Microbiology Commons^™

Analysis Of Bacterial Diversity In Arctic Soil And Sediment Samples From Ny-Alesund, Norway Using Denaturing Gradient Gel Electrophoresis., Yew Wen Chyin

Student Works (2010-2019)

Bacterial diversity in soil and sediment samples from eighteen sites in and around Dasan Station, Ny-Ålesund, Norway was analyzed using Denaturing Gradient Gel Electrophoresis (DGGE), and was correlated with the environmental variables. Samples analysed included terrestrial soils, beach soil, periglacier soils, inland lake bank sediments, melt lake sediments, and marine sediments. Spearman rank order correlation showed significant correlations (P = 0.001) between conductivity (r = 0.470) and pH (r = 0.294) with the bacterial diversity. Soil from the tundra site (sample 17) appeared to have the most diverse bacterial community while inland lake bank sediment from the …

Bacterial Acquisition In Juveniles Of Several Broadcast Spawning Coral Species, Koty H. Sharp, Kim B. Ritchie

Arts & Sciences Faculty Publications

Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, …

Bryostatins: Biological Context And Biotechnological Prospects, Amaro E. Trindade-Silva, Grace E. Lim-Fong, Koty H. Sharp

Arts & Sciences Faculty Publications

Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and Bryostatins are a family of protein kinase C modulators that have potential applications in biomedicine. Found in miniscule quantities in a small marine invertebrate, lack of supply has hampered their development. In recent years, bryostatins have been shown to have potent bioactivity in the central nervous system, an uncultivated marine bacterial symbiont has been shown to be the likely natural source of the bryostatins, the bryostatin biosynthetic genes have been identified and characterized, and bryostatin analogues with promising biological activity have been developed and tested. Challenges in …

Introducing Mothur: Open-Source, Platform-Independent, Community-Supported Software For Describing And Comparing Microbial Communities, Courtney Robinson

Department of Biology Faculty Publications

mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

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

Biology Faculty Publications

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

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 …

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 …

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.

Altered Regulation Of Aquaporin Gene Expression In Allergen And Il-13-Induced Mouse Models Of Asthma, Carissa M. Krane, Bijia Deng, Venkateshwar Mutyam, Casey A. Mcdonald, Stephen Pazdziorko, Lawrence Mason, Samuel Goldman, Marion Kasaian, Divya Chaudhary, Cara Williams, Melisa W.Y. Ho

Biology Faculty Publications

IL-13 is known to affect many processes that contribute to an asthmatic phenotype, including inflammation, fibrosis, and mucus production. Members of the aquaporin (AQP) family of transmembrane water channels are targets of regulation in models of lung injury and inflammation. Therefore, we examined AQP mRNA and protein expression in allergen and IL-13-induced mouse models of asthma. Lungs from ovalbumin sensitized and ovalbumin challenged (OVA/OVA) and IL-13 treated mice showed airway thickening, increased mucus production, and pulmonary eosinophilia. Pulmonary function tests showed a significant increase in methacholine-induced airway hyperreactivity in OVA/OVA and IL-13-treated mice as compared with controls. Quantitative PCR analysis …

Molecular Coevolution Of Pacific Northwest Hantaviruses And Their Host, The Deer Mouse, Peromyscus Maniculatus, Philip Darren Jones

Dissertations and Theses

Sin Nombre virus (SNV, family Bunyaviridae, genus Hantavirus), hosted by the deer mouse, Peromyscus maniculatus (family Cricetidae, Subfamily Neotominae), is the primary etiological agent of Hantavirus pulmonary syndrome (HPS) in the western United States. HPS, with known pathogenicity only to humans and for which there is no cure or prophylaxis, affects the epithelium of the lungs by making the capillaries leaky, thereby resulting in bilateral infiltrates, and eventually leading to respiratory failure and death by drowning in approximately 38% of hospitalized patients.

In the Americas, Peromyscus has been co-evolving with hantaviruses for approximately 12–20 million years, since the first …

Overexpression Of Mazfsa In Staphylococcus Aureus Induces Bacteriostasis By Selectively Targeting Mrnas For Cleavage, Zhibiao Fu, Sandeep Tamber, Guido Memmi, Niles P. Donegan, Ambrose L. Cheung

Dartmouth Scholarship

The role of chromosomally encoded toxin-antitoxin (TA) loci in bacterial physiology has been under debate, with the toxin proposed as either an inducer of bacteriostasis or a mediator of programmed cell death (PCD). We report here that ectopic expression of MazFSa, a toxin of the TA module from Staphylococcus aureus, led to a rapid decrease in CFU counts but most cells remained viable as determined by differential Syto 9 and propidium iodide staining after MazFSa induction. This finding suggested that the toxin MazFSa induced cell stasis rather than cell death. We also showed that MazFSa selectively cleaves cellular mRNAs in …

Structure-Function Analysis Of Endoproteolytic Cleavage: Site-Directed Mutagenesis Studies Of The Α-Msh Cleavage Site In Silurana Tropicalis Pomc, Quinn Kun Chen

Electronic Theses and Dissertations

The maturation process of many prohormone molecules typically requires endoproteolytic cleavage C-terminal of dibasic residues, such as the K¹⁴¹R¹⁴²↓ site N-terminal of the α-melanocyte stimulating hormone (α-MSH) sequence in Silurana tropicalis proopiomelanocortin (POMC). In order to determine the absolute requirement of basic amino acid residues in the cleavage process, site-directed mutagenesis was employed to substitute alanine for the wild-type residues in the frog POMC open reading frame. Specifically, the following underlined residues were individually targeted for alanine substitution: R ¹³⁷ Q ¹³⁸ E ¹³⁹ N ¹⁴⁰ K ¹⁴¹ R ¹⁴²↓. The mouse pancreatic αTC1.9 cell …

Afforestation Alters The Composition Of Functional Genes In Soil And Biogeochemical Processes In South American Grasslands, Sean T. Berthrong, Christopher W. Schadt, Gervasio Piñeiro, Robert B. Jackson

Scholarship and Professional Work - LAS

Soil microbes are highly diverse and control most soil biogeochemical reactions. We examined how microbial functional genes and biogeochemical pools responded to the altered chemical inputs accompanying land use change. We examined paired native grasslands and adjacent Eucalyptus plantations (previously grassland) in Uruguay, a region that lacked forests before European settlement. Along with measurements of soil carbon, nitrogen, and bacterial diversity, we analyzed functional genes using the GeoChip 2.0 microarray, which simultaneously quantified several thousand genes involved in soil carbon and nitrogen cycling. Plantations and grassland differed significantly in functional gene profiles, bacterial diversity, and biogeochemical pool sizes. Most grassland …

A Global Meta-Analysis Of Soil Exchangeable Cations, Ph, Carbon, And Nitrogen With Afforestation, Sean T. Berthrong, Esteban G. Jobbagy, Robert B. Jackson

Scholarship and Professional Work - LAS

Afforestation, the conversion of non-forested lands to forest plantations, can sequester atmospheric carbon dioxide, but the rapid growth and harvesting of biomass may deplete nutrients and degrade soils if managed improperly. The goal of this study is to evaluate how afforestation affects mineral soil quality, including pH, sodium, exchangeable cations, organic carbon, and nitrogen, and to examine the magnitude of these changes regionally where afforestation rates are high. We also examine potential mechanisms to reduce the impacts of afforestation on soils and to maintain long-term productivity.

Across diverse plantation types (153 sites) to a depth of 30 cm of mineral …

Compensatory Evolution Of Gene Regulation In Response To Stress By Escherichia Coli Lacking Rpos, Daniel M. Stoebel, Karsten Hokamp, Michael S. Last, Charles J. Dorman

All HMC Faculty Publications and Research

The RpoS sigma factor protein of Escherichia coli RNA polymerase is the master transcriptional regulator of physiological responses to a variety of stresses. This stress response comes at the expense of scavenging for scarce resources, causing a trade-off between stress tolerance and nutrient acquisition. This trade-off favors non-functional rpoS alleles in nutrient-poor environments. We used experimental evolution to explore how natural selection modifies the regulatory network of strains lacking RpoS when they evolve in an osmotically stressful environment. We found that strains lacking RpoS adapt less variably, in terms of both fitness increase and changes in patterns of transcription, than …

Host And Seasonal Effects On The Infection Dynamics Of Skrjabinoptera Phrynosoma (Ortlepp) Schulz, 1927, A Parasitic Nematode Of Horned Lizards, Kathryn Claire Hilsinger

College of Graduate Studies: Theses & Dissertations

Author's Abstract: Skrjabinoptera phrynosoma (Ortlepp) Schulz, 1927 is a common parasitic nematode of horned lizards. The life cycle of S. phrynosoma was described by Lee in 1957, but has received little attention since. The present study addressed effect of season as well as host characteristics on the infection dynamics in lizard hosts. In the Alvord Basin in southeastern Oregon, S. phrynosoma were collected from Phrynosoma platyrhinos Gerard 1852 horned lizards via stomach flushes, cloaca flushes and fecal pellet collections. Parasite load variables (number of nematodes per host, length of those nematodes, and total worm burden (ΣL)) were analyzed within three …

Contributions Of Gut Bacteria To Bacillus Thuringiensis-Induced Mortality Vary Across A Range Of Lepidoptera, Nichole Broderick, Courtney Robinson, Matthew Mcmahon, Kenneth Raffa

Department of Biology Faculty Publications

Gut microbiota contribute to the health of their hosts, and alterations in the composition of this microbiota can lead to disease. Previously, we demonstrated that indigenous gut bacteria were required for the insecticidal toxin of Bacillus thuringiensis to kill the gypsy moth, Lymantria dispar. B. thuringiensis and its associated insecticidal toxins are commonly used for the control of lepidopteran pests. A variety of factors associated with the insect host, B. thuringiensis strain, and environment affect the wide range of susceptibilities among Lepidoptera, but the interaction of gut bacteria with these factors is not understood. To assess the contribution of gut …

Patterning Defects In Silkworm Embryos Analysed Through Cuticle Preparations, Amit Singh, Madhuri Kango-Singh, K. P. Gopinathan

Biology Faculty Publications

The mulberry silkworm, Bombyx mori, a holometabolous lepidopteran insect, has a metameric body plan. Due to its functional adaptation, B. mori presents some unique deviations in its pal/ern from the evolutionarily advanced dipteran insect, Drosophila melanogaster. Previous studies on mutant phenotype analysis in B. mori have been carried out in late stages of larval development. Here we employ, the cuticle preparation approach during embryonic development to study morphological landmarks associated with B. mori, Eri, another race a/silkworm, and pattern defects associated with Ekp mutant of B.mori. The homeotic mutant Ekp, generates ectopic abdominallegs, a feature …

An Algorithm For Identifying Novel Targets Of Transcription Factor Families: Application To Hypoxia-Inducible Factor 1 Targets, Yue Jiang, Bojan Cukic, Donald A. Adjeroh, Heath D. Skinner, Jie Lin, Qingxi J. Shen, Bing-Hua Jiang

Electrical & Computer Engineering Faculty Research

Efficient and effective analysis of the growing genomic databases requires the development of adequate computational tools. We introduce a fast method based on the suffix tree data structure for predicting novel targets of hypoxia-inducible factor 1 (HIF-1) from huge genome databases. The suffix tree data structure has two powerful applications here: one is to extract unknown patterns from multiple strings/sequences in linear time; the other is to search multiple strings/sequences using multiple patterns in linear time. Using 15 known HIF-1 target gene sequences as a training set, we extracted 105 common patterns that all occur in the 15 training genes …

A Cell Biology Laboratory Exercise To Study Sub-Cellular Organelles In Drosophila, Meghana Tare, Amit Singh

Biology Faculty Publications

The fast-changing scenario of undergraduate education puts emphasis on introducing students to hands-on techniques as part of their laboratory courses. In order to cater to large numbers of students and the time constraints involved with undergraduate level laboratory courses, there is a need for development of experiments that are cost effective and can be completed in a defined time frame. We have devised a laboratory exercise for teaching cell biology using the Drosophila melanogaster model. Drosophila can be reared in a short period of time in a cost effective manner. We used Drosophila tissue to study the sub-cellular organization of …

Molecular Characterisation Of A Bovine-Like Rotavirus Detected From A Giraffe, Emily Mulherin, Jill Bryan, Marijke Beltman, Luke O'Grady, Eugene Pidgeon, Lucie Garon, Andrew Lloyd, John Bainbridge, Helen O'Shea, Paul Whyte, Séamus Fanning

Department of Biological Sciences Publications

Background

Rotavirus (RV), is a member of the Reoviridae family and an important etiological agent of acute viral gastroenteritis in the young. Rotaviruses have a wide host range infecting a broad range of animal species, however little is known about rotavirus infection in exotic animals. In this paper we report the first characterisation of a RV strain from a giraffe calf.

Results

This report describes the identification and detailed molecular characterisation of a rotavirus strain detected from a 14-day-old Giraffe (Giraffa camelopardalis), presenting with acute diarrhea. The RV strain detected from the giraffe was characterized molecularly as G10P[11]. …

Global Analysis Of Gene Expression Changes During Retinoic Acid-Induced Growth Arrest And Differentiation Of Melanoma: Comparison To Differentially Expressed Genes In Melanocytes Vs Melanoma, Mary H. Estler, Goran Boskovic, James Denvir, Sarah Miles, Donald A. Primerano, Richard M. Niles

Biochemistry and Microbiology

BACKGROUND: The incidence of malignant melanoma has significantly increased over the last decade. Some of these malignancies are susceptible to the growth inhibitory and pro-differentiating effects of all-trans-retinoic acid (RA). The molecular changes responsible for the biological activity of RA in melanoma are not well understood.

RESULTS: In an analysis of sequential global gene expression changes during a 4-48 h RA treatment of B16 mouse melanoma cells, we found that RA increased the expression of 757 genes and decreased the expression of 737 genes. We also compared the gene expression profile (no RA treatment) between non-malignant melan-a mouse melanocytes and …

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 …

Rules Of Engagement: Interspecies Interactions That Regulate Microbial Communities, Ainslie Little, Courtney Robinson, S Peterson, Kenneth Raffa, Jo Handelsman

Department of Biology Faculty Publications

Microbial communities comprise an interwoven matrix of biological diversity modified by physical and chemical variation over space and time. Although these communities are the major drivers of biosphere processes, relatively little is known about their structure and function, and predictive modeling is limited by a dearth of comprehensive ecological principles that describe microbial community processes. Here we discuss working definitions of central ecological terms that have been used in various fashions in microbial ecology, provide a framework by focusing on different types of interactions within communities, review the status of the interface between evolutionary and ecological study, and highlight important …

Louis Pasteur’S Views On Creation, Evolution, And The Genesis Of Germs, Alan L. Gillen, Frank Sherwin

Faculty Publications and Presentations

“There is no remembrance of men of old, and even those who are yet to come will not be remembered by those who follow.” Ecclesiastes 1:11 (NIV)

In past years revisionist historians have been rewriting the worldview of Christians who have made some of the major discoveries in biology and medicine. It appears that postmodern revisionists are rewriting history to support their agenda of a more “secular” explanation to science. The Judeo-Christian worldview is not politically correct in most universities. This is true in regard to past scientists such as Louis Pasteur who believed in creation. According to reliable, primary …

Isolation And Characterization Of Vibrio Tubiashii Outer Membrane Proteins And Determination Of A Toxr Homolog, Broderick Eribo

Department of Biology Faculty Publications

Outer membrane proteins (OMPs) expressed by Vibrio tubiashii under different environmental growth conditions were characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, N-terminal amino acid sequencing, and PCR analyses. Results showed the presence of a 38- to 40-kDa OmpU-like protein and ompU gene, a maltoporin-like protein, several novel OMPs, and a regulatory toxR homolog.

Characteristics And Dyes Biodegradation Potential Of Crude Lignolytic Enzymes From White-Rot Fungus Crepidotus Variabilis Isolated In Coastal Tanzania, G. Y. S. Gys Mtui

Tanzania Journal of Science

Lignocellulosic enzymes from Crepidotus variabilis collected from mangrove forests of coastal Tanzania were investigated by using standard methods, and their ability to degrade aromatic compounds were elucidated. The fungal crude enzyme filtrates had maximum laccase (Lac), lignin peroxidase (LiP) and manganese peroxidase (MnP) activities of 70 U/mL, 16 U/mL and 8, U/mL respectively. The crude enzyme extracts were able to oxidize rhemazol brilliant blue-R (RBB-R) dye, phenol, "-naphthol and pyrogallol. Also, they could remove up to 58% and 92% color from raw textile effluent and aromatic dyes, respectively, after 14 days of incubation at 30ºC and pH 4.5. Desalted and …

Genomic Resources For Myzus Persicae: Est Sequencing, Snp Identification, And Microarray Design, John S. Ramsey, Alex C. C. Wilson, Marin De Vos, Qi Sun, Cecilia Tamborindeguy, Agnese Winfield, Gaynor Malloch, Dawn M. Smith, Brian Fenton, Stewart M. Gray, Georg Jander

Biology Articles and Papers

Backgorund

The green peach aphid, Myzus persicae (Sulzer), is a world-wide insect pest capable of infesting more than 40 plant families, including many crop species. However, despite the significant damage inflicted by M. persicae in agricultural systems through direct feeding damage and by its ability to transmit plant viruses, limited genomic information is available for this species.

Results

Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs). Aphids for library construction were raised on Arabidopsis thaliana, Nicotiana benthamiana, Brassica oleracea, B. napus, and Physalis floridana (with and without Potato leafroll virus infection). The …

The Potential Role Of Probiotics In Reducing Poverty-Associated Infections In Developing Countries, Kingsley Anukam

Data and Test Instruments

Probiotics are defined by the Food and Agricultural Organization/ World Health Organization as “live microorganisms which when administered in adequate amounts confer a health benefit on the host” [1]. The potential benefits of their use have not been adequately investigated, especially in the developing world. Japan introduced Yakult, a probiotic fermented food drink in 1935, and in the Northern hemisphere, research and use of probiotics has gained an unprecedented momentum in the last decade [2]. Use of probiotics is not uncommon in Europe [3], but in many developing countries use of probiotics in its present definition is a foreign concept. …

Biophysical Study Of The Sh2 Domain Of Human Tensin, Yogesh Mohan Kulkarni

Doctoral Dissertations

Cell migration is a key characteristic of embryogenesis, inflammation, wound healing, tumor cell metastasis and a broad range of other normal and pathological processes. Accumulating evidence suggests that the protein tensin provides a physical link between transmembrane receptors, proteins commonly associated with signal transduction, and the actin cytoskeleton. Adhesion involves three broad classes of macromolecules: ExtraCellular Matrix (ECM) molecules, transmembrane adhesion receptors, and intracellular adhesion plaque proteins. Tensin is particularly enriched in Fibrillar Adhesions (FA's), though it is also present to a modest extent in Focal Contacts (FC's). Src Homology 2 (SH2) domains function in the transmission of molecular signals …