Laboratory and Basic Science Research Commons^™

Whole Genome Sequencing As A Tool For Identifying Phenotypic Properties And Underlying Genetic Mechanisms In Staphylococcus Pseudintermedius, Matthew C. Riley

Doctoral Dissertations

Staphylococcus pseudintermedius is a Gram-positive bacterial opportunistic pathogen commonly associated with dermal infections in canines, but capable of causing serious disease in other species. Reports of human infections caused by S. pseudintermedius along with an increase in resistance to multiple antibiotics highlights the importance of this organism. Whole genome sequencing can allow large scale investigation of genetic mechanisms underlying phenotypic properties that contribute to the expansion of successful S. pseudintermedius clonal lineages.

The increase in multidrug and methicillin-resistant S. pseudintermedius (MRSP) may result from horizontal transfer of genetic material between bacterial isolates, yet is thought to be rare in Staphylococci …

Replication-Transciption Switch In Human Mitochondria, Karen Agaronyan

Graduate School of Biomedical Sciences Theses and Dissertations

Coordinated replication and expression of mitochondrial genome is critical for metabolically active cells during various stages of development. However, it is not known whether replication and transcription can occur simultaneously without interfering with each other and whether mtDNA copy number can be regulated by the transcription machinery. Human mitochondrial RNA polymerase (mtRNAP) is a central enzyme involved in gene expression in mitochondria. It generates genome-size polycistronic transcripts and also makes replication primers at two origins of replication. MtRNAP is distantly related to phage T7 RNAP. While T7 RNAP is optimized to produce large amounts of transcripts to overcompete the bacterial …

Contribution Of A Putative Up Element Dna Sequence To The Activity Of A Newly Identified Phage Promoter, Courtney Hamilton

Mahurin Honors College Capstone Experience/Thesis Projects

In transcription, a universal step in gene expression, information from a DNA sequence is copied into RNA. A key component in gene expression is the promoter sequence, a region of DNA to which RNA polymerase binds during the initiation of transcription of downstream genes. Most bacterial promoters contain a -10 and a -35 sequence that are bound by the RNA polymerase. Some promoters also contain an Upstream Promoter (UP) element. UP elements have been shown to boost promoter activity. We recently identified a new promoter in a mutant bacteriophage that grows on a bacterial host that prevents antitermination of phage …

Relationship Between Morphogenesis And Secretion In The Filamentous Fungus Aspergillus Nidulans, Lakshmi Preethi Yerra

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

Filamentous fungi have a long history in biotechnology for the production of food ingredients, pharmaceuticals and enzymes. The advancements made in recent years have earned filamentous fungi such as Aspergillus species a dominant place among microbial cell factories. Although the model fungus A. nidulans has been extensively studied, the genetic and regulatory networks that underlie morphogenesis and development have yet to be fully characterized. The Rho GTPases (Cdc42 and RacA) are one of the most important regulators of the morphogenetic processes among diverse eukaryotic organisms. Although the functions of these GTPases are relatively well-characterized, little is known about their downstream …

Identification, Characterization, And Life Cycle Of Intein-Associated Homing Endonucleases, Joshua J. Skydel

Honors Scholar Theses

Inteins are molecular parasites that have been identified in unicellular organisms from the three domains of life. The intein self-excises following translation of the host gene, and therefore incurs a fitness cost for its carrier. The symbiotic state of the intein to its host is dependent on the presence or absence of a homing endonuclease domain, which facilitates horizontal transfer of the molecule. Identification of this domain provides information on the evolutionary history of the intein, as well as patterns of horizontal gene transfer in microbial communities. I have therefore developed Hidden Markov Models (HMMs) to identify homing endonuclease domains …

Characterization Of The Marine Sponge Amphimedon Compressa Microbiome Across A Spatial Gradient, Renee Michelle Potens

HCNSO Student Theses and Dissertations

Diverse and ecologically important microbial communities (microbiomes) are symbiotic within marine sponges. In this study, the microbiome of Amphimedon compressa from three sample locations (Broward and Dade Counties, Southeast Florida, USA and the Southern Caribbean, Bocas del Toro, Panama) is characterized using 16S rRNA Illumina sequencing. The predominant taxa are Proteobacteria and Cyanobacteria, as expected for Low Microbial Abundance sponges, accounting for over 53% of the total microbiome community. The numbers of Operational Taxonomic Units (OTUs) decrease from Broward County (2,900) to Dade County (2,300) and then Bocas del Toro (1,200). The correlates to a decreasing north-south gradient of …

Role Of Stemloop D In Terminally Deleted Coxsackievirus B3 Replication, Lee K. Jaramillo

Theses & Dissertations

Coxsackievirus B3 (CVB3) is an enterovirus with no known form of latency. However, assays designed to detect enteroviral RNA have shown that CVB3 RNA can persist for weeks beyond the acute infection both naturally and experimentally. Our previous work with coxsackievirus revealed an inhibited version of enteroviral replication where the progeny virus, termed terminally deleted (TD) virus, was missing a maximum of 49 nucleotides from the beginning of the 5’ non-translated region (NTR). The largest terminally deleted virus, TD50, effaced stem a, stemloop b, and stemloop c from the secondary structure, the cloverleaf. We hypothesized that further deletion beyond those …

Insights Into Determinants That Contribute To Colonization, Virulence And Antibiotic Resistance In Enterococci, Maria Camila Montealegre

Dissertations & Theses (Open Access)

Enterococcus faecalis and Enterococcus faecium are increasingly common as causative agents of human infections, many of which are very difficult to treat due to multi-drug resistance. The work presented in the first part of this dissertation elucidates a mechanism for the regulation of pilus expression. I showed that ATT is the initiation codon of ebpA, the first gene of an operon that codes for the endocarditis and biofilm-associated pili (Ebp), a recognized virulence factor in E. faecalis. The presence of this rare start codon downregulates EbpA translation and protein levels, diminishing biofilm and binding abilities of …

Non-Essentiality Of Alr And Muri Genes In Mycobacteria, Philion L. Hoff, Denise Zinniel, Raúl G. Barletta

UCARE Research Products

Amino acids are the building blocks of life. If DNA is the blueprint, amino acids are the lumber that proteins are built with. Proteins are built with left-handed, L- forms of amino acids. Bacteria have an essential cell wall component that happens to be an exception: peptidoglycan. Bacteria have enzymes called racemases that convert L- amino acid forms into right-handed, D- forms. Amino acids participate in many reactions with keto acids. Transaminases allow conversion between amino acids by transfer of an amino group.

Previous reports claimed there is no D-ala transaminase activity in mycobacteria and thus alr and murI genes …

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 …