Microbiology Commons^™

Investigation Of Bacillus Subtilis As A Biopesticide Against Botrytis Cinerea, Kenneth K. Ng

Master's Theses

The objective of this thesis was to investigate BiOWiSH^TM-Aqua, a commercial dry solid formulation containing a consortium of bacteria and yeast, as a biopesticide for treatment of Botrytis cinerea, a gray mold that affects strawberries. BiOWiSH^TM-Aqua was compared with another commercial product specifically used as a fungicide and bacteriocide, Serenade® Garden Disease Control Spray (concentrated Bacillus subtilis strain QST 713). Both laboratory tests as well as in vivo lab tests were conducted. BiOWiSH^TM-Aqua results varied widely from plate to plate, regardless of experimental conditions. In some of these plates, inhibition zones were observed …

Modeling Of Early Siv/Hiv Infection, Krista Schaefer, Cecilia Noecker, Kelly Zaccheo, Vitaly Gunasov, Judy Day, Yiding Yang

Symposium on Research and Creative Expression (SORCE)

Although HIV has infected over 20 million people worldwide, it is a rather poorly transmitted virus since less than 1 out of 100 to 1,000 acts of sexual intercourse results in virus transmission. The factors that could potentially explain why the probability of transmission is so small are poorly understood. It is nearly impossible to study HIV replication in the first 2-3 weeks of infection because the virus is undetectable until after that duration. By using stochastic simulations of mathematical models of early virus replication, we investigate how the duration of the eclipse phase prior to virus production (eclipse stage) …

Large-Scale Experimental Studies Show Unexpected Amino Acid Effects On Protein Expression And Solubility In Vivo In E. Coli, W. Nicholson Price Ii, Samuel K. Handelman, John K. Everett, Saichiu N. Tong, Ana Bracic, Jon D. Luff, Victor Naumov, Thomas Acton, Philip Manor, Rong Xiao, Burkhard Rost, Gaetano T. Montelione, John F. Hunt

Articles

The biochemical and physical factors controlling protein expression level and solubility in vivo remain incompletely characterized. To gain insight into the primary sequence features influencing these outcomes, we performed statistical analyses of results from the high-throughput protein-production pipeline of the Northeast Structural Genomics Consortium. Proteins expressed in E. coli and consistently purified were scored independently for expression and solubility levels. These parameters nonetheless show a very strong positive correlation. We used logistic regressions to determine whether they are systematically influenced by fractional amino acid composition or several bulk sequence parameters including hydrophobicity, sidechain entropy, electrostatic charge, and predicted backbone disorder. …

Neurodegeneration - A Means To An End, Amit Singh

Biology Faculty Publications

Cell death, a global phenomenon found throughout the animal kingdom, is a mechanism to maintain tissue homeostasis and for adaptation to changes in the environment [1,2]. Millions of cells die in our body daily- they succumb to stress and commit suicide by a mechanism referred to as cell death or apoptosis [2-4]. Under normal conditions cells are continuously replaced by new cells from the stemor progenitor- cells. For example, an optimum balance in shedding of dead cells from the skin and their replenishment by new ones maintain our health and hygiene. In this context, apoptosis is a mechanism to eliminate …

Response Of A Single 'Mega Intramuscular Dose' Of Vitamin D On Serum 25ohd And Parathyroid Hormone Levels, Aysha Habib, Dileep K Rohra, Shakil A Saghir, Shamsa K Udani, Richard Wood, Abdul Jabbar

Department of Pathology and Laboratory Medicine

Objective: To determine the changes produced in serum 25OHD and iPTH levels after 600,000 IU of injection cholecalciferol in volunteers. Study Design: Interventional study. Place and Duration of Study: Section of Chemical Pathology, Department of Pathology and Microbiology, the Aga Khan University Hospital, Karachi, from June 2009 - June 2010. Methodology: Volunteers of either gender aged 18-40 years with known 25OHD, calcium (Ca), creatinine (Cr) and phosphorous (P) levels were included in the study. Subjects on therapy like vitamin D and calcium supplements, corticosteroids or anti-epileptic medicines, primary hyperparathyroidism and hypercalcaemia, with co-morbidity like renal failure, liver disease and history …

Effects Of The Parasitic Dinoflagellate Hematodinium Sp. On Blue Crab (Callinectes Sapidus) Activity Predation And Habitat Selection, John M. Tiggelaar Ii

Biological Sciences Theses & Dissertations

The blue crab Callinectes sapidus occurs along the Atlantic and Gulf coasts of the United States, and in high salinity regions, they are subject to lethal infection by the parasitic dinoflagellate Hematodinium. In Virginia's seaside estuaries, the prevalence of Hematodinium infection of C. sapidus can sometimes exceed 50%, threatening the commercial fishery for this species. Indeed, other commercially important crustacean fisheries have approached collapse due to Hematodinium infections. Most studies of this host-parasite interaction have focused on epidemiology, host-pathogen dynamics, and pathogen transmission, and little is known about the impact of the parasite on host behavior and population dynamics. …

Characterization Of Species C Human Adenovirus Serotype 6 (Ad6), Eric A. Weaver, Reeti Khare, Mathew L. Hillestad, Donna Palmer, Philip Ng, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

Adenovirus serotype (Ad5) is the most studied Ad. Ad1, 2, and 6 are also members of species C Ad and are presumed to have biologies similar to Ad5. In this work, we have compared the ability of Ad1, 2, 5, and 6 to infect liver and muscle after intravenous and intramuscular injection. We found that Ad6 was surprisingly the most potent at liver gene delivery and that Ad1 and Ad2 were markedly weaker than Ad5 and 6. To understand these differences, we sequenced the Ad6 genome. This revealed that the Ad6 fiber protein is surprisingly three shaft repeats shorter than …

Assessing The Microbial Consequences Of Remediation: Surrogate Microbial Screening And Native Metabolic Signatures In Tc(Vii) Contaminated Sediments, Kathryn Lafaye Bailey

USF Tampa Graduate Theses and Dissertations

The chemical and physical processes controlling contaminant fate and transport in the vadose zone limit the options for application of many remedial technologies. Foam delivery technology (FDT) has been developed as a potential solution to overcome these limitations for remediating subsurface and deep vadose zone environments using reactive amendments. Although there are many advantages to utilizing FDT for treatment in the deep vadose zone, little information is available on how the addition of these surfactants and remedial amendments affect the indigenous microbial communities in the deep vadose zone as well as the impact of biological transformations of surfactant-based foams on …

Heme Oxygenase-1 Regulates The Immune Response To Influenza Virus Infection And Vaccination In Aged Mice, Nathan W. Cummins, Eric A. Weaver, Shannon M. May, Anthony J. Croatt, Oded Foreman, Richard B. Kennedy, Gregory A. Poland, Michael A. Barry, Karl A. Nath, Andrew D. Badley

Nebraska Center for Virology: Faculty Publications

Underlying mechanisms of individual variation in severity of influenza infection and response to vaccination are poorly understood. We investigated the effect of reduced heme oxygenase-1 (HO-1) expression on vaccine response and outcome of influenza infection. HO-1-deficient and wild-type (WT) mice (kingdom, Animalia; phylum, Chordata; genus/species, Mus musculus) were infected with influenza virus A/PR/8/34 with or without prior vaccination with an adenoviral-based influenza vaccine. A genome-wide association study evaluated the expression of single-nucleotide polymorphisms (SNPs) in the HO-1 gene and the response to influenza vaccination in healthy humans. HO-1-deficient mice had decreased survival after influenza infection compared to WT mice (median …

Hemoglobin E Syndromes In Pakistani Population., Bushra Moiz, Amna Nasir, Anila Rashid, Tariq Moatter, Mashhooda Rasool Hashmi

Department of Pathology and Laboratory Medicine

Background:Hemoglobin E is an important hemoglobin variant with a worldwide distribution. A number of hemoglobinopathies have been reported from Pakistan. However a comprehensive description of hemoglobin E syndromes for the country was never made. This study aimed to describe various hemoglobin E disorders based on hematological parameters and chromatography. The sub-aim was to characterize hemoglobin E at molecular level.

Methods:

This was a hospital based study conducted prospectively for a period of one year extending from January 1 to December 31, 2008. EDTA blood samples were analyzed for completed blood counts and hemoglobin variants through automated hematology analyzer and …

Evidence For Viral Infection In The Copepods Labidocera Aestiva And Acartia Tonsa In Tampa Bay, Florida, Darren Stephenson Dunlap

USF Tampa Graduate Theses and Dissertations

Mesozooplankton are of critical importance to marine food webs by transferring energy from the microbial food web to higher trophic levels and depositing energy to the deeper ocean layers through fecal deposition. While decades of research have shown that viruses have significant impacts in the oceans, and infect a wide range of organisms from bacteria to whales, there is still little known about the impacts of viruses on the mesozooplankton community. As copepods are the most abundant mesozooplankton group, this study sought to characterize the viruses present in natural populations of the calanoid copepods Acartia tonsa and Labidocera aestiva in …

Antifungal Activity Of Lactobacillus Against Microsporum Canis, Microsporum Gypseum And Epidermophyton Floccosum, Jiahui Guo, Brid Brosnan, Ambrose Furey, Elke K. Arendt, Padraigin Murphy

Department of Biological Sciences Publications

A total of 220 lactic acid bacteria isolates were screened for antifungal activity using Aspergillus fumigatus and Aspergillus niger as the target strains. Four Lactobacillus strains exhibited strong inhibitory activity on agar surfaces. All four were also identified as having strong inhibitory activity against the human pathogenic fungi Microsporum canis, Microsporum gypseum and Epidermophyton floccosum. One of the four lactobacilli, namely Lb. reuteri ee1p exhibited the most inhibition against dermatophytes. Cell-free culture supernatants of Lb. reuteri ee1p and of the non-antifungal Lb. reuteri M13 were freeze-dried and used to access and compare antifungal activity in agar plate assays …

Paramecium Bursaria Chlorella Virus 1 Encodes A Polyamine Acetyltransferase, Zachary Charlop-Powers, Jean Jakoncic, James R. Gurnon, James L. Van Etten, Ming-Ming Zhou

Nebraska Center for Virology: Faculty Publications

Background: PBCV-1 gene a654l encodes a protein with sequence similarity to GCN5 histone acetyltransferases.

Results: A crystal structure of A654L bound to coenzyme A reveals how A654L acetylates polyamines, not histone lysines.

Conclusion: A654L functions as a polyamine acetyltransferase.

Significance: As the first viral polyamine acetyltransferase, A654L has a possible role in host polyamine catabolism in viral replication.

Paramecium bursaria chlorella virus 1 (PBCV-1), a large DNA virus that infects green algae, encodes a histone H3 lysine 27-specific methyltransferase that functions in global transcriptional silencing of the host. PBCV-1 has another gene a654l that encodes a protein with sequence similarity …

Soil Bacterial Communities Of A Calcium-Supplemented And A Reference Watershed At The Hubbard Brook Experimental Forest (Hbef), New Hampshire, Usa, Ganapathi Sridevi, Rakesh Minocha, Swathi A. Turlapati, Katherine C. Goldfarb, Eoin L. Brodie, Louis S. Tisa, Subhash C. Minocha

New Hampshire Agricultural Experiment Station Publications

Soil Ca depletion because of acidic deposition-related soil chemistry changes has led to the decline of forest productivity and carbon sequestration in the northeastern USA. In 1999, acidic watershed (WS) 1 at the Hubbard Brook Experimental Forest (HBEF), NH, USA was amended with Ca silicate to restore soil Ca pools. In 2006, soil samples were collected from the Ca-amended (WS1) and reference watershed (WS3) for comparison of bacterial community composition between the two watersheds. The sites were about 125 m apart and were known to have similar stream chemistry and tree populations before Ca amendment. Ca-amended soil had higher Ca …

Regulation Of The Vapbc-1 Toxin-Antitoxin Locus In Nontypeable Haemophilus Influenzae, Susan D. Cline, Sehresh Saleem, Dayle A. Daines

Biological Sciences Faculty Publications

Nontypeable Haemophilus influenzae (NTHi) are human-adapted commensal bacteria that can cause a number of chronic mucosal infections, including otitis media and bronchitis. One way for these organisms to survive antibiotic therapy and cause recurrent disease is to stop replicating, as most antimicrobials target essential biosynthetic pathways. Toxin-antitoxin (TA) gene pairs have been shown to facilitate entry into a reversible bacteriostatic state. Characteristically, these operons encode a protein toxin and an antitoxin that associate following translation to form a nontoxic complex, which then binds to and regulates the cognate TA promoter. Under stressful conditions, the labile antitoxin is degraded and the …

Links From Mantle To Microbe At The Lau Integrated Study Site: Insights From A Back-Arc Spreading Center, Margaret K. Tivey, Erin Becker, Roxanne Beinart, Charles R. Fisher, Peter Girguis, Charles H. Langmuir, Peter J. Michael, Anna-Louise Reysenbach

Biology Faculty Publications and Presentations

The Lau Integrated Study Site (ISS) has provided unique opportunities for study of ridge processes because of its back-arc setting in the southwestern Pacific. Its location allows study of a biogeographical province distinct from those of eastern Pacific and mid-Atlantic ridges, and crustal compositions along the ridge lie outside the range of mid-ocean ridge crustal compositions. The Lau ISS is located above a subduction zone, at an oblique angle. The underlying mantle receives water and other elements derived from the downgoing lithospheric slab, with an increase in slab influence from north to south. Water lowers the mantle melting temperature and …

Partial Characterization Of The Antimicrobial Activity Of Ccl28, Bin Liu

Theses and Dissertations

This research focuses on the antimicrobial activity of the mouse chemokine CCL28. In addition to their well characterized chemotactic activity, many chemokines have been shown to be antimicrobial in vitro, including the mucosally expressed chemokine CCL28. I have investigated the primary sequence features required for antimicrobial activity, salt sensitive nature of killing/binding mechanism, and in vivo microbial interactions of CCL28. Through the use of protein mutation and expression techniques, I have shown that the holoprotein (108 amino acids) is necessary for full antimicrobial activity of CCL28. Furthermore, the C terminal region of CCL28 is essential for microbial killing as an …

Genetic Reporter System For Positioning Of Proteins At The Bacterial Pole, Kathryn R. Fixen, Anuradha Janakiraman, Sean Garritty, Daniel J. Slade, Andrew N. Gray, Nilay Karahan, Ann Hochschild, Marcia C. Goldberg

Publications and Research

Spatial organization within bacteria is fundamental to many cellular processes, although the basic mechanisms underlying localization of proteins to specific sites within bacteria are poorly understood. The study of protein positioning has been limited by a paucity of methods that allow rapid large-scale screening for mutants in which protein positioning is altered. We developed a genetic reporter system for protein localization to the pole within the bacterial cytoplasm that allows saturation screening for mutants in Escherichia coli in which protein localization is altered. Utilizing this system, we identify proteins required for proper positioning of the Shigella autotransporter IcsA. Autotransporters, widely …

Molecular Diagnostics: The Changing Culture Of Medical Microbiology, Susan Bullman, Brigid Lucey, Roy D. Sleator

Department of Biological Sciences Publications

Diagnostic molecular biology is arguably the fastest growing area in current laboratory-based medicine. Growth of the so called ‘omics’ technologies has, over the last decade, led to a gradual migration away from the ‘one test, one pathogen’ paradigm, toward multiplex approaches to infectious disease diagnosis, which have led to significant improvements in clinical diagnostics and ultimately improved patient care.

Humanized Mice As A Model To Study Human Viral Pathogenesis And Novel Antiviral Drugs, Freddy Mauricio Sanchez Tumbaco

Theses and Dissertations

Animal models have greatly contributed to the understanding of different aspects of human biology, as well as a variety of human-related pathogens and diseases. In order to study them, humanized mice susceptible to pathogens that replicate in human immune cells have been developed (e.g., humanized Rag2-/-γc-/- mice). These animals are engrafted with human hematopoietic stem cells (HSCs), resulting in the de novo development and maturation of the major functional components of the human adaptive immune system and the production of a variety of human cell types. Primary and secondary lymphoid organs in the mouse are populated with human cells, and …