Microbiology Commons^™

Streptococcus Agalactiae Strains With Chromosomal Deletions Evade Detection With Molecular Methods, Isabella A. Tickler, Fred C. Tenover, Scott Dewell, Victoria M. Le, Rachel N. Blackman, Richard V. Goering, Amy E. Rogers, Heather Piwonka, Brittney D. Jung-Hynes, Derrick J. Chen, Michael J. Loeffelholz, Devasena Gnanashanmugam, Ellen Jo Baron

Biology Faculty Publications

Surveillance of circulating microbial populations is critical for monitoring the performance of a molecular diagnostic test. In this study, we characterized 31 isolates of Streptococcus agalactiae (group B Streptococcus [GBS]) from several geographic locations in the United States and Ireland that contain deletions in or adjacent to the region of the chromosome that encodes the hemolysin gene cfb, the region targeted by the Xpert GBS and GBS LB assays. PCR-negative, culture-positive isolates were recognized during verification studies of the Xpert GBS assay in 12 laboratories between 2012 and 2018. Whole-genome sequencing of 15 GBS isolates from 11 laboratories revealed …

Evaluating Fungal Pathogen Inoculum Loads In Field Seed Banks, Taryn Lori Williamson

Theses and Dissertations

Quantification of soilborne pathogen inoculum loads is important in both agricultural and wildland settings. Quantitative Polymerase Chain Reaction (qPCR) methods using SYBR Green chemistry have been shown to be useful for quantifying fungal inoculum loads in environmental samples. The purpose of this study was to develop a method to quantify fungal pathogen inoculum loads in soil seed banks using a qPCR method with SYBR Green chemistry. The invasive annual grass Bromus tectorum was chosen for this seed bank study. There were three objectives: 1) to design target-specific primers for three fungal pathogens known to be important in Bromus tectorum seed …

Regulation Of Vaccinia Virus Replication: A Story Of Viral Mimicry And A Novel Antagonistic Relationship Between Vaccinia Kinase And Pseudokinase, Annabel T. Olson

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

Poxviruses employ sophisticated signaling pathways that thwart cellular defense mechanisms and simultaneously ensure viral factors are modulated properly. Yet, our understanding of these complex signaling networks are incomplete. For example, the vaccinia B1 kinase plays a vital role in inactivating the cellular antiviral factor BAF, and is suggested to orchestrate other pathways. B1 is highly conserved among poxviruses and exhibits a remarkable degree of similarity to VRKs, a family of cellular kinases, suggesting that the viral enzyme has evolved to mimic VRK activity. Indeed, B1 and VRKs have been demonstrated to target a shared substrate, the DNA binding protein BAF, …

Genomics Based Approaches To Fungal Evolution, Aaron J. Robinson, Donald O. Natvig

Biology ETDs

Advances in DNA sequencing and data analysis make it possible to address questions in population genetics and evolution at the genomic level. Fungi are excellent subjects for such studies, because they are found in diverse environments, have short generation times, can be maintained in culture and have relatively small genomes. My research employed genetic approaches using a variety of sequencing technologies and methods of analysis to explore questions in fungal evolution.

In one study, I explored the genetics behind differences in thermotolerance between isolates of Neurospora discreta from Alaska and New Mexico. Isolates from the two states exhibited differences in …

Modelling Non-Linear Functional Responses In Competitive Biological Systems., Nickolas Goncharenko

Western Research Forum

One of the most versatile and well understood models in mathematical biology is the Competitive Lotka Volterra (CLV) model, which describes the behaviour of any number of exclusively competitive species (that is each species competes directly with every other species). Despite it's success in describing many phenomenon in biology, chemistry and physics the CLV model cannot describe any non-linear environmental effects (including resource limitation and immune response of a host due to infection). The reason for this is the theory monotone dynamical systems, which was codeveloped with the CLV model, does not apply when this non-linear effect is introduced. For …

Characterization Of The Φctx-Like Pseudomonas Aeruginosa Phage Dobby Isolated From The Kidney Stone Microbiota, Genevieve Johnson, Alan J. Wolfe, Catherine Putonti

Biology: Faculty Publications and Other Works

Bacteriophages (phages) are vital members of the human microbiota. They are abundant even within low biomass niches of the human body, including the lower urinary tract. While several prior studies have cultured bacteria from kidney stones, this is the first study to explore phages within the kidney stone microbiota. Here we report Dobby, a temperate phage isolated from a strain of Pseudomonas aeruginosa cultured from a kidney stone. Dobby is capable of lysing clinical P. aeruginosa strains within our collection from the urinary tract. Sequencing was performed producing a 37 152 bp genome that closely resembles the temperate P. aeruginosa …

Further Understanding Of Bacteriophages That Infect The Bacterial Family Enterobacteriaceae, Paul Flake

Undergraduate Honors Theses

Despite the eclectic nature of bacteriophage genomes, nucleotide comparison is an effective method for grouping phages into cluster and subcluster classifications. This process is facilitated by making preliminary cluster assignations based on the identity of the major capsid protein. As more phages continue to be sequenced and integrated into cluster/subcluster groupings, adjustments may need to be made to the genomic similarity percentages that have previously defined cluster/subcluster classifications. Implementing proteomic comparison in addition to nucleotide homology may provide added clarity to this process. Protein conservation and diversity among lytic phages that infect the bacterial family Enterobacteriaceae is discussed and the …

Effect Of Environmental Factors And Residual Sanitizers On Survival And Attachment Of Indicator Organism And Human Pathogens On Fresh Produce, Vijay Singh Chhetri

LSU Doctoral Dissertations

A comprehensive understanding of the behavior of microbial contaminants on produce surfaces in agricultural farms and during post-harvest activities is essential for the development of produce safety risk management strategies. Our studies investigated the survival and the attachment of E. coli on watermelon surfaces in agricultural settings with different levels of vegetation, and the effect of residual sanitizers on the survival and the attachment of E. coli O157: H7 and L. monocytogenes on spinach leaves. The attachment strength (S_R) of the E. coli cells on watermelon surfaces significantly increased (P<0.05) from 0.04 to 0.99 in the first 24 h, which was primarily due to the decrease in loosely attached population, given that the population of strongly attached cells was constant. The daily die-off rate of E. coli ranged from -0.12 …

Functional Cell Separation Of Transformable Microoragnisms From Complex Microbial Niches, Tamara Zaza, Shubha R.L. Malla, Shannon E. Weigum

Research Horizons Day Posters

No abstract provided.

Two-Component Signaling System Baesr Of Escherichia Coli In Development Of Antibiotic Resistance, Y. Savanie Fernando, Carolina Dolislager

Research Horizons Day Posters

No abstract provided.

Symbiosis In Archaea: Functional And Phylogenetic Diversity Of Marine And Terrestrial Nanoarchaeota And Their Hosts, Emily Joyce St. John

Dissertations and Theses

The Nanoarchaeota are an enigmatic lineage of Archaea found in deep-sea hydrothermal vents and geothermal springs across the globe. These small (~100-400 nm) hyperthermophiles live ectosymbiotically with diverse hosts from the Crenarchaeota. Despite their broad distribution in high-temperature environments, very few Nanoarchaeota have been successfully isolated in co-culture with their hosts and nanoarchaeote genomes are poorly represented in public databases. However, the Nanoarchaeota provide unique insights into the structure and function of symbiosis in the archaeal domain. This study describes novel nanoarchaeotes from multiple geothermal habitats, using a combination of direct cultivation techniques and genomic analysis. A new nanoarchaeote …

Serum Amyloid P Component Binds Fungal Surface Amyloid And Decreases Human Macrophage Phagocytosis And Secretion Of Inflammatory Cytokines, Nicole E. Behrens, Peter N. Lipke, Darrell Pilling, Richard H. Gomer, Stephen A. Klotz

Publications and Research

In patients with invasive fungal diseases, there is often little cellular inflammatory response. We tested the idea that binding of the human constitutive plasma protein serum amyloid P component (SAP) (also called PTX2) to Candida albicans dampens the innate immune response to this fungus. Many pathogenic fungi have cell surface amyloid-like structures important for adhesion and biofilm formation. Human SAP bound to fungi that expressed functional cell surface amyloid, but SAP had minimal binding to fungi with reduced expression of cell surface amyloid. In the absence of SAP, phagocytosis of fungi by human macrophages was potentiated by expression of amyloid …

Establishment Of Listeria Monocytogenes In The Gastrointestinal Tract, Morgan L. Davis, Steven C. Ricke, Janet R. Donaldson

Faculty Publications

Listeria monocytogenes is a Gram positive foodborne pathogen that can colonize the gastrointestinal tract of a number of hosts, including humans. These environments contain numerous stressors such as bile, low oxygen and acidic pH, which may impact the level of colonization and persistence of this organism within the GI tract. The ability of L. monocytogenes to establish infections and colonize the gastrointestinal tract is directly related to its ability to overcome these stressors, which is mediated by the efficient expression of several stress response mechanisms during its passage. This review will focus upon how and when this occurs and how …

A Human Papillomavirus-Independent Cervical Cancer Animal Model Reveals Unconventional Mechanisms Of Cervical Carcinogenesis, Chunbo He, Xiangmin Lv, Cong Huang, Peter C. Angeletti, Guohua Hua, Jixin Dong, Jin Zhou, Zhengfeng Wang, Bowen Ma, Xingcheng Chen, Paul F. Lambert, Bo R. Rueda, John S. Davis, Cheng Wang

Nebraska Center for Virology: Faculty Publications

HPV infections are common in healthy women and only rarely cause cervical cancer, suggesting that individual genetic susceptibility may play a critical role in the establishment of persistent HPV infection and the development of cervical cancer. Here, we provide convincing in vitro and in vivo evidence showing that differential expression and activation of YAP1 oncogene determine individual susceptibility to HPV infection and cervical carcinogenesis. We found that hyperactivation of YAP1 in mouse cervical epithelium was sufficient to induce invasive cervical cancer. Cervical epithelial cell-specific HPV16 E6/E7 and YAP1 double-knockin mouse model demonstrated that high-risk HPV synergized with hyperactivated YAP1 to …

Targeted Therapy For The Future: The Use Of Novel Antimicrobial Peptides Against P. Aeurginosa, Matthew Froid

UNO Student Research and Creative Activity Fair

Pathogenic bacteria, such as the gram-negative bacterium Pseudomonas aeruginosa, are becoming resistant to our current arsenal of antibiotics at an alarming rate. P. aeruginosa is a leading cause of nosocomial acquired infections and is a primary co-morbidity in patients with compromised immune systems. One potential source of new antibiotic agents is antimicrobial peptides. Antimicrobial peptides (AMPs) are small proteins, and some have shown a high degree of efficacy and broad-spectrum activity against both Gram-positive and Gram-negative bacteria. An experimental AMP that has been developed by Dr. Wang at UNMC, DASamp2, has shown to be effective against virulent bacteria, including P. …

Microbiological Safety Of Areca Nut-Containing, Ready-To-Eat Chewing Substances Common Among Pakistani Paediatric Population: A Pilot Study, Anjiya Sulaiman, Hina Saeed Zuberi, Seema Irfan, Kulsoom Ghias

Department of Biological & Biomedical Sciences

Objective: To evaluate microbiological contamination of areca nut-containing, ready-to-eat chewing substances easily accessible to vulnerable paediatric population.
Methods: A pilot study was conducted at the Aga Khan University Medical College from June to October 2016 on twelve samples of areca nut-containing chewing substances (four supari, paan masala and gutka each) collected from various localities of Karachi. These were evaluated individually for total colony counts, hygiene indicator organisms, pathogenic organisms, and levels of aflatoxin. Microbial contamination was analysed using pour-plate method. Fungal aflatoxin levels were measured by enzyme-linked immunosorbent assay (ELISA)..
Results: Wet gutka preparations were contaminated by Escherichia coli and …

Rnd Efflux Pump Systems In Acinetobacter, With Special Emphasis On Theirrole In Quorum Sensing, Bindu Subhadra, Man Hwan Oh, Chul Hee Choi

Faculty Publications - Biological Sciences

Acinetobacter is an important opportunistic, multidrug resistant pathogen causing majority of nosocomial infections worldwide. The multidrug resistance is attributed by a plethora of efflux pumps and the overexpression of the same mediates export of antimicrobial agents. Quorum sensing (QS) is the cell-to-cell communication system in which bacteria produces specific signaling molecules which are transported out to the surrounding environment to communicate with other bacterial cells. It has been noticed that multidrug efflux pumps like resistance-nodulation-cell division (RND) efflux pumps play an important role in QS by exporting these signaling molecules. This review discusses various RND efflux pumps and the current …

Diversity Of Resistance Mechanisms In Carbapenem-Resistant Enterobacteriaceae At A Health Care System In Northern California, From 2013 To 2016, Fiona Senchyna, Rajiv L. Gaur, Johanna Sandlund, Cynthia Truong, Guillaume Tremintin, Dietmar Kültz, Carlos A. Gomez, Fiona B. Tamburini, Tessa Andermann, Ami Bhatt, Isabella A. Tickler, Nancy Watz, Indre Budvytiene, Gongyi Shi, Fred C. Tenover, Niaz Banaei

Biology Faculty Publications

The mechanism of resistance in carbapenem-resistant Enterobacteriaceae (CRE) has therapeutic implications. We comprehensively characterized emerging mechanisms of resistance in CRE between 2013 and 2016 at a health system in Northern California. A total of 38.7% (24/62) of CRE isolates were carbapenemase gene-positive, comprising 25.0% (6/24) blaOXA-48 like, 20.8% (5/24) bla_KPC, 20.8% (5/24) bla_NDM, 20.8% (5/24) bla_SME, 8.3% (2/24) bla_IMP, and 4.2% (1/24) bla_VIM. Between carbapenemases and porin loss, the resistance mechanism was identified in 95.2% (59/62) of CRE isolates. Isolates expressing bla_KPC were 100% susceptible to ceftazidime–avibactam, meropenem–vaborbactam, …

A Comparative Analysis Of The Fermentation Capabilities Of Various Bifidobacterium Strains, Ella Oney

Honors Program: Senior Projects (Public)

Bifidobacterium is a genus of anaerobic bacteria that are commonly found to inhabit the gastrointestinal tract of many members of the animal kingdom. These microorganisms are adapted to obtain their carbon from the breakdown of complex carbohydrates. Marmosets, a mammal whose gut microbiome is inhabited by high levels of Bifidobacteria, consume gum Arabic as a major part of their diet. The purpose of this experiment is to determine whether Bifidobacterium strains isolated from the guts of marmosets are able to degrade and ferment this complex carbohydrate or one of its main constituents, arabinose. This was accomplished by inoculating isolates of …

Pas Kinase And Tor, Controllers Of Cell Growth And Proliferation, Brooke Jasmyn Cozzens

Theses and Dissertations

Nutrient sensing kinases lie at the heart of cellular health and homeostasis, allowing cells to quickly adapt to changing environments. Target of Rapamycin (TOR) and PAS kinase (PASK, or PASKIN) are two such nutrient kinases, conserved from yeast to man. In yeast, these kinases each have paralogs. The two TOR paralogs in yeast mimic the mammalian TORC1 and TORC2 complexes, except both Tor1 and Tor2 may contribute to TORC1 or TORC2 function. The two PAS kinase paralogs are paired with the TOR paralogs, meaning that both Psk1 and Psk2 regulate TORC1, while Psk2 suppresses a temperature-sensitive allele of Tor2. Herein …