Microbiology Commons^™

Scanning Labyrinthulomycete Genomes For Yeast Transcription Factor Binding Site Motifs, Jackie L. Collier, Joshua Rest

Interdisciplinary Research Data

To develop broadly useful methods for the genetic manipulation of Labyrinthulomycetes (a diverse group of ubiquitous osmoheterotrophic marine protists), it is essential to understand the similarities and differences in regulation of gene expression among them. Toward this end we have used FIMO from the MEME suite (http://meme-suite.org/doc/fimo.html) to identify potential transcription factor binding sites in each of the three available genome sequences: Aplanochytrium kerguelense PBS07, Schizochytrium aggregatum ATCC 28209, and Aurantiochytrium limacinum ATCC MYA-1381

Proteomic Approach For Extracting Cytoplasmic Proteins From Streptococcus Sanguinis Using Mass Spectrometry, Fadi Elrami, Kristina Nelson, Ping Xu

Philips Institute for Oral Health Research Publications

Streptococcus sanguinis is a commensal and early colonizer of oral cavity as well as an opportunistic pathogen of infectious endocarditis. Extracting the soluble proteome of this bacterium provides deep insights about the physiological dynamic changes under different growth and stress conditions, thus defining “proteomic signatures” as targets for therapeutic intervention. In this protocol, we describe an experimentally verified approach to extract maximal cytoplasmic proteins from Streptococcus sanguinis SK36 strain. A combination of procedures was adopted that broke the thick cell wall barrier and minimized denaturation of the intracellular proteome, using optimized buffers and a sonication step. Extracted proteome was quantitated …

A Comparative Analysis Of Stress Responses In Diverse Acanthamoeba Isolates, Mallory Jean Douthitt

Theses, Dissertations and Capstones

Acanthamoeba are free-living amoebae which can differentiate from vegetative, trophozoite forms into dormant cysts upon encountering unfavorable conditions. Acanthamoeba isolates FLA9, BP, and FLA22 are known to have unusual tolerance to environmental conditions which would promote encystment in the type strain, Neff. To facilitate further research into the behavior of these isolates, the phenotypic variables of instantaneous growth rate (μ), mean exponential encystment rate (Ԑ), and overall encystment success are calculated for the study isolates a variety of environmental conditions. Results indicate that BP and FLA22 may prefer growth conditions that are intolerable to the Neff strain. Findings suggest genomic …

Antibiotic Resistance Genes In Minnesota Soil Bacteria From Areas Of High And Low Ferric Iron, Gunner L. Drossel, Presley Martin Phd

Departmental Honors Projects

Naturally-occurring antibiotic resistance genes in soil bacteria represent a potentially important reservoir of genes that could contribute to antibiotic resistance of human pathogens. It has been reported that over 40 genes in bacterial genomes are controlled by concentrations of ferric iron. We examined the effect of soil metal content on the level of resistance to two antibiotics, ampicillin (Amp) and tetracycline (Tet), and the presence of multiple genes that code for efflux pump-mediated resistance. These pumps act to export toxins (e.g. heavy metals and antibiotics, perhaps). Because of this, growth in heavy metal-contaminated soils might select for antibiotic resistance. Ninety-six …

Annotation And Identification Of Several Glycerolipid Metabolic Related Ortholog Genes; Mrub_0437, Mrub_1813 And Mrub_2759 In The Organism Meithermus Ruber And Their Predicted Respective Orthologs B3926, B4042 And Bo514 Found In E.Coli., Abdul Rahman Abdul Kader, Dr. Lori R. Scott

Meiothermus ruber Genome Analysis Project

We predict Mrub_0437 encodes the enzyme glycerol kinase (DNA coordinates [417621..419183), which is an intermediary step of the glycerolipid metabolic pathway (KEGG map00561), It catalyzes the conversion of glycerol to sn-Glycerol-3-phosphate. The E. coli K12 MG1655 ortholog is predicted to be b3926.

We predict Mrub_1813 encodes the enzyme diacylglycerol kinase (DNA coordinates [1864659..1865063), which is an intermediary step of the glycerolipid metabolic pathway (KEGG map00561), It catalyzes the conversion of 1,2-diacyl-sn-glycerol to 1,2-diacyl-sn-glycerol 3-phosphate. The E. coli K12 MG1655 ortholog is predicted to be b4042.

We predict Mrub_2759 encodes the enzyme glycerol kinase (DNA coordinates [2799712..2800665), which is an intermediary …

Serine Biosynthesis And Glycine Biosynthesis/Degradation: Mrub_0173 Is Orthologous To E. Coli B2913 (Sera); Mrub_0125 Is Orthologous To E. Coli B4388 (Serb); Mrub_2910 Is Orthologous To E. Coli B2551 (Glya)., Megan M. Janssen, Dr. Lori R. Scott

Meiothermus ruber Genome Analysis Project

ABSTRACT. This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_0173, Mrub_0125, and Mrub_ 2910. We predict that Mrub_0173 encodes the enzyme phosphoglycerate dehydrogenase (DNA coordinates 152982 ... 154347), which is the 1st step of the serine biosynthesis pathway (KEGG map number 00680). It catalyzes the conversion of NAD+ + 3-phospho-D-glycerate → NADH H+ + 3-phospho-hydroxypyruvate. The E. coli K12 MG1655 ortholog is predicted to be b2913, which has …

The Effect Of Gram-Positive Staphylococcus Aureus Cell Wall Components Lipoteichoic Acid And Peptidoglycan On Cytokine Production, Cytoskeletal Arrangement, And Cell Viability On Raw 264.7 Murine Macrophages, Gabrielle String

Browse all Theses and Dissertations

In this study, gram positive Staphylococcus aureus cell wall components such as lipoteichoic acid (LTA) and peptidoglycan (PGN) were used to study the potential inflammatory and anti-inflammatory cytokine response, cytoskeletal arrangement and cell viability on RAW264.7 murine macrophages over 24 hours. The effect of S.aureus LTA and PGN (5 µg/mL) on RAW 264.7 macrophages was evaluated every six hours for twenty-four hours. Inflammatory cytokine (TNF-a) production peaked at 6 hours before decreasing over time. Anti-inflammatory cytokine (IL-10) production peaked between 12 and 18 hours. During the first twenty-four hours, cytotoxicity of treated macrophages, as defined as the release of lactate …

Effects Of Socs1 And Socs3 Peptide Mimetics On Macrophage Phagocytosis Of Malignant Cells, Colt Dylan Capan

Browse all Theses and Dissertations

Macrophages play a key role in both the innate and adaptive immune system responses to foreign materials. Suppressors of cytokine signaling (SOCS) proteins are known as regulators of the immune response through various JAK/STAT pathways. This study examined the roles of SOCS1 and SOCS3 peptide mimetics on the phagocytosis of fluorescently labeled malignant target cell by RAW264.7 murine macrophages. The malignant cells used were Neuro-2a cells, a murine neuroblastoma cell line. A prominent "eat me" signal found in neuroblastoma cells is calreticulin (CRT), which permits macrophages to recognize and then phagocytize the malignant cells. When M1 (pro-inflammatory) polarized macrophages were …

Identification And Characterization Of Fungal Isolates From Land-Applied Sewage Sludge, Vaille Swenson, Hope L. Juntunen, R Honour, R C. Hale, Michael Gaylor, Patrick Videau

Research & Publications

Approximately eight million dry tons of sewage sludge is generated in the U.S. each year, with more than half of that now land-applied as the primary method of disposal. Despite the proliferation of this practice, little is known about the microbial constituents of these noxious materials. To address this knowledge gap, we isolated and characterized fungi present in archived samples of land-disposed sewage sludge collected from the Snoqualmie National Forest (Washington State). Sludge samples were resuspended in sterile water and 15 fungal isolates were selected and purified on sabouraud dextrose agar plates supplemented with 50 mg/L of chloramphenicol. Fungal morphology …

The Hetz Gene Regulates Heterocyst Formation In Anabaena Sp. Strain Pcc 7120, Patrick Videau, Vaille Swenson, Michael Gaylor, S M. O'Hanlon, L M. Cozy

Research & Publications

To form a complex multicellular organism, stem cells must differentiate into each cell/tissue type along proper spatiotemporal scales. The study of differentiation and organismal development has historically been conducted in prokaryotes due to their genetic and morphological simplicity. Anabaena sp. strain PCC 7120 is a multicellular filamentous cyanobacterium that differentiates a morphologically distinct secondary cell type, the heterocyst, in response to a lack of combined environmental nitrogen. Heterocysts are regularly spaced along filaments and fix atmospheric dinitrogen to maintain organismal viability in its absence. Previous work suggested that the hetZ gene is involved in heterocyst differentiation, but the insertional mutants …

Toward A Rapid Production Of Multivirus-Specific T Cells Targeting Bkv, Adenovirus, Cmv, And Ebv From Umbilical Cord Blood, Hema Dave, Min Luo, J.W. Blaney, Shabnum Patel, Cecilia Barese, Conrad Russell Cruz, Elizabeth J. Shpall, Catherine M. Bollard, Patrick J. Hanley

Pediatrics Faculty Publications

Umbilical cord blood (CB) has emerged as an effective alternative donor source for hematopoietic stem cell transplantation. Despite this success, the prolonged duration of immune suppression following CB transplantation and the naiveté of CB T cells leave patients susceptible to viral infections. Adoptive transfer of ex vivo-expanded virus-specific T cells from CB is both feasible and safe. However, the manufacturing process of these cells is complicated, lengthy, and labor-intensive. We have now developed a simplified method to manufacture a single culture of polyclonal multivirus-specific cytotoxic T cells in less than 30 days. It eliminates the need for a live virus …

The External Microbiome Of Bats: Effects Of Season, Site, Host Species, And Body Region, Kyle G. George

Master's Theses and Doctoral Dissertations

White-nose syndrome is a cutaneous fungal disease that has been detrimental to North American bats for over 10 years, but few investigators have examined the natural microbiota living on these mammals. I explored the influence of season, geographic site, host species, and body region on the external microbiome of four cave-hibernating and two migratory species. Automated ribosomal intergenic spacer analysis was used to profile bacterial communities from three cutaneous regions of 222 bats across winter and summer sites in Michigan, Illinois, and Kentucky. Season, site, host species, and body region all influenced the composition of external bacterial communities, but geographic …

Cytokine Expression, Cytoskeleton Organization, And Viability Of Sim-A9 Microglia Exposed To Staphylococcus Aureus-Derived Lipoteichoic Acid And Peptidoglycan, Erin Roberts

Browse all Theses and Dissertations

In these experiments, SIM-A9 microglia were exposed to Staphylococcus aureus cell wall components lipoteichoic acid (LTA) and peptidoglycan (PGN) at a concentration of 5 ug/mL for six, twelve, eighteen, and twenty-four hours and the cytokine expression, cytoskeleton organization, and cell viability of the cells were observed. Following LTA and PGN exposure, TNF-a; secretion increased at each time interval and was highest observed at 24 hours. No significant IL-10 secretion was detected. Over the 24 hour period, cell viability and cytotoxicity of LTA and PGN treatment groups were not significantly different from the control, indicating the observed inflammatory cytokine response was …

Genomic Vs. Non-Genomic Role Of The Ahr In Human Immunoglobulin Expression, Nasser Alhamdan

Browse all Theses and Dissertations

The immunoglobulin heavy chain gene (Igh) in various animal models is regulated by numerous regulatory elements including the 3’Igh regulatory region (3’IghRR). Several transcription factors are involved in modulating the 3’IghRR including the aryl hydrocarbon receptor (AhR). The AhR is a ligand-activated transcription factor that mediates the transcription of genes involved in the metabolism of environmental toxicants such as TCDD. TCDD binds AhR and regulates immunoglobulin (Ig) expression in B cells. This modulation appears to be directly mediated by binding of the AhR to dioxin response elements (DRE) within the 3’IghRR. In human B cells, IgG secretion inhibited by TCDD …

Effects Of Socs1 And Socs3 Peptide Mimetics On Macrophage Phagocytosis Of Malignant Cells, Colt Dylan Capan

Browse all Theses and Dissertations

Macrophages play a key role in both the innate and adaptive immune system responses to foreign materials. Suppressors of cytokine signaling (SOCS) proteins are known as regulators of the immune response through various JAK/STAT pathways. This study examined the roles of SOCS1 and SOCS3 peptide mimetics on the phagocytosis of fluorescently labeled malignant target cell by RAW264.7 murine macrophages. The malignant cells used were Neuro-2a cells, a murine neuroblastoma cell line. A prominent “eat me” signal found in neuroblastoma cells is calreticulin (CRT), which permits macrophages to recognize and then phagocytize the malignant cells. When M1 (pro-inflammatory) polarized macrophages were …

A Survey Of Β-Lactam Antibiotic Resistance Genes And Culturable Ampicillin Resistant Bacteria In Minnesota Soils, Emily M. Wollmuth

Departmental Honors Projects

Since the discovery of penicillin, antibiotics have been an essential tool in the treatment of bacterial infections and diseases. It is estimated that antibiotics and antibiotic resistance genes have existed for billions of years. With the increasing appearance of resistant pathogenic bacteria, there has been growing concern. β-lactam antibiotics make up the largest portion of the global market, so resistance to these antibiotics is especially alarming. It has been theorized that frequency and type of antibiotic resistance genes vary by area. Previous studies suggest that these differences may be related to antibiotic use in agricultural and urban areas. To survey …

Carbapenem-Resistant Klebsiella Pneumoniae In Barbados: Driving Change In Practice At The National Level., Corey Forde, Bryan Stierman, Pilar Ramon-Pardo, Thais Dos Santos, Nalini Singh

Psychiatry and Behavioral Sciences Faculty Publications

Introduction

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is of growing concern globally. The risk for transmission of antimicrobial resistant organisms across several continents to the Caribbean is a real one given its tourism industry. After a cluster of cases of CRKP were detected, several studies detailed in this report were initiated to better characterize the problem.

Methods

A hospital-wide point prevalence study and active surveillance were performed at Queen Elizabeth Hospital (QEH) in Barbados in 2013 to assess the prevalence of CRKP infection/colonization. Following this, a 1-year longitudinal study measured the prevalence of CRKP isolates in the hospital and across all healthcare …

Clinical And Mucosal Immune Correlates Of Hiv-1 Semen Levels In Antiretroviral-Naive Men., Brendan J W Osborne, Angie K Marsh, Sanja Huibner, Kamnoosh Shahabi, Cindy Liu, Tania Contente, Nico J D Nagelkerke, Colin Kovacs, Erika Benko, Lance Price, Kelly S Macdonald, Rupert Kaul

Environmental and Occupational Health Faculty Publications

Background.

This study was done to characterize parameters associated with semen human immunodeficiency virus (HIV)-1 ribonucleic acid (RNA) viral load (VL) variability in HIV-infected, therapy-naive men. Methods.

Paired blood and semen samples were collected from 30 HIV-infected, therapy-naive men who have sex with men, and 13 participants were observed longitudinally for up to 1 year. Human immunodeficiency virus RNA, bacterial load by 16S RNA, herpesvirus (Epstein-Barr virus and cytomegalovirus [CMV]) shedding, and semen cytokines/chemokines were quantified, and semen T-cell subsets were assessed by multiparameter flow cytometry. Results.

Semen HIV RNA was detected at 93% of visits, with >50% of men …

Media Optimization, Scale-Up And Repeated Fed-Batch Operations For The Production Of 1,3-Propanediol From Glycerol By Halanaerobium Hydrogeniformans, Shivani Kalia

Masters Theses

"The development of renewable energy sources, such as biofuels, is of great interest in today's world due to depletion of fossil fuels and concerns about climate change. The production of the main by-product, crude glycerol, in biodiesel production presents an opportunity for the production of industrially relevant commodities. Crude glycerol in biodiesel waste is highly impure and possesses high salt concentrations and alkalinity, making it infeasible for direct industrial utilization. Moreover, current glycerol purification methods are highly cost-intensive, necessitating a search for cost-effective approaches that are feasible to employ. Genome data analysis of Halanaerobium hydrogeniformans, revealed the metabolic capability …

Review Of The Algal Biology Program Within The National Alliance For Advanced Biofuels And Bioproducts, Clifford J. Unkefer, Richard T. Sayre, Jon K. Magnuson, Daniel B. Anderson, Ivan Baxter, Ian K. Balby, Judith K. Brown, Michael Carleton, Rose Ann Cattolico, Taraka Dale, Timothy P. Devarenne, C. Meghan Downes, Susan K. Dutcher, David T. Fox, Ursula Goodenough, Jan Jaworski, Jonathan E. Holladay, David M. Kramer, Andrew T. Koppisch, Mary S. Lipton, Babetta L. Marrone, Margaret Mccormick, István Molnár, John B. Mott, Kimberly L. Ogden, Ellen A. Panisko, Matteo Pellegrini, Juergen Polle, James W. Richardson, Martin Sabarsky, Shawn R. Starkenburg, Gary D. Stormo, Munehiro Teshima, Scott N. Twary, Pat J. Unkefer, Joshua S. Yuan, José A. Olivares

Publications and Research

In 2010,when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortiumbegan, littlewas known about themolecular basis of algal biomass or oil production. Very fewalgal genome sequenceswere available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played bymetabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome …