Microbiology Commons^™

The Role Of Household Antimicrobials In The Proliferation Of Antibiotic Resistance During Anaerobic Digestion, Daniel Elliott Carey

Dissertations (1934 -)

Antimicrobial chemicals in consumer personal care products have been found to increase antibiotic resistance in pure culture studies. Although many studies focus on antibiotic resistance development pertinent to medical scenarios, resistance developed in natural and engineered environments might be significant and has become an emerging concern for human health. This dissertation focuses on the antimicrobial chemicals triclosan and triclocarban. These compounds are distinctly different from antibiotics and are used in products like soaps that are labelled as “antibacterial”. Municipal wastewater treatment plants receive triclocarban and triclosan loads higher than most contaminants of emerging concern because they are frequently used in …

Identification And Characterization Of Ion Channel Activity Of The M2 Protein From Influenza Virus D (Dm2), Jianing Liu

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

Viral ion channels are membrane proteins of influenza viruses that play essential roles in the replication cycle, which enables them to be targeted by antiviral drugs. M2 of influenza type A virus, BM2 of influenza type B virus, and CM2 from influenza type C virus have been characterized as ion channel proteins and antiviral drug amantadine was developed to control influenza type A virus. However, few studies have been conducted to clarify the properties of the M2 protein (DM2) of influenza type D virus, a novel influenza virus genus identified in 2014. To identify the ion channel activity of DM2, …

Experimental Demonstration Of An Allee Effect In Microbial Populations, Rajreni B. Kaul, Andrew M. Kramer, Fred C. Dobbs, John M. Drake

OES Faculty Publications

Microbial populations can be dispersal limited. However, microorganisms that successfully disperse into physiologically ideal environments are not guaranteed to establish. This observation contradicts the Baas-Becking tenet: ‘Everything is everywhere, but the environment selects’. Allee effects, which manifest in the relationship between initial population density and probability of establishment, could explain this observation. Here, we experimentally demonstrate that small populations of Vibrio fischeri are subject to an intrinsic demographic Allee effect. Populations subjected to predationby the bacterivore Cafeteria roenbergensis display both intrinsic and extrinsic demographic Allee effects. The estimated critical threshold required to escape positive densitydependence is around 5, 20 or …

No Nonsense: The Protection Of Wild-Type Mrnas From Nonsense-Mediated Mrna Decay In Saccharomyces Cerevisiae, Krista D. Patefield

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

Gene regulation in eukaryotes is tightly controlled at multiple levels to ensure proper expression and cellular homeostasis. Misregulation of gene expression is a common source of genetic disease. One mechanism by which cells are able to control gene expression is through the synthesis and degradation of the mRNA molecules encoding the genes. The transcription and degradation of mRNA molecules controls the pool mRNAs that are available to the translational machinery. One of the well-studied mRNA decay pathways is the Nonsense-Mediated mRNA Decay pathway (NMD). Originally, NMD was discovered as a posttranscriptional mRNA surveillance mechanism responsible for the deadenylation-independent decapping and …

Identifying Genetic Factors In The Development Of Diabetes In The Wasatch Front Population 2013-2014, Julianne H. Grose

Journal of Undergraduate Research

The academic objectives of this MEG were to train undergraduate and graduate students on the scientific process while providing valuable insight into the genetic factors that may play a role in the development of diabetes in the Wasatch front population. We were able to meet these objectives as evidenced by the training of two graduate students and seven undergraduates and by the identification of a novel genetic allele which most likely contributes to diabetes.

Examining The Relative Contributions Of Genes, Diet, And The Gut Microbiome To The Development Of Obesity And Diabetes, Laura C. Bridgewater

Journal of Undergraduate Research

This project began as a collaboration with Dr. Julianne Grose in MMBIO to study the effect of PAS kinase on diabetes and obesity in a mouse model system. Due to our initial findings, the study has grown to include Dr. Ben Bickman in PDBIO (an expert in metabolism) and Dr. Scott Weber in MMBIO (an immunologist). We have found that PAS kinase knockout mice have an increased metabolic rate—not only in their overall system but also specifically in skeletal muscle. Metabolic rate can have a profound influence on the immune system, so we began working with Dr. Weber to measure …

Analysis Of The Kinetics And Recombinatorial Mechanisms Of Hiv-1 Evolution In Vivo In Humanized Mice, Bradford Berges

Journal of Undergraduate Research

Several of my students have moved on to future positions, as follows: Medical school: Sterling Adams, German Cuadra, Art Lee (still interviewing), and Tyler White (still interviewing) Graduate school: Steve Hallam

See below in the ‘academic deliverables’ section for further details on presentations, grant funding awarded directly to students, and publications.

Final Report For 2013 Meg: Improving The Memory Response Of Pathogen Specific Helper T Cells, Scott Weber

Journal of Undergraduate Research

The following two aims are from my 2013 MEG. We made great progress and completed most of both Aim 1 and Aim 2. Details on the progress for each aim are described below.

Mentoring Environment: This MEG allowed me to expand the size of my lab and increase the amount and quality of mentoring. I met with student each week in lab meeting as well as individually. I also had each student email me a weekly update. Students were given opportunities to do hands on work, be involved in the data analysis and presentation at local and regional meetings.

BYU …

Characterization Of Bacterial Diversity In Cold-Water Anthothelidae Corals, Stephanie Nichole Lawler

USF Tampa Graduate Theses and Dissertations

Cold-water corals, similar to tropical corals, contain a diverse and complex microbial landscape. Comprised of vital microscopic organisms (i.e. bacteria, viruses, archaea), the coral microbiome is a driving factor in the proliferation and survival of the coral host. Bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic …

Community-Scale Water Treatment Systems In The Dominican Republic, Water Supply In The Dr

Engagement & Service-Learning Summit

No abstract provided.

Î?- Lactam-Induced Changes In Cell Wall Composition And Autolytic Properties Of Daptomycin Resistant Staphylococcus Aureus, Michael Krzyskowski

Theses and Dissertations

Staphylococcus aureus is a major human pathogen that is well known for its ability to develop resistance to antimicrobial therapies. Recent studies have identified a combination of β-lactam antibiotic and daptomycin (DAP) to be highly effective at killing single and multi-drug-resistant S. aureus. Of particular interest is this drug combinationâ??s efficiency with which it kills strains classified as DAP-resistant methicillin-resistant Staphylococcus aureus (DAP-R MRSA). The goals of the present study were two-fold: to provide a physiological profile of a DAP-R S. aureus strain undergoing beta-lactam treatment by observing changes in autolytic rate, susceptibility to lytic enzymes, levels of peptidoglycan O-acetylation, …

Borrelia Burgdorferi Induces A Type I Interferon Response During Early Stages Of Disseminated Infection In Mice, Mary M. Petzke, Radha Iyer, Andrea Love, Zoe Spieler, Andrew Brooks, Ira Schwartz

NYMC Faculty Publications

BACKGROUND: Lyme borrelia genotypes differ in their capacity to cause disseminated disease. Gene array analysis was employed to profile the host transcriptome induced by Borrelia burgdorferi strains with different capacities for causing disseminated disease in the blood of C3H/HeJ mice during early infection.

RESULTS: B. burgdorferi B515, a clinical isolate that causes disseminated infection in mice, differentially regulated 236 transcripts (P < 0.05 by ANOVA, with fold change of at least 2). The 216 significantly induced transcripts included interferon (IFN)-responsive genes and genes involved in immunity and inflammation. In contrast, B. burgdorferi B331, a clinical isolate that causes transient skin infection but does not disseminate in C3H/HeJ mice, stimulated changes in only a few genes (1 induced, 4 repressed). Transcriptional regulation of type I IFN and IFN-related genes was measured by quantitative RT-PCR in mouse skin biopsies collected from the site of infection 24 h after inoculation with B. burgdorferi. The mean values for transcripts of Ifnb, Cxcl10, Gbp1, Ifit1, Ifit3, Irf7, Mx1, and Stat2 were found to be significantly increased in B. burgdorferi strain B515-infected mice relative to the control group. In contrast, transcription of these genes was not significantly changed in response to B. burgdorferi strain B331 or B31-4, a mutant that is unable to disseminate.

CONCLUSIONS: These results establish a positive association between the disseminating capacity of B. burgdorferi and early type I IFN induction in a murine model of Lyme disease.

Drought Responsive Gene Expression Regulatory Divergence Between Upland And Lowland Ecotypes Of A Perennial C4 Grass, John T. Lovell, Scott Schwartz, David B. Lowry, Eugene V. Shakirov, Jason E. Bonnette, Xiaoyu Weng, Mei Wang, Jenifer Johnson, Avinash Sreedasyam, Christopher Plott, Jerry Jenkins, Jeremy Schmutz, Thomas E. Juenger

Biological Sciences Faculty Research

Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C₄ grass, Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. …

Phylogenetic Organization Of Bacterial Activity., Ember M Morrissey, Rebecca L Mau, Egbert Schwartz, J Gregory Caporaso, Paul Dijkstra, Natasja Van Gestel, Benjamin J Koch, Cindy M. Liu, Michaela Hayer, Theresa A Mchugh, Jane C Marks, Lance B. Price, Bruce A Hungate

Environmental and Occupational Health Faculty Publications

Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism's ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with (13)C and (18)O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing …

Analysis Of Johne's Disease Elisa Status And Associated Performance Parameters In Irish Dairy Cows, A. E. Kennedy, N. Byrne, A. B. Garcia, Jim O'Mahony, R. G. Sayers

Department of Biological Sciences Publications

Background

Infection with Mycobacterium avium subspecies paratuberculosis (MAP) has been associated with reductions in milk production in dairy cows and sub optimal fertility. The aim of this study was to highlight the production losses associated with testing MAP ELISA positive in Irish dairy cows. Secondary objectives included investigation of risk factors associated with testing MAP ELISA positive. A survey of management practices on study farms was also conducted, with examination of associations between management practices and herd MAP status.

Blood samples were collected from 4188 breeding animals on 22 farms. Samples were ELISA tested using the ID Screen Paratuberculosis Indirect …

Factors Affecting Transduction Efficiency Of Pseudotyped Viral Vectors Incorporating Alphaviral Glycoproteins, Aditi Kesari

Open Access Dissertations

The genome of an organism has the complete set of biochemical instructions required for sustenance of life. Mutations or abnormalities in this genome lead to genetic disorders. Currently available therapeutic options mostly focus on treating the symptoms, but not curing them. Gene therapy promises to be a curative form of medicine. In gene therapy cells carrying a defective gene are targeted and replaced with a healthy copy of that gene. The vehicles used for delivering this gene are known as vectors. Retroviruses are popularly used gene therapy/transfer vectors. However, retroviruses are limited in the range of cells they can enter …

Phagephisher: A Pipeline For The Discovery Of Covert Viral Sequences In Complex Genomic Datasets, Thomas Hatzopoulos, Siobhan C. Watkins, Catherine Putonti

Bioinformatics Faculty Publications

Obtaining meaningful viral information from large sequencing datasets presents unique challenges distinct from prokaryotic and eukaryotic sequencing efforts. The difficulties surrounding this issue can be ascribed in part to the genomic plasticity of viruses themselves as well as the scarcity of existing information in genomic databases. The open-source software PhagePhisher (http://www.putonti-lab.com/phagephisher) has been designed as a simple pipeline to extract relevant information from complex and mixed datasets, and will improve the examination of bacteriophages, viruses, and virally related sequences, in a range of environments. Key aspects of the software include speed and ease of use; PhagePhisher can be used with …

Biological Nanomotors With A Revolution, Linear, Or Rotation Motion Mechanism, Peixuan Guo, Hiroyuki Noji, Christopher M. Yengo, Zhengyi Zhao, Ian Grainge

Nanobiotechnology Center Faculty Publications

The ubiquitous biological nanomotors were classified into two categories in the past: linear and rotation motors. In 2013, a third type of biomotor, revolution without rotation (http://rnanano.osu.edu/movie.html), was discovered and found to be widespread among bacteria, eukaryotic viruses, and double-stranded DNA (dsDNA) bacteriophages. This review focuses on recent findings about various aspects of motors, including chirality, stoichiometry, channel size, entropy, conformational change, and energy usage rate, in a variety of well-studied motors, including F_oF₁ ATPase, helicases, viral dsDNA-packaging motors, bacterial chromosome translocases, myosin, kinesin, and dynein. In particular, dsDNA translocases are used to illustrate how …

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 …

Shaping The Growth Behaviour Of Biofilms Initiated From Bacterial Aggregates, Gavin Melaugh, Jaime B. Hutchison, Kasper N. Kragh, Yasuhiko Irie, Aled E. L. Roberts, Thomas Bjarnsholt, Stephen P. Diggle, Vernita Gordon, Rosalind J. Allen

Biology Faculty Publications

Bacterial biofilms are usually assumed to originate from individual cells deposited on a surface. However, many biofilm-forming bacteria tend to aggregate in the planktonic phase so that it is possible that many natural and infectious biofilms originate wholly or partially from pre-formed cell aggregates. Here, we use agent-based computer simulations to investigate the role of pre-formed aggregates in biofilm development. Focusing on the initial shape the aggregate forms on the surface, we find that the degree of spreading of an aggregate on a surface can play an important role in determining its eventual fate during biofilm development. Specifically, initially spread …