Microbiology Commons^™

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

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+ …

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 …

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 …

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, …

Caenorhabditis Elegans Endorse Bacterial Nanocellulose Fibers As Functional Dietary Fiber Reducing Lipid Markers, Amanda Muñoz-Juan, Adrien Assié, Anna Esteve-Codina, Marta Gut, Núria Benseny-Cases, Buck S Samuel, Esther Dalfó, Anna Laromaine

Faculty, Staff and Students Publications

Bacterial nanocellulose (BNC) is a promising dietary fiber with potential as a functional food additive. We evaluated BNC fibers (BNCf) in the Caenorhabditis elegans model to obtain insight into the BNCf's biointeraction with its gastrointestinal tract while reducing the variables of higher complex animals. BNCf were uptaken and excreted by worms without crossing the intestinal barrier, confirming its biosafety regarding survival rate, reproduction, and aging for concentrations up to 34 μg/ml BNCf. However, a slight decrease in the worms' length was detected. A possible nutrient shortage or stress produced by BNCf was discarded by measuring stress and chemotactic response pathways. …

Engineering Small-Molecule And Protein Drugs For Targeting Bone Tumors, Yixian Wang, Chenhang Wang, Meng Xia, Zeru Tian, Joseph Zhou, Julian Meyer Berger, Xiang H-F Zhang, Han Xiao

Faculty, Staff and Students Publications

Bone cancer is common and severe. Both primary (e.g., osteosarcoma, Ewing sarcoma) and secondary (e.g., metastatic) bone cancers lead to significant health problems and death. Currently, treatments such as chemotherapy, hormone therapy, and radiation therapy are used to treat bone cancer, but they often only shrink or slow tumor growth and do not eliminate cancer completely. The bone microenvironment contributes unique signals that influence cancer growth, immunogenicity, and metastasis. Traditional cancer therapies have limited effectiveness due to off-target effects and poor distribution on bones. As a result, therapies with improved specificity and efficacy for treating bone tumors are highly needed. …

Angiogenic Gene Therapy For Refractory Angina: Results Of The Exact Phase 2 Trial, Kenta Nakamura, Timothy D Henry, Jay H Traverse, David A Latter, Nahush A Mokadam, Geoffrey A Answini, Adam R Williams, Benjamin C Sun, Christopher R Burke, Faisal G Bakaeen, Marcelo F Dicarli, Bernard R Chaitman, Mark W Peterson, Dawn G Byrnes, E Magnus Ohman, Carl J Pepine, Ronald G Crystal, Todd K Rosengart, Elaine Kowalewski, Gary G Koch, Howard C Dittrich, Thomas J Povsic, Exact Trial Investigators

Faculty, Staff and Students Publications

Background: XC001 is a novel adenoviral-5 vector designed to express multiple isoforms of VEGF (vascular endothelial growth factor) and more safely and potently induce angiogenesis. The EXACT trial (Epicardial Delivery of XC001 Gene Therapy for Refractory Angina Coronary Treatment) assessed the safety and preliminary efficacy of XC001 in patients with no option refractory angina.

Methods: In this single-arm, multicenter, open-label trial, 32 patients with no option refractory angina received a single treatment of XC001 (1×1011 viral particles) via transepicardial delivery.

Results: There were no severe adverse events attributed to the study drug. Twenty expected severe adverse events in 13 patients …

Mechanisms Driving Fasting-Induced Protection From Genotoxic Injury In The Small Intestine, Kali Deans-Fielder, Timothy Wu, Thanh Nguyen, Sarah To, Yang-Zhe Huang, Steven J Bark, Jason C Mills, Noah F Shroyer

Faculty, Staff and Students Publications

Genotoxic agents such as doxorubicin (DXR) can cause damage to the intestines that can be ameliorated by fasting. How fasting is protective and the optimal timing of fasting and refeeding remain unclear. Here, our analysis of fasting/refeeding-induced global intestinal transcriptional changes revealed metabolic shifts and implicated the cellular energetic hub mechanistic target of rapamycin complex 1 (mTORC1) in protecting from DXR-induced DNA damage. Our analysis of specific transcripts and proteins in intestinal tissue and tissue extracts showed that fasting followed by refeeding at the time of DXR administration reduced damage and caused a spike in mTORC1 activity. However, continued fasting …

Sialic Acid-Siglec-E Interactions Regulate The Response Of Neonatal Macrophages To Group B Streptococcus, Sean J Lund, Pamela G B Del Rosario, Asami Honda, Kaitlin J Caoili, Marten A Hoeksema, Victor Nizet, Kathryn A Patras, Lawrence S Prince

Faculty, Staff and Students Publications

The mammalian Siglec receptor sialoadhesin (Siglec1, CD169) confers innate immunity against the encapsulated pathogen group B Streptococcus (GBS). Newborn lung macrophages have lower expression levels of sialoadhesin at birth compared with the postnatal period, increasing their susceptibility to GBS infection. In this study, we investigate the mechanisms regulating sialoadhesin expression in the newborn mouse lung. In both neonatal and adult mice, GBS lung infection reduced Siglec1 expression, potentially delaying acquisition of immunity in neonates. Suppression of Siglec1 expression required interactions between sialic acid on the GBS capsule and the inhibitory host receptor Siglec-E. The Siglec1 gene contains multiple STAT binding …

The Influence Of Environmental Conditions On Gordonia Terrae -Specific Bacteriophage Distribution And Diversity, Gt M. Moore

Biology Theses

Bacteriophages are viruses that infect a diverse range of bacteria, with certain strains serving medical and industrial significance. Actinobacteriophages are viruses that specifically infect Phylum Actinobacteria hosts including the environmentally abundant Gordonia terrae. Some species of Gordonia, including G. terrae, have also been isolated from human infections. The isolation and characterization of novel phages that can infect Gordonia can therefore be significant to both genomics and potential phage therapy. Actinobacteriophages that infect these bacteria have been isolated from soil environments, but optimal environmental parameters for isolation have not been fully evaluated. This study examined the relationships between environmental …

Screening Of Orthodontic Patients And Age-Matched Non- Orthodontic Samples For High-Risk Oncogenic Human Papillomavirus (Hpv) Strains, Hunter Hinton

UNLV Theses, Dissertations, Professional Papers, and Capstones

Introduction: The human papillomavirus (HPV) is known to cause cancer in several tissues and organs, including the cervix and the oral cavity. Several oncogenic or high-risk strains have been identified, which include HPV16 and HPV18.However, other research has demonstrated that additional oncogenic, high-risk strains exist - including HPV31, HPV33, HPV35, HPV52 and HPV58, although much less is known about their prevalence. Based upon this lack of knowledge, the primary objective of this project is to address the prevalence of these strains among pediatric and adult patients through screening of saliva samples from the UNLV-SDM and orthodontic clinic populations.

Methods: The …

Quaternary Ammonium Compound Resistance Of Klebsiella Pneumoniae And Klebsiella Quasipneumoniae Strains Isolated From The International Space Station, Natasha Svetlana Sushenko

UNLV Theses, Dissertations, Professional Papers, and Capstones

The International Space Station (ISS) has been continuously inhabited for twenty-three years and harbors a diverse population of microorganisms under conditions of microgravity, elevated radiation, and relative isolation, including Biosafety Level 2 (BSL-2) opportunistic pathogens. To sanitize surfaces on the ISS, astronauts use a combination of four antimicrobial quaternary ammonium compounds (QACs). As the stresses of space flight are known to stimulate virulence and antimicrobial resistance in bacteria, the frequent use of QAC disinfectants on the ISS is of concern to NASA. This not only poses risks to astronauts during future long-term space travel, but there is also a concern …

Enhancement Of Favipiravir With Compound X In A Hamster Model Of Yellow Fever Virus Infection, Hunter Stanger

Undergraduate Honors Capstone Projects

Yellow fever virus (YFV) has long been a worldwide health concern, and recent outbreaks in South America and Africa have resulted in significant mortality. There is currently an effective vaccine to prevent infection, but there are no currently developed antiviral drugs to treat patients that have already contracted the disease. Because of this, an effective antiviral is needed to combat unanticipated cases or emergence in areas that have previously been unaffected by this virus. A drug called favipiravir has shown promising results previously. This compound acts as a nucleoside analog to halt the replication of the virus and stop infection. …

Exploring Novel Nutrient Acquisition Mechanisms For Maintaining Energy Metabolism In Toxoplasma Gondii, Melanie Key

All Dissertations

Toxoplasma gondii is an infectious intracellular parasite that establishes infection within various mammalian hosts, including humans. Toxoplasma infects approximately one-third of the global population, making it an impactful pathogen of study. T. gondii is the causative agent of toxoplasmosis, an opportunistic infection that causes severe illness or fatality in immunocompromised individuals or pregnant women. The parasite possesses a very effective invasion strategy, allowing it to cross different tissue types to disseminate infection across the placental and blood-brain barrier. Although there are a few treatments for acute toxoplasmosis, these drugs can produce adverse side effects. These options are not effective against …

Physico-Chemical, Organoleptic, And Antioxidant Properties Of Black Soybean Flour (Glycine Soja (L.) Merrit) Flakes With The Addition Of Bangle (Zingiber Purpureum Roxb.), Ika Dyah Kumalasari, Nurkhasanah Nurkhasanah, Sepitriani Sepitriani

Pharmaceutical Sciences and Research

Flakes are products that are generally made from cereals. In this study, we are interested to use black soybean (Glycine soja (L) Merrit) and bangle (Zingiber purpureum Roxb.) as flakes ingredients. Black soybeans have high antioxidant components, while bangle contains high antioxidant and fiber components, which enables it to capture free radicals. This study aimed to find the most favorable formula with good physical, chemical, and organoleptic characteristics, which also has the highest antioxidant activity. We used the Completely Randomized Design (CRD) method and the variation of formulation used was the ratio of black soybean flour to bangle …

Bootstrapping For Estimating The Conservative Kill Ratio Of The Surrogate To The Pathogen For Use In Thermal Process Validation At The Industrial Scale, Arshpreet Kaur Khattra, Surabhi Wason, Kevin Thompson, Andy Mauromostakos, Jeyamkondan Subbiah, Jennifer C. Acuff

Food Science Faculty Publications and Presentations

A surrogate is commonly used for process validations. The industry often uses the target log cycle reduction for the test (LCR_Test) microorganism (surrogate) to be equal to the desired log cycle reduction for the target (LCR_Target) microorganism (pathogen). When the surrogate is too conservative with far greater resistance than the pathogen, the food may be overprocessed with quality and cost consequences. In aseptic processing, the Institute for Thermal Processing Specialists recommends using relative resistance (D_Target)/(D_Test) to calculate LCR_Test (product of LCR_Target and relative resistance). This method uses the mean values …

Microbiological Quality Of Irrigation Water And Leafy Vegetables In Dar Es Salaam, Tanzania, Bubelwa L. Kamara, Godwill D. Mrema, Thomas J. Lyimo

Tanzania Journal of Science

The quality of water used for the irrigation of leafy vegetables in urban settings is in doubt due to contamination associated with poor hygiene and water pollution. This study examined the microbiological quality of irrigation water and leafy vegetables at Chang’ombe in Dar es Salaam, Tanzania as well as the perceptions and level of awareness of nearby consumers. Water and leafy vegetable samples were analysed for faecal coliform (FC) using standard techniques. Perception and awareness of consumers were collected using a questionnaire survey. The results showed an average FC count of 406.1 ± 16.40 MPN/100 ml for the irrigation water. …

The Immune Contribution To Postpartum Remodeling, Jessica Caroline Ming

Master's Theses

Following parturition, the uterus must undergo significant changes in size and structure through a process called postpartum remodeling. This process is known to have both pro- and anti- inflammatory components. However, how various immune cells contribute to remodeling and the pathways that promote inflammation are not well understood. We hypothesize that immune cells that infiltrate the uterus postpartum modulate inflammation to promote postpartum remodeling. Our preliminary data suggests that inflammatory cell death may contribute to the inflammation present in the early postpartum period, and thus further studies will analyze caspase-1, gasdermin D, and IL-1β and IL-18. To analyze the immune …

Genetic, In Vitro Phenotypic, And Clinical Characterization Of Atypical Enteropathogenic E. Coli Infection And Pathogenesis, Sarah E. Kralicek

Dissertations

Enteropathogenic E. coli (EPEC) are enteric pathogens that are non-invasive, lack Shiga toxin, and use a type 3 secretion system encoded on the locus of enterocyte effacement (LEE) pathogenicity island to translocate bacterial effector proteins into host intestinal epithelial cells leading to diarrhea. Atypical EPEC (aEPEC), in contrast to typical EPEC (tEPEC), lack bundle-forming pili, likely altering adherence and pathogenicity. Detection of aEPEC with co-infecting pathogens and in some asymptomatic individuals leads to questions regarding aEPEC virulence, especially in adults. I aimed to characterize the clinical manifestations of aEPEC infection and the genetic and in vitro phenotypic factors that contribute …

Elucidating The Underlying Mechanisms Polyamines Play On Coxsackievirus B3 Infection, Mason Richard Firpo

Dissertations

Polyamines are a class of metabolites consisting of small carbon chains that contain amine groups and are positively charged at cellular pH. They play many important roles within the cell and are necessary for cell growth, membrane function, transcription, and translation. They are also required by a myriad of viruses for a productive infection. This includes the non-polio enterovirus Coxsackievirus B3 (CVB3). CVB3 is a cardiotropic virus that can readily infect the heart and cause irreversible damage which can eventually lead to dilated cardiomyopathy and the need for a heart transplant. Unfortunately, there are no approved antivirals or vaccines that …

Inactivation Of Escherichia Coli, Salmonella Enterica, And Listeria Monocytogenes Using The Contamination Sanitization Inspection And Disinfection (Csi-D) Device, Jennifer Mccoy Sanders, Vanessa Alarcon, Grace Marquis, Amanda Tabb, Jo Ann Van Kessel, Jakeitha Sonnier, Brad J. Haley, Insuck Baek, Jianwei Qin, Moon Kim, Fartash Vasefi, Stanislav Sokolov, Rosalee S. Hellberg

Food Science Faculty Articles and Research

The Contamination Sanitization Inspection and Disinfection (CSI-D) device is a handheld fluorescence-based imaging system designed to disinfect food contact surfaces using ultraviolet-C (UVC) illumination. This study aimed to determine the optimal CSI-D parameters (i.e., UVC exposure time and intensity) for the inactivation of the following foodborne bacteria plated on non-selective media: generic Escherichia coli (indicator organism) and the pathogens enterohemorrhagic E. coli, enterotoxigenic E. coli, Salmonella enterica, and Listeria monocytogenes. Each bacterial strain was spread-plated on non-selective agar and exposed to high-intensity (10 mW/cm²) or low-intensity (5 mW/cm²) UVC for 1–5 s. Control …

Antimicrobial Activity Of Cat Flea (Ctenocephalides Felis) Gut Proteins On Different Days After Blood Feeding, Dhruva K. Karnik

Honors College Theses

Cat fleas (Ctenocephalides felis) are a blood-feeding ectoparasitic insect and a common domestic pest found throughout the world. Because of their reliance on host blood, fleas are exposed to blood-borne pathogens; however, the flea gut lumen is a hostile environment for microbial colonization. For example, the gut epithelia differentially express immune genes in response to feeding. In the present study, we measured the antimicrobial activity of gut proteins from cat fleas at different days after feeding (2, 5, 7, and 14). Dissected flea guts were homogenized, passed through a syringe filter, and measured in a protein assay kit. …

Trna Anticodon Cleavage By Target-Activated Crispr-Cas13a Effector, Ishita Jain, Matvey Kolesnik, Konstantin Kuznedelov, Leonid Minakhin, Natalia Morozova, Anna Shiriaeva, Alexandr Kirillov, Sofia Medvedeva, Alexei Livenskyi, Laura Kazieva, Kira S Makarova, Eugene V Koonin, Sergei Borukhov, Konstantin Severinov, Ekaterina Semenova

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Type VI CRISPR-Cas systems are among the few CRISPR varieties that target exclusively RNA. The CRISPR RNA–guided, sequence-specific binding of target RNAs, such as phage transcripts, activates the type VI effector, Cas13. Once activated, Cas13 causes collateral RNA cleavage, which induces bacterial cell dormancy, thus protecting the host population from the phage spread. We show here that the principal form of collateral RNA degradation elicited by Leptotrichia shahii Cas13a expressed in Escherichia coli cells is the cleavage of anticodons in a subset of transfer RNAs (tRNAs) with uridine-rich anticodons. This tRNA cleavage is accompanied by inhibition of protein synthesis, thus …

Investigating Vital Neutrophil Extracellular Trap Pathogen Response In Neutropenic Individuals, Ryan Illig

Thinking Matters Symposium

Neutrophils, also called polymorphonuclear leukocytes (PMNs), constitute the majority of innate immune cells. These cells possess a complex arsenal of functions that allow them to detect and eliminate a broad spectrum of pathogens. Neutropenia is characterized by decreased levels of neutrophils in the bloodstream, typically falling below the normal range. Moderate to severe neutropenia can increase the risk of pathogenic infections and without treatment can be life-threatening. Although the concentration of neutrophils in neutropenic individuals is decreased, upon activation, neutrophils still release neutrophil extracellular traps (NETs). NETs are pivotal in combating a spectrum of pathogens through their non-selective nature. Overreactive …

Identification Of Plant Growth Promoting Rhizobacteria For Ballona Wetlands Restoration, Caroline Ehren, Michelle Lum

Honors Thesis

The Ballona Wetlands Ecological Reserve (BWER) is home to many California native plant species which contribute to ecosystem services of flood and erosion mitigation, water quality improvement, carbon sequestration, and habitat provisions for threatened and endangered species. Plant growth promoting rhizobacteria (PGPR) improve plant tolerance to abiotic stressors and suppress pathogens through the alteration of nutrient absorption, water uptake, and enzymatic activity, and have potential in conservation strategies by aiding revegetation methods. Eight bacterial strains were isolated from native Frankenia salina and Baccharis pilularis in the BWER to determine whether these microbes act as PGPR. The strains were characterized using …

Gut Check: Exploring The Role Of Acinetobacter In Intestinal Inflammation, Janiece Sharmell Glover

MUSC Theses and Dissertations

Inflammatory Bowel Disease (IBD) is a chronic disorder characterized by excessive intestinal inflammation. Alterations in the gut microbiota have been consistently observed in individuals with IBD, but it is unclear which bacteria participate in driving inflammation. A comprehensive survey of publicly available RNA-sequencing datasets revealed that Acinetobacter species are elevated in the gastrointestinal tract of IBD patients. We found that A. calcoaceticus was particularly elevated in Crohn’s Disease patients; a subset of IBD. It is well documented that Acinetobacter species are resistant to several antibiotics, but there is very little information on the effects of Acinetobacter in the gut and …

Exploration Of Enterococcus Faecalis Bacteriophages Diversity: Comprehensive Phylogenetic Analysis And Discovery Isolation Of Enterococcus Faecalis Phage From A Soil Sample In South Florida, Hailey N. Jauernick

All HCAS Student Capstones, Theses, and Dissertations

Enterococcus faecalis is a commensal bacterium found in the gastrointestinal tract, oral cavity, and vagina of humans, which can transition to pathogenic states, leading to diverse infections. Many E. faecalis infections are becoming progressively challenging to treat, stemming from the lack of effective antibiotic therapies against its virulence factors, including biofilm formation and antibiotic resistance. Phage therapy emerges as a promising alternative, targeting bacteria with minimal impact on host flora. However, despite phages' ubiquitous presence and potential applications in medicine and biotechnology, their diversity and ecological niches are vastly understudied. Here, we investigated the diversity of sequenced E. faecalis phages …