Life Sciences Commons^™

Inflammatory Cytokine Gene Expression In Mesenteric Adipose Tissue During Acute Experimental Colitis, William Conan Mustain, Marlene E. Starr, Joseph Daniel Valentino, Donald A. Cohen, Daiki Okamura, Chi Wang, B. Mark Evers, Hiroshi Saito

Markey Cancer Center Faculty Publications

BACKGROUND: Production of inflammatory cytokines by mesenteric adipose tissue (MAT) has been implicated in the pathogenesis of inflammatory bowel disease (IBD). Animal models of colitis have demonstrated inflammatory changes within MAT, but it is unclear if these changes occur in isolation or as part of a systemic adipose tissue response. It is also unknown what cell types are responsible for cytokine production within MAT. The present study was designed to determine whether cytokine production by MAT during experimental colitis is depot-specific, and also to identify the source of cytokine production within MAT.

METHODS: Experimental colitis was induced in 6-month-old C57BL/6 …

Comparative Genomics And Functional Analysis Of Rhamnose Catabolic Pathways And Regulons In Bacteria, Irina A. Rodionova, Xiaoqing Li, Vera Thiel, Sergey Stolyar, Krista Stanton, James K. Fredrickson, Donald A. Bryant, Andrei L. Osterman, Aaron A. Best, Dmitry A. Rodionov

Faculty Publications

L-rhamnose (Rha) is a deoxy-hexose sugar commonly found in nature. L-Rha catabolic pathways were previously characterized in various bacteria including Escherichia coli. Nevertheless, homology searches failed to recognize all the genes for the complete L Rha utilization pathways in diverse microbial species involved in biomass decomposition. Moreover, the regulatory mechanisms of L-Rha catabolism have remained unclear in most species. A comparative genomics approach was used to reconstruct the L-Rha catabolic pathways and transcriptional regulons in the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, and Thermotogae. The reconstructed pathways include multiple novel enzymes and transporters involved in the utilization of L-Rha and …

Nutrient Limitation In Three Lowland Tropical Forests In Southern China Receiving High Nitrogen Deposition: Insights From Fine Root Responses To Nutrient Additions, Feifei Zhu, Muneoki Yoh, Frank S. Gilliam, Xiankai Lu, Jiangming Mo

Biological Sciences Faculty Research

Elevated nitrogen (N) deposition to tropical forests may accelerate ecosystem phosphorus (P) limitation. This study examined responses of fine root biomass, nutrient concentrations, and acid phosphatase activity (APA) of bulk soil to five years of N and P additions in one old-growth and two younger lowland tropical forests in southern China. The old-growth forest had higher N capital than the two younger forests from long-term N accumulation. From February 2007 to July 2012, four experimental treatments were established at the following levels: Control, N-addition (150 kg N ha^–1 yr^–1), P-addition (150 kg P ha^–1 yr^{–1 …}

Divergent Antibody Subclass And Specificity Profiles But Not Protective Hla-B Alleles Are Associated With Variable Antibody Effector Function Among Hiv-1 Controllers, Jennifer I. Lai, Anna F. Licht, Anne-Sophie Dugast, Todd Suscovich, Ickwon Choi, Chris Bailey-Kellogg, Galit Alter, Margaret E. Ackerman

Dartmouth Scholarship

Understanding the coordination between humoral and cellular immune responses may be the key to developing protective vaccines, and because genetic studies of long-term HIV-1 nonprogressors have associated specific HLA-B alleles with spontaneous control of viral replication, this subject group presents an opportunity to investigate relationships between arms of the adaptive immune system. Given evidence suggesting that cellular immunity may play a role in viral suppression, we sought to determine whether and how the humoral immune response might vary among controllers. Significantly, Fc-mediated antibody effector functions have likewise been associated with durable viral control. In this study, we compared the effector …

Novel Thermophilic Bacteria Isolated From Marine Hydrothermal Vents, Christine Demko Sislak

Dissertations and Theses

As part of a large study aimed at searching for patterns of diversity in the genus Persephonella along the north to south geochemical gradient of the ELSC, ten novel strains of Alphaproteobacteria were isolated unexpectedly. Using defined media under microaerophilic conditions to enrich for Persephonella from chimney samples collected at the seven vent fields on the ELSC and the dilution to extinction by serial dilution method to purify cultures, a total of ten strains belonging to the Alphaproteobacteria were isolated. Two of these isolates, designate MN-5 and TC-2 were chosen for further characterization and are proposed as two new species …

Identification Of The Binding Partners For Hspb2 And Cryab Reveals Myofibril And Mitochondrial Protein Interactions And Non-Redundant Roles For Small Heat Shock Proteins, Kelsey Murphey Langston

Theses and Dissertations

Small Heat Shock Proteins (sHSP) are molecular chaperones that play protective roles in cell survival and have been shown to possess chaperone activity. As such, mutations in this family of proteins result in a wide variety of diseases from cancers to cardiomyopathies. The sHSPs Beta-2 (HspB2) and alpha-beta crystalline (CryAB) are two of the ten human sHSPs and are both expressed in cardiac and skeletal muscle cells. A heart that cannot properly recover or defend against stressors such as extreme heat or cold, oxidative/reductive stress, and heavy metal-induced stress will constantly struggle to maintain efficient function. Accordingly, CryAB is required …

Characterizing The Human Vaginal Microbiome Using High-Throughput Sequencing, Jean Megan E. Macklaim

Electronic Thesis and Dissertation Repository

The human vaginal microbiome undoubtedly has a significant role in reproductive health and for protection from infectious organisms. Recent efforts to characterize the bacterial species of the vagina using molecular techniques have uncovered an unexpected diversity. Using high-throughput sequencing I sought to describe the structure and function of the vaginal microbiome under different physiological states including healthy, bacterial vaginosis (BV), post-menopausal vaginal atrophy, and acute vulvovaginal candidiasis (VVC).

Partial 16S rRNA gene sequencing revealed that healthy, asymptomatic women most often have vaginal biotas dominated by Lactobacillus iners or L. crispatus. In contrast, BV is a heterogeneous, highly diversified condition …

Use Of Irf-3 And/Or Irf-7 Knockout Mice To Study Viral Pathogenesis: Lessons From A Murine Retrovirus-Induced Aids Model, Megan A. O'Connor, William R. Green

Dartmouth Scholarship

Interferon regulatory factor (IRF) regulation of the type I interferon response has not been extensively explored in murine retroviral infections. IRF-3(-/-) and select IRF-3/7(-/-) mice were resistant to LP-BM5-induced pathogenesis. However, further analyses strongly suggested that resistance could be attributed to strain 129-specific contamination of the known retrovirus resistance gene Fv1. Therefore, caution should be taken when interpreting phenotypes observed in these knockout mice, as strain 129-derived genetic polymorphisms may explain observed differences.

Effects Of Biodiesel Concentration On Microbial Deterioration Of Polyethylene In A Simulated Fuel Storage Tank, Juan Manuel Restrepo-Florez

Electronic Thesis and Dissertation Repository

In this study a simulated fuel storage tank was used to investigate the effect of biodiesel concentration on biodegradation of polyethylene. This research is relevant in the field of fuel storage. The simulated storage system consisted of a number of identical conical flasks. Each flask was comprised of two layers, an upper one consisting of a fuel blend of diesel with biodiesel in concentrations ranging from 0 to 100% of biodiesel and the bottom layer containing an aqueous mineral media inoculated with a community obtained from a real fuel storage facility. Polyethylene slabs cut to a specific size were immersed …

The Glycine And Proline Reductase Systems: An Evolutionary Perspective And Presence In Enterobacteriaceae, Joshua Witt

HIM 1990-2015

The Glycine and Proline Reduction systems are two of the best characterized selenoenzymes in bacteria and have been found to occur in a wide variety of clostridia [1-5]. These enzymes are utilized to reduce glycine or D-proline to obtain energy via substrate level phosporylation or membrane gradients, respectively [6, 7]. This includes the pathogens C. difficile and C. botulinum [5, 8]. Strains of C. difficile are activate toxigenic pathways whenever either of these pathways is active within the cell [5, 8]. Though evolutionary studies have been conducted on ammonia producing bacteria [9] none has been done to directly characterize these …

Wood Decomposition In A Warmer World, Emily Elizabeth Austin

Doctoral Dissertations

Climatic warming is altering species distributions and ecosystem functions across the globe. Wood is an important carbon pool and the fungal communities in wood are relatively simple compared to those in soil. These factors make decomposing wood an ideal system for exploring the influence of decomposer community on the response of decomposition to warming. My research has focused on the effects of warming wood decomposition rates and wood decomposing communities. Using field and lab- based manipulative experiments and field observations I explore the influence of tree species, wood decomposition stage, geography and warming on fungal community structure and activity. In …

Impact Of Wheat Streak Mosaic Virus And Triticum Mosaic Virus On Transmission By Aceria Tosichella Keifer (Eriophyidae) And Virus Epidemiology In Wheat, Camila F. De Oliveira

Department of Entomology: Dissertations, Theses, and Student Research

The wheat curl mite (WCM), Aceria tosichella Keifer, transmits a complex of viruses, Wheat streak mosaic virus (WSMV), Triticum mosaic virus (TriMV) and Wheat mosaic virus (WMoV), to wheat, Triticum aestivum, in the Great Plains. Co-infection of wheat by these viruses is frequently observed, increasing disease severity and yield loss.

Current genetic work classifies WCM populations into two genotypes, Type 1 and Type 2. It has been shown that different mite genotypes are able to transmit viruses at varying rates. WCM-virus relations are very specific and can impact vector biology. In this study, the primary objective was to determine …

The Incidence Of Antibiotic Resistance In Mesophilic Aeromonas Isolated From The Buffalo River And From A Non-Urban Site Upstream, Amy L. Chapman

Biology Theses

Antibiotics are commonly used in agriculture and industry and their discharge is commonly seen in rivers, like the Buffalo River. This antibiotic discharge may cause a selective environment which favors the growth of antibiotic resistant Aeromonas. To study the effect of urban pollution on the antibiotic resistance in Aeromonas, 229 Aeromonas isolates were collected from fish tissues as well as sediment and water samples collected from the Buffalo River and a non-urban site (Cazenovia Creek). Seven different Aeromonas taxa were identified using biochemical tests. There were 124 (54%) isolates that were classified as atypical, which was the most commonly …

Investigating Potential Bioactive Compounds From Rhodococcus And Their Effects On Mcf7 Breast Cancer Cells, Megan N. Crabtree

Electronic Theses and Dissertations

Many drugs used in the treatment of various cancers are derived from or influenced by compounds from nature. The soil bacterium Rhodococcus is of interest because of its identified secondary metabolic pathways and the production of novel natural antibiotics from several strains. In this study, a solid agar extraction method was used to collect compounds from strains of Rhodococcus. These bacterial compound extracts were then tested using a MTT assay in order to evaluate their effectiveness in augmenting MCF7 breast cancer cell death. The results of two way ANOVA analyses revealed 18 compound extracts from 15 strains of Rhodococcus that …

Identification And Characterization Of Genetic Factors Involved In Candida-Bacterial Interactions, Sean J. Fox

Electronic Theses and Dissertations

Throughout existence, fungi and bacteria have long shared ecological niches and thus engage in numerous interactions to mutually enhance survival or antagonistically gain competitive advantages. Of importance to human health are those interactions that involve bacteria with the opportunistic fungi, Candida albicans. An important virulence factor of C. albicans is the ability to control morphology, which allows the transition between yeast, pseudohyphal, and hyphal phenotypes. Morphological control in C. albicans is governed by quorum sensing and the secreted autoregulatory molecule farnesol. Quorum sensing allows individual cells to sense the environment and respond as a group. Bacteria also use quorum …

Electrotransfer Of Single-Stranded Or Double-Stranded Dna Induces Complete Regression Of Palpable B16.F10 Mouse Melanomas, Loree Heller, Vesba Todorovic, Maja Cemazar

Bioelectrics Publications

Enhanced tumor delivery of plasmid DNA with electric pulses in vivo has been confirmed in many preclinical models. Intratumor electrotransfer of plasmids encoding therapeutic molecules has reached Phase II clinical trials. In multiple preclinical studies, a reduction in tumor growth, increased survival or complete tumor regression have been observed in control groups in which vector or backbone plasmid DNA electrotransfer was performed. This study explores factors that could produce this antitumor effect. The specific electrotransfer pulse protocol employed significantly potentiated the regression. Tumor regression was observed after delivery of single-stranded or double-stranded DNA with or without CpG motifs in both …

An Argument And Plan For Promoting The Teaching And Learning Of Neglected Tropical Diseases, Kevin M. Bonney

Publications and Research

Neglected tropical diseases constitute a significant public health burden, affecting over one billion people globally, yet this group of diseases is underrepresented in the appropriation of both monetary and intellectual capital for developing improved therapies and public health campaigns. The topic of neglected tropical diseases has been similarly marginalized in the biology classrooms of our nation’s high schools and colleges, despite offering an opportunity to teach and learn about a diverse area of microbiology with far-reaching public health, social, and economic implications. Discussed herein is an argument for increasing the representation of neglected tropical diseases in microbiology education as a …

Characterization Of The Role(S) Of Env Protein Of Human Endogenous Retrovirus-K In Multiple Human Cancers, Ming Li

Dissertations & Theses (Open Access)

Human endogenous retroviruses (HERVs) are remnants from ancient retroviral infections, and most of them are inactive in normal tissues. One family of HERV, HERV-K, is found to be associated with multiple human cancers including breast cancer, pancreatic cancer and melanoma, but the causal relationship between HERV-K and cancer is still unclear. Increased expression of HERV-K in melanoma cells correlates with malignant transformation, while a serological response to HERV-K in breast cancer or melanoma patients correlates with survival probability. However, the mechanism behind these observations remains obscure. Our laboratory reported that anti-HERV-K envelope (Env) protein antibodies show antitumor potential in targeting …

C-Jun N-Terminal Kinases Regulate Adenovirus-Mediated Autophagy And Antigen Presentation, Sarah R. Klein

Dissertations & Theses (Open Access)

Targeted immunotherapy with recombinant, oncolytic adenoviruses is under investigation for the treatment of cancer. Evidence indicates adenoviruses induce autophagy that is required for oncolysis, but the molecular regulation of autophagy in infected cells remains under investigation. Our data suggested the canonical pathway regulating starvation-induced autophagy was not implemented in adenovirus-induced autophagy; however, adenovirus infection triggered phosphorylation of c-Jun N-terminal kinases (JNK) that was essential for autophagy. Adenoviral replication within the host cell elicited JNK pathway activation leading to B cell lymphoma-2 (Bcl-2) phosphorylation. JNK-dependent Bcl-2 phosphorylation stimulated the dissociation of Bcl-2/beclin 1 heterodimers, enabling beclin 1 to initiate autophagy. Moreover, …

Validation Of Thermal Destruction Of Pathogenic Bacteria In Rendered Animal Products, Mary Hayes

All Dissertations

This study tested enumeration techniques for high fat food matrices and determined thermal death times in rendering animal products. Standard Class O phosphate/magnesium chloride dilution buffer series (Dilution Series A) and a modified (pre-warmed to 32oC) lecithin phosphate dilution buffer series (Dilution Series B) were used to enumerate a Salmonella cocktail from both poultry and beef rendering materials. Results of this study indicate use of a modified lecithin buffer did not improve Salmonella enumeration accuracy from rendering materials. Instead, the results suggested use of xylose lysine deoxycholate agar (XLD) with either buffer system accurately enumerated Salmonella from rendering materials. The …

The Performance Of Bacterial Phytosensing Transgenic Tobacco Under Field Conditions, Michael Harrison Fethe

Masters Theses

Currently the platforms for wide-area detection of environmental contamination are limited. Therefore, there is interest in developing new platforms, especially for use in crop plants to detect and report the presence of biotic and abiotic stress agents. A biosensor uses a biological organism or substrate to detect the presence of an elicitor (i.e., heavy metal, TNT, or bacteria). The foundational groundwork to create biosensors in transgenic plants exists. The creation of bacterial phytosensing transgenic tobacco containing an orange fluorescent protein (OFP) reporter driven by synthetic pathogen-inducible promoters provides a fluorescent signal when infected with phytopathogens for earlier detection in the …

A Synthetic Biology Approach To Engineering New Anticancer Agents, Shane Robert Wesener

Theses and Dissertations

Histone deacetylase (HDAC) inhibitors are becoming increasingly valuable therapeutic agents in treatment of several types of malignancies. FK228 is a depsipeptde anticancer compound produced by Chromobacterium violaceum no. 968 through a nonribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) hybrid assembly line. In the present study, reconstitution of the biosynthetic pathway responsible for the production of FK228 revealed cross-talk between modular PKS and fatty acid synthase. This pathway contains two PKS modules on the DepBC enzymes that lack a functional acyltransferase (AT) domain, and no apparent AT-encoding gene exists within the gene cluster or its vicinity. We reported through heterologous expression of …

Bacterially-Mediated Formation Of Rock Coatings In Kärkevagge, Swedish Lapland: A Mineralogical And Micro-Environmental Analog For Mars, Cassandra L. Marnocha

Graduate Theses and Dissertations

The search for past or present life on Mars is, for now, limited to surface environments. An often neglected surface environment that could have served as an abode for life and could presently preserve evidence of that life is that of rock coatings. Rock coatings are mineral accretions on rock surfaces. On Earth, they are widespread and occur with considerable chemical diversity. There is growing evidence for a biotic role in their formation on Earth, particularly with respect to rock varnish. As a result, rock varnish has become a target of astrobiological interest on Mars, where varnish-like coatings have been …

Proximity-Labeling Of Near Neighbors Of Lamin A And Lamin A-Δ50 (Progerin)., Mohammad Sabri

Undergraduate Honors Theses

In an attempt to isolate and identify proteins that differentially interact with or locate near lamin A and progerin, we used a previously described method named BioID (proximity-dependent biotin identification). This method is based on fusion of a promiscuous E. coli biotin-protein ligase (BL) to a targeting protein (in this study, lamin A-GFP and progerin-GFP). The biotin ligase biotinylates amino residues in proteins that are near-neighbors of the fusion protein. To create the fusion proteins, BL was sub-cloned from a pcDNA3.1 MCS-BirA(R118G)-HA plasmid donated by Kyle Roux from University of South Dakota. The BL fragment was ligated into a pNEBR-X1-lamin …

The Influence Of Hydrogeomorphology, Soil Redox Conditions, And Salinity On The Spatial Zoning Of Saltgrass, Salt Rush, And Cattails In Scotts Creek Marsh, Swanton Pacific Ranch, Ca, Mark D. Gormley

Master's Theses

Scotts Creek Marsh (SCM) is a small coastal wetland ecosystem in Davenport, CA. The vegetation of SCM is dominated by three halophytic zones comprised of saltgrass, salt rush, cattails. The objectives of the study were (i) to investigate the variables that influence the zoning of the three dominant halophyte communities in SCM and (ii) to the test the effectiveness of Indicator of Reduction in Soil (IRIS) tubes to indicate the reduction of S. The study examined the following parameters from April 6 to July 21, 2013: (i) the HGM of Scotts Creek Marsh, (ii) soil oxidation and reduction (redox) conditions, …

Environmental Constraints On Cyanomyophage Abundance In The Subtropical Pacific Ocean, Tiana Maria Pimentel

Masters Theses

Viruses are abundant in the world’s oceans and are thought to be important participants in marine biogeochemical cycling. Of these viruses, cyanophages are considered especially important because they infect and lyse cyanobacteria, which are some of the main primary producers in marine environments. Cyanophages are thought to influence the abundance and diversity of cyanobacterial populations and impart significant mortality, thereby affecting primary productivity and microbial community structure. Despite their ecological relevance, little is known about how environmental factors shape cyanophage abundance and diversity over large temporal and spatial scales. To address this gap in knowledge, seawater samples were collected during …

Studies Of Molecular Mechanisms Of Cranberry Mediated Healthspan Promotion In Caenorhabditis Elegans, Sujay Guha

All Dissertations

Extensive studies have demonstrated the potent ability of many nutraceuticals to alleviate the symptoms of aging and stress. We found that cranberry extract (CBE) supplementation at an optimum concentration could prolong Caenorhabditis elegans (C. elegans) lifespan in a manner of daf-16 and osr-1 dependence. Considering that aging is a progressive degeneration of physiological functions, it is intriguing to know whether CBE consumption may delay the age-related degenerative changes in animals. Thus, we examined the effect of CBE consumption on healthspan in C. elegans populations with different ages and age-related disorders. Our results suggest that long-term CBE supplementation leads to a …

Role Of The Cipa Scaffoldin Protein In Cellulose Solubilization, As Determined By Targeted Gene Deletion And Complementation In Clostridium Thermocellum, Daniel G. Olson, Richard J. Giannone, Robert L. Hettich, Lee R. Lynd

Dartmouth Scholarship

The CipA scaffoldin protein plays a key role in the Clostridium thermocellum cellulosome. Previous studies have revealed that mutants deficient in binding or solubilizing cellulose also exhibit reduced expression of CipA. To confirm that CipA is, in fact, necessary for rapid solubilization of crystalline cellulose, the gene was deleted from the chromosome using targeted gene deletion technologies. The CipA deletion mutant exhibited a 100-fold reduction in cellulose solubilization rate, although it was eventually able to solubilize 80% of the 5 g/liter cellulose initially present. The deletion mutant was complemented by a copy of cipA expressed from a replicating plasmid. In …

Tracking The Cellulolytic Activity Of Clostridium Thermocellum Biofilms, Alexandru Dumitrache, Gideon M. Wolfaardt, David Allen, Steven N. Liss, Lee R. Lynd

Dartmouth Scholarship

Microbial cellulose conversion by Clostridium thermocellum 27405 occurs predominantly through the activity of substrate-adherent bacteria organized in thin, primarily single cell-layered biofilms. The importance of cellulosic surface exposure to microbial hydrolysis has received little attention despite its implied impact on conversion kinetics.

Iron-Regulated Cyanobacterial Predominance And Siderophore Production In Oligotrophic Freshwater Lakes, Ryan J. Sorichetti

Electronic Thesis and Dissertation Repository

The frequency and intensity of cyanobacterial blooms (cyanoblooms) is increasing globally. Contrary to existing phosphorus (P) and nitrogen (N) paradigms describing cyanobloom proliferation in eutrophic (nutrient-rich) freshwater lakes, many of the recent cyanobloom reports pertain to oligotrophic (nutrient-poor) freshwater lakes with no prior history of cyanobloom occurrence. There exists a critical research need to re-visit existing conceptual models, identify regulating factors currently unaccounted for and improve our ability to effectively detect and measure cyanobacterial toxins (cyanotoxins) in lakes. Iron (Fe) is required in nearly all pathways of cyanobacterial macronutrient use, though its direct role in regulating cyanobacterial biomass is not …