Microbiology Commons^™

Examination Of Germination Receptors Of B. Subtilis And B. Megaterium, Shruti Patel, Alessio Luinetti, Ernesto Abel-Santos, Eduardo Robleto

Undergraduate Research Opportunities Program (UROP)

Many bacterial species including those in the Bacilli group form spores as a mechanism to survive harsh conditions such as extreme temperature, radiation, chemicals, and nutrient starvation. By forming spores, they can remain metabolically dormant for an extended period and revert to their vegetative form when environment becomes favorable. This resumption of metabolism and growth is marked by a process called germination that is triggered by exogenous nutrients such as amino acids, sugars, and nucleotides. The (Ger) germination receptors that are postulated to respond to these germinants, in the case of B. subtilis and B. megaterium, are a complex of …

Evaluating Snow Microbial Assemblages, Jenny Lam, Jessica K. Guy, Ryan Brock, Matt Oates, Alison E. Murray

Undergraduate Research Opportunities Program (UROP)

Psychrophiles are organisms that grow optimally below 20C (1). The US Great Basin is home to many mountain peaks with an abundance of alpine snow environments perfect for psychrophilic habitation. We analyzed samples from three different locations, Wheeler Peak, Pacific Crest Trail, and Mount Conness, characterizing and comparing the psychrophilic communities at varying depth intervals in the snow. Polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) showed no notable difference in community structure with depth, but there was a distinct difference when comparing different snow environments (i.e. shaded vs. full sun exposure). The chlorophyll concentration decreased as the …

Evaluation Of Virb Binding Site Contribution To The Regulation Of The Icsp Promoter In Shigella Flexneri, Juan C. Duhart, Maria I. Castellanos, Helen J. Wing

Undergraduate Research Opportunities Program (UROP)

Shigella species are gram-negative, rod-shaped bacteria that are closely related to Escherichia coli. Virulent Shigella spp. are intracellular pathogens that invade, replicate and spread through epithelial cells of the lower intestine and cause bacillary dysentery in humans. This disease is characterized by a robust inflammatory response that results in fever, abdominal pain, and bloody diarrhea (3). According to the CDC, approximately 14,000 cases are reported each year in the United States alone. This number however, does not reflect the actual incidence of this disease as many cases go unreported. The molecular pathogenesis of these bacteria lies in the large virulence …

Modifying The Amino Acid Sequence In The Surface-Exposed Loops Of The Omptin Family Of Proteins To Determine Their Effect On Function, Natiera Magnuson, Eun-Hae Kim, Christian Ross, Helen J. Wing

Undergraduate Research Opportunities Program (UROP)

The omptin family of proteins consists of proteases which lie in the outer membrane of some gram-negative, pathogenic bacteria such as Escherichia coli (OmpT), Shigella flexneri (IcsP), Salmonella typhimurium (PgtE), and Yersinia pestis (Pla). These proteases are highly conserved, sharing approximately 50% sequence identity and a β-barrel shape (fig. 1D). The differences in the structure of these four proteins are in the surface-exposed loop region surrounding the active site, but not in the active site itself [4]. These proteases are important for the virulence of many bacteria. For example, OmpT of E. coli cleaves an antimicrobial peptide secreted by epithelial …

Transcriptional Regulation Of The Shigella Flexneri Icsp Promoter: Silencing And Anti-Silencing By H-Ns And Virb, Dustin Harrison

UNLV Theses, Dissertations, Professional Papers, and Capstones

Shigella species are gram-negative intracellular pathogens that cause bacillary dysentery in humans. Many genes required for virulence of Shigella are carried on a large 230 kb plasmid and many of these are under the transcriptional control of the histone-like nucleoid structuring protein (H-NS) and by the major virulence regulator VirB. At the non-permissive temperature of 30⁰C, H-NS represses transcription, while at 37⁰C VirB alleviates this repression. This mechanism of gene regulation has been coined "silencing/anti-silencing" and is commonly found in many important bacterial pathogens including Salmonella spp. and Yersinia spp. The icsP gene, encoded by the Shigella virulence plasmid, is …

The Domains Of The Catalytic Subunit Of The Eukaryotic Rna Degrading Exosome, Rrp44p, Have Distinct Functions, Daneen Schaeffer

Dissertations and Theses (Open Access)

The exosome is a 3’ to 5’ exoribonuclease complex that consists of ten essential subunits. In the cytoplasm, the exosome degrades mRNA in a general mRNA turnover pathway and in several mRNA surveillance pathways. In the nucleus, the exosome processes RNA precursors to form small, stable, mature RNA species, including rRNA, snRNA, and snoRNA. In addition to processing these RNAs, the nuclear exosome is also involved in degrading aberrantly processed forms of these RNAs, and others, including mRNA.

The 3’ to 5’ exoribonuclease activity of the exosome is contributed by the RNB domain of the only catalytically active subunit, Rrp44p, …

Constraint-Based Model Of Shewanella Oneidensis Mr-1 Metabolism: A Tool For Data Analysis And Hypothesis Generation, Grigoriy E. Pinchuk, Eric A. Hill, Oleg V. Geydebrekht, Jessica De Ingeniis, Xiaolin Zhang, Andrei Osterman, James H. Scott

Dartmouth Scholarship

Shewanellae are gram-negative facultatively anaerobic metal-reducing bacteria commonly found in chemically (i.e., redox) stratified environments. Occupying such niches requires the ability to rapidly acclimate to changes in electron donor/acceptor type and availability; hence, the ability to compete and thrive in such environments must ultimately be reflected in the organization and utilization of electron transfer networks, as well as central and peripheral carbon metabolism. To understand how Shewanella oneidensis MR-1 utilizes its resources, the metabolic network was reconstructed. The resulting network consists of 774 reactions, 783 genes, and 634 unique metabolites and contains biosynthesis pathways for all cell constituents. Using constraint-based …

Fetal Programming By Nicotine Increases Cardiac Susceptibility To Ischemic Injury, Jennifer Charlotte Alexie Lawrence

Loma Linda University Electronic Theses, Dissertations & Projects

Fetal programming is the area of study that focuses on the prenatal origins of adult onset disorders. Previous studies have associated an adverse prenatal environment with the onset of physiologic and metabolic diseases during adulthood. Fetal malnutrition, hypoxia, and exposure to drugs - such as cocaine and nicotine - have been associated with adult disease states. Cigarette smoking is the number one cause of preventable death in the developed world. Among the many dangerous chemicals found in tobacco products is nicotine, the compound responsible for the addictive nature of tobacco use. Nicotine use during pregnancy is a known cause of …

Regulation Of Pim1 Under Hypoxia In Prostate Cancer, Eva Sahakian

Loma Linda University Electronic Theses, Dissertations & Projects

A defining characteristic of solid tumors is the capacity to divide and spread under conditions of nutrient deprivation and limited oxygen availability. These microenvironmental stresses arise from structural abnormalities in tumor vessels that lead to aberrant microcirculation. Hypoxia acts as a physiological “selection pressure” in the progression of cancer by activating pathways and enhancing the expression of specific genes in tumor cells which eventually diminish their apoptotic potential. Ultimately, hypoxic microenvironment functions as a “stress factor”, selecting cells with the ability to survive and divide under anoxic conditions. The members of the PIM family of cytoplasmic serine threonine kinases are …

Natural Competence In Thermoanaerobacter And Thermoanaerobacterium Species, A Joe Shaw, David A. Hogsett, Lee R. Lynd

Dartmouth Scholarship

Low-G+C thermophilic obligate anaerobes in the class Clostridia are considered among the bacteria most resistant to genetic engineering due to the difficulty of introducing foreign DNA, thus limiting the ability to study and exploit their native hydrolytic and fermentative capabilities. Here, we report evidence of natural genetic competence in 13 Thermoanaerobacter and Thermoanaerobacterium strains previously believed to be difficult to transform or genetically recalcitrant.

In Thermoanaerobacterium saccharolyticum JW/SL-YS485, natural competence- mediated DNA incorporation occurs during the exponential growth phase with both replicating plasmid and homologous recombination-based integration, and circular or linear DNA. In T. saccharolyticum, disruptions of genes similar to …

Functional Characterization Of Mat1-1-Specific Mating-Type Genes In The Homothallic Ascomycete Sordaria Macrospora Provides New Insights Into Essential And Nonessential Sexual Regulators, V. Klix, M. Nowrousian, C. Ringelberg, J. J. Loros

Dartmouth Scholarship

Mating-type genes in fungi encode regulators of mating and sexual development. Heterothallic ascomycete species require different sets of mating-type genes to control nonself-recognition and mating of compatible partners of different mating types. Homothallic (self-fertile) species also carry mating-type genes in their genome that are essential for sexual development. To analyze the molecular basis of homothallism and the role of mating-type genes during fruiting-body development, we deleted each of the three genes, SmtA-1 (MAT1-1-1), SmtA-2 (MAT1-1-2), and SmtA-3 (MAT1-1-3), contained in the MAT1-1 part of the mating-type locus of the homothallic ascomycete species Sordaria macrospora. Phenotypic analysis of deletion mutants revealed …

The Role Of Transcription In Stationary Phase Mutagenesis In Bacillus Subtilis, Holly Anne Martin

UNLV Theses, Dissertations, Professional Papers, and Capstones

Stationary phase mutagenesis, also known as stress-induced or adaptive mutagenesis, is defined as the accumulation of mutations during conditions of no net growth or conditions of stress. This process has been implicated in acquiring antibiotic resistance and evasion of host immune responses in microbial pathogens and in the generation of mutations that lead to neoplasia in animal cells. Previous work has shown that defects in DNA synthesis and repair systems contribute to the formation of adaptive mutations; however the role of transcription in the accumulation of mutations is still being examined. It is speculated that transcriptional derepression leads to an …

Electrically Mediated Delivery Of Plasmid Dna To The Skin, Using A Multielectrode Array, Richard Heller, Yolmari Criz, Loree C. Heller, Richard A. Gilbert, Mark J. Jaroszeski

Bioelectrics Publications

The easy accessibility of skin makes it an excellent target for gene transfer protocols. To take full advantage of skin as a target for gene transfer, it is important to establish an efficient and reproducible delivery system. Electroporation is a strong candidate to meet this delivery criterion. Electroporation of the skin is a simple, direct, in vivo method to deliver genes for therapy. Previously, delivery to the skin was performed by means of applicators with relatively large distances between electrodes, resulting in significant muscle stimulation and pain. These applicators also had limitations in controlling the directionality of the applied field. …

Structural Dynamics And Signaling Roles Of The Aer Pas And F1 Regions, Asharie J. Campbell

Loma Linda University Electronic Theses, Dissertations & Projects

The Aer aerotaxis receptor in Escherichia coli mounts such a rapid response to redox that E. coli changes its swimming behavior within 100 ms after an oxygen pulse. This receptor is a membrane-bound homodimer, and it monitors internal energy (redox) via an FAD cofactor bound to a cytoplasmic N-terminal PAS domain. Understanding PAS sensing is important, as PAS domains comprise a superfamily of more than 25,000 members from all kingdoms. This study focused on the Aer N-terminal PAS sensor, as well as the region tethering it to the membrane anchor, known as the F1. Previous genetic studies on these regions …

Farnesol Induces Hydrogen Peroxide Resistance In Candida Albicans Yeast By Inhibiting The Ras-Cyclic Amp Signaling Pathway, Aurélie Deveau, Amy E. Piispanen, Angelyca A. Jackson, Deborah A. Hogan

Dartmouth Scholarship

Farnesol, a Candida albicans cell-cell signaling molecule that participates in the control of morphology, has an additional role in protection of the fungus against oxidative stress. In this report, we show that although farnesol induces the accumulation of intracellular reactive oxygen species (ROS), ROS generation is not necessary for the induction of catalase (Cat1)-mediated oxidative-stress resistance. Two antioxidants, α-tocopherol and, to a lesser extent, ascorbic acid effectively reduced intracellular ROS generation by farnesol but did not alter farnesol-induced oxidative-stress resistance. Farnesol inhibits the Ras1-adenylate cyclase (Cyr1) signaling pathway to achieve its effects on morphology under hypha-inducing conditions, and we demonstrate …

The Role Of Cuticle, Fatty Acids, And Lipid Signaling In Plant Defense, Ye Xia

Theses and Dissertations--Plant Pathology

Systemic acquired resistance (SAR) is initiated upon recognition of specific microbial effectors by cognate plant resistance proteins and immunizes distal tissues of plants against secondary infections. SAR involves the generation of a mobile signal at the site of primary infection, which then translocates to and activates defense responses in the distal tissues via some unknown mechanism(s). This study shows that an ACYL CARRIER PROTEIN 4 (ACP4), GLABRA1 (GL1) and ACYL CARRIER BINDING PROTEINS (ACBP) are required for the processing of the mobile SAR signal in distal tissues of Arabidopsis. Although acp4, gl1 and acbp plants generate the mobile signal, …

Plasmid Injection And Application Of Electric Pulses Alter Endogenous Mrna And Protein Expression In B16.F10 Mouse Melanomas, L. C. Heller, Y. L. Cruz, B. Ferraro, H. Yang, R. Heller

Bioelectrics Publications

The application of electric pulses to tissues causes cell membrane destabilization, allowing exogenous molecules to enter the cells. This delivery technique can be used for plasmid gene therapy. Reporter gene expression after plasmid delivery with eight representative published protocols was compared in B16.F10 mouse melanoma tumors. This expression varied significantly based on the pulse parameters utilized for delivery. To observe the possible influence of plasmid injection and/or pulse application on endogenous gene expression, levels of stress-related mRNAs 4 and 24 h after delivery were determined by PCR array. Increases in mRNA levels for several inflammatory chemokines and cytokines were observed …

Chlorella Viruses Encode Most, If Not All, Of The Machinery To Glycosylate Their Glycoproteins Independent Of The Endoplasmic Reticulum And Golgi, James L. Van Etten, James Gurnon, Giane M. Yanai-Balser, David Dunigan, Michael V. Graves

Nebraska Center for Virology: Faculty Publications

In contrast to all other viruses that use the host machinery located in the endoplasmic reticulum and Golgi to glycosylate their glycoproteins, the large dsDNA-containing chlorella viruses encode most, if not all, of the components to glycosylate their major capsid proteins. Furthermore, all experimental results indicate that glycosylation occurs independent of the endoplasmic reticulum and Golgi. (Review article)

Enterobacterial Repetitive Intergenic Consensus-Pcr (Eric-Pcr) Analysis Among Raw Vegetables Isolates Of Campylobacter Jejuni., Tuan Suraya Tuan Soh

Student Works (2010-2019)

A total of 20 (n=20) raw vegetable isolates of Campylobacter jejuni were examined for the presence of virulence genes and genetic diversity using enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) analysis. All C. jejuni isolates were obtained from the laboratory of Food Science and Biotechnology, University Putra Malaysia, Serdang, Selangor. When specific PCR amplification were determined, all raw vegetables isolates of Campylobacter jejuni contained cadF and ceuE genes. Whereas, 12 (12/20) isolates were positive cdtB and 6 (6/20) were positive cdtC. None of the C. jejuni isolates was cdtA positive. Using ERIC-PCR analysis, all 20 isolates of C. jejuni were …

Application Of Pcr-Based Serogrouping Of Salmonella Enterica., Mohammed Elbagir Mohammed Elhassan Nori

Student Works (2010-2019)

Serotyping is the most fundamental approach in epidemiological surveillance and outbreak investigations for Salmonella. Many multiplex PCR assays have been reported for serotyping Salmonella based on O and H antigens. The aim of this study was to apply and improve the approach in differentiation and serotyping Salmonella enterica strains by combination of sequential multiplex PCRs targeting the O, H and Vi antigens of Salmonella, and this achieved by working on 126 strains. All the strains were purified on BSA and produced black colonies of Salmonella. The strains were confirmed by PCR amplification gene that targets the hilA. 122 of 126 …

Increased Perfusion And Angiogenesis In A Hindlimb Ischemia Model With Plasmid Fgf-2 Delivered By Noninvasive Electroporation, B. Ferraro, Y. L. Cruz, M. Baldwin, D. Coppola, R. Heller

Bioelectrics Publications

Gene therapy approaches delivering fibroblast growth factor-2 (FGF-2) have shown promise as a potential treatment for increasing blood flow to ischemic limbs. Currently, effective noninvasive techniques to deliver plasmids encoding genes of therapeutic interest, such as FGF-2, are limited. We sought to determine if intradermal injection of plasmid DNA encoding FGF-2 (pFGF) followed by noninvasive cutaneous electroporation (pFGFE+) could increase blood flow and angiogenesis in a rat model of hindlimb ischemia. pFGFE+ or control treatments were administered on postoperative day 0. Compared to injection of pFGF alone (pFGFE-), delivery of pFGFE+ significantly increased FGF-2 expression for 10 days. Further, the …

Analysing The Effects Of Loss Of Sin3 In Drosophila Melanogaster, Aishwarya Swaminathan

Wayne State University Dissertations

Sin3A has been previously shown to be an essential gene for Drosophila viability and is implicated in the regulation of cell cycle. In this study, we show that SIN3 is not only required for embryonic viability but also for post-embryonic development. Genetic analysis suggests that the different isoforms of SIN3 may regulate unique sets of genes during development. The developmental lethality occurring due to ubiquitous knock down of SIN3 is hypothesized to be to the result of defects in cell proliferation. Conditional knock down of SIN3 in the wing discs results in a curly wing phenotype in the adult fly. …

Neuroaids In Africa, Kevin Robertson, Jeff Liner, James Hakim, Jean-Louis Sankalé, Igor Grant, Scott Letendre, David Clifford, Amadou Gallo Diop, Assan Jaye, Georgette Kanmogne, Alfred Njamnshi, T. Dianne Langford, Tufa Gemechu Weyessa, Charles Wood, Mwanza Banda, Mina Hosseinipour, Ned Sacktor, Noeline Nakasuja, Paul Bangirana, Robert Paul, John Joska, Joseph Wong, Michael Boivin, Penny Holding, Betsy Kammerer, Annelies Van Rie, Prudence Ive, Avindra Nath, Kathy Lawler, Clement Adebamowo, Walter Royal Iii, Jeymohan Joseph

Nebraska Center for Virology: Faculty Publications

In July 2009, the Center for Mental Health Research on AIDS at the National Institute of Mental Health organized and supported the meeting “NeuroAIDS in Africa.” This meeting was held in Cape Town, South Africa, and was affiliated with the 5th IAS Conference on HIV Pathogenesis, Treatment and Prevention. Presentations began with an overview of the epidemiology of HIV in sub-Saharan Africa, the molecular epidemiology of HIV, HIV-associated neurocognitive disorders (HANDs), and HAND treatment. These introductory talks were followed by presentations on HAND research and clinical care in Botswana, Cameroon, Ethiopia, The Gambia, Kenya, Malawi, Nigeria, Senegal, South Africa, Uganda, …

Functional Properties Of The Hiv-1 Subtype C Envelope Glycoprotein Associated With Mother-To-Child Transmission, Hong Zhang, Marzena Rola, John T. West, Damien C. Tully, Piotr Kubis, Jun He, Chipepo Kankasa, Charles Wood

Nebraska Center for Virology: Faculty Publications

Understanding the properties of viruses capable of establishing infection during perinatal transmission of HIV-1 is critical for designing effective means of limiting transmission. We previously demonstrated that the newly transmitted viruses (in infant) were more fit in growth, as imparted by their envelope glycoproteins, than those in their corresponding mothers. Here, we further characterized the viral envelope glycoproteins from six mother-infant transmission pairs and determined whether any specific envelope functions correlate with HIV-1 subtype C perinatal transmission. We found that most newly transmitted viruses were less susceptible to neutralization by their maternal plasma compared to contemporaneous maternal viruses. However, the …

Chronology And Evolution Of The Hiv-1 Subtype C Epidemic In Ethiopia, Damien C. Tully, Charles Wood

Nebraska Center for Virology: Faculty Publications

Objective—To reconstruct the onset date and evolutionary history of the HIV-1 subtype C epidemic in Ethiopia - one of the earliest recorded subtype C epidemics in the world.

Design—HIV-1 C env sequences with a known sampling year isolated from HIV-1 positive patients from Ethiopia between 1984 and 2003.

Methods—Evolutionary parameters including origin and demographic growth patterns were estimated using a Bayesian coalescent-based approach under either strict or relaxed molecular clock models.

Results—Bayesian evolutionary analysis indicated a most recent common ancestor date of 1965 with three distinct epidemic growth phases. Regression analysis of root-to-tip distances revealed a highly similar estimate for …

Enhancement Of Autophagy During Lytic Replication By The Kaposi’S Sarcoma-Associated Herpesvirus Replication And Transcription Activator, Hui-Ju Wen, Zhilong Yang, You Zhou, Charles Wood

Nebraska Center for Virology: Faculty Publications

Autophagy is one of two major degradation systems in eukaryotic cells. The degradation mechanism of autophagy is required to maintain the balance between the biosynthetic and catabolic processes and also contributes to defense against invading pathogens. Recent studies suggest that a number of viruses can evade or subvert the host cell autophagic pathway to enhance their own replication. Here, we investigated the effect of autophagy on the KSHV (Kaposi’s sarcoma-associated herpesvirus) life cycle. We found that the inhibition of autophagy reduces KSHV lytic reactivation from latency, and an enhancement of autophagy can be detected during KSHV lytic replication. In addition, …

Transcription Analysis Of The Chlorovirus Paramecium Bursaria Chlorella Virus-1, Giane M. Yanai

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

Paramecium bursaria chlorella virus (PBCV-1), a member of the family Phycodnaviridae, is a large dsDNA, plaque-forming virus that infects the unicellular green alga Chlorella NC64A. The 331 kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To follow global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDS) was constructed. Competitive hybridization experiments were conducted employing cDNAs from poly A-containing RNAs obtained from cells at seven time points after virus infection. The results led to the following conclusions: i) the PBCV-1 replication cycle is temporally programmed and regulated; ii) 360 …

Drosophila Adult Eye Model To Teach Scanning Electron Microscopy In An Undergraduate Cell Biology Laboratory, Meghana Tare, Oorvashi Roy Puli, Sarah M. Oros, Amit Singh

Biology Faculty Publications

We have devised an undergraduate laboratory exercise to study tissue morphology using fruit fly, Drosophila melanogaster, as the model organism. Drosophila can be reared in a cost effective manner in a short period of time. This experiment was a part of the undergraduate curriculum of the cell biology laboratory course aimed to demonstrate the use of scanning electron microscopy (SEM) technique to study the morphology of adult eye of Drosophila. The adult eye of Drosophila is a compound eye, which comprises of 800 unit eyes, and serves as an excellent model for SEM studies. We used flies that …

Protection Against Mucosal Shiv Challenge By Peptide And Helper-Dependent Adenovirus Vaccines, Eric A. Weaver, Pramod N. Nehete, Bharti P. Nehete, Stephanie J. Buchl, Donna Palmer, David C. Montefiori, Philip Ng, K. Jagannadha Sastry, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

Groups of rhesus macaques that had previously been immunized with HIV-1 envelope (env) peptides and first generation adenovirus serotype 5 (FG-Ad5) vaccines expressing the same peptides were immunized intramuscularly three times with helperdependent adenovirus (HD-Ad) vaccines expressing only the HIV-1 envelope from JRFL. No gag, pol, or other SHIV genes were used for vaccination. One group of the FG-Ad5- immune animals was immunized three times with HD-Ad5 expressing env. One group was immunized by serotype-switching with HD-Ad6, HD-Ad1, and HD-Ad2 expressing env. Previous work demonstrated that serum antibody levels against env were significantly higher in the serotype-switched group than in …

The Role Of Human Endogenous Retroviruses In Renal Cell Carcinoma, Michele D. Tisdale

Biological Sciences Theses & Dissertations

Human endogenous retroviruses make up approximately 8-9% of the human genome. A number of expressed HERVs, those that are actively transcribing, have been associated with various cancers. Suppression mechanisms that control HERV expression often fail or become more permissive in tissues where expression should be restricted. Previous studies have identified HERV expression in breast cancer tissues, whereas normal tissue HERV expression remained suppressed. In addition, studies of DNA hypermethylation have correlated with the ability to contribute to cancer development. Hypermethylation of several tumor suppressor genes occurs frequently in cancers and alterations in promoter regions could contribute to the development of …