Microbiology Commons^™

Preface To Special Issue

Aliso: A Journal of Systematic and Floristic Botany

No abstract provided.

Exploring Diversity Of Nitrate Reducing Thermophiles In Nevada Hot Springs, Jenny Lam, Jeremy A. Dodsworth, Brian P. Hedlund

Undergraduate Research Opportunities Program (UROP)

High rates of denitrification have been measured in Nevada geothermal hot springs, but little is known about the thermophiles that contribute to this activity. We hypothesize that heterotrophic bacteria in the genus Thermus are the most important denitrifiers in the springs. Alternatively, other microorganisms including chemolithotrophs may also be important. To test these hypotheses, several different strategies will be used to try to enrich and isolate nitrate-reducing microorganisms. Isolates will be identified by 16S rRNA gene PCR and sequencing. Subsequently, representative isolates will be chosen for nitrate reductase gene (narG) sequencing and for studies on the kinetics of nitrate reduction …

Baseline Microbial Characterizations Of An Imperiled Aquatic Diversity Hotspot: Ash Meadows National Wildlife Refuge, Jessica Newburn, Jim Bruckner, Jenny C. Fisher, Duane P. Moser

Undergraduate Research Opportunities Program (UROP)

Located in the discharge zone of the Death Valley Flow System, Ash Meadows National Wildlife Refuge is a spring-fed desert oasis and biodiversity hotspot about 90 miles northwest of Las Vegas. These critical wetlands are potentially threatened by groundwater pumping, exotic species invasions, and climate change. Although a major component of the lower food web, very little is known about the microbial makeup of this ecosystem. As a first step towards understanding the microbial and biogeochemical aspects of this system, a detailed molecular-based characterization of microbial communities, baseline chemistry, and physical characteristics of various springs of Ash Meadows will be …

The Role Of Rpoe In Stationary Phase Mutagenesis In Bacillus, Turquoise C. Alexander, Eduardo A. Robleto

Undergraduate Research Opportunities Program (UROP)

Stationary phase mutagenesis is a phenomenon whereby random mutations are generated in non-dividing cells. In order to understand how these mutations arise, we use Bacillus subtilis, a gram positive rod-shaped model organism. It is hypothesize that increased transcription promotes stationary phase mutagenesis in this organism. We therefore examined the role of rpoE, a gene that encodes RNA polymerase ! subunit and proposed to influence efficiency of transcription. To this end, we will first generate a strain bearing a deletion in the rpoE gene. In order to determine if this gene is important for mutagenesis, we will examine the accumulation of …

Germination And Characterization Of Bacillus Anthracis And Bacillus Cereus, Ann Desdemonia Nde-Neh Fowajuh, Ernesto Abel-Santos

Undergraduate Research Opportunities Program (UROP)

Bacillus cereus and Bacillus anthracis are micro organisms found in soil. Normally, only their spores are found in soil. We recently showed that, B. anthracis and B. cereus do not germinate in soil. Thus, how does B. cereus and B. anthracis continue their life cycle if they can not replicate in soil? We hypothesize that B. cereus and B. anthracis spores may germinate in the gut of nematodes. Caenorhabditis elegans was used as our model nematode to investigate this possibility. Subsequently, the goal of our research is to determine the effect of C. elegans on the life cycle of B. …

Martian Life Detection With Xylose Enantiomers, Arturo White, Gaosun Zhang, Henry J. Sun

Undergraduate Research Opportunities Program (UROP)

Ability of Martian soil to degrade carbohydrates, shown by the Viking mission, has two interpretations. One possibility is that the soil harbors living microorganisms. Alternatively, the soil is sterile but chemically oxidizing, i.e. it is laden with photochemical oxidants. It was shown by REU research last summer that these two possibilities can be distinguished by the use of glucose enantiomers. Life is selective: Earth organisms use D-glucose, but ignore Lglucose. This stereo selectivity is absent in chemical reactions. The goal of this project is to test if xylose, a five carbon sugar, is also suitable for chiral life detection. Mixed …

Attempts To Cultivate Bacteria From Deep Subsurface Aquifers And Mountaintop Plant Communities, Eric D. Hughes, J. C. Bruckner, Duane P. Moser

Undergraduate Research Opportunities Program (UROP)

In the late 1990s, the limits of life were pushed even further when microorganisms were discovered thriving 2.5 km below the surface of the Earth in deep South African gold mines. These very simple communities were dominated by a single species of bacteria from within the phylum, Firmicutes. Desulforudis audaxviator remains unique to a sizeable portion of the South African deep subsurface. At depths below 2.5km, it comprises well over 99% of all organisms present, which presents a unique circumstance in which the environment has provided a natural pure culture. From this naturally occurring pure culture, environmental genomics was applied …

The Role Of Recn In Stationary Phase Mutagenesis In Bacillus Subtilis, Lauren E. Johnson, Katherine R. Ona, Eduardo A. Robleto, Ronald E. Yasbin

Undergraduate Research Opportunities Program (UROP)

Here, we examine mutagenic programs that are independent of growth, such aspects of the evolutionary process are novel and have been implicated in the formation of cancers in animal cells and the acquisition of antibiotic resistance in animal pathogens. Adaptive or stationary phase mutagenesis is a genetic program to in increase diversity in cells under conditions of stress whereby cells escape non-dividing conditions. Previous research has shown that recombination functions are required to generate mutations that promote growth in Escherichia coli cells starved for carbon. This project tests the hypothesis that recombination functions are required for the generation of mutations …

Martian Life Detection With Amino Acid Enantiomers, Ali Jamil, Gaosen Zhang, Henry J. Sun

Undergraduate Research Opportunities Program (UROP)

The Viking mission showed that Martian soil can degrade a heterotrophic medium to carbon dioxide as if live microorganisms were present. The result is considered inconclusive, however, because abiotic oxidants, such as superoxides, may also exist on Mars and would explain the Viking result. One way to resolve this ambiguity is to repeat the Viking experiment with a isomerically pure medium. The consumption of one isomer, either D or L, would indicate biological activity. Indiscriminate destruction of both isomers would indicate abiotic redox processes. This idea was validated for glucose by REU research last summer (Sun et al. 2009). The …

Long Distance Microbial Transport In Air: Global Change Implications, Bradley J. Davey, J. C. Bruckner, Jenny C. Fisher, Duane P. Moser

Undergraduate Research Opportunities Program (UROP)

The first manifestations of global change will most likelv be observed in the Earth's atmosphere. Changing wind patterns, for example, may effect the long distance dispersal of microor-g anisms. The overall objective of this research is to correlate molecular assessments of microbial community structure from cloud water and snow samples, obtained from DRI's Storm Peak Laboratory atop Mt. Werner in Colorado, with atmospheric data and calculated air mass back trajectories. Our activities for summer of 2009 will be a focused proof-of-concept exercise to determine if intact microbial DNA and viable cells can be recovered from cloud water and alpine snow …

Survival Of Shigella Flexneri In Swimming Pool Water, Monique Gomez, Helen J. Wing

Undergraduate Research Opportunities Program (UROP)

Shigellosis is a disease caused by the pathogenic bacterium Shigella flexneri. The bacterium causes bloody diarrheadiarrhea, fever and abdominal pain. Infections can be and may cause fatal. . The disease may also cause bloody diarrhea and intense intestinal crampings. In the United States, there have been many outbreaks of shigellosis have been traced back to associated with inadequately disinfectedchlorinated public swimming pools and wading pools. These outbreaks of sShigellosis are most commonly seen among small children who play in these pools. . My goal is to determine how well Shigella survives in freshly chlorinated pool water and in pool water …

The Regulation Of The Icsp Promoter Of Shigella Flexneri By Ryhb, Lia A. Africa, Helen J. Wing

Undergraduate Research Opportunities Program (UROP)

Iron is an essential element in the metabolism of many organisms, including bacteria. In many pathogenic bacteria, the levels of iron present trigger the expression of many virulence genes. In Shigella, a gram-negative bacterium that causes dysentery in humans, the expression of a small regulatory RNA, ryhB, is blocked in the presence of iron. Studies have revealed that ryhB represses virB, a global regulator of virulence genes in Shigella.

The icsP gene is under the direct control of VirB. icsP encodes an outer membrane protease that cleaves a protein necessary for the actin tail assembly of Shigella in vitro. In …

Differential Localization Of Icsa And Icsp In The Outer Membrane Of Shigella Flexneri, Robin Herlands, Helen Wing

Undergraduate Research Opportunities Program (UROP)

Our goal is to visualize IcsP on the surface of S. flexneri and determine how its localization changes during growth versus stationary phases. We hypothesize IcsP will be present on the surface of S. flexneri differentially during growth and stationary phases of cell cycle. We hypothesize greater levels of IcsP seen during stationary phase (simultaneous with lower, more unipolar IcsA, due to IcsP mediated cleavage). During growth phase, we expect less IcsP to be present on the surface, and IcsA to be more evenly distributed around the cell surface.

Adding Upstream Sequence And A Downstream Reporter To The Bile Acid Inducible Promoter Of Clostridium Scindens Vpi 12708, Bryan Patrick Mason

Masters Theses & Specialist Projects

Bile acids in the small intestines of animals serve to breakdown fats and fatsoluble vitamins. Most of the bile acids are reabsorbed into the enterohepatic circulation, but approximately five percent of these bile acids pass into the large intestine. These bile acids are swiftly deconjugated by the bacterial population, and then subjected to further intestinal bacterial chemical modifications. The most significant of these modifications are 7α-dehydroxylations which form secondary bile acids (deoxycholate and lithocholate). Much research has illuminated the 7α-dehydroxylation pathway: of particular interest is the bile acid inducible operon, for which Clostridium scindens VPI 12708 serves as the model …

Anticancer Properties Of Research-Grade Hydrastis Canadensis (Goldenseal) And Characterization Of Its Effect On The Mdr1-Encoded Phosphoglycoprotein Efflux Pump, Sara Garrett

All Theses

Multiple drug resistance (MDR) in tumors, observed both in vivo and in vitro, is generally attributed to efflux-mediated reduced drug accumulation via mdr1/P-gp. Notoriously chemoresistant colorectal cancers exhibit the highest P-gp expression, account for 9% of all cancer deaths, and are the third most common cancer in men and women. P-gp, a 170kDa protein, contains twelve transmembrane segments with two ATP-binding domains used to extrude intracellular compounds of broad specificity against a concentration gradient. Studies concerning natural health products are becoming more prevalent in the search for safe anti-P-gp remedies and Hydrastis canadensis (goldenseal) was studied for its anti-cancer properties. …

Red Raspberries Possess Anticarcinogenic And Immunostimulatory Potential, Jason God

All Dissertations

Despite the great strides made in the treatment of cancer, considerably little progress has been made towards prevention of the disease. In light of this reality, it has become apparent that a greater focus needs to be devoted to research into means of cancer prevention. Due to the significant role that nutrition plays in the development of cancer, the diet presents an attractive and logical target for such research.
Epidemiology has consistently shown an inverse relationship between fruit and vegetable consumption and risk for developing cancer. Additionally, countless in vitro studies on natural products isolated from fruits and vegetables have …

Cloning And Expression Of A Putative Exported Protein Coding Gene Sas1089 From An Invasive Community Associated Staphylococcus Aureus Strain Mssa476, Nailah Alzaki

All-Inclusive List of Electronic Theses and Dissertations

Originally, methicillin resistant Staphylococcus aureus (MRSA) occurred primarily in the hospital setting and was designated hospital- associated MRSA (HA-MRSA). In recent years, isolates of Staphylococcus aureus from the community (CA-MRSA), found to be methicillin resistant, are not as resistant tooth~ antibiotics as HA-MRSA. However, community strains are noted for their invasiveness causing soft tissue infections with propensity for invasion to deeper sites.

Rapid Evolution Of Sex-Pheromone-Producing Enzyme In Drosophila, Troy R. Shirangi, Héloïse D. Dufour, Thomas M. Williams, Sean B. Carroll

Biology Faculty Publications

A wide range of organisms use sex pheromones to communicate with each other and to identify appropriate mating partners. While the evolution of chemical communication has been suggested to cause sexual isolation and speciation, the mechanisms that govern evolutionary transitions in sex pheromone production are poorly understood. Here, we decipher the molecular mechanisms underlying the rapid evolution in the expression of a gene involved in sex pheromone production in Drosophilid flies. Long-chain cuticular hydrocarbons (e.g., dienes) are produced female-specifically, notably via the activity of the desaturase DESAT-F, and are potent pheromones for male courtship behavior in Drosophila melanogaster. We …

The Helicobacter Pylori Anti-Sigma Factor Flgm Is Predominantly Cytoplasmic And Cooperates With The Flagellar Basal Body Protein Flha, Melanie Rust, Sophie Borchert, Eike Niehus, Sarah A. Gripp, Afrodita Bajceta, Jonathan L. Mcmurry, Sebastian Suerbaum, Kelly T. Hughes, Christine Josenhans

Faculty Articles

Helicobacter pylori requires flagellar motility and orientation to persist actively in its habitat. A particular feature of flagella in most Helicobacter species including H. pylori is a membraneous flagellar sheath. The anti-sigma factor FlgM of H. pylori is unusual, since it lacks an N-terminal domain present in other FlgM homologs, e.g., FlgM of Salmonella spp., whose regulatory function is intimately coupled to its secretion through the flagellar type III secretion system. The aim of the present study was to characterize the localization and secretion of the short H. pylori FlgM in the presence of a flagellar sheath and to elucidate …

Population Study Of 1311 C/T Polymorphism Of Glucose 6 Phosphate Dehydrogenase Gene In Pakistan - An Analysis Of 715 X-Chromosomes., Bushra Moiz, Amna Nasir, Tariq Moatter, Zulfiqar Ali Naqvi, Mohammad Khurshid

Department of Pathology and Laboratory Medicine

Background:Nucleotide 1311 polymorphism at exon 11 of G6PD gene is widely prevalent in various populations of the world. The aim of the study was to evaluate 1311 polymorphism in subjects carrying G6PD Mediterranean gene and in general population living in Pakistan.

Results:

Patients already known to be G6PD deficient were tested for 563C-T (G6PD Mediterranean) and 1311 C-T mutation through RFLP based PCR and gene sequencing. A control group not known to be G6PD deficient was tested for 1311C/T only.C-T transition at nt 1311 was detected in 60/234 X-chromosomes with 563 C-T mutation (gene frequency of 0.26) while in …

Cis-Regulatory Sequence And Co-Regulatory Transcription Factor Functions In Erα-Mediated Transcriptional Repression, Richard Leroy Smith

Theses and Dissertations

Estrogens exert numerous actions throughout the human body, targeting healthy tissue while also enhancing the proliferative capacity of breast cancers. Estrogen signaling is mediated by the estrogen receptor (ER), which binds DNA and ultimately affects the expression of adjacent genes. Current understanding of ER-mediated transcriptional regulation is mostly limited to genes whose transcript levels increase following estrogen exposure, though recent studies demonstrate that direct down-regulation of estrogen-responsive genes is also a significant feature of ER action. We hypothesized that differences in cis-regulatory DNA was a factor in determining target gene expression and performed computational and experimental studies to test this …

Overexpression Of A Mutant Form Of Ehraba, A Unique Rab Gtpase Of Entamoeba Histolytica, Alters Endoplasmic Reticulum Morphology And Localization Of The Gal/Galnac Adherence Lectin, B. H. Welter, Lesly A. Temesvari

Publications

Entamoeba histolytica is a protozoan parasite that causes amoebic dysentery and liver abscess. Vesicle trafficking events, such as phagocytosis and delivery of plasma membrane proteins, have been implicated in pathogenicity. Rab GTPases are proteins whose primary function is to regulate vesicle trafficking; therefore, understanding the function of Rabs in this organism may provide insight into virulence. E. histolytica possesses a number of unique Rabs that exhibit limited homology to host Rabs. In this study we examined the function of one such Rab, EhRabA, by characterizing a mutant overexpressing a constitutively GTP-bound version of the protein. Overexpression of mutant EhRabA resulted …

Escherichia Coli O157:H7 And Other E. Coli Strains Share Physiological Properties Associated With Intestinal Colonization, Lisa Jacobsen, Lisa Durso, Tyrell Conway, Kenneth W. Nickerson

Kenneth Nickerson Papers

Escherichia coli isolates (72 commensal and 10 O157:H7 isolates) were compared with regard to physiological and growth parameters related to their ability to survive and persist in the gastrointestinal tract and found to be similar. We propose that nonhuman hosts in E. coli O157:H7 strains function similarly to other E. coli strains in regard to attributes relevant to gastrointestinal colonization.

Section Abstracts: Biology And Microbiology & Molecular Biology

Virginia Journal of Science

Abstracts of the Biology Section and Microbiology & Molecular Biology for the 87th Annual Meeting of the Virginia Academy of Science, May 27th-29th, 2009, Virginia Commonwealth University, Richmond, VA.

Native Cellular Architecture Of Treponema Denticola Revealed By Cryo-Electron Tomography, Jacques Izard, Chyong-Ere Hsieh, Ronald J. Limberger, Carmen A. Mannella, Michael Marko

Department of Food Science and Technology: Faculty Publications

Using cryo-electron tomography, we are developing a refined description of native cellular structures in the pathogenic spirochete Treponema denticola. Tightly organized bundles of periplasmic flagella were readily observed in intact plunge-frozen cells. The periplasmic space was measured in both wild-type and aflagellate strains, and found to widen by less than the diameter of flagella when the latter are present. This suggests that a structural change occurs in the peptidoglycan layer to accommodate the presence of the flagella. In dividing cells, the flagellar filaments were found to bridge the cytoplasmic cylinder constriction site. Cytoplasmic filaments, adjacent to the inner membrane, …

Inhibition Of Yeast Hexokinase By The Antimalarial Drug Artemisinin: Probing Mechanism Of Action With A Model Enzyme, Jennifer S. Spence

Biological Sciences Theses & Dissertations

A leading infectious cause of death, malaria threatens approximately half of the world's population, and drug-resistant strains of Plasmodium falciparum have created immense difficulty in chemotherapy of the disease. The artemisinin (ART) class of antimalarials may represent a powerful solution. In addition to their safety, effectiveness, and moderate cost, they are the only drugs in use for which there has been no widespread evidence of clinical resistance. The exact parasiticidal mechanism of ART is highly contested, but evidence suggests that protein alkylation may play a role in cytotoxicity. in vitro essays were performed using yeast hexokinase (HK) to demonstrate a …

Designing A Microbial Prolyl Peptidase Delivery System For The Treatment Of Celiac Disease, Matthew J. Shurtleff

Master's Theses

Celiac disease is an autoimmune enteropathy resulting from the ingestion of gluten and gluten-like proteins from wheat, barley and rye in afflicted individuals. Indigestible gluten-derived peptides rich in proline residues are known to be responsible for eliciting the inappropriate immune response characteristic of the disease. In this investigation, surface level expression of prolyl peptidase activity by genetically engineered probiotic lactobacilli was postulated to be a possible treatment for this disease. Plasmid-based reporter vectors were constructed utilizing a novel, homology-based cloning technique to assess the expression and localization signals from the S-layer protein gene of Lactobacillus acidophilus. These plasmids were mutated …

Contribution Of Ledgf/P75 To Prostate Cancer Chemoresistance, Melanie Mediavilla-Varela

Loma Linda University Electronic Theses, Dissertations & Projects

Prostate cancer (PCa) is the second leading cause of male cancer death in the United States, and is considered a health disparity because of its disproportionate incidence and mortality in African American (AA) males. A major challenge in PCa treatment is its recurrence into hormone refractory prostate cancer (HRPC). Docetaxel is the standard of care for first line chemotherapy to HRPC. Unfortunately, most patients ultimately manifest resistance to DTX and succumb to the disease. Circumventing DTX resistance in HRPC will require better understanding of the mechanisms by which this drug kills prostate tumor cells, and the genes that promote this …

Studies In Prolonged Oxidative Stress Resistance In Porphyromonas Gingivalis, Rachelle Mckenzie

Loma Linda University Electronic Theses, Dissertations & Projects

Porphyromonas gingivalis is a gram negative, anaerobic bacterium implicated as a major etiological agent in chronic adult periodontitis. In the inflammatory environment of the periodontal pocket, the organism must overcome oxidative stress as a result of exposure to air in the oral cavity as well as to reactive oxygen species (ROS) generated by host immune cells. A comprehensive mechanism for oxidative stress resistance in P. gingivalis is yet to be fully elucidated. In this study we examined the modulation of gene expression under conditions of oxidative stress by whole-genome DNA microarray analysis. Our findings indicated that numerous genes are involved …

Localization And Expression Of The Aer Receptor In Escherichia Coli, Daniel Salcedo

Loma Linda University Electronic Theses, Dissertations & Projects

In Escherichia coli, chemotactic movement towards an energetically-favorable environment is mediated by five transmembrane chemoreceptors. These sensory proteins respond to numerous environmental signals, including amino acids, sugars, and pH. The aerotaxis receptor, Aer, is an intracellular sensor that responds to oxygen concentration and other parameters affecting cellular energy levels. Bacterial chemotaxis receptors form dimeric signaling units that organize into tetramers and hexamers and form large clusters at the cell poles. A cluster arrangement could increase receptor sensitivity by lateral communication between dimers, thus amplifying the signal from one dimer. We have shown that Aer forms dimers, trimer of dimers, …