Microbiology Commons^™

Investigating Oxidative Stress And Large-Scale Genomic Reduction In Vibrio Natriegens Through The Development And Application Of New Genetic Techniques, Elizabeth Glasgo

Doctoral Dissertations

Vibrio natriegens is the fastest replicating bacterium and recent work has demonstrated its potential for biotechnology and synthetic biology applications. While these industries have been the focus of V. natriegens research, it offers a promising system for diverse laboratory studies. However, currently a complete understanding of V. natriegens biology is lacking. As such, there is a need to advance genetic techniques and physiological understanding to better inform all aforementioned applications. Here we describe our contributions to the growing field of V. natriegens genetics and the application of these new techniques to study physiological processes and themes in genome evolution. Briefly, …

Antimicrobials Produced By Ants: Chemical Properties And Microbe Specificity, Katy Chon, Clint A. Penick

Master's Theses

Antibiotic resistance is a growing public health concern worldwide, and for over a decade, we have been witnessing the growth of difficult to treat infectious diseases caused by bacteria that are becoming resistant to antibiotics. This resistance can be mostly related to the misusing and improper use of antibiotics in both humans and animals. To restore this problem, humans have turned to new sources for the production of antibiotics. In this study, we focused on using ants. Social insects, including ants and bees, have faced strong disease pressures during their evolution and have developed a range of methods to fight …

Investigating The Development Of Alcohol Tolerance In The Eskape Pathogens, Hannah Durkee

West Chester University Master’s Theses

Antiseptics and disinfectants are used globally to kill or inhibit the growth of bacteria to prevent infection. Considering the well-documented development of antibiotic resistance, the potential for evolved tolerance to alcohol-based antimicrobial agents raises concern. The ESKAPE bacterial pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) are a major cause of healthcare-associated mortality and present a threat to public health due to the progression of multi-drug resistance. We conducted an experiment to determine if the ESKAPE pathogens develop an increased tolerance to ethanol upon repeated exposure by selecting for survivors after a …

Probiotic Compounds Inhibit Staphylococcus Aureus Biofilm Formation, Reduce Virulence, & Improve Antibiotic Sensitivity, Kyle R. Leistikow

Dissertations (1934 -)

Multidrug-resistant (MDR) bacterial infections are a top five global public health threat, causing 2.8 million infections and 35,000 deaths annually in the US alone. Staphylococcus aureus is one of the most clinically important MDR pathogens in the world with infections leading to high rates of morbidity and mortality in both humans and animals. This bacterium's ability to form protective biofilms further complicates classical antibiotic interventions, highlighting the need for new therapeutics with novel mechanisms of action. The goal of this dissertation was to investigate antibiofilm mechanisms employed by probiotic bacteria to reduce S. aureus virulence and mitigate antimicrobial resistance evolution …

Impacts Of Bacterial Evolution On Host Lethality In Drosophila, Andrew Preston

College of Arts & Sciences Senior Honors Theses

Evolution is the process by which species change their genetic traits, such as the pathogenicity of bacteria, over time in response to changes in their environment. Although the genetic mechanisms underlying many evolutionary processes have been revealed, it is still not well understood how opportunistic pathogens, such as Pseudomonas aeruginosa, become virulent. The overall goal of this thesis is to test the Coincidental Evolution Hypothesis, which proposes that the virulence of opportunistic pathogens evolves coincidentally as a by-product of their interaction with their natural predators. I hypothesized that the virulence of ancestral Pseudomonas aeruginosa changes over time if it co-evolves …

Effect Of Sub-Inhibitory Wastewater Stressors On Mutation Frequency In Clinically Relevant Aeromonas Species, Brandon Michael Schultz

Theses and Dissertations

Antimicrobial resistance among pathogens is steadily increasing resulting in untreatable infections and elevated mortality rates, with an estimation of claiming 10 million lives worldwide by 2050. A common factor accelerating resistance is the presence of sub-inhibitory microbial stressors (e.g. antimicrobials, heavy metals, and disinfectants), which can drive horizontal gene transfer and mutagenesis in various environments. Improper disposal of pharmaceuticals, excretion of antimicrobial byproducts from humans and livestock, and excess storm runoff are common sources of these pollutants. An environmental reservoir rich in stressors and bacterial populations, including the emerging pathogen Aeromonas, is wastewater. Our objective in this study was to …

On The Relationship Of Diabetes And Sleep Apnea: Evolution And Epigenetics, Nancy Wilson

Undergraduate Honors Theses

This thesis gives an overview of the relationship between diabetes, sleep apnea, obesity, and heart disease. It then addresses evidence that the traditional understanding of this relationship is incomplete or misleading. In the process, there is a brief discussion of the evolutionary rationale for the development and retention of sleep apnea in light of blood sugar dysregulation, as an adaptive mechanism in response to environmental stressors, followed by a brief overview of the general concepts of epigenetics. Finally, this paper presents the results of a literature search on the epigenetic marks and changes in gene expression found in sleep apnea …

Why Do Antibiotics Exist?, Fabrizio Spagnolo, Monica Trujillo, John J. Dennehy

Publications and Research

In the struggle with antibiotic resistance, we are losing. There is now a serious threat of moving into a postantibiotic world. High levels of resistance, in terms of both frequency and strength, have evolved against all clinically approved antibiotics worldwide. The usable life span of new clinically approved antibiotics is typically less than a decade before resistance reaches frequencies so high as to require only guarded usage. However, microbes have produced antibiotics for millennia without resistance becoming an existential issue. If resistance is the inevitable consequence of antibiotic usage, as has been the human experience, why has it not become …

A Cophylogenetic Analysis Of Fungus Gardening Ants And Their Symbiotic Fungi, Katherine Beigel

Biology Theses

Fungus-growing ants (Tribe Attini) and their fungal cultivars share a 50-million-year coevolutionary history. Large scale phylogenetic analyses depict a strong co-phyletic signal among ants and their farmed fungi yet fungus sharing among unrelated ant lineages is somewhat widespread. An overview of sharing has been hampered by a lack of genetic markers that exhibit intraspecific variation and surveys across geographic regions. For example, previous studies have shown similar sequences of the internal transcribed spacer (ITS) region of fungus in different species of Trachymyrmex, suggesting that these ant species are farming the same fungal clone. To examine whether this was a …

From Genes To Ecosystems: Resource Availability And Dna Methylation Drive The Diversity And Abundance Of Restriction Modification Systems In Prokaryotes, Spiridon E. Papoulis

Doctoral Dissertations

Together, prokaryotic hosts and their viruses numerically dominate the planet and are engaged in an eternal struggle of hosts evading viral predation and viruses overcoming defensive mechanisms employed by their hosts. Prokaryotic hosts have been found to carry several viral defense systems in recent years with Restriction Modification systems (RMs) were the first discovered in the 1950s. While we have biochemically elucidated many of these systems in the last 70 years, we still struggle to understand what drives their gain and loss in prokaryotic genomes. In this work, we take a computational approach to understand the underlying evolutionary drivers of …

Effects Of Evolution On Laboratory Sublines Of Myxococcus Xanthus Dk1622, Mackenzie Ryan, Francesca Scribano, Kimberly Murphy

Celebration of Learning

Microbes have served as effective models for studying evolution because of their ability to be easily replicated, stored, and manipulated. Myxococcus xanthus is a soil bacterium that has served as a model organism in many laboratories. The unique social and motile behaviors exhibited by this bacterium make it ideal for phenotypic assays. A wild-type strain of M. xanthus, DK1622, has been distributed to laboratories across the United States and therefore we now have DK1622 sublines. The genomes of a number of these sublines have been sequenced and their social and motile phenotypes have been analyzed. When nine of these sublines …

Tetrameric Photosystem I: From Initial Discovery And Characterization In Chroococcidiopsis Sp. Ts-821 To Exploration Of Its Distribution And Understanding Of Its Significance In Cyanobacteria, Meng Li

Doctoral Dissertations

Photosystem I (PSI) forms trimeric complexes in most characterized cyanobacteria. We had reported the tetrameric form of PSI in the unicellular cyanobacterium, Chroococcidiopsis sp. TS-821 (TS-821). Using Cryo-EM, a 3D model of the PSI tetramer structure at 11.5 [Angstrom] resolution was obtained and a 2D map within the membrane plane of at 6.1 [Angstrom]. In contrast to the three-fold symmetry in trimeric PSI crystal structure from T. elongatus, two different inter-monomer interactions involving PsaLs are found in the PSI tetramer. Phylogenetic analysis based on PsaL protein sequences shows that TS-821 is closely related to heterocyst-forming cyanobacteria. Additionally, this tetrameric …

Discovery And Characterization Of A New Group Of Is10 Insertion Sequences, Rachel Marie Kinzelman

Theses and Dissertations

Insertion sequences (ISs) are small mobile genetic elements that can have significant impact on the genotype and phenotype of a host organism. Previous work in this laboratory revealed an insertion sequence that disrupted the luxA gene in Vibrio harveyi strain BCB451, knocking out light production. Phylogenetic analysis of this insertion sequence, dubbed IS451, reveals that it is in the IS10 family, but represents a novel variant that is only 79% identical to other known IS10 sequences. Twelve copies of IS451 were isolated from a genomic library and sequenced, and were found to be essentially identical, but located in dispersed chromosomal …

Investigating Physiological Collaborations Between A Lower Termite And Its Symbionts, Brittany F. Peterson

Open Access Dissertations

This project was completed in an effort to better understand the contributions of symbiotic microbes to the biology of Reticulitermes flavipes, the eastern subterranean termite. Lower-termites, like R. flavipes, house symbionts from all three domains of life within their hindgut paunch. This intimate association is reflected in nearly every aspect of termite biology. Here, I investigate these physiological collaborations as they relate to digestion and immunity. My efforts focused on 1) quantifying the role of bacteria in wood digestion within the termite gut, 2) evaluating the role of symbionts in protection against pathogens, and 3) identifying gene products that bacterial …

An Exploration Of The Phylogenetic Placement Of Recently Discovered Ultrasmall Archaeal Lineages, Jeffrey M. O'Brien

Honors Scholar Theses

In recent years, several new clades within the domain Achaea have been discovered. This is due in part to microbiological sampling of novel environments, and the increasing ability to detect and sequence uncultivable organisms through metagenomic analysis. These organisms share certain features, such as small cell size and streamlined genomes. Reduction in genome size can present difficulties to phylogenetic reconstruction programs. Since there is less genetic data to work with, these organisms often have missing genes in concatenated multiple sequence alignments. Evolutionary Biologists have not reached a consensus on the placement of these lineages in the archaeal evolutionary tree. There …

Genetic Diversity, Population Structure, And Evolution Of Virulence In Toxoplasma Gondii, Elliot Keats Cullen Shwab

Doctoral Dissertations

Toxoplasma gondii is among the most widespread eukaryotic pathogens known. It chronically infects approximately one third of the world’s human population and has been isolated from an extremely diverse array of globally distributed mammals and birds. Understanding the structure of the worldwide T. gondii population enhances our understanding of the factors that have shaped that structure and led to the proliferation of one of the most evolutionarily successful pathogens on Earth. Herein we collate genotypic data from global isolates, demonstrating that T. gondii possesses a unique population structure in which only a small number of genotypes dominate throughout the northern …

Mysteries Of The Trypanosomatid Maxicircles: Characterization Of The Maxicircle Genomes And The Evolution Of Rna Editing In The Order Kinetoplastida, Preethi Ranganathan Iyengar

Theses and Dissertations

The trypanosomatid protists belonging to Order Kinetoplastida are some of the most successful parasites ever known to mankind. Their extreme physiological diversity and adaptability to different environmental conditions and host systems make them some of the most widespread parasites, causing deadly diseases in humans and other vertebrates.

This project focuses on their unique mitochondrion, called the kinetoplast, and more specifically involves the characterization of a part of their mitochondrial DNA (also called kinetoplast DNA or kDNA), the maxicircles, which are functional homologs of eukaryotic mitochondrial DNA in the kinetoplastid protists. We have sequenced and characterized the maxicircle genomes of 20 …

Herbert W. Conn: Formative Decades Of Microbiology And Evolutionary Biology, Frederick M. Cohan, Alexa Boesel

Frederick M. Cohan

Herbert W. Conn (1859–1917) made outstanding contributions to both microbiology and evolutionary biology, reflecting his intellectual command of several biological disciplines. Conn endeavored to make the unseen world of microbes familiar, real, and consequential to members of the general public. He presciently considered the role of bacteria in our own bodies, describing them as being both harmful and beneficial to our health. He also contributed to our understanding of the concept of species, how they originate, and what those ideas might mean in terms of bacterial speciation. In Conn’s spirit, microbial ecologists studying speciation eschew the “species” taxa of bacterial …

Characterization Of Phycoerythrin Physiology In Low-Light Adapted Prochlorococcus Ecotypes, Kathryn H. Roache-Johnson

Electronic Theses and Dissertations

The marine cyanobacteria Prochlorococcus and Synechococcus are the most abundant phototrophs in the oceans. They cohabit the oligotrophic ocean and thus have coevolved together, yet they have distinctly different methods for harvesting light. Synechococcus, like other cyanobacteria, possess phycobilisomes with various combinations of phycobiliproteins to capture wavelengths of light not otherwise available to chlorophyll. Prochlorococcus lack phycobilisomes and use divinyl chlorophyll b (Chl b2) as their primary accessory pigment to divinyl chlorophyll a (Chl a2) to capture light energy. In addition to the divinyl chlorophylls, Prochlorococcus has genes associated with the phycobiliprotein phycoerythrin (PE), the role of which is still …

Complete Genome Sequences And Phylogeny Of West Nile Virus Isolates From Southeastern United States, 2003-2012, Crystal Wedin

USF Tampa Graduate Theses and Dissertations

The study of the evolution and phylogeny of West Nile virus (WNV) has been an important area of research since the introduction of WNV in 1999. However, genome sequencing of isolates from the Southeastern part of the United States has been somewhat limited. To determine how WNV has evolved at a more localized level, ten isolates from Florida and Georgia from 2003-2012 were completely sequenced using Illumina's next-generation technology. In addition, a phylogenetic comparison of both the complete genome and select partial genomes was completed to ensure consistency among the results. This study further demonstrated the dominance of the North …

The Evolution Of Host Specificity In The Vertebrate Gut Symbiont Lactobacillus Reuteri, Steven Frese

Department of Food Science and Technology: Dissertations, Theses, and Student Research

The vertebrate gut is home to one of the densest populations of life on Earth. This microbial community has a profound effect on host health, nutrition, development, behavior, and evolution. However, very little is known about how these microbes have evolved with their vertebrate hosts, how and whether they select hosts or how they remain associated with their hosts. Recent work identified Lactobacillus reuteri as an organism that is composed of host-specific sub-populations, each population associated with a different host animal. Representatives from each host-associated population were tested for their ability to colonize gnotobiotic mice, which only rodent strains could …

Two Boundaries Separate Borrelia Burgdorferi Populations In North America, Gabriele Margos, Jean I. Tsao, Santiago Castillo-Ramirez, Yvette A. Girard, Anne G. Hoen

Dartmouth Scholarship

Understanding the spread of infectious diseases is crucial for implementing effective control measures. For this, it is important to obtain information on the contemporary population structure of a disease agent and to infer the evolutionary processes that may have shaped it. Here, we investigate on a continental scale the population structure of Borrelia burgdorferi, the causative agent of Lyme borreliosis (LB), a tick-borne disease, in North America. We test the hypothesis that the observed d population structure is congruent with recent population expansions and that these were preceded by bottlenecks mostly likely caused by the near extirpation in the 1900s …

Prospects For The Study Of Evolution In The Deep Biosphere, Jennifer F. Biddle, Jason B. Sylvan, William J. Brazelton, Katina J. Edwards, Craig L. Moyer, John F. Heidelberg, William C. Nelson

Biology Faculty and Staff Publications

Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in …

Intra And Interhost Dynamics Shaping Arbovirus Adaptation And Evolution, Alexander T. Ciota

Legacy Theses & Dissertations (2009 - 2024)

Arthropod-borne viruses (arboviruses), which are predominately mosquito-borne and almost exclusively RNA viruses, are maintained in nature in complex transmission cycles involving blood sucking invertebrates and vertebrate hosts. Although over 120 arboviruses are human pathogens responsible for causing a significant and expanding global health burden, a detailed understanding of the complex interactions between these pathogens and their hosts, particularly invertebrate hosts, is lacking. Defining these interactions is necessary if we are to understand the selective pressures and, therefore, evolutionary, adaptive, and epidemiological potential of arboviruses. This requires experimental infection and evolution studies, particularly in vivo, with natural hosts. The results presented …

Evidence Of A Rudimentary Colon In Leucoraja Erinacea, Alyssa M. Simeone

Honors Theses

During the transition of animals from water onto land, the colon is believed to have evolved as an essential water-absorbing organ in terrestrial vertebrates to prevent desiccation. The class Chondrichthyes, comprised of sharks, rays, and skates, are isotonic to their marine environment, and thus do not require a functional colon. The Chondrichthyes are an excellent organism for developmental and physiological studies in evolutionary context because they have undergone little evolutionary change since their appearance 450 million years ago. Previous histochemical studies demonstrate potential water absorbing properties in the digestive tract of the little skate, Leucoraja erinacea (Theodosiou et al., 2007). …

A Messenger Molecule Governs Interdependency In An Evolved Pseudomonas Aeruginosa Biofilm Community, Thomas Macelliott Johnson

Honors Theses and Capstones

Biofilm populations are known to harbor great diversity, but the importance of this diversity is not fully understood. A likely contributor to this variation is the second messenger molecule cyclic-di-GMP: low levels associate with a planktonic lifestyle while high levels favor biofilm formation. In ongoing studies of an evolving biofilm population of Pseudomonas aeruginosa (PA), we observed extensive ecological diversification that may relate to this lifestyle switch. In PA, the gene bifA encodes a phosphodiesterase that is known to degrade cyclic-di-GMP and reduce biofilm. This gene was cloned onto a plasmid under control of an inducible promoter and the plasmid …

Levels Of Biological Organization And The Origin Of Novelty, Brian Hall, Ryan Kerney

Ryan Kerney

The concept of novelty in evolutionary biology pertains to multiple tiers of biological organization from behavioral and morphological changes to changes at the molecular level. Identifying novel features requires assessments of similarity (homology and homoplasy) of relationships (phylogenetic history) and of shared developmental and genetic pathways or networks. After a brief discussion of how novelty is used in recent literature, we discuss whether the evolutionary approach to homology and homoplasy initially formulated by Lankester in the 19th century informs our understanding of novelty today. We then discuss six examples of morphological features described in the recent literature as novelties, and …

Access To Mutualistic Endosymbiotic Microbes: An Underappreciated Benefit Of Group Living, Michael Lombardo

Michael P Lombardo

"The original publication is available at www.springerlink.com"

A central question in behavioral ecology has been why animals live in groups. Previous theories about the evolution of sociality focused on the potential benefits of decreased risk of predation, increased foraging or feeding efficiency, and mutual aid in defending resources and/or rearing offspring. This paper argues that access to mutualistic endosymbiotic microbes is an underappreciated benefit of group living and sets out to reinvigorate Troyer’s hypothesis that the need to obtain cellulolytic microbes from conspecifics influenced the evolution of social behavior in herbivores and to extend it to nonherbivores. This extension is …

On The Evolution Of Sexually Transmitted Diseases In Birds, Michael Lombardo

Michael P Lombardo

"The definitive version is available at www.blackwell-synergy.com".

Sexually transmitted diseases (STDs) in animals are caused by pathogens that are transmitted during copulation. Birds have played an important role in the development of STD-centered theories of mating behavior. However, it is not known whether STDs exist in wild bird populations. While the avian cloaca with its dual functions of gamete transfer and excretion seemingly predisposes birds for the evolution of STDs, the life history patterns of most birds (i.e., seasonal breeders with relatively brief annual periods of sexual activity) suggest otherwise. The importance of STDs as selective forces that shape host …

Comparing Models Of Evolution For Ordered And Disordered Proteins, Celeste J. Brown, Audra K. Johnson, Gary W. Daughdrill

Molecular Biosciences Faculty Publications

Most models of protein evolution are based upon proteins that form relatively rigid 3D structures. A significant fraction of proteins, the so-called disordered proteins, do not form rigid 3D structures and sample a broad conformational ensemble. Disordered proteins do not typically maintain long-range interactions, so the constraints on their evolution should be different than ordered proteins. To test this hypothesis, we developed and compared models of evolution for disordered and ordered proteins. Substitution matrices were constructed using the sequences of putative homologs for sets of experimentally characterized disordered and ordered proteins. Separate matrices, at three levels of sequence similarity ( …