Microbiology Commons^™

To Love Your Neighbor: A Christian Perspective On The Study Of Microbiology And Immunology, Joy Doan

Faith Learning Integration Papers

I have been blessed with enough of a sense of adventure to have experienced the awe-inspiring beauty of a rain forest at night, the top of Half Dome at Yosemite National Park, the sheer cliffs and rushing waters of the Narrows at Zion National Park, Plateau Point—which seems suspended in the Grand Canyon, and the top of a 14,000-foot peak in the Rocky Mountains of Colorado. These are the types of places about which one of the characters in Robert Pirsig’s Zen and the Art of Motorcycle Maintenance observes, “This is the hardest stuff in the world to photograph. You …

Metabolic Engineering Of A Thermophilic Bacterium To Produce Ethanol At High Yield, A. Joe Shaw, Kara K. Podkaminer, Sunil G. Desai, John S. Bardsley, Stephen R. Rogers, Philip G. Thorne, David A. Hogsett, Lee R. Lynd

Dartmouth Scholarship

We report engineering Thermoanaerobacterium saccharolyticum, a thermophilic anaerobic bacterium that ferments xylan and biomass-derived sugars, to produce ethanol at high yield. Knockout of genes involved in organic acid formation (acetate kinase, phosphate acetyltransferase, and L-lactate dehydrogenase) resulted in a strain able to produce ethanol as the only detectable organic product and substantial changes in electron flow relative to the wild type. Ethanol formation in the engineered strain (ALK2) utilizes pyruvate:ferredoxin oxidoreductase with electrons transferred from ferredoxin to NAD(P), a pathway different from that in previously described microbes with a homoethanol fermentation. The homoethanologenic phenotype was stable for >150 generations …

Multidimensional Protein Fractionation Using Proteomelab Pf 2d™ For Profiling Amyotrophic Lateral Sclerosis Immunity: A Preliminary Report, Joshua Schlautman, Wojciech Rozek, Robert Stetler, R. Lee Mosley, Howard Gendelman, Pawel Ciborowski

Nebraska Center for Virology: Faculty Publications

Background: The ProteomeLab™ PF 2D platform is a relatively new approach to global protein profiling. Herein, it was used for investigation of plasma proteome changes in amyotrophic lateral sclerosis (ALS) patients before and during immunization with glatiramer acetate (GA) in a clinical trial.
Results: The experimental design included immunoaffinity depletion of 12 most abundant proteins from plasma samples with the ProteomeLab™ IgY-12 LC10 column kit as first dimension separation, also referred to as immuno-partitioning. Second and third dimension separations of the enriched proteome were performed on the PF 2D platform utilizing 2D isoelectric focusing and RP-HPLC with the resulting fractions …

Oriented Cell Growth On Self-Assembled Bacteriophage M13 Thin Films, Jianhua Rong, L. Andrew Lee, Kai Li, Brandon Harp, Charlene M. Mello, Zhongwei Niu, Qian Wang

Faculty Publications

Fibrillar M13 bacteriophages were used as basic building blocks to generate thin films with aligned nanogrooves, which, upon chemical grafting with RGD peptides, guide cell alignment and orient the cell outgrowth along defined directions.

The Bile Response Repressor Brer Regulates Expression Of The Vibrio Cholerae Breab Efflux System Operon, Francisca A. Cerda-Maira, Carol S. Ringelberg, Ronald K. Taylor

Dartmouth Scholarship

Enteric pathogens have developed several resistance mechanisms to survive the antimicrobial action of bile. We investigated the transcriptional profile of Vibrio cholerae O1 El Tor strain C6706 under virulence gene-inducing conditions in the presence and absence of bile. Microarray analysis revealed that the expression of 119 genes was affected by bile. The mRNA levels of genes encoding proteins involved in transport were increased in the presence of bile, whereas the mRNA levels of genes encoding proteins involved in pathogenesis and chemotaxis were decreased. This study identified genes encoding transcriptional regulators from the TetR family (vexR and breR) and …

Phylogeographical Structure And Evolutionary History Of Two Buggy Creek Virus Lineages In The Western Great Plains Of North America, Abinash Padhi, Amy T. Moore, Mary Bomberger Brown, Jerome E. Foster, Martin Pfeffer, Kathryn P. Gaines, Valerie A. O'Brien, Stephanie A. Strickler, Allison E. Johnson, Charles R. Brown

School of Natural Resources: Faculty Publications

Buggy Creek virus (BCRV) is an unusual arbovirus within the western equine encephalitis complex of alphaviruses. Associated with cimicid swallow bugs (Oeciacus vicarius) as its vector and the cliff swallow (Petrochelidon pyrrhonota) and house sparrow (Passer domesticus) as its amplifying hosts, this virus is found primarily in the western Great Plains of North America at spatially discrete swallow nesting colonies. For 342 isolates collected in Oklahoma, Nebraska, Colorado, and North Dakota, from 1974 to 2007, we sequenced a 2076 bp region of the 26S subgenomic RNA structural glycoprotein coding region, and analyzed phylogenetic relationships, …

Mortality Among Hiv-1- And Human Herpesvirus Type 8 – Affected Mother-Infant Pairs In Zambia, Janet Wojcicki, Mulindi Mwanahamuntu, Veenu Minhas, Boris Djokic, Chipepo Kankasa, Winslow Klaskala, Brad Brayfield, Saul Phiri, Charles Wood, Charles Mitchell

Nebraska Center for Virology: Faculty Publications

Objective: To determine the respective trends in mortality of Zambian mother-infant pairs based on maternal infection with HIV-1 and human herpesvirus type 8 (HHV-8).
Methods: A prospective cohort study was done on Zambian mother-infant pairs, stratified by maternal serologic status and followed from 6 weeks postdelivery for 48 months. Statistical analysis of the differences in the calculated mortality rates among the four groups was done using Stata 7.0. Kaplan-Meier analysis and Cox proportional hazard models were used to measure subject survival time.
Results: Between September 1998 and March 2002, a total of 1,425 mother-infant pairs were enrolled. …

Tissue And Stage-Specific Juvenile Hormone Esterase (Jhe) And Epoxide Hydrolase (Jheh) Enzyme Activities And Jhe Transcript Abundance In Lines Of The Cricket Gryllus Assimilis Artificially Selected For Plasma Jhe Activity: Implications For Jhe Microevolution, Anurag Anand, Erica Crone, Anthony J. Zera

Anthony Zera Publications

Fat body and midgut juvenile hormone esterase (JHE) and juvenile hormone epoxide hydrolase (JHEH) specific activities, and plasma JHE activity, were measured throughout the last stadium in two pairs (blocks) of lines of the cricket Gryllus assimilis, each pair of which had been artificially selected for high- or low-plasma JHE activity. Highly significant differences were observed between high- and low-activity lines of each block on most days for fat body JHE, and on one day for midgut JHE activity. In each block, line differences in developmental profiles for fat body JHE activity paralleled line differences in plasma JHE activity …

New And Interesting Laboulbeniales From Brazil, Walter Rossi, Ernesto Bergonzo

Aliso: A Journal of Systematic and Floristic Botany

Two new species of Laboulbeniales are described: Laboulbenia parasyphraeae, parasitic on Parasyphraea sp. (Coleoptera, Chrysomelidae, Alticinae), and L. skelleyi, parasitic on Pselaphacus rubricatus and P. signatus (Coleoptera, Erotylidae). Other recorded species are Chaetomyces pinophili, Chitonomyces aurantiacus, Corethromyces ophitis, Dimorphomyces platensis, Dioicomyces anthici, D. cf. notoxi, Hesperomyces coccinelloides, Hydrophilomyces rhynchophorus, Laboulbenia arnaudii, L. funeralis, L. pachystoma, and L. systenae. Six ‘‘morphospecies’’ of Chitonomyces (C. appendiculatus, C. hyalinus, C. prolongatus, C. simplex, C. uncinatus, and C. cf. zonatus) parasitic on …

A New Species Of Genus Laboulbenia (Laboulbeniales) On Craspedophorus Formosanus (Coleoptera, Carabidae) From Taiwan, With A Note On Laboulbenia Asiatica, Katsuyuki Terada, Meng-Hao Hsu, Wen-Jer Wu

Aliso: A Journal of Systematic and Floristic Botany

Laboulbenia taiwaniana sp. nov. on Craspedophorus formosanus is described from Taiwan and illustrated with photographs. It is characterized by a long, asymmetrical perithecium with an oblique apex and a pale-colored lower wall, a slender, evenly tapered receptacle with cylindrical cell I and II and trapezoidal cell IV, well developed appendages with black septa concentrated in the basal portion of the appendage system, and especially by black septa on the distal end of cell g. Laboulbenia asiatica, which was described from an Asian carabid---"Casnonia sp."---in 1899 and was illustrated in 1908 by Thaxter, is reviewed and compared …

Laboulbeniales On Semiaquatic Heteroptera. A New Species Of Triceromyces (Ascomycota, Laboulbeniales) On Microvelia (Heteroptera, Veliidae) From Spain, Sergio Santamaria

Aliso: A Journal of Systematic and Floristic Botany

A new species of fungal genus Triceromyces (Laboulbeniales) is described: Triceromyces benjaminii. The description is based on several thalli found on the insect host Microvelia pygmaea (Heteroptera, Veliidae), collected in two localities from SE Spain. Characteristics of male and female thalli of this dioecious species are discussed and compared with other dioecious taxa. The characteristics of male thalli require some adjustment in generic limits. This is the first species of Triceromyces known to parasitize a species of Microvelia, a semiaquatic heteropteran genus. The new species is described and illustrated with line drawings and photographs. A table collates information …

The Genus Prolixandromyces (Laboulbeniales) In The Old World Prolixandromyces (Laboulbeniales), Alex Weir

Aliso: A Journal of Systematic and Floristic Botany

Two new species of Prolixandromyces (Laboulbeniales) parasitic on Rhagovelia (Heteroptera: Veliidae) are described and illustrated: Prolixandromyces benjaminii from the Philippine Islands and P. lanceolatus from Africa (Madagascar, Malawi, Nigeria, Sierra Leone, and South Africa) and Asia (Indonesia: Sulawesi, Sumba, Timor; Malaysia: Selangor; and Sri Lanka). In order to accommodate these species the circumscription of Prolixandromyces is emended. The new taxa are compared with the one known species from the Old World, P. triandrus from Spain, and with the five known New World taxa.

New Species Of Cucujomyces (Laboulbeniales) On Chilean Leiodidae, Walter Rossi, Alex Weir

Aliso: A Journal of Systematic and Floristic Botany

Four new species of Cucujomyces (Laboulbeniales) parasitic on Leiodidae (Coleoptera) from Chile are described and illustrated: Cucujomyces dasypelatis on Dasypelates nebulosus, C. gratiellae on Hydnodietus brunneus, C. neohydnobii on Neohydnobius argentinicus, and C. newtonii on Metahydnobius spp. The new taxa are compared with other known species of Cucujomyces. Morphological variation encountered in one of the new species, C. gratiellae, encompasses attributes of both Cucujomyces and Balazucia, necessitating Balazucia to be placed in synonymy under Cucujomyces. On the basis of this, two new combinations, Cucujomyces bilateralis and C. japonicus, are proposed.

Methods Used By Dr. R. K. Benjamin, And Other Mycologists, To Isolate Zygomycetes, Gerald L. Benny

Aliso: A Journal of Systematic and Floristic Botany

The methods that Dr. Richard K. Benjamin used to isolate Zygomycetes are discussed. These processes involved the following five steps: (1) collection, (2) plating, (3) isolation, (4) culture, and (5) maintenance. Additional methods, materials, and modifications used to isolate Zygomycetes are summarized. The author considers the flattening of the aerial hyphae onto the substrate of the faster- and higher-growing Mucorales for several consecutive days to be the critical step in isolating species of Coemansia, Piptocephalis, Syncephalis, and Dimargaritales. The methods used by other scholars to isolate, culture, and study many taxa in Zygomycetes also are discussed.

Recombinant G3 Domain Protein Of The Rat Laminin-5 Α3 Chain Binds To Integrins On Tumorogenic Breast Cancer Cells To Induce Apoptosis, Brittany Turner

All Dissertations

The extracellular matrix (ECM) is a network of proteins for holding tissues and cells together. Among the constituents of the ECM is the large molecular weight glycoprotein laminin. Laminin is predominately found in the basement membrane of tissues. Laminins are composed of α, β, and γ chains with 5 globular (G) subdomains at the carboxyl (C) terminal end of the α chain. Of the 12 different laminin isoforms, laminin-5 has been targeted for cancer research. Specifically, the G3 domain has been studied as the specific binding domain. Cells are able to migrate through cell surface adhesion receptors known as integrins. …

The Antioxidant Defense Network: Synergistic Combinations To Prevent Oxidative Damage, Amy Marie Clement

Theses and Dissertations

One of the matchless ironies of the human body is its requirement for the highly reactive oxygen molecule, which has been clearly implicated in many diseases and the aging processes. Oxidants produced by metabolic processes damage cells by starting chemical chain reactions including oxidation of DNA and proteins as well as lipid peroxidation. Damage to DNA can cause mutations and lead to cancer if not reversed by DNA repair mechanisms. Damage to proteins causes enzyme inhibition, denaturation and protein degradation. Lipid peroxidation can cause cell lysis as well as creating mutagenic and carcinogenic by-products. The human body contains antioxidants and …

Identification Of Chlamydial Iron-Responsive Proteins During Intracellular Growth., Brian D. Dill

Electronic Theses and Dissertations

Chlamydia trachomatis is an obligate intracellular bacterium and the most prevalent cause of bacterial sexually transmitted disease. Genital chlamydial infections, marked by chronic, intense inflammation, can lead to genital tissue scarring and infertility and is a contributing factor to development of pelvic inflammatory disease and ectopic pregnancy. Iron is required as a cofactor for numerous highly conserved pathways, and nearly all studied organisms rely on iron for growth. In response to iron restriction, the chlamydial developmental cycle arrests at the intracellular reticulate body stage, resulting in a phenomenon termed persistence. Persistence likely plays a role in chlamydial pathogenesis through the …

The Effects Of Host Physiological Conditions On The Expression Of Icsp In Shigella Flexneri, Karen Levy, Helen Wing

Undergraduate Research Opportunities Program (UROP)

Shigella flexneri is a gram-negative bacterium capable of causing diarrhea and dysentery known as shigellosis. It is estimated there are 167.4 million shigellosis episodes throughout the world each year causing 1.1 million deaths. Shigella invades cells in the lower intestine through an induced phagocytosis. Once in the cytoplasm, bacteria move from one cell to another using actin-based motility. The Shigella outer membrane protease IcsP regulates actin-based motility and cell-to-cell spread by cleaving the actin assembly protein IcsA from the bacterial cell surface. We hypothesize that IcsP may serve additional functions during infection. By examining which environmental signals trigger icsP expression, …

The Effect Of Cody On Stationary Phase Mutagenesis In Bacillus Subtilis, May Yared, Holly Martin, Eduardo A. Robleto, Ronald E. Yasbin

Undergraduate Research Opportunities Program (UROP)

We examine the notion that cells in conditions of stress accumulate mutation is in genes under selection via transcription processes. CodY is a global transcriptional regulator in many Gram positives, including soil and pathogenic microbes. In conditions of exponential growth and when branch chain amino acids and GTP are in abundance CodY acts as a transcriptional repressor of many metabolic operons. This transitional repression saves the cell energy and allows efficient use of resources. In conditions of starvation, CodY relieves repression of genes involved in acquisition of nutrients and degradation of carbon sources (genes under selection). Here, we compare the …

Microbial Nitrogen Cycling In Nevada Geothermal Springs, Mitchell G. Chaires, Jeremy A. Dodsworth, Brian P. Hedlund

Undergraduate Research Opportunities Program (UROP)

Hot spring habitats above maximum photosynthetic temperature (73 ºC) are not well understood with respect to nitrogen (N) cycling. Few predictions have been made, and even fewer measurements of in situ activities have been reported. Thermodynamic calculations based on in situ chemical and temperature measurements will be used to predict the occurrence of the specific N-cycling reactions. In addition, these measurements in two springs will aid in an attempt to cultivate ammonia oxidizing species.

Potential Antimicrobial Properties Of The Cyanobacterium Microcoleus Vaginatus In Relationship To The Moss Bryum Argenteum, Crystal Erickson, Lloyd Stark

Undergraduate Research Opportunities Program (UROP)

Biological soil crusts play important ecological roles in arid desert regions. These crusts cycle nutrients, prevent wind/water erosion, and form the basis of food chains and soil formation in desert communities. Primary components of these structures include two desert moss species Bryum argenteum and Syntrichia caninervis, and Microcoleus vaginatus, a cyanobacterium. Our Phase I experiment strongly suggests that in an environment of intense light, a condition of stress to Syntrichia caninervis, there is an increase in shoot regeneration when cyanobacteria are present compared to when they are absent. Microcoleus is a highly motile species and our lab observations of fewer …

Microbial Ecology Of Keane Wonder Spring, Death Valley National Park, Alexander B. Michaud, Duane P. Moser

Undergraduate Research Opportunities Program (UROP)

This research is focused on developing a better understanding of he physiological and phylogenetic diversity as well as environmental abundance of bacteria of the genus: Shewanella in selected desert ecosystems. Prior research from this laboratory has revealed that these bacteria are very abundant in sulfurand organic-rich aquatics habitats. We have selected a number of habitats for detailed investigation (cultivation, molecular ecology and relevant environmental chemistry) including the Tropicana Wash, spring in Death Valley, the lower Virgin River and possibly Big Soda Lame, Nevada.

The Regulation Of The Icsp Promoter Of Shigella Flexneri By The Virulence Factor Virb, Maria Castellanos, Dustin Harrison, Helen Wing

Undergraduate Research Opportunities Program (UROP)

Shigella flexneri is a pathogenic bacterium that causes severe dysentery in humans commonly known as shigellosis. Shigella encodes an outer membrane protease called IcsP. The regulation of icsP expression is under direct control of a transcriptional factor called VirB, which controls the expression of many virulence genes in Shigella. Previous work has shown through deletion analysis of the icsP promoter region that sequences as far as 1368 base pairs upstream of the transcription starting site are important for the regulation of the icsP gene by VirB. However, it is still unclear whether VirB activation requires sequences within the icsP promoter …

Aerobic Respiration By Two Sulfate Reducing Magnetotactic Bacteria, Strains Rs-1 And Fh-1, Paul Howse, Sabrina Schubbe, Dennis A. Bazylinski

Undergraduate Research Opportunities Program (UROP)

Magnetotactic bacteria is the categorical name for a group of prokaryotes that biomineralize magnetosomes which are intracellular, membrane-bounded magnetic iron mineral crystals. The focus of this study is on two magnetiteproducing, magnetotactic sulfate-reducing bacteria (SRB), Desulfovibrio magneticus strain RS-1 and strain FH-1 which also belongs in the genus Desulfovibrio in the δ-Proteobacteria. SRB utilize sulfate as a terminal electron acceptor under anaerobic conditions reducing sulfate to sulfide. A large number of organic compounds as well as some inorganic compounds have been shown to provide electrons for sulfate reduction. Traditionally, because no SRB have been shown to convincingly grow with O2 …

Kinetics Of Bacillus Anthracis And Bacillus Cereus Spore Germination In Soil And The C. Elegans Intestine, Maclean Hall, Ernesto Abel-Santos

Undergraduate Research Opportunities Program (UROP)

Bacillus anthracis and Bacillus cereus are both described as soil bacteria, but are almost exclusively found as spores within the soil. Soil is generally not a nutrient-rich environment and may lack the amino acids and nucleosides necessary for spore germination and vegetative reproduction. We aim to determine if soil alone can cause germination in these two species in order to produce vegetative cells that can reproduce. In addition, nematodes, decaying meat, maggots, and plant roots will be tested for their ability to cause germination in these species.

Genomic Foundations Of Carbon Fixation In Bacteria Living In Hot Springs, Rachel K. Skinner, Brian P. Hedlund, Jeremy A. Dodsworth

Undergraduate Research Opportunities Program (UROP)

Photosynthesis does not occur above 73°C, so organisms living above this temperature must obtain useable carbon by some other mechanism. It is generally assumed that carbon is fixed by thermophiles through the process of chemolithoautotrophy; however, primary production has never been demonstrated to occur in hot springs >73°C. We have shown that two organisms, Thermocrinis and Pyrobaculum, make up more than 90% of the cells in an 80°C Great Basin hot spring, Great Boiling Spring. We hypothesize that these organisms fix carbon in the hot spring via the reverse tricarboxylic acid (rTCA) cycle. To test this hypothesis we will: i) …

Denitrification In Great Basin Hot Springs, Austin Mcdonald, Brian P. Hedlund

Undergraduate Research Opportunities Program (UROP)

Hydrogen has been proposed to fuel primary production in the Aquificae dominated hot springs of Yellowstone National Park (Spear, et al. 2005), a finding the authors generalized to all hot springs. However, clone libraries derived from Great Basin springs contain few 16S ribosomal RNA (rRNA) gene sequences from Aquificae and many from unknown microorganisms. In the same springs, alternative electron donors rival the reducing power of hydrogen. This project will try to cultivate the uncharacterized microbes of two Great Basin springs and determine which electron donors they can use.

Nitrogen is key to life. In its reduced form, ammonia, it …

Characterization Of The Omptin Protease, Ompt, In Escherichia Coli, Amanda Yates, Eun-Hae Kim, Helen Wing

Undergraduate Research Opportunities Program (UROP)

Omptins are outer membrane proteases found in gram negative bacteria that cause diseases in humans, such as pathogenic Escherichia coli, Shigella flexneri, Salmonella typhimurium, and Yersinia pestis. Bacterial species that express omptins cause diseases such as highly fatal plague and severe diarrhea and dysentery. The genes that encode these proteases are ompT, icsP, pgtE, and pla, respectively. These proteases are highly related in structure and share approximately 50% sequence identity. In S. flexneri, IcsP has been shown to cleave a key virulence determinant, IcsA (Egile et al., 1997). IcsA recruits host actin and allows for intracellular movement within host cells …

Altered Expression Of Cell Cycle And Apoptotic Proteins In Chronic Hepatitis C Virus Infection., Saira Sarfraz, Saeed Hamid, Anwar Ali Siddiqui, Snawar Hussain, Shahid Pervez, Graeme Alexander

Department of Biological & Biomedical Sciences

Background: A disrupted cell cycle progression of hepatocytes was reported in chronic hepatitis C virus (HCV) infection, which can contribute significantly in the associated pathogenesis. The present study aimed to further elaborate these disruptions by evaluating the expression of key cell cycle and apoptotic proteins in chronic HCV infection with particular reference to genotype 3. Archival liver biopsy specimens of chronic HCV-infection (n = 46) and normal histology (n = 5) were analyzed by immunohistochemistry using antibodies against proliferation marker Mcm-2, G1 phase marker Cyclin D1, S phase marker Cyclin A, cell cycle regulators p21 (CDK inhibitor) and p53 (tumor …

Relationship Of Lactobacillus Casei To Prevention Of Antibiotic Associated Diarrhea Due To Clostridium Difficile, Kayal K. Chandramohan

All-Inclusive List of Electronic Theses and Dissertations

The purpose of this research was to study the effectiveness of Lactobacillus casei in preventing the occurrence of antibiotic associated diarrhea related to Clostridium difficile. Twenty-six patients, above the age of sixty years, who were prescribed antibiotic therapy and admitted to the Rehabilitation or Orthopedics Units at Union Hospital and who met the eligibility criteria were recruited for the study. Equal numbers of patients (13 in each group) were assigned to the Control and the Experimental group based on their admission date to the hospital and their willingness to consume a probiotic yogurt type drink. The patients in the experimental …