Microbiology Commons^™

Role Of Epstein-Barr Virus Induced Gene Ii (Ebi2) In Epstein-Barr Virus Infection And B-Cell Chemotaxis, Brian Poole

Journal of Undergraduate Research

The academic objectives of this proposal were met. Using the funding provided by the MEG, we generated data that was used to publish three peer-reviewed journal articles:

Post-Translational Modifications Of Thymidine Kinase 1, Dr. Kim O'Neill

Journal of Undergraduate Research

Thymidine kinase 1 (TK1) is one diagnostic and prognostic marker which has shown promising potential in a variety of solid tumors and hematological malignancies. Unfortunately there have been challenges associated with developing a clinically useful immunoassay which have prevented TK1 from being fully utilized in the clinical setting at present. One of the major goals of this study was to produce a dependable, reproducible, immunoassay to detect TK1 in serum from cancer patients. There have been many attempts at detecting protein or genetic material in the serum or sputum of lung cancer patients but these all have failed due to …

Rekayasa Ekofisiologis Tanaman Teh Belum Menghasilkan Klon Gmb 7 Melalui Pemberian Asam Humat Dan Pupuk Hayati Konsorsium, Intan Ratna Dewi Anjarsari, Santi Rosniawaty, Cucu Suherman

Jurnal Kultivasi

Teh merupakan komoditas perkebunan penting di Indonesia. Rekayasa ekologis yang dilakukan untuk meningkatkan produktivitas tanaman teh di perkebunan adalah melalui tindakan pemupukan. Sejalan dengan prinsip pertanian berkelanjutan kini pihak pekebun pada umumnya menggunakan input yang lebih ramah lingkungan, diantaranya dengan menggunakan asam humat dan pupuk hayati konsorsium. Saat ini asam humat telah dimanfaatkan sebagai pelengkap pupuk yang dapat meningkatkan pemanfaatan pupuk dan meningkatkan pertum-buhan tanaman. Selain asam humat, salah satu alternatif untuk meningkatkan pertumbuhan tanaman teh belum menghasilkan adalah dengan pemeberian pupuk hayati konsorsium yang terdiri dari bakteri pelarutf posfat, bakteri penambat nitrogen dan bakteri pelarut kalium.Tujuan penelitian adalah untuk …

Elucidating A Precise Role For The Small Heat Shock Proteins Cryab And Hspb2 In Cardiac Robustness, Julianne H. Grose

Journal of Undergraduate Research

Evaluation of how well the academic objectives of the proposal were met

• Specific Aim 1: Perform yeast two-hybrid screens on wild type CryAB, R120G CryAB, and HspB2 in order to create a protein-protein interaction network and identify potential substrates.
• Achievements: Large-scale yeast-two hybrid screens were performed on wild type CryAB, R120G CryAB and HspB2 in order to identify their protein-protein interaction networks and to identify putative substrates.
• Specific Aim 2: Validate the protein-protein interaction network via Y2H dependency tests (A), affinity purification from mammalian cells (B) and chaperone activity assays (C).
• Achievements: Y2H dependency tests were performed for all three …

Validation Of An Nbmp2 Mutant Mouse Model, Laura C. Bridgewater

Journal of Undergraduate Research

Work in the Bridgewater Lab over the last several years has focused on elucidating the function of a novel protein we discovered, nBmp2. The initial discovery presenting work performed in cultured cells (rather than whole animals) was published back in 2010 and we subsequently constructed a mutant mouse line in which nBmp2 is disrupted. Much evidence was accumulating to show that the mice have problems with muscle function, neurological function, and immune function, but some fundamental experiments necessary to validate the mouse model had been giving us problems. The absence of that data prevented us from publishing any reports on …

Identification Of The Ps1 Thr147ile Variant In A Family With Very Early Onset Dementia And Expressive Aphasia, James Denvir, Shirley Neitch, Jun Fan, Richard M. Niles, Goran Boskovic, Bernard G. Schreurs, Donald A. Primerano, Daniel L. Alkon

Biochemistry and Microbiology

Background: Early onset dementias have variable clinical presentations and are often difficult to diagnose. We established a family pedigree that demonstrated consistent recurrence of very early onset dementia in successive generations.

Objective and Method: In order to refine the diagnosis in this family, we sequenced the exomes of two affected family members and relied on discrete filtering to identify disease genes and the corresponding causal variants.

Results: Among the 720 nonsynonymous single nucleotide polymorphisms (SNPs) shared by two affected members, we found a C to T transition that gives rise to a Thr147Ile missense substitution in the presenilin 1 (PS1) …

New Functionally-Enhanced Soy Proteins As Food Ingredients With Anti-Viral Activity, Aizhan Sabirzhanovna Turmagambetova, Nadezhda Sergeevna Sokolova, Andrey Pavlinovich Bogoyavlenskiy, Vladimir Eleazvich Berezin, Mary Ann Lila, Diana M. Cheng, Vyacheslav Dushenkov

Publications and Research

Respiratory viruses are a major public health problem because of their prevalence and high morbidity rate leading to considerable social and economic implications. Cranberry has therapeutic potential attributed to a comprehensive list of phytochemicals including anthocyanins, flavonols, and unique A-type proanthocyanidins. Soy flavonoids, including isoflavones, have demonstrated anti-viral effects in vitro and in vivo. Recently, it was demonstrated that edible proteins can efficiently sorb and concentrate cranberry polyphenols, including anthocyanins and proanthocyanins, providing greatly stabilized matrices suitable for food products. The combination of cranberry and soy phytoactives may be an effective dietary anti-viral resource. Anti-viral properties of both cranberry juice-enriched …

Characterization Of Genomic Variations In Snps Of Pe_Pgrs Genes Reveals Deletions And Insertions In Extensively Drug Resistant (Xdr) M. Tuberculosis Strains From Pakistan., Akber Kanji, Zahra Hasan, Ruth Mcnerney, Mridul Nair, Asho Ali, Kim Mallard, Taane G. Clark, Ambreen Zaver, Sana Jafri,, Rumina Hasan

Department of Pathology and Laboratory Medicine

BACKGROUND:

Mycobacterium tuberculosis (MTB) PE_PGRS genes belong to the PE multigene family. Although the function of PE_PGRS genes is unknown, it is hypothesized that the PE_PGRS genes may be associated with antigenic variability in MTB.

MATERIAL AND METHODS:

Whole genome sequencing analysis was performed on (n=37) extensively drug-resistant (XDR) MTB strains from Pakistan, which included Lineage 1 (East African Indian, n=2); Other lineage 1 (n=3); Lineage 3 (Central Asian, n=24); Other lineage 3 (n=4); Lineage 4 (X3, n=1) and T group (n=3) MTB strains.

RESULTS:

There were 107 SNPs identified from the analysis of 42 PE_PGRS genes; of these, 13 …

Fluoroquinolone-Resistant Tuberculosis: Implications In Settings With Weak Healthcare Systems, Kauser Jabeen, Sadia Shakoor, Rumina Hasan

Department of Pathology and Laboratory Medicine

Fluoroquinolones (FQ) play an essential role in the treatment and control of multidrug-resistant tuberculosis (MDR-TB). They are also being evaluated as part of newer regimens under development for drug-sensitive TB. As newer FQ-based regimens are explored, knowledge of FQ resistance data from high TB burden countries becomes essential. We examine available FQ resistance data from high TB burden countries and demonstrate the need for comprehensive surveys to evaluate FQ resistance in these countries. The factors driving FQ resistance in such conditions and the cost of such resistance to weak healthcare systems are discussed. The need for a comprehensive policy for …

Promoting Genome Stability Via Multiple Dna Repair Pathways, Scott Cukras

USF Tampa Graduate Theses and Dissertations

Maintaining genome integrity is indispensible for cells to prevent and limit accruement of deleterious mutations and to promote viable cell growth and proliferation. Cells possess a myriad of mechanisms to detect, prevent and repair incurred cellular damage. Here we discuss various proteins and their accompanying cellular pathways that promote genome stability. We first investigate the NEDD8 protein and its role in promoting homologous recombination repair via multiple Cullin E3 ubiquitin ligases. We provide specific mechanisms through which, UBE2M, an E2 conjugating enzyme, neddylates various Cullin ligases to render them catalytically active to degrade their substrates by the proteasome. We show …

Cyanobacteria, Algae And Microfungi Present In Biofilm From Božana Cave (Serbia), Slađana Popović, Gordana Subakov Simić, Miloš Stupar, Nikola Unković, Dragana Predojević, Jelena Jovanović, Milica Ljaljević Grbić

International Journal of Speleology

Phototrophic microorganisms (cyanobacteria and algae) and microfungi, were identified from biofilm on the walls of the entrance of BožanaCavein west Serbia. Temperature, relative humidity and light intensity were measured, and chlorophyll a content determined. Light intensity differed from the entrance inwards. However, Chl a content was not proportional to light intensity, instead it was positively correlated to biofilm weight. Biofilm samples from two sites were also observed using a scanning electron microscope. Coccoid forms of cyanobacteria were abundant at the sampling site with the lowest light intensity, while members of the order Nostocales were predominant at the sampling site with …

The Bifunctional Alcohol And Aldehyde Dehydrogenase Gene, Adhe, Is Necessary For Ethanol Production In Clostridium Thermocellum And Thermoanaerobacterium Saccharolyticum, Jonathan Lo, Tianyong Zheng, Shuen Hon, Daniel G. Olson, Lee Lynd

Dartmouth Scholarship

Thermoanaerobacterium saccharolyticum and Clostridium thermocellum are anaerobic thermophilic bacteria being investigated for their ability to produce biofuels from plant biomass. The bifunctional alcohol and aldehyde dehydrogenase gene, adhE, is present in these bacteria and has been known to be important for ethanol formation in other anaerobic alcohol producers. This study explores the inactivation of the adhE gene in C. thermocellum and T. saccharolyticum. Deletion of adhE reduced ethanol production by >95% in both T. saccharolyticum and C. thermocellum, confirming that adhE is necessary for ethanol formation in both organisms. In both adhE deletion strains, fermentation products shifted from ethanol …

Helicobacter Pylori: Genomic Insight Into The Host-Pathogen Interaction, Kathryn P. Haley, Jennifer A. Gaddy

Peer Reviewed Articles

The advent of genomic analyses has revolutionized the study of human health. Infectious disease research in particular has experienced an explosion of bacterial genomic, transcriptomic, and proteomic data complementing the phenotypic methods employed in traditional bacteriology. Together, these techniques have revealed novel virulence determinants in numerous pathogens and have provided information for potential chemotherapeutics. The bacterial pathogen, Helicobacter pylori, has been recognized as a class 1 carcinogen and contributes to chronic inflammation within the gastric niche. Genomic analyses have uncovered remarkable coevolution between the human host and H. pylori. Perturbation of this coevolution results in dysregulation of the …

Long-Term Impacts Of Disturbance On Nitrogen-Cycling Bacteria In A New England Salt Marsh, Anne E. Bernhard, Courtney Dwyer, Adrian Idrizi, Geoffrey Bender, Rachel Zwick

Biology Faculty Publications

Recent studies on the impacts of disturbance on microbial communities indicate communities show differential responses to disturbance, yet our understanding of how different microbial communities may respond to and recover from disturbance is still rudimentary. We investigated impacts of tidal restriction followed by tidal restoration on abundance and diversity of denitrifying bacteria, ammonia-oxidizing bacteria (AOB), and ammonia-oxidizing archaea (AOA) in New England salt marshes by analyzing nirS and bacterial and archaeal amoA genes, respectively. TRFLP analysis of nirS and betaproteobacterial amoA genes revealed significant differences between restored and undisturbed marshes, with the greatest differences detected in …

Genome-Wide Comparison Of Pu.1 And Spi-B Binding Sites In A Mouse B Lymphoma Cell Line, Lauren A. Solomon, Stephen K. H. Li, Jan Piskorz, Li S. Xu, Rodney P. Dekoter

Microbiology & Immunology Publications

Background

Spi-B and PU.1 are highly related members of the E26-transformation-specific (ETS) family of transcription factors that have similar, but not identical, roles in B cell development. PU.1 and Spi-B are both expressed in B cells, and have been demonstrated to redundantly activate transcription of genes required for B cell differentiation and function. It was hypothesized that Spi-B and PU.1 occupy a similar set of regions within the genome of a B lymphoma cell line.

Results

To compare binding regions of Spi-B and PU.1, murine WEHI-279 lymphoma cells were infected with retroviral vectors encoding 3XFLAG-tagged PU.1 or Spi-B. Anti-FLAG chromatin …

Concomitant Uptake Of Antimicrobials And Salmonella In Soil And Into Lettuce Following Wastewater Irrigation, J. Brett Sallach, Yuping Zhang, Laurie Hodges, Daniel D. Snow, Xu Li, Shannon L. Bartelt-Hunt

Department of Civil and Environmental Engineering: Faculty Publications

The use of wastewater for irrigation may introduce antimicrobials and human pathogens into the food supply through vegetative uptake. The objective of this study was to investigate the uptake of three antimicrobials and Salmonella in two lettuce cultivars. After repeated subirrigation with synthetic wastewater, lettuce leaves and soil were collected at three sequential harvests. The internalization frequency of Salmonella in lettuce was low. A soil horizon-influenced Salmonella concentration gradient was determined with concentrations in bottom soil 2 log CFU/g higher than in top soil. Lincomycin and sulfamethoxazole were recovered from lettuce leaves at concentrations as high as 822 ng/g and …

Synthesis Of Bioinspired Carbohydrate Amphiphiles That Promote And Inhibit Biofilms, Eric L. Dane, Alicia E. Ballok, George A. O'Toole, Mark W. Grinstaff

Dartmouth Scholarship

The synthesis and characterization of a new class of bioinspired carbohydrate amphiphiles that modulate Pseudomonas aeruginosa biofilm formation are reported. The carbohydrate head is an enantiopure poly-amido-saccharide (PAS) prepared by a controlled anionic polymerization of β-lactam monomers derived from either glucose or galactose. The supramolecular assemblies formed by PAS amphiphiles are investigated in solution using fluorescence assays and dynamic light scattering. Dried samples are investigated using X-ray, infrared spectroscopy, and transmission electron microscopy. Additionally, the amphiphiles are evaluated for their ability to modulate biofilm formation by the Gram-negative bacterium Pseudomonas aeruginosa. Remarkably, from a library of eight amphiphiles, we identify …

Search For Host Factors Involved In Attachment Of Agrobacterium Tumefaciens To Plants, Anna Petrovicheva

Dissertations, Theses, and Capstone Projects

Agrobacterium tumefaciens is able to infect a diverse array of plants and causes crown gall disease. Typically these bacteria attach to plant roots and transform the plant cells to induce tumors. The mechanism of this attachment in the infection process is not yet fully understood. Using wild type Arabidopsis thaliana, Columbia-0, and several Arabidopsis mutant lines as a binding target, we screened for A. thaliana mutants with altered adhesion.

The A. thaliana mutant lines were selected in The Arabidopsis Information Resource (TAIR) according to possible location of the resulting protein and similarity to known transformation mutants. Of these mutants …

Whole Genome Sequencing Based Characterization Of Extensively Drug-Resistant Mycobacterium Tuberculosis Isolates From Pakistan, Asho Ali, Zahra Hasan, Ruth Mcnerney, Kim Mallard, Grant Hill Cawthorne, Francesc Coll, Mridul Nair, Arnab Pain, Taane G. Clark, Rumina Hasan

Department of Pathology and Laboratory Medicine

Improved molecular diagnostic methods for detection drug resistance in Mycobacterium tuberculosis (MTB) strains are required. Resistance to first- and second- line anti-tuberculous drugs has been associated with single nucleotide polymorphisms (SNPs) in particular genes. However, these SNPs can vary between MTB lineages therefore local data is required to describe different strain populations. We used whole genome sequencing (WGS) to characterize 37 extensively drug-resistant (XDR) MTB isolates from Pakistan and investigated 40 genes associated with drug resistance. Rifampicin resistance was attributable to SNPs in the rpoB hot-spot region. Isoniazid resistance was most commonly associated with the katG codon 315 (92%) mutation …

Inclusion Of Fermented Foods In Food Guides Around The World, Stephanie N. Chilton, Jeremy P. Burton, Gregor Reid

Microbiology & Immunology Publications

Fermented foods have been a well-established part of the human diet for thousands of years, without much of an appreciation for, or an understanding of, their underlying microbial functionality, until recently. The use of many organisms derived from these foods, and their applications in probiotics, have further illustrated their impact on gastrointestinal wellbeing and diseases affecting other sites in the body. However, despite the many benefits of fermented foods, their recommended consumption has not been widely translated to global inclusion in food guides. Here, we present the case for such inclusion, and challenge health authorities around the world to consider …

Immunotherapy For Human Breast Cancer, Nasrah Ali Al Kamal

Browse all Theses and Dissertations

Al Kamal, Nasrah. M.S. Program of Microbiology and Immunology, Wright State University, 2015.Immunotherapy for Human Breast Cancer. The study focuses on the methodologies that are used in breast cancer therapy. The review finds major evolutions of these methods and the influence they have made on the increased survival rates in cancer patients. There is also a projection of the processes that are involved in the therapy practices and the way the protocols have been improved over time. The various stages of cancer treatment project the various aspects of better performance articulations in the therapy sector. There is also reference to …

The Frequency Of Ticks Carrying Rickettsia Sp., Sarah C. Canterberry, Daniel J. Bennett, Robert J. Wiggers

Faculty Publications

No abstract provided.

Subsistence Strategies In Traditional Societies Distinguish Gut Microbiomes, Alexandra J. Obregon-Tito, Raul T. Tito, Jessica Metcalf, Krithvivasa Sankaranarayanan, Jose C. Clemente, Luke K. Ursell, Zhenjiang Zech Xu, Will Van Treuren, Rob Knight, Morris Foster

Division of Research and Economic Development Faculty & Staff Publications

Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2-2.5 MB, coverage depth x26-513) and functional potential …

Making The Leap From Research Laboratory To Clinic: Challenges And Opportunities For Next-Generation Sequencing In Infectious Disease Diagnostics., Brittany Goldberg, Heike Sichtig, Chelsie Geyer, Nathan Ledeboer, George M Weinstock

Pediatrics Faculty Publications

Next-generation DNA sequencing (NGS) has progressed enormously over the past decade, transforming genomic analysis and opening up many new opportunities for applications in clinical microbiology laboratories. The impact of NGS on microbiology has been revolutionary, with new microbial genomic sequences being generated daily, leading to the development of large databases of genomes and gene sequences. The ability to analyze microbial communities without culturing organisms has created the ever-growing field of metagenomics and microbiome analysis and has generated significant new insights into the relation between host and microbe. The medical literature contains many examples of how this new technology can be …

Early Initiation Of Antiretroviral Therapy Can Functionally Control Productive Hiv-1 Infection In Humanized-Blt Mice, Qingsheng Li, For Yue Tso, Guobin Kang, Wuxun Lu, Yue Li, Wenjin Fan, Zhe Yuan, Christopher J. Destache, Charles Wood

Nebraska Center for Virology: Faculty Publications

Background—Recent reports showed that functional control of HIV-1 infection for a prolonged time is possible by early anti-retroviral therapy (ART); however its underlying mechanism needs to be studied with a suitable animal model. Recently, humanized-BLT (bone marrow, liver and thymus) mouse (hu-BLT) was shown to be an excellent model for studying HIV-1 infection. We thus tested the feasibility of studying functional control of HIV-1 infection using hu-BLT mice.

Methods—Animals in three treatment groups (Rx-6h, Rx-24h, Rx-48h) and untreated group were infected with HIV-1, followed by ART initiation at 6, 24 or 48 hours post-infection and continued daily for two weeks. …

The Role Of Dendritic Cell Subsets And Innate Immunity In The Pathogenesis Of Type 1 Diabetes And Other Autoimmune Diseases, Jeffrey D. Price, Kristin V. Tarbell

Nebraska Center for Virology: Faculty Publications

Dendritic cells (DCs) are key antigen-presenting cells that have an important role in autoimmune pathogenesis. DCs control both steady-state T cell tolerance and activation of pathogenic responses. The balance between these two outcomes depends on several factors, including genetic susceptibility, environmental signals that stimulate varied innate responses, and which DC subset is presenting antigen. Although the specific DC phenotype can diverge depending on the tissue location and context, there are four main subsets identified in both mouse and human: conventional cDC1 and cDC2, plasmacytoid DCs, and monocyte-derived DCs. In this review, we will discuss the role of these subsets in …

Application Of Supervised Machine Learning Algorithms For Rapid Identification Of Mrsa Pfge Strain Types, Michael L. Bernauer

Biomedical Informatics Seminar Series (BioMISS)

Introduction: Pulsed-field gel electrophoresis (PFGE) is a molecular typing method used in epidemiologic surveillance of MRSA. PFGE relies on electrophoretic migration of restricted DNA fragments, resulting in characteristic fingerprints which can be used to classify organisms. Current methods of analysis, such as Gel Compar II and BioNumerics rely on unsupervised hierarchical clustering algorithms to group organisms based on pairwise similarity. These methods are labor intensive, often requiring a significant amount of user intervention and oversight. This study presents an automated approach to PFGE typing to reduce the amount of user involvement and time required for analysis.

Methods: A total of …

Adar1 Facilitates Hiv-1 Replication In Primary Cd4+ T Cells., Eloy Cuadrado, Thijs Booiman, John L Van Hamme, Machiel H Jansen, Karel A Van Dort, Adeline Vanderver, Gillian I Rice, Yanick J Crow, Neeltje A Kootstra, Taco W Kuijpers

Neurology Faculty Publications

Unlike resting CD4+ T cells, activated CD4+T cells are highly susceptible to infection of human immunodeficiency virus 1 (HIV-1). HIV-1 infects T cells and macrophages without activating the nucleic acid sensors and the anti-viral type I interferon response. Adenosine deaminase acting on RNA 1 (ADAR1) is an RNA editing enzyme that displays antiviral activity against several RNA viruses. Mutations in ADAR1 cause the autoimmune disorder Aicardi-Goutieères syndrome (AGS). This disease is characterized by an inappropriate activation of the interferon-stimulated gene response. Here we show that HIV-1 replication, in ADAR1-deficient CD4+T lymphocytes from AGS patients, is blocked at the level of …

Herpes Virus Infections, Inflammatory Markers And Risk Of Developing T2dm And Cvd: An Analysis Of Nhanes With Adults, Aged 20-49, 1999-2010, Margarita Irizarry-De La Cruz

Walden Dissertations and Doctoral Studies

Herpes simplex viruses (HSVs), are among the most virulent and widespread pathogens; they affect 60-90% of the population worldwide. Substantial evidence indicates a possible association between pathogens and chronic disease. HSVs, among other viruses, have been associated with increased risk for inflammatory diseases. However, prior findings have been inconsistent on the role of infection in triggering autoimmune response and chronic disease. This study builds on the premise that pathogens can induce an inflammatory response and increase the risk for disease development. A representative U.S. sample from NHANES, a national population-based cross-sectional survey, was used to examine the relationship between HSVs …

Signaling Between Two Sensor Kinases Controls Biofilms And Host Colonization In A Bacterial Symbiont, Allison N. Norsworthy

Dissertations

Organisms within all domains of life must acclimate to fluctuating environments to survive. To do this, cells utilize sensory circuits, which function to connect environmental stimuli to an intracellular response. One common sensory pathway utilized by bacteria is two-component signaling (TCS), composed of an environmental sensor (the sensor kinase, SK) and a cognate, intracellular effector (the response regulator, RR). The marine bacterium Vibrio fischeri uses an elaborate TCS phosphorelay containing a hybrid SK, RscS, and two RRs, SypE and SypG, to colonize its natural squid host, Euprymna scolopes. This TCS pathway regulates V. fischeri's ability to form a biofilm, or …