterochromatinized, extrachromosomal episome in the nucleus, which can be reverted to euchromatin in response to certain stimuli, like stress. KSHV has evolved to exploit numerous host proteins to orchestrate its lifecycle, especially …

The Impact Of Polymycovirus 1 On Aspergillus Fumigatus Pathogenesis During Lung Infection, Alexander W. Rapp

Dartmouth College Ph.D Dissertations

The genus Aspergillus comprises over 250 species of fungi. Within this genus, only a handful of species cause disease in humans. One species is Aspergillus fumigatus (A.f.), an environmentally ubiquitous, saprophytic fungal pathogen. Lung infections due to A.f. range from invasive infection to allergic forms of the disease. Allergic bronchopulmonary aspergillosis (ABPA) is one of the most severe forms and presents as a hypersensitivity that often results in off-target damage to the surrounding airways. Patients with ABPA are sensitized to fungal antigens and this is commonly seen in cystic fibrosis and genetic predispositions. Recent data from our lab shown how …

Abstract 2587 Recombinant Expression And Purification Of A. Vinelandii Cown In E. Coli, Julie Takei, Cedric P. Owens, Katie Sanders, Neeraja Gajendran

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The goal of this project is to study the protein CowN in the diazotroph Azotobacter vinelandii (Av) in comparison to CowN in Gluconacetobacter diazotrophicus (Gd). Nitrogenase is an enzyme that catalyzes the reduction of nitrogen gas into ammonia in diazotrophic bacteria. In many diazotrophs, the protein CowN prevents nitrogenase inhibition from the environmental gas carbon monoxide (CO). Previous work studied CowN in the diazotroph G. diazotrophicus. In G. diazotrophicus, CowN binds to nitrogenase and weakens CO binding to its active site. The mechanism of CowN has only been investigated in G. diazotrophicus. Thus, we are interested in determining if CowN's …

Functional Characterization Of Uncharacterized Essential Genes In The Oral Pathogen Streptococcus Mutans, Courtney Dover

Student Theses and Dissertations

Streptococcus mutans is a pathogen associated with the formation of dental caries, and its genome contains many uncharacterized genes, including some which are classified as essential genes. These genes are required for the growth of the organism. Characterizing the function of these genes is important for understanding the organism, as well as identifying potential antimicrobial targets. This project used a CRISPRi (CRISPR interference) system to repress seven experimentally uncharacterized genes within the S. mutans genome and investigated the effects of their repression via RNA-seq transcriptomics, phylogenetic analysis, and TEM. The gene annotated as SMU_393 was then prioritized for further analysis …

Colonization-Persistence Trade-Offs In The Human Microbiome, Liam F. Nokes

Environmental Studies Senior Theses

Understanding how diverse microbial taxa coexist in the human body without competitively excluding one another remains a key challenge in microbiome ecology. One proposed explanation is the colonization-persistence trade-off, where species with high colonization ability are poor persisters, and vice versa. We test for this trade-off across human associated microbial communities among many individuals and in multiple body sites using a large-scale participant-level meta-analysis of longitudinal microbiome datasets curated from the MGnify database. We applied island biogeography-based models to calculate effective colonization and persistence rates for microbial families and genera across 606 individuals over twenty-six studies. Regression of the log-transformed …

Genetic And Biochemical Analyses Reveal Litr's Role In Vibrio Fischeri Biofilm Formation, Brittany Loi Fung

Dissertations

Quorum sensing controls numerous processes ranging from production of virulence factors to biofilm formation. Biofilms, communities of bacteria that are attached to one another and/or a surface, are common in nature and, when they form, can produce a quorum of bacteria. One model system to study biofilms is the bacterium Vibrio fischeri, which forms a biofilm that promotes colonization of its symbiotic host. Many factors promote V. fischeri biofilm formation in vitro, including the symbiosis polysaccharide (SYP), cellulose, and the LapV adhesin but, so far, only a handful of studies have probed connections between biofilm formation and quorum sensing. In …

Investigating The Consequences Of Conjugated And Secreted Isg15 On Coronavirus Pathogenesis, Mudassir Syed Ali

Dissertations

Coronaviruses have evolved a breadth of mechanisms to antagonize host innate immune responses. One widely studied mechanism is the ability to deconjugate ISG15 from target proteins in a process called deISGylation, which is catalyzed by the papain-like protease (PLP) domain of viral non-structural protein (nsp) 3. Since PLP activity is required for viral replication, it has been challenging to generate an infectious virus with a PLP that maintains protease activity but has lost deISGylase activity. In this study, we generated a chimeric MHV-A59 with its PLP2 domain replaced with that of the human coronavirus HKU1, which has been documented to …

Interrogating The Dispersal Process And Relevant Genes In Vibrio Fischeri, Jeremy Esin

Dissertations

Biofilms are aggregates of bacteria encased in a matrix that shields bacteria from environmental hazards. These structures are formed in response to cues from the environment and drive colonization of new niches. Biofilms can be both beneficial and detrimental. Largely, research focuses on biofilms that have negative outcomes in clinical, environmental, and economical settings. However, the value of beneficial biofilms is recognized and studied. The marine bacterium Vibrio fischeri is part of a model system for studying symbiotic biofilms in a eukaryotic host. V. fischeri produces a transient biofilm at the surface of a specialized light organ and then disperses …

Culture Harder: Use More Specimen To Increase Methicillin-Resistant Staphylococcus Aureus Culture Yield Relative To Pcr, Arvette E. Mitchell, Arpit P. Patel, Jennifer Dicandilo, Zachary W. Rebollido, Matthew Pettengill

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Methicillin-resistant Staphylococcus aureus (MRSA) causes considerable morbidity and mortality in both community-acquired and healthcare-associated infections, but detecting colonization with MRSA has been shown to improve patient outcomes in certain clinical settings. MRSA colonization detection has been carried out in a variety of ways, with molecular assays having superior sensitivity in most studies relative to culture, but culture is disadvantaged in some comparisons by utilization of low specimen volumes. We compared a commercial molecular assay to both low-volume (10 µl) and high-volume (650 µl) cultures and found that increasing the volume utilized for culture led to the detection of 25% more …

Belowground Biomass Shifts Along A Temperate Forest Edge, Lara Holbrook Roelofs

Dartmouth College Undergraduate Theses

Anthropogenic land use change and development has caused widespread global forest fragmentation, resulting in a greater proportion of forests at or near a forest edge. Temperate forests are the most fragmented forest biome, and forests in the Northeastern U.S. are particularly fragmented due to a history of intense land use and development pressure. Nearly a quarter of these forests are now within 30 meters of a forest edge. These edge ecosystems have distinct abiotic and biotic gradients that differentiate them from forest interiors, including increased light, temperature, and exposure to wind and other disturbances, as well as decreases in humidity …

Investigating A Link Between Dna Repair And Dna Replication In Escherichia Coli Using A Bacterial Two-Hybrid System, Lo Cooper

University Honors Theses

Cells rely on nucleotide excision repair (NER) to remove bulky DNA lesions, such as those caused by UV light. In Escherichia coli, NER involves the UvrABC complex, and includes two main pathways, global genomic repair and transcription-coupled repair (TCR). While TCR, which preferentially removes lesions that block RNA polymerase on the transcribed strand of active genes, is well studied, less is known about whether a similar coupling between repair proteins and replisomes blocked by damaged DNA exists. Such a process has been suggested by a high throughput interactome study, using the replisome subunit HolC as bait and the damage …

Digesting The Details: How Cooking Shapes The Microbiome And Influences Obesity, Tracy Lieu

University Honors Theses

Obesity is a growing global health concern linked to chronic diseases and changes in the gut microbiome. While diet is known to affect gut microbes, less attention has been given to how food processing methods, such as heating, fermentation, and cold processing, change food in ways that influence the gut microbiome and health. This thesis reviews research on how different cooking and preparation techniques affect the availability of nutrients for microbial fermentation and the resulting effects on microbial diversity and metabolism. The findings show that fermentation and cold processing are the most supportive of gut health. These methods help preserve …

Evaluation Of Nature-Based Engineering Stream Restoration Of Plaster Creek Through Leisure Creek Condominium Association, Julie Wildschut, Rebecca Evenhouse, Andrea Lubberts, Dave Warners, Haley Weesies

Faculty and Professional Research

When land that was once covered with vegetation and soil becomes dominated by impervious concrete and rooftops, the amount of water infiltrated by the ground plumets. As a result, most suburban areas contribute to the impairment of streams by adding excess water, nutrients, and pollutants to nearby waterways each time it rains. One harmful result of this is the erosion of stream banks. The rapid influx of water that occurs after rain events can destabilize and erode stream banks, resulting in excess sediment in the water. One location where this happened very prominently was a section of Plaster Creek which …

Seroprevalence And Associated Risk Factors Of Caprine Arthritis Encephalitis (Cae) And Peste Des Petits Ruminants (Ppr) Among Deer In An Institutional Farm In Malaysia, Krishnan Nair Balakrishnan, Faez Firdaus Abdullah Jesse, Bura Thlama Paul, Shalonagiftsal Stephen C Charles, Ummul Rifhan Najiha Noor Zaman, Eric Lim Teik Chung, Nur Amira Azhar, Abdirahman Barre, Muhammed Mikail, Mohd Azmi Mohd Lila

The Thai Journal of Veterinary Medicine

Caprine arthritis encephalitis (CAE) and peste des petits ruminants (PPR) are significant viral diseases impacting small ruminants, leading to substantial economic losses and posing a potential threat to livestock health. Although seroprevalence evidence of these viruses has been documented in ruminants, there is a lack of data regarding their presence among farmed deer in Malaysia. This preliminary study aimed to determine the seroprevalence and associated risk factors for CAEV and PPRV infections among deer in Malaysia. A total of ninety-two blood sera from an institutional deer farm were screened for CAEV and PPRV antibodies using commercially available indirect ELISA test …

From Epidemics To Experimental Treatments: Amphibian Mass Mortality Events And A Potential Treatment For Chytridiomycosis, Daniel Callahan

Graduate Masters Theses

Worldwide, amphibian populations have experienced dramatic declines due to a variety of threats. Among them, disease has been particularly deleterious and continues to impact populations. In the United States and Canada, the three leading causes of amphibian mass mortality events are ranavirosis, chytridiomycosis, and severe perkinsea infection, all caused by infectious pathogens. While research and policy have helped populations recover from these diseases, more work needs to be done to develop practical and efficient treatments for these infections. Of these three diseases, chytridiomycosis has had the most devastating effects on amphibian populations globally. Caused by the chytrid fungi Batrachochytrium dendrobatidis …

Characterization Of Sars-Cov-2 Replication And Transcription Complexes Via Structural And Evolutionary Approaches, Amelie Ghirardo, Ben Shabatian, Avishai Aghelian, Kyle Tau, Eleonora Gianti

Undergraduate Research

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused around 700M cases and over 7M COVID-19-related deaths recorded worldwide (World Health Organization, March 2025). Aiming to effectively combat this and other disease-causing Coronaviruses (CoV), unprecedented research efforts led to the development of new vaccines and antiviral therapies. Due to emergence of variants of concern (VOCs) with increased transmissibility, immune evasion from vaccination, and potential to resist the available treatments, SARS-CoV-2 continues to represent a major threat to global health. Hence, there is a pressing need to discover new antivirals with broad-spectrum efficacy against multiple SARS-CoV-2 variants and related CoVs. This project …

A Complete Transfer Learning-Based Pipeline For Discriminating Between Select Pathogenic Yeasts From Microscopy Photographs, Ryan A. Parker, Danielle S. Hannagan, Jan H. Strydom, Christopher J. Boon, Jessica Fussell, Chelbie A. Mitchell, Katie L. Moerschel, Aura G. Valter-Franco, Christopher Cornelison

Faculty Articles

Pathogenic yeasts are an increasing concern in healthcare, with species like Candida auris often displaying drug resistance and causing high mortality in immunocompromised patients. The need for rapid and accessible diagnostic methods for accurate yeast identification is critical, especially in resource-limited settings. This study presents a convolutional neural network (CNN)-based approach for classifying pathogenic yeast species from microscopy images. Using transfer learning, we trained the model to identify six yeast species from simple micrographs, achieving high classification accuracy (93.91% at the patch level, 99.09% at the whole image level) and low misclassification rates across species, with the best performing model. …

Impacts Of Land Development On Soil Microdiversity And Antibiotic Production, Dennis Guillen Castro, Robert Garcia, Jonathan Castro, Davida Smyth

Masters Theses (Archived)

The impact of land development on soil microbial diversity and antibiotic production is critical due to industrial expansion and the scarcity of effective antibiotics. Low Impact Development (LID) aims to preserve ecosystems, but its effectiveness in maintaining microbial diversity is uncertain. This study compares soil samples from nine sites: undisturbed (UD), residential (RD), and Madla Greenway (GW) within the VIDA development area and Texas A&M University-San Antonio campus. Isolated microbes were screened for antibiotic production and genetically characterized. Preliminary findings indicate that UD sites harbor greater microbial abundance, and a higher proportion of antibiotic-producing microbes compared to GW and RD …

Assessing The Efficiency Of Methotrexate (Mtx) As An Antiviral Drug Against Gammaherpes Virus Replication, Yennifer A. Gaspar Garcia

Honors Projects

It is estimated that ~15% of all cancers are caused by oncogenic virus infections. Two of the top seven cancer-causing human viruses are members of the gammaherpesvirus family: Epstein Barr Virus (EBV) and Kaposi’s Sarcoma Herpesvirus (KSHV). Our lab uses Murine Herpesvirus 68 (MHV-68), a mouse gammaherpesvirus with shares significant genetic homology to KSHV and EBV, as a model system to understand how gammaherpesviruses alter the metabolism of their host during lytic infection to promote their replication. We recently metabolically profiled MHV-68 infected host cells at various time points during the lytic infectious cycle. Our data showed nucleotide metabolism is …