Microbiology Commons^™

Biology And Epidemiology Of Dengue Viruses In The El Paso And The Surrounding Usa And Mexico Border Communities, Pedro Miguel Palermo Infante

Open Access Theses & Dissertations

Dengue is considered one of the most important human arboviral diseases worldwide. Dengue cases have increased in the last three decades in the Americas, especially along the United States (US)- Mexico (MX) border region, where the main vector of dengue, Aedes aegypti mosquito, is widely distributed. Explosive outbreaks of dengue in northern Mexico have been associated with imported and local transmission of dengue in the US border communities, especially in the Southeast Texas area, also known as Rio Grande Valley. Due to the unknown if dengue virus (DENV) is present in other areas in the US border located west of …

The Effects Of Tubulin Post-Translational Modifications On The Flagellar Motility Of Trypanosoma Brucei, Katherine Wentworth

All Theses

Trypanosoma brucei is a parasitic kinetoplastid that causes African trypanosomiasis and is transmitted to a mammalian host by the tsetse fly (Glossina spp.). T. brucei relies on its flagellar motility to carry out its morphological changes from the procyclic form (predominant in the fly vector) to the bloodstream form (infectious form in mammals) and navigate the bloodstream of its host. The driving structure within the flagellum is the axoneme, which is composed of microtubules and dynein motor proteins. The tubulin code hypothesis suggests that cells regulate microtubule motor protein activity through post-translational modifications (PTMs) of alpha and beta …

Combining Isotopic And Genetic Analyses To Quantify Microbial Facilitation Of Recalcitrant Resource Use By Terrestrial And Aquatic Consumers, Alexi Christina Besser

Biology ETDs

Quantifying the flow of energy and nutrients through food webs is foundational to understanding the structure and function of ecosystems. Here, I utilize the stable carbon and nitrogen isotope analysis of individual amino acids to trace the movement of essential amino acids through terrestrial and freshwater food webs in New Mexico, USA. I first explore isotopic patterns among co-occurring terrestrial plants and aquatic algae. I then combine this molecular isotopic approach with 16S and 18S rRNA sequencing to demonstrate the importance of gut microbiota as sources of essential amino acids to wild mammalian hosts. Next, I explore the roles of …

A Pooling Strategy For Detecting Carbapenem Resistance Genes By The Xpert Carba-R Test In Rectal Swab Specimens, Fred C. Tenover, Peng Zhang, Qi Wang, Chaoe Zhou, Feifei Zhang, Xinghui Gao, Yi-Wei Tang, Hui Wang

Biology Faculty Publications

Rapid and accurate detection of carriers of carbapenemase-producing organisms (CPO) in hospitalized patients is critical for infection control and prevention. This study aimed to evaluate a pooling strategy for the detection of carbapenem resistance genes (CRG) in multiple specimens using the Xpert Carba-R test. Two rectal swabs each were collected from 415 unique patients. One swab was tested by Carba-R on the five specimen-pooled strategy. The other swab was tested individually by culture followed by DNA sequence analysis for CRG as the reference. At the first 5:1 pooling testing, 22 of 83 pools were positive, which yielded 34 positives from …

College Of Natural Sciences Newsletter, September & October 2022, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 3, Issue 6

Page 1 Dean's Message
Page 2 Awards & Recognition
Page 3 Midwest Regional ACS Meeting
Page 4 North Central ASM Meeting
Page 5 Geography Department Travel
Page 6-7 Media Coverage of CNS
Page 7 REMAST Program at SDState receives national spotlight
Page 8 Celebrating the lives of those who touched the College
Page 9 Innovative Learning Spaces
Page 10 Open PRAIRIE Data
Page 11 2022 CNS Scholarship Brunch
Page 12-14 Fall 2022 Outreach Events

Viruses In Astrobiology, Ignacio De La Higuera, Ester Lázaro

Biology Faculty Publications and Presentations

Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very …

Bird Species Define The Relationship Between West Nile Viremia And Infectiousness To Culex Pipiens Mosquitoes, Jefferson A. Vaughan, Robert Newman, Michael J. Turrell

Biology Faculty Publications

The transmission cycle of West Nile virus (WNV) involves multiple species of birds. The relative importance of various bird species to the overall transmission is often inferred from the level and duration of viremia that they experience upon infection. Reports utilizing in vitro feeding techniques suggest that the source and condition of blood in which arboviruses are fed to mosquitoes can significantly alter the infectiousness of arbovirus to mosquitoes. We confirmed this using live hosts. A series of mosquito feedings with Culex pipiens was conducted on WNV-infected American robins and common grackles over a range of viremias. Mosquitoes were assayed …

Leaf Phenology And Freeze Tolerance Of The Invasive Tree Pyrus Calleryana (Roseaceae) And Potential Native Competitors, Margaret E. Maloney, Abby Hay, Eric B. Borth, Ryan W. Mcewan

Biology Faculty Publications

Pyrus calleryana is one of the most problematic invasive species in the eastern United States. The mechanisms that enable Py. calleryana to establish and outcompete native plants are not fully understood but likely include a profile of advantageous traits. Extended leaf phenology is a characteristic noted in many woody invasive plants. Leaf phenology of Py. calleryana and two native woody species, Populus deltoides and Platanus occidentalis, was observed in natural areas near Dayton, OH from December 2019 to November 2020. A frost event in May also gave us the serendipitous opportunity to assess frost tolerance of these species. We …

Characterisation And Antimicrobial Potential Of Actinobacteria Isolated From Momela Soda Lakes, Tanzania, Witness S. Lema, Ally Mahadhy, Modester Damas, Joan J.E. Munissi, Thomas J. Lyimo

Tanzania Journal of Science

Extreme environments such as soda lakes are potential sources of microbes with biotechnological applications in different sectors. This study aimed at isolation, characterization and investigation of antibacterial potential of actinobacteria from Momela Soda Lakes, at Arusha National Park in Tanzania. One hundred and twenty (120) isolates were recovered from soil and water samples using the dilution plate technique. The isolates were morphologically and biochemically characterized, and further, screened for antimicrobial activity by disc diffusion method as well as the micro dilution technique. Cytotoxic effects were determined using the brine shrimp lethality test. Results showed that, all 120 isolates were Gram-positive …

Chemical Composition And Bioactive Potential Of Extracts From Diospyros Capricornuta F. White Against Aspergillus Flavus And Aspergillus Parasiticus, Princess W. Ngowi, Juma A. Mmongoyo, Lilian D. Kaale

Tanzania Journal of Science

Diospyros capricornuta is an endemic species widely distributed along the coast of Tanzania that is used as food condiments and traditional medicine. The chemical compositions of Diospyros capricornuta leaves, stem-bark, and root-bark extracts; and their bioactive potentials against Aspergillus flavus and Aspergillus parasiticus were investigated. The leaves, stem-bark, and root-bark samples of D. capricornuta were extracted using Soxhlet apparatus and the resultant extracts were analyzed using Gas Chromatography-Mass Spectrometry (GC-MS). A total of 14 compounds were identified from the extracts, whereby 2,4-di-tert-butylphenol was the most abundant compound in all extracts. The growth and aflatoxin production inhibitions against A. flavus and …

Pulse-Field Analysis Diversity Of Extended Spectrum Beta Lactamases Producing Gram Negative Bacteria Isolated From Periplaneta Americana (Cockroaches), Omolara D. Popoola, Moses O. Efuntoye, Georgia C. Agu, Benjamin T. Thomas

Tanzania Journal of Science

Extended spectrum beta lactamase (ESBL) producing bacteria are organisms of public health significance that have been implicated in prolonged hospital stay, treatment failures and higher fatalities. These organisms were originally thought to be widely distributed in hospital, but have since grown in terms of their epidemiological coverage. This study was therefore aimed at using pulse-field gel electrophoresis (PFGE) to understand the diversity of ESBL producing organisms originating from cockroaches in Ago-Iwoye, Nigeria. The diversity was determined by using a set of twenty six (26) ESBL producing bacterial strains isolated from cockroaches sampled in Ago-Iwoye community, Ogun State, Nigeria. PFGE analysis …

Forty Years Without Family: Three Novel Bacteriophages With High Similarity To Spp1 Reveal Decades Of Evolutionary Stasis Since The Isolation Of Their Famous Relative, Veronique A. Delesalle, Brianne E. Tomko, Albert C. Vill, Katherine B. Lichty, Gregory P. Krukonis

Biology Faculty Publications

SPP1, an extensively studied bacteriophage of the Gram-positive Bacillus subtilis, is a model system for the study of phage–host interactions. Despite progress in the isolation and characterization of Bacillus phages, no previously fully sequenced phages have shared more than passing genetic similarity to SPP1. Here, we describe three virulent phages very similar to SPP1; SPP1 has greater than 80% nucleotide sequence identity and shares more that 85% of its protein coding genes with these phages. This is remarkable, given more than 40 years between the isolation of SPP1 and these phages. All three phages have somewhat larger genomes and more …

Genetic Determinants Of Carotenoid Pigmentation In The Opportunistic Pathogen Mycobacterium Kansasii, Niklas Janisch

Dissertations, Theses, and Capstone Projects

Mycobacterium kansasii (Mk) is an opportunistic pulmonary pathogen causing infections, predominantly in immunocompromised people, with symptoms similar to those caused by its close relative Mycobacterium tuberculosis (Mt). In contrast to the latter, little work has been done on Mk genetics and even less on its defining characteristic of photochromogenicity, the controlled expression of carotenoid pigments in response to light exposure.

This work represents major progress in the investigation of pigmentation-related genetic factors in Mk. We report the creation of a large-scale, random transposon-insertion mutant library of Mk and its subsequent screening for mutants with an aberration in the …

Nla28 Activator Modulates Σ54-Dependent Gene Regulation In Myxococcus Xanthus, Muqing Ma

Dissertations - ALL

The complex life cycle of Myxococcus xanthus makes it a model organism for studying multicellular developmental processes in bacteria. In response to environmental changes, M. xanthus cells collectively and dramatically adjust their morphology, physiological functions, and biosynthesis. Particularly, M. xanthus copes with starvation by producing fruiting bodies filled with dormant and stress-resistant spores. During secondary metabolism, it synthesizes polyketide (PK) and non-ribosomal peptide (NRP) natural products that are crucial sources of antibiotics. Bacteria including M. xanthus, require the alternative σ54 regulatory system to initiate the transcription of necessary genes for settling stress and completing developmental process. This dissertation introduces in …

Mechanisms Of Carbapenemase-Mediated Resistance Among High-Risk Pseudomonas Aeruginosa Lineages In Peru, Isabella A. Tickler, Juan Carlos Gomez De La Torre, Luis Alvarado, Anne E. Obradovich, Fred C. Tenover

Biology Faculty Publications

Objectives: Pseudomonas aeruginosa is one of the leading causes of healthcare-associated infections globally. High-risk carbapenemase-encoding P. aeruginosa clones are disseminating in many regions. The aim of this study was to learn more about the lineages and mechanisms of resistance of P. aeruginosa circulating in Peru.

Methods: A total of 141 carbapenemase-producing isolates recovered from hospitalized and ambulatory patients in Lima were sequenced and analyzed to infer their lineages through whole-genome sequence typing (wgST) and to identify their antimicrobial resistance genes.

Results: wgST identified nine sequence types (STs); ST111 and ST357 were the most frequently encountered (44.0% and 38.3%, respectively), followed …

Microbial Dimension Of Symbiosis And Dysbiosis In Fungus–Gardening Ants, Blake S. Bringhurst

Biology Theses

With symbiotic partners, the means by which a host obtain a symbiont influence the specificity between the host and the symbiont. One such system where symbiont specificity is seen to varying degrees is with higher attine ants. Higher attine ants have symbiotic relationships with the fungal cultivar they grow and the bacterial symbionts in their microbiomes. Among the higher attines, there are two broad groups of fungi. Most ants in the genus Trachymyrmex tend to grow Clade–B fungi, which are a group of undescribed Leucocoprinus species, while leaf–cutting ants in the genera Acromyrmex and Atta tend to grow Clade–A fungi …

Complete Genome Sequences Of Two Temperate Bacillus Subtilis Phages Isolated At Tumamoc Hill Desert Laboratory, Gregory P. Krukonis, Amanda K. Kemp, Katie F. Storrie, Vivian R. Chavira, Hayden W. Lantrip, Victoria D. Perez, Desiree A. Reyes, Julian A. Truax, Rachel Loney, Veronique A. Delesalle

Biology Faculty Publications

Bacteriophages are important in structuring bacterial communities, including desert soils dominated by Bacillus species. Here, we describe two genetically similar temperate phages isolated on a Bacillus subtilis strain from soil in Tucson, Arizona. Their double-stranded DNA (dsDNA) genomes contain 98 and 102 genes, with a set of 4 genes being found in only one phage.

Effects Of Mass Death On Community Structure And Ecosystem Function, Abby Kimpton Jones

Theses and Dissertations

Death and decomposition are natural processes that are generally well-understood. However, large events of death, such as mass mortality events (MMEs) are increasing in frequency and their impacts on the ecosystem are largely unknown. These events may have both bottom-up effects from increased nutrient input as well as top-down effects from loss of an ecological functional group by the affected population. Different functional MMEs may result in different top-down effects, creating cascading effects. In Chapter 1, I test the hypothesis that scavenger and herbivore simulated MMEs generate novel bottom-up and top-down effects. Results indicate that MMEs have a significant effect …

Genome Sequence Of The Estuarine Synechococcus Sp. Strain Nb0720_010, Campbell A. Mackenzie, Marcia F. Marston, Javier F. Tabima, Nathan A. Ahlgren

Arts & Sciences Faculty Publications

Synechococcus spp. are unicellular cyanobacteria widely distributed in the world's oceans. We report the complete genome sequence of Synechococcus sp. strain NB0720_010, isolated from Narragansett Bay, Rhode Island. NB0702_10 has several large (.3,000-amino acid) protein-coding genes that may be important in its interactions with other cells, including grazers in estuarine habitats.

College Of Natural Sciences Newsletter, July & August 2022, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 3, Issue 5

Page 1 Dean's Message
Page 2 Awards & Recognition
Page 3 Resources for Student Success
Page 4 Welcome to New Faculty & Staff
Page 5 Summer Activities in CNS
Page 9 Celebrating the lives of those who touched the College
Page 10 Media Coverage of CNS
Page 12 Open PRAIRIE Data
Page 13 Snaps from he start of the semester
Page 14 Science as Art Competition

An Overview Of The Extracurricular Polysaccaride Production Of Probiotic Lactic Acid Bacteria, Olujimi Babajide Olowokere

Theses (2016-Present)

The study focuses on a comprehensive review of lactic acid bacteria and their production of extracellular polysaccharide substrates (EPS). Two important factors are addressed in the work; and these are 1) identification of LAB stains found in the commercially sold daily milk, 2) significant factors impacting polysaccharide production. Motivation behind these focus points is to allow further inquiries and studies on exploring these strains of bacteria for human wellness promotion. With microbial EPS production being a recent interest of study among healthcare and food industries sectors, new species of bacteria are extensively exploited for further investigation to improve human health, …

Arsr Family Regulator Msmeg_6762 Mediates The Programmed Cell Death By Regulating The Expression Of Hnh Nuclease In Mycobacteria, Xiangke Duan, Xue Huang, Junqi Xu, Xue Li, Jingjing Niu, Xiaoli Du, Xiaoyu Wang, Jiang Li, Michael Kelly, Jiaohan Guo, Ke Zhang, Yu Huang, Biao Kan, Jianping Xie

Biology Student Work

Programmed cell death (PCD) is the result of an intracellular program and is accomplished by a regulated process in both prokaryotic and eukaryotic organisms. Here, we report a programed cell death process in Mycobacterium smegmatis, an Actinobacteria species which involves a transcription factor and a DNase of the HNH family. We found that over-expression of an ArsR family member of the transcription factor, MSMEG_6762, leads to cell death. Transcriptome analysis revealed an increase in the genes’ transcripts involved in DNA repair and homologous recombination, and in three members of HNH family DNases. Knockout of one of the DNase genes, MSMEG_1275, …

Increasing The Resilience Of Plant Immunity To A Warming Climate, Jong Hum Kim, Christian Castroverde, Shuai Huang, Chao Li, Richard Hilleary, Adam Seroka, Reza Sohrabi, Diana Medina-Yerena, Bethany Huot, Jie Wang, Sharon Marr, Mary Wildermuth, Tao Chen, John Macmicking, Sheng Yang He

Biology Faculty Publications

Extreme weather conditions associated with climate change affect many aspects of plant and animal life, including the response to infectious diseases. Production of salicylic acid (SA), a central plant defence hormone, is particularly vulnerable to suppression by short periods of hot weather above the normal plant growth temperature range via an unknown mechanism. Here we show that suppression of SA production in Arabidopsis thaliana at 28 °C is independent of PHYTOCHROME B (phyB) and EARLY FLOWERING 3 (ELF3), which regulate thermo-responsive plant growth and development. Instead, we found that formation of GUANYLATE BINDING PROTEIN-LIKE 3 (GBPL3) defence-activated biomolecular condensates (GDACs) …

Antibiotic-Resistant Escherichia Coli And EnterococcusSpp. In Sand And Water At Tampa Bay Beaches, Jennifer K. Sabater

USF Tampa Graduate Theses and Dissertations

As antibiotic resistance in the environment continues to rise there is an increased concern that infections may become harder to treat as bacteria acquire genes for multidrug resistance. Recreational beach waters in the Tampa Bay area are routinely monitored by the Florida Department of Environmental Protection for the presence of fecal indicator bacteria (FIB) such as Escherichia coli and enterococci. Exceedances of beach action values (BAV) 235 CFU/100 mL (E. coli) and 70 CFU/100 mL (enterococci) indicate the presence of fecal contamination which is associated with an increased risk of disease for beachgoers. Antibiotic-resistant E. coli and Enterococcus spp. have …

Investigating The Antagonistic Activity Of Asymptomatic Bacteriuria Against Uropathogenic E. Coli., Ciara Kenneally

ORBioM (Open Research BioSciences Meeting)

Asymptomatic bacteriuria (ABU) is the presence of bacteria in urine, resembling a state of commensalism. Bacteria are characterised as ABU when they have been isolated from two consecutive urine samples (≥ 10⁵ CFU/ml) from individuals, but without symptoms attributable to a urinary tract infection (UTI). ABU Escherichia coli strains have evolved from uropathogenic ancestors and lack virulence factors associated with uropathogenic E. coli (UPEC). UPEC are the main etiological agent of urinary tract infections (UTIs), attributable to > 80% of cases. The frequency at which multidrug-resistant UPEC are isolated is affecting guidelines for use of former first-line antibiotics for UTIs, …

College Of Natural Sciences Newsletter, May & June 2022, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 3, Issue 4

Page 1 Dean's Message
Page 2 Awards and Recognition
Page 3-4 The path to a Doctorate Degree
Page 4 American Indian Student Center Native Graduate Honoring Ceremony
Page 5 Celebrating the lives of those who touched the College
Page 6 Media coverage of CNS
Page 7 Open PRAIRIE
Page 8-10 CNS Graduation Festivities
Page 11-14 Spring 2022 Dean's List
Page 16 Richard and Janice Vetter Endowed Professorship in Biotechnology.position

Biomass Estimation Of Marine Biofilms On Plastic Surfaces, Kian Banihashemi, Fernando Javier Gil

Biological Sciences

Plastics have become a major source of marine pollution, which threatens food safety and quality, human health, and marine ecosystems. Due to the drastic negative effects of plastics in a marine environment, alternative biodegradable plastics are being generated that are more eco-friendly and have less environmental impact. Though some of these plastics are known to biodegrade, the process of degradation for bioplastics has not been heavily studied in a marine environment. This pilot project sought to both quantify the process of biodegradation and compare across different methods for effectiveness of biomass estimation, which serves as an indicator of biodegradation. Plastics …

The Nature Of Phenotypes: Provoking And Measuring The Dynamic Processes Of Swarm Expansion, Predation, And Antibiotic Resistance In Myxococcus Xanthus, Linnea Judith Ritchie

Dissertations - ALL

The question of how genotype affects phenotype has fascinated and puzzled scientists for generations. Regardless of organism, the correlation between observation and underlying condition is necessary for scientists to understand the world around us. Myxococcus xanthus, a fascinating organism with a large genome (7,314 genes), is known for complex social behaviors and is an excellent model system for the study of this relationship. Upon starvation, M. xanthus cells condense into large multicellular aggregates to await renewed nutrient availability. M. xanthus cells swarm together on surfaces as a predatory biofilm, lysing and killing prey as a singular unit. During predation, swarms …

Detecting Potentially Neurotoxic Pseudo-Nitzschia Species In The Grand Strand Area, Chesney Price

Honors Theses

Pseudo-nitzschia is a globally distributed diatom genus which contains 26 neurotoxin (domoic-acid) producing species. In shallow coastal waters these diatoms are associated with both the development of harmful algal blooms and the bio-accumulation of toxins in shellfish that can impact human health. Pilot data recovered in 2018 indicated the presence of multiple species of Pseudo-nitzschia, including domoic-acid producing taxa. We hypothesize that we will recover a similar species diversity using multiple sampling dates during the summer of 2021. Environmental DNA (eDNA) samples taken from the public shellfish harvesting area waters at Huntington Beach State Park (SC) over a two month …

Effect Of Mycorrhizae Inoculation On The Growth And Success Of Three Taxodium Distichum Hybrids In Saline - Impacted Coastal Soils, Elif Ilhan

Electronic Theses and Dissertations

In 2008, Galveston Island was severely impacted by Hurricane Ike, resulting in high salt deposition in the soil and groundwater. This caused a loss of many native plant species. A study was initiated to determine effective ways to promote the growth conditions of three bald cypress genotypes (Taxodium distichum var distichum and Taxodium distichum var mexicanum crosses) in salt-affected soils. The treatments applied were mycorrhizae inoculation, fertilizer application, and a combination of mycorrhizae inoculation and fertilizer application. A total of sixty (60) trees planted in plots of three rows and divided into five randomized replication blocks of four treatments …