Biology Commons^™

Rna-Seq Of Borrelia Burgdorferi In Multiple Phases Of Growth Reveals Insights Into The Dynamics Of Gene Expression, Transcriptome Architecture, And Noncoding Rnas, William K. Arnold, Christina R. Savage, Catherine A. Brissette, Janakiram Seshu, Jonathan Livny, Brian Stevenson

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Borrelia burgdorferi, the agent of Lyme disease, differentially expresses numerous genes and proteins as it cycles between mammalian hosts and tick vectors. Insights on regulatory mechanisms have been provided by earlier studies that examined B. burgdorferi gene expression patterns during cultivation. However, prior studies examined bacteria at only a single time point of cultivation, providing only a snapshot of what is likely a dynamic transcriptional program driving B. burgdorferi adaptations to changes during culture growth phases. To address that concern, we performed RNA sequencing (RNA-Seq) analysis of B. burgdorferi cultures at early-exponential, mid-exponential, and early-stationary phases …

Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, Jillian L. Mccool Ms., Nick Hum, Gabriela G. Loots

STAR Program Research Presentations

The CRISPR-Cas system is an adaptive immune system found in bacteria which helps protect against the invasion of other microorganisms. This system induces double stranded breaks at precise genomic loci (1) in which repairs are initiated and insertions of a target are completed in the process. This mechanism can be used in eukaryotic cells in combination with sgRNAs (1) as a tool for genome editing. By using this CRISPR-Cas system, in addition to the “safe harbor locus,” ROSAβ26, the incorporation of a target gene into a site that is not susceptible to gene silencing effects can be achieved through few …

Patterns In Richness And Community Structure: From Bacteria To Apex Predators, Ara S. Winter

Biology ETDs

Patterns of community structure and richness provide context for studies from microbial ecology, global macroecology, languages, to Bayesian statistics. Diversity patterns for animals on land and their predictor variables are well studied. However, diversity patterns for bacterial communities and marine macroorganisms are not well studied or understood. Here I examine diversity patterns in caves, on the external surface of Chiroptera (bats), and in marine ecosystems. At the local to regional scale we investigate factors that drive bacterial community patterns in richness and composition in lava cave microbial mats and microbes on bats. Lastly, out of the cave and into the …

Impacts From The Use Of Antibiotics In Livestock: Methods Of Transmission Of Antibiotic Resistance From Livestock To Humans, Kristin M. Walden

Biology: Student Scholarship & Creative Works

Antibiotic use in livestock production has been around since the 1950s. Antibiotic feed is used in livestock and other meat producing animals for three reasons: illness prevention, illness treatment, and growth promotion. Unfortunately, since the time that antibiotics were first invented, antibiotic resistant bacteria have become a threat to public health. There are many studies showing methods of transmission of antibiotic resistance from livestock to humans. Antibiotic resistance can spread from livestock to soil, water, insects, and food, which ultimately comes into contact with humans. A proposed study to measure antibiotic resistance when eliminating antibiotic feed will provide a hypothesis …

Antibiotic Resistant Bacteria In Natural Environments Within Kentucky., Steve Tran

College of Arts & Sciences Senior Theses

Rates of antibiotic resistance in bacteria are rapidly rising; this is, in part, due to overuse of antibiotics resulting in a great burden on the U.S. healthcare system. With the rise of resistant bacteria, a large-scale outbreak of antibiotic resistant bacterial infections may also occur. Research on developing antibiotics has also decreased. Thus healthcare is at a great disadvantage in the arms race against bacteria. The environmental reservoirs of antibiotic resistance are currently being explored in Kentucky, in which bacteria have been collected from a broad spectrum of natural environments to analyze their antibiotic resistant capabilities and their interactions with …

An Analysis Of Bacterial Contamination Of Chicken Eggs And Antimicrobial Resistance, Holly Spitzer

All College Thesis Program, 2016-2019

Chicken eggs are a major component of American diets, with an average yearly consumption of approximately 250 eggs per person (American Humane Society). While highly nutritious, eggs are also one of the leading causes of food poisoning and food borne illness in the United States. Eggs may become contaminated by a number of different types of bacteria during production, including Salmonella, a group of bacteria that, according to the CDC, causes more than 1.2 million cases of food borne illness in the United States every year. In an effort to decrease the frequency of bacterial contamination, many food producers …

The Signature Of God In Medicine And Microbiology An Apologetic Argument For Declarative Design In The Discoveries Of Alexander Fleming, Alan L. Gillen, Michael Cargill

Faculty Publications and Presentations

In logic and reasoning, a signature indicates the presence of an author; likewise, the characteristics of staphylococci indicate the presence of a Creator. Staphylococci and its “kind” are common bacteria, particularly in colonized people.1 Staphylococcus aureus has a complex molecular mechanism of assembling its golden pigment, staphyloxanthin. The biosynthesis of staphyloxanthin is a stellar example of irreducible complexity. Similar to staphylococci, the life and works of Alexander Fleming show the fingerprints of Providence. The so-called “serendipitous” achievements of Fleming have contributed to modern medicine, convincing Fleming and others that God was at work in his life. Fleming recognized that …

Isolation And Characterization Of Microbial Community Associated With Diadumene Lineata, The Orange-Striped Sea Anemone, Tiffany Lin, Andrew Weir

Student and Faculty Research Days

The orange-striped sea anemone, Diadumene lineata, is a marine invertebrate that can be found in the Northern Hemisphere. Distribution of Diadumene lineata ranges from Japan to the Gulf of Argentina. This invasive anemone originated from the Pacific Coast of Asia and serves as a host for a diverse microbial community including a photosynthetic alga. The epiphytic bacteria adhere to the outer surface as well as to the gastrovascular cavity of the host. The microbial community associated with Diadumene lineata is relatively unknown. This study attempted to isolate and identify bacteria commonly associated with this invasive marine invertebrate. Diadumene lineata was …

The Loss Of Methanol Utilization In Methylobacteria, Justin T. Skariah

Theses and Dissertations

Methylobacteria primary uses Cl substrates as a carbon and energy source. This experiment was performed to see if Methylobacteria would lose the ability to use Cl compound methanol after prolonged exposure to multi-carbon substrates. To determine this, the bacteria was grown on MR2A3 (multi-carbon substrates) and MOM (single-carbon substrates) for multiple generations and tested for loss of function on a series of generations. These tests include streaking plates of MOM and R2A with bacteria from MR2A3 then getting a bacterial colony count and also toothpick transfers of the colonies to verify findings. After 20 generations there were no significant decrease …

A Comprehensive Benchmarking Study Of Protocols And Sequencing Platforms For 16s Rrna Community Profiling, Rosalinda D’Amore, Umer Zeeshan Ijaz, Melanie Schirmer, John G. Kenny, Richard Gregory, Alistair C. Darby, Migun Shakya

Dartmouth Scholarship

In the last 5 years, the rapid pace of innovations and improvements in sequencing technologies has completely changed the landscape of metagenomic and metagenetic experiments. Therefore, it is critical to benchmark the various methodologies for interrogating the composition of microbial communities, so that we can assess their strengths and limitations. The most common phylogenetic marker for microbial community diversity studies is the 16S ribosomal RNA gene and in the last 10 years the field has moved from sequencing a small number of amplicons and samples to more complex studies where thousands of samples and multiple different gene regions are interrogated. …

Isolation And Identification Of Bacterial Endosymbionts In The Brooding Brittle Star Amphipholis Squamata, Abbey Rose Tedford

Honors Theses and Capstones

Symbiotic associations with subcuticular bacteria (SCB) have been identified and studied in numerous echinoderms, including the SCB of the brooding brittle star, Amphipholis squamata. These SCB, however, have not been studied using current next generation sequencing technologies. Previous studies on the SCB of A. squamata placed these bacteria in the genus Vibrio (γ-Proteobacteria), but subsequent studies suggested that the SCB are primarily composed of α-Proteobacteria. The present study examines the taxonomic composition of SCB associated with A. squamata from the Northwest Atlantic. DNA was extracted using a CTAB protocol and 16S rRNA sequences were amplified …

Scardovia Wiggsiae Prevalence In Orthodontic Patients, Brandon Joseph Streiff

UNLV Theses, Dissertations, Professional Papers, and Capstones

Dental caries has mainly been associated with Streptococcus, Lactobacillus, Actinomyces and Veillonella species. But in recent salivary studies a new cariogenic pathogen, has been identified. This new bacteria, Scardovia wiggsiae (SW), is currently being tested within the UNLV School of Dental Medicine patient population. Although these current studies are being conducted to study its prevalence in both pediatric and adult populations, it has not been evaluated among patients with an altered oral environment as seen in patients with orthodontic appliances. Fixed orthodontic appliances increase the difficulty of removing daily plaque on and in between the teeth with standard oral hygiene …

A Newly Discovered Bordetella Species Carries A Transcriptionally Active Crispr-Cas With A Small Cas9 Endonuclease, Yury V. Ivanov, Nikki Shariat, Karen B. Register, Bodo Linz, Israel Rivera, Kai Hu, Edward G. Dudley, Eric T. Harvill

Biology Faculty Publications

Background

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) are widely distributed among bacteria. These systems provide adaptive immunity against mobile genetic elements specified by the spacer sequences stored within the CRISPR.

Methods

The CRISPR-Cas system has been identified using Basic Local Alignment Search Tool (BLAST) against other sequenced and annotated genomes and confirmed via CRISPRfinder program. Using Polymerase Chain Reactions (PCR) and Sanger DNA sequencing, we discovered CRISPRs in additional bacterial isolates of the same species of Bordetella. Transcriptional activity and processing of the CRISPR have been assessed via RT-PCR.

Results

Here we …

Comparative Analysis Of Anti-Bd Bacteria From Six Malagasy Frog Species Of Ranomafana National Park, Kelsey Savage

Senior Honors Projects, 2010-2019

As Malagasy amphibians are facing an impending extinction crisis from the lethal skin fungus Batrachochytrium dendrobatidis (Bd), it has become imperative to proactively mitigate the threat. Bd sporangia develop in the skin of infected amphibians and cause the skin to thicken, leading to ionic imbalance and eventual heart failure. It has been shown that certain bacterial species are able to inhibit Bd growth on amphibians by producing antifungal metabolites. Community-based probiotics are one approach used to combat chytridomycosis by inoculating an environment with Bd-inhibitory bacteria so that many amphibian species are treated at once. With this method, it is important …

Root Associated Microbes: The Mediators Between Plants And Soil, Sarah Livingston Dean

Biology ETDs

Globally, increasing human populations have either caused or accelerated several types of environmental change. Symbiotic microbes have powerful effects on plant fitness, yet little study has been done on how microbial-plant relationships are affected by environmental changes. In two different ecosystems I explore how either nitrogen (N) pollution or drought can alter root associated microbe (RAM)-plant relationships using Next Generation Sequencing. In moist-meadow alpine tundra at Niwot Ridge, CO, I examine the relative contribution of host identity, N enrichment, and plant neighborhood on RAM diversity and community composition in two co-dominant plant species; Geum rossii and Deschampsia cespitosa. In New …

Is There Specificity In A Defensive Mutualism Against Soil Versus Lab Nematodes, Dictyostelium Discoideum Farmers And Their Bacteria?, Boahemaa Adu-Oppong,, David C. Queller, Joan E. Strassmann

Biology Faculty Research

Background: The social amoeba Dictyostelium discoideum is a soil-dwelling microbe, which lives most of its life cycle in the vegetative stage as a predator of bacteria and as prey for nematodes. When bacteria are sparse, amoebae aggregate into a multicellular fruiting body. Some clones of D. discoideum have agriculture (Brock et al., 2011). They carry bacteria through the social stage, eat them prudently, and use some bacteria as defence against non-farming D. discoideum competitors. Caenorhabditis elegans preys on D. discoideum in the laboratory but does not encounter it in nature because C. elegans lives on rotten fruit. The nematode …

Varying Influences Of Selection And Demography In Host-Adapted Populations Of The Tick-Transmitted Bacterium, Anaplasma Phagocytophilum Speciation And Evolutionary Genetics, Matthew Aardema, Friederike D. Von Loewenich

Department of Biology Faculty Scholarship and Creative Works

Background: The host range of a pathogenic bacterial strain likely influences its effective population size, which in turn affects the efficacy of selection. Transmission between competent hosts may occur more frequently for host generalists than for specialists. This could allow higher bacterial population densities to persist within an ecological community and increase the efficacy of selection in these populations. Conversely, specialist strains may be better adapted to their hosts and consequently achieve greater within-host population densities, with corresponding increases in selection efficacy. To assess these different hypotheses, we examined the effective population sizes of three strains of the bacterium Anaplasma …

Assessment Of A Metaviromic Dataset Generated From Nearshore Lake Michigan, Siobhan C. Watkins, Neil Kuehnle, C Anthony Ruggeri, Kema Malki, Katherine Bruder, Jinan Elayyan, Kristina Damisch, Naushin Vahora, Paul O'Malley, Brianne Ruggles-Sage, Zachary Romer, Catherine Putonti

Bioinformatics Faculty Publications

Bacteriophages are powerful ecosystem engineers. They drive bacterial mortality rates and genetic diversity, and affect microbially mediated biogeochemical processes on a global scale. This has been demonstrated in marine environments; however, phage communities have been less studied in freshwaters, despite representing a potentially more diverse environment. Lake Michigan is one of the largest bodies of freshwater on the planet, yet to date the diversity of its phages has yet to be examined. Here, we present a composite survey of viral ecology in the nearshore waters of Lake Michigan. Sequence analysis was performed using a web server previously used to analyse …

Characterization Of Two Biochars Derived From Horse Muck And Their Ability To Reduce Pathogen Transport In Soil, David Griffith

Theses and Dissertations--Biosystems and Agricultural Engineering

Biochars have been created and characterized from a variety livestock manure biomass including poultry, dairy, and swine. However, no research has been conducted on the physical and chemical makeup of biochar pyrolyzed from horse muck. Two horse muck derived biochars containing either straw (HS) or woodchip (HW) bedding were pyrolyzed at 700°C and characterized for their physical and chemical properties. Tests revealed both biochars had high alkalinity, moderate specific conductivity, and low surface area as compared to other biochars in the literature. HS contained more mineral structures than HW. Scanning electron microscopy presented differences in particle shape, size, and presence …

Purification And Characterization Of Bcsc; An Integral Component Of Bacterial Cellulose Export, Emily D. Wilson Ms

Theses and Dissertations (Comprehensive)

Biofilms are a growing concern in the medical field due to their increased resistance to antibiotics. When found in a biofilm, bacteria can have antibiotic resistance 10-1000 times that of their planktonic counterparts. Therefore, it is important to study the formation of biofilms. Cellulose biofilms are formed by Enterobacteriaceae, such as many Escherichia coli and Salmonella spp. strains. Biofilms provide these species with benefits including antimicrobial protection, development of bacterial communities, promotion of DNA exchange, uptake of nutrients, and, in the case of cellulose biofilms, immune system evasion. Cellulose biofilms are controlled by the Bacterial cellulose synthesis (Bcs) complex located …

Characterization Of The Interaction Between Ftsz-Ring Stabilizer Zapc And The Conserved Protease Clpxp In E. Coli Cytokinesis, Andrea Cardenas Arevalo

Dissertations and Theses

Cell division in bacteria requires the assembly of a macromolecular protein machinery at midcell that is spatiotemporally regulated during the bacterial cell cycle. Central to the process of division is the assembly of a cytokinetic ring-like structure, termed the Z-ring, formed by polymers of the essential tubulin-homolog FtsZ. Polymerization of FtsZ is regulated by a number of proteins that bind FtsZ and regulate its assembly/disassembly mechanisms. Despite being extensively studied, the molecular nature of the diverse protein-protein interactions that regulate the assembly of FtsZ during early stages of division is not well understood. Here, I focus on an FtsZ-ring stabilizer …

Impact Of Biofilm Formation And Composition On Antibiotic Resistance In Environmental Isolates Of Escherichia Coli And Salmonella Spp., Raluca Tutulan

Theses and Dissertations (Comprehensive)

Escherichia coli and Salmonella spp., like most bacteria, prefer to grow in biofilms. These biofilms provide bacteria with protection from harsh environmental factors (such as desiccation and changes in pH), aid in the evasion of host immune responses and provide increased antibiotic resistance. Biofilms are present in non-host environments (e.g. water pipes) as well as in mammalian hosts (in the healthy gastrointestinal microbiota and in over 65% of nosocomial infections). Two important components utilized by E. coli and Salmonella spp. to form biofilms are cellulose and curli fimbriae. Curli fimbriae mediate the attachment of bacteria to abiotic surfaces and …

Acute Effects Of Tio2 Nanomaterials On The Viability And Taxonomic Composition Of Aquatic Bacterial Communities Assessed Via High-Throughput Screening And Next Generation Sequencing, Binh Chu, Tiezheng Tong, Jean-François Gaillard, Kimberley A. Gray, John J. Kelly

Biology: Faculty Publications and Other Works

The nanotechnology industry is growing rapidly, leading to concerns about the potential ecological consequences of the release of engineered nanomaterials (ENMs) to the environment. One challenge of assessing the ecological risks of ENMs is the incredible diversity of ENMs currently available and the rapid pace at which new ENMs are being developed. High-throughput screening (HTS) is a popular approach to assessing ENM cytotoxicity that offers the opportunity to rapidly test in parallel a wide range of ENMs at multiple concentrations. However, current HTS approaches generally test one cell type at a time, which limits their ability to predict responses of …

Characterization Of A Putative Cephalotoxin From The Hemocytes Of Euprymna Scolopes, Jessie E. Scott

University Scholar Projects

Many organisms have beneficial microbial symbionts, and complex interactions between the immune system and the bacteria must occur to allow these symbioses to persist. The host immune system must recognize and preferentially tolerate the beneficial microorganisms, while simultaneously eliminating harmful pathogens. The Hawaiian bobtail squid, Euprymna scolopes, is a model organism for host-microbe interactions because of the unique light organ symbiosis. Hemocytes, the squid’s primary immune cell, infiltrate and patrol the light organ and continuously interact with the symbiont Vibrio fischeri. Using this model, several innate immunity genes have been shown to be differentially expressed in the hemocytes …

Antimicrobial Resistance Of Channel Catfish Intestinal Microflora In The Arkansas And Ninnescah Rivers In Kansas, Jordan R. Hofmeier

Master's Theses or Doctor of Nursing Practice

Antimicrobial compounds have been used by humans to counteract bacterial infections since 1910. Overuse of these compounds in clinical and agricultural applications has led to rapid evolution and global spread of antimicrobial resistance and rivers are the main receiving body for antimicrobials and resistant bacteria from urban effluents and agricultural runoff. When antimicrobial-resistant bacteria enter the aquatic environment, water acts as a physical pathway for their distribution. Subsequently, resistance genes become established in natural systems and pose threats to human health and ecological processes. Due to these potential threats, antimicrobial resistance in the aquatic environment should be closely monitored. To …

Dispersal Of Antibiotic-Resistant Bacteria Near Central Great Plains Feedlots, Jennifer R. Pfannenstiel-Klaus

Master's Theses or Doctor of Nursing Practice

Antibiotic resistance is a growing concern in medical and veterinary settings. Resistance can be worsened by misuse and overuse of antibiotics. Such situations can give rise to highly resistant organisms. Ciprofloxacin, a synthetic, broad-spectrum antibiotic used to treat gram-positive and gram-negative infections in humans, has similar chemical structure to enrofloxacin, which is used to treat animals. Cross-resistance might arise because of that similarity. This research describes the dispersal and prevalence of bacteria that exhibit ciprofloxacin resistance in relation to feedlots in the central Great Plains region. Six times in 2013, six feedlots were sampled for airborne bacterial communities at, upwind …

Antimicrobial And Antiinsectan Phenolic Metabolites Of Dalea Searlsiae, Gil Belofsky, Mario Aronica, Eric Foss, Jane Diamond, Felipe Santana, Jacob Darley, Patrick F. Dowd, Christina M. Coleman, Daneel Ferreira

All Faculty Scholarship for the College of the Sciences

Continued interest in the chemistry of Dalea spp. led to investigation of Dalea searlsiae, a plant native to areas of the western United States. Methanol extractions of D. searlsiae roots and subsequent chromatographic fractionation afforded the new prenylated and geranylated flavanones malheurans A–D (1–4) and known flavanones (5 and 6). Known rotenoids (7 and 8) and isoflavones (9 and 10) were isolated from aerial portions. Structure determination of pure compounds was accomplished primarily by extensive 1D- and 2D-NMR spectroscopy. The absolute configurations of compounds 1–5, 7 …

Bacteria As Bioindicators: Bioassessment In The Bonneville Basin Of Utah, Mark Merkley, Russell Rader

Journal of Undergraduate Research

Bioassessment is the practice of using organisms to detect environmental health and integrity. Ecosystem health and integrity depend on the interaction between living organism and ecosystem function. All organisms or groups of organisms do not respond the same to environmental stress. Depending on various disturbance characteristics, each group may respond at different rates and provide different information (Rader, 2001). Besides the usual macrophytes, macroinvertebrates, or algae, bacteria have the capability of being strong bioindicators. Because of their extremely small size, bacteria have the highest surface-to volume ratios of any living organisms. Thus, bacteria should be the most environmentally aware organisms, …

Effect Of Prey Richness On A Consumer’S Intrinsic Growth Rate, Brian J. Darby, Michael A. Herman

School of Biological Sciences: Faculty Publications

The intrinsic growth rate of nonselective microbivores increases asymptotically with increasing prey biomass, but we do not know how intrinsic growth rate is affected by prey richness. The objective of this experiment was to determine the effect of prey richness on the growth kinetics of nematode predators while grazing on mixed bacterial lawns. We found that the intrinsic growth rate of Caenorhabditis elegans in laboratory culture increased asymptotically with prey richness. The mechanism of this pattern was primarily due to the best available prey species in the mixture: the intrinsic growth rate of the consumer feeding on a mixture of …

Structure-Function Analysis Of Zapc, An Ftsz-Ring Stabilizer, In Escherichia Coli Cytokinesis, Lukasz Tchorzewski

Dissertations and Theses

In Escherichia coli, cell division is defined by the polymerization and constriction of a cytokinetic ring (Z ring) formed by FtsZ, a tubulin-like GTPase, at midcell. Division also involves the formation of a multi-protein complex at midcell known as the divisome. Several divisome proteins promote the assembly/disassembly processes of FtsZ, thereby exercising spatiotemporal control over division. Among FtsZ regulatory proteins are the FtsZ ringassociated proteins (Zap), which either directly or indirectly stabilize the Z-ring by increasing lateral interactions amongst FtsZ protofilaments in the Z-ring. ZapA-D are recruited during early cytokinesis and have overlapping functions in stabilizing FtsZ at midcell, but …