Microbiology Commons^™

Function Of The Enterobactin Operon Of A. Actinomycetemcomitans In The Presence Of Catecholmines And Iron., Taylor Johnson

Electronic Theses and Dissertations

Background: Aggregatibacter actinomycetemcomitans (Aa) possesses a two-component system, QseBC, which is key in biofilm formation/virulence and is activated in the presence of iron-catecholamine complexes. Aa does not synthesize enterobactin, a catechol-based siderophore, yet possesses the machinery for recognition and uptake. We hypothesize that Aa is able to acquire iron by catecholamine mediation through the enterobactin receptor/transporter. Methods: By insertional mutation, we attempted to delete the enterobactin permease from the genome using suicide vector pJT1. A growth curve of truncated mutant ΔfepA was also conducted to observe growth in the presence of iron and catecholamines. Statistical significance was determined by ANOVA …

Range-Wide Prevalence And Impacts Of Pseudocercosporella Inconspicua On Lilium Grayi And An Assessment Of L. Superbum And L. Michauxii As Reservoirs, Cindy L. Barrett

Electronic Theses and Dissertations

Lilium grayi (Gray’s Lily), a southern Appalachian endemic species, is threatened by a Lilium-specific fungal pathogen, Pseudocercosporella inconspicua. The disease is characterized by tan lesions that can cause early senescence, while also lowering seed production and viability. This project tested for P. inconspicua conidia and accessed health at nine locations. The disease was present and ubiquitous across the range of L. grayi. Through identification of P. inconspicua conidia in the field, L. superbum (Turk’s Cap Lily) was identified as an additional host, while L. michauxii (Michaux’s Lily) was disease-free. However, infection was inducible in both species. With …

Proteomic Identification Of Histone Post-Translational Modifications Induced By Dna Double-Strand Breaks And Novel Proteins Involved In The Dna Damage Response, Pingping Wang

Dissertations and Theses (Open Access)

Inaccurate repair of DNA double-strand breaks (DSBs) can lead to DNA mutation and chromosome rearrangements, causing human diseases such as cancer. Although we know the basic mechanisms of DSB repair, the added complexities in the chromatin context are unclear. This is partially due to the lack of unbiased systems for identifying proteins and post-translational modifications (PTMs) involved in DSB repair. In this work, we established a novel method, termed DSB-ChAP-MS (Double Strand Break-Chromatin Affinity Purification with Mass Spectrometry), for the affinity purification of a sequence-specific single copy endogenous chromosomal locus containing a DSB, followed by the proteomic identification of enriched …

The Bovine Rumen Microbiome Revealed By Different Fractions Of Rumen Contents, Ashlee L. Breakstone

Animal Science Undergraduate Honors Theses

The bovine rumen microbiota is very important in terms of animal functionality and digestion. The fermentative capability of the rumen provides means for the digestion of complex plant material that is indigestible by humans. The rumen is the working ground for millions of microorganisms, primarily bacteria, to digest and ferment feed into volatile fatty acids and bacterial protein for the animal’s energy and protein needs, respectively. Of significant importance is the rumen microbiomes ability to conform to certain factors such as genetics, feed, or geographic location. These changes can have a direct measure on animal growth, health, and performance. The …

Isolation Of A Mycobacterium Virus With The Infectivity Rate Tested At Various Temperatures, Katie Wegenast

Undergraduate Theses

Isolation techniques developed by the HHMI and the SEA-PHAGES program were used to obtain a bacteriophage from a mixture of loamy clay soil. The sample was retrieved from a forest edge in central Kentucky. The isolate produced large lytic plaques on a lawn of the bacterium Mycobacterium smegmatis. The bacteriophage was purified, amplified, and analyzed using restriction digest analysis with visualization by gel electrophoresis. Restriction digest analysis suggests the virus belongs to a group known as “A”. Mycobacteriophages are placed into distinct groups based on DNA sequences comparison. The next step in the procedure will be to document with …

Accumulation And Expression Of Multiple Antibiotic Resistance Genes In Arcobacter Cryaerophilus That Thrives In Sewage, Jess A. Millar, Rahul Raghavan

Biology Faculty Publications and Presentations

We explored the bacterial diversity of untreated sewage influent samples of a wastewater treatment plant in Tucson, AZ and discovered that Arcobacter cryaerophilus, an emerging human pathogen of animal origin, was the most dominant bacterium. The other highly prevalent bacteria were members of the phyla Bacteroidetes and Firmicutes, which are major constituents of human gut microbiome, indicating that bacteria of human and animal origin intermingle in sewage. By assembling a near-complete genome of A. cryaerophilus, we show that the bacterium has accumulated a large number of antibiotic resistance genes (ARGs) probably enabling it to thrive in the wastewater. We also …

Does High Relatedness Promote Cheater-Free Multicellularity In Synthetic Lifecycles?, R F. Inglis, E Ryu, O Asikhia, Joan E. Strassmann, David C. Queller

Biology Faculty Research

The evolution of multicellularity is one of the key transitions in evolution and requires extreme levels of cooperation between cells. However, even when cells are genetically identical, noncooperative cheating mutants can arise that cause a breakdown in cooperation. How then, do multicellular organisms maintain cooperation between cells? A number of mechanisms that increase relatedness amongst cooperative cells have been implicated in the maintenance of cooperative multicellularity including single-cell bottlenecks and kin recognition. In this study, we explore how relatively simple biological processes such as growth and dispersal can act to increase relatedness and promote multicellular cooperation. Using experimental populations of …

Molecular Detection Of Candidatus Bartonella Mayotimonensis In North American Bats, Thomas M. Lilley, Cali Ann Wilson, Riley F. Bernard, Emma V. Wilcox, Eero J. Vesterinen, Quinn Mr Webber, Laura Ann Kurpiers, Jenni M. Prokkola, Imran Ejotre, Allen Kurta, Kenneth A. Field, Deeann M. Reeder, Arto T. Pulliainen

Faculty Journal Articles

Candidatus Bartonella mayotimonensis was detected in 2010 from an aortic valve sample of a patient with endocarditis from Iowa, the United States of America. The environmental source of the potentially new endocarditis-causing Bartonellaremained elusive. We set out to study the prevalence and diversity of bat-associated Bartonella in North America. During 2015, mist nets and harp traps were used to capture 92 bats belonging to two species: little brown myotis (Myotis lucifugusLe Conte 1831, n = 73) and the gray myotis (M. grisescens A.H. Howell 1909, n = 19) in Kentucky, Michigan, Pennsylvania, and Tennessee. DNA preparations …

The Incidence Of Mrsa Infections In The United States: Is A More Comprehensive Tracking System Needed?, Kevin T. Kavanagh, Said Abusalem, Lindsay E. Calderon

EKU Faculty and Staff Scholarship

A review of epidemiological studies on the incidence of MRSA infections overtime was performed along with an analysis of data available for download from Hospital Compare (https://data.medicare.gov/data/hospital-compare). We found the estimations of the incidence of MRSA infections varied widely depending upon the type of population studied, the types of infections captured and in the definitions and terminology used to describe the results. We could not find definitive evidence that the incidence of MRSA infections in U.S. community or facilities is decreasing significantly. Of concern are recent data reported to the National Healthcare Safety Network (NHSN) on MRSA bloodstream infections which …

Trafficking Receptor Signatures Define Blood Plasmablasts Responding To Tissue-Specific Immune Challenge, Yekyung Seong, Nicole Lazarus, Lusijah Sutherland, Aida Habtezion, Tzvia Abramson, Xiao-Song He, Harry Greenberg, Eugene Butcher

Faculty Publications, Biological Sciences

Antibody-secreting cells are generated in regional lymphoid tissues and traffic as plasmablasts (PBs) via lymph and blood to target sites for local immunity. We used multiparameter flow cytometry to define PB trafficking programs (TPs, combinations of adhesion molecules and chemoattractant receptors) and their imprinting in patients in response to localized infection or immune insults. TPs enriched after infection or autoimmune inflammation of mucosae correlate with sites of immune response or symptoms, with different TPs imprinted during small intestinal, colon, throat, and upper respiratory immune challenge. PBs induced after intramuscular or intradermal influenza vaccination, including flu-specific antibody–secreting cells, display TPs characterized …

Microflora In The Cheek Pouches Of Ord's Kangaroo Rat (Dipodomys Ordii) From The Nebraska Sandhills, Devin M. Christensen

UNO Student Research and Creative Activity Fair

The microflora living within the Ord’s kangaroo rat (Dipodymis ordii) cheek pouches has never been extensively studied before. Kangaroo rats use their cheek pouches to transport seeds and grasses in their mouths that they later store. It is predicted that the cheek pouches harbor fungal and bacterial growth that could be either helpful or harmful to the kangaroo rat and its environment. 8 kangaroo rats were humanely captured using Sherman live traps in the Nebraska Sandhills; their cheek pouches were swabbed, and the microorganisms obtained were grown on agar plates and in liquid media until an adequate amount …

Draft Genome Sequences Of Three Closely Related Isolates Of The Purple Nonsulfur Bacterium Rhodovulum Sulfidophilum, Michael S. Guzman, Beau Mcginley, Natalia Santiago-Merced, Dinesh Gupta, Arpita Bose

Biology Faculty Research

We report here the draft genome sequences of three isolates of Rhodovulum sulfidophilum from a single population that will serve as a model system for understanding genomic traits that underlie metabolic variation within closely related marine purple nonsulfur bacteria in natural microbial communities.

The Human Microbiome: An Emerging Tool In Forensics, Jarrad T. Hampton-Marcell, Jose V. Lopez, Jack A. Gilbert

Biology Faculty Articles

No abstract provided.

Sequential Displacement Of Type Vi Secretion System Effector Genes Leads To Evolution Of Diverse Immunity Gene Arrays In Vibrio Cholerae, Paul C. Kirchberger, Daniel Unterweger, Daniele Provenzano, Stefan Pukatzki, Yan Boucher

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Type VI secretion systems (T6SS) enable bacteria to engage neighboring cells in contact-dependent competition. In Vibrio cholerae, three chromosomal clusters each encode a pair of effector and immunity genes downstream of those encoding the T6SS structural machinery for effector delivery. Different combinations of effector-immunity proteins lead to competition between strains of V. cholerae, which are thought to be protected only from the toxicity of their own effectors. Screening of all publically available V. cholerae genomes showed that numerous strains possess long arrays of orphan immunity genes encoded in the 3' region of their T6SS clusters. Phylogenetic analysis reveals that these …

Ticks Elicit Variable Fibrinogenolytic Activities Upon Feeding On Hosts With Different Immune Backgrounds, Ashish Vora, Vikas Taank, John F. Anderson, Durland Fish, Daniel E. Sonenshine, John D. Catravas, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

Ticks secrete several anti-hemostatic factors in their saliva to suppress the host innate and acquired immune defenses against infestations. Using Ixodes scapularis ticks and age-matched mice purchased from two independent commercial vendors with two different immune backgrounds as a model, we show that ticks fed on immunodeficient animals demonstrate decreased fibrinogenolytic activity in comparison to ticks fed on immunocompetent animals. Reduced levels of D-dimer (fibrin degradation product) were evident in ticks fed on immunodeficient animals in comparison to ticks fed on immunocompetent animals. Increased engorgement weights were noted for ticks fed on immunodeficient animals in comparison to ticks fed on …

Identification And Characterization Of An Efficient Acyl-Coa:Diacylglycerol Acyltransferase 1 (Dgat1) Gene From The Microalga Chlorella Ellipsoidea, Xuejie Guo, Chengming Fan, Yuhong Chen, Jingqiao Wang, Weibo Yin, Richard R. C. Wang, Zanmin Hu

Forage and Range Research Laboratory Publications

Background: Oil in the form of triacylglycerols (TAGs) is quantitatively the most important storage form of energy for eukaryotic cells. Diacylglycerol acyltransferase (DGAT) is considered the rate-limiting enzyme for TAG accumulation. Chlorella, a unicellular eukaryotic green alga, has attracted much attention as a potential feedstock for renewable energy production. However, the function of DGAT1 in Chlorella has not been reported.

Results: A full-length cDNA encoding a putative diacylglycerol acyltransferase 1 (DGAT1, EC 2.3.1.20) was obtained from Chlorella ellipsoidea. The 2,142 bp open reading frame of this cDNA, designated CeDGAT1, encodes a protein of 713 amino acids showing …

A Blueprint To Evaluate One Health, Simon R. Rüegg, Barry J. Mcmahon, Barbara Häsler, Roberto Esposito, Helen O'Shea, Et Al

Department of Biological Sciences Publications

One Health (OH) positions health professionals as agents for change and provides a platform to manage determinants of health that are often not comprehensively captured in medicine or public health alone. However, due to the organization of societies and disciplines, and the sectoral allocation of resources, the development of transdisciplinary approaches requires effort and perseverance. Therefore, there is a need to provide evidence on the added value of OH for governments, researchers, funding bodies, and stakeholders. This paper outlines a conceptual framework of what OH approaches can encompass and the added values they can provide. The framework was developed during …

Microbiome And Bacterioplankton Rrna Gene Sequence Data Collected From Gulf Of Mexico Seawater Samples, Cruises Dp01 And Dp02 From May 2015 - August 2015, Cole Easson, Jose V. Lopez

DEEPEND Datasets

Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during two planned DEEPEND cruise expeditions to the GOM. Filters were stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable region was generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Bioinformatics analyses in QIIME and R was used to quality filter and assess microbial community diversity and taxonomic composition. These baseline characterizations track alpha and beta diversity at different depths ranging from 0 – …

The Subject Librarian Newsletter, Biology, Spring 2017, Sandy Avila

Libraries' Newsletters

No abstract provided.

Evolutionary Adaptations Of Biofilms Infecting Cystic Fibrosis Lungs Promote Mechanical Toughness By Adjusting Polysaccharide Production, Kristin Kovach, Megan Davis-Fields, Yasuhiko Irie, Kanishk Jain, Shashvat Doorwar, Katherine Vuong, Numa Dhamani, Kishore Mohanty, Ahmed Touhami, Vernita D. Gordon

Biology Faculty Publications

Biofilms are communities of microbes embedded in a matrix of extracellular polymeric substances, largely polysaccharides. Multiple types of extracellular polymeric substances can be produced by a single bacterial strain. The distinct polymer components of biofilms are known to provide chemical protection, but little is known about how distinct extracellular polysaccharides may also protect biofilms against mechanical stresses such as shear or phagocytic engulfment. Decades-long infections of Pseudomonas. aeruginosa biofilms in the lungs of cystic fibrosis patients are natural models for studies of biofilm fitness under pressure from antibiotics and the immune system. In cystic fibrosis infections, production of the extracellular …

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 …

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 …

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 …

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 …

Investigating The Sources And Dynamics Of Escherichia Coli In A Missouri Ozarks Watershed, Kaleb Bassett

Masters Theses

"Escherichia coli, an intestinal bacterium, can serve as an indication of the presence of pathogenic microorganisms in water systems used by humans for recreation, agriculture, or drinking water. Many aquatic systems in the United States exceed the E. coli standard, set by the Environmental Protection Agency, for safe drinking water and recreational use. During 2016, a water sampling program was established in the Mill Creek watershed, a rural watershed located near the city of Newburg in Phelps County, Missouri. Water samples were collected before, during, and after storms throughout the year to examine the relationship between E. coli …

Surveillance Of Emerging Livestock Viruses, Faten A. Okda

Electronic Theses and Dissertations

Accurate and rapid diagnostic tests are essential for the management and control of emerging infectious diseases. Therefore, the overall goals of studies presented in this dissertation were to provide improved diagnostic and surveillance capabilities for several emerging viral diseases impacting the livestock industry and to provide insight into appropriate control strategies. Recent, severe outbreaks of porcine epidemic diarrhea virus (PEDV) in Asia and North America highlighted the need for well-validated diagnostic tests for identification of PEDV infected animals and evaluation of their immune status. PEDV was first detected in the U.S. in May 2013 and another swine coronavirus, porcine deltacoronavirus …

Molecular Diversity Of Foliar Fungal Endophytes In Relation To Defense Strategies And Disease In Whitebark Pine, Lorinda Bullington

Graduate Student Theses, Dissertations, & Professional Papers

An invasive fungal pathogen, Cronartium ribicola (the causative agent of white pine blister rust) infects and kills whitebark pine (Pinus albicaulis) throughout the western US. Blister rust has decreased whitebark pine populations by over 90% in some areas. Whitebark pine, a keystone species, has been proposed for listing under the Endangered Species Act in the U.S., and the loss of this conifer is predicted to have severe impacts on forest composition and function in high elevations. Hundreds of asymptomatic fungal species live inside whitebark pine tissue, and recent studies suggest that these fungi can influence the frequency and …

Characterizing Regulatory Factors Of The Sumoylation System, David Quintanar

Open Access Theses & Dissertations

The effects that influenzaâ??s seasonal epidemics have on human health and the global economy have been clearly noted; while they are indeed very impressive, the impact of influenza pandemics arguably surpass other known infectious agents. Influenza A virus attaches to, enters, and infect cells by releasing its segmented genome which localize to the nucleus then use the hostâ??s cellular machinery to replicate and create viral progeny. The virus is able to hijack transcriptional components as well as to interact with other known and unknown host proteins which ultimately allows for a balance between cell viability and viral propagation. One known …