Molecular Biology Commons^™

Finding Rna-Dna Hybrid Viruses, Jeremy Filip, Geoffery S. Diemer, Kenneth M. Stedman

Student Research Symposium

Until extremely recently it was thought that recombination between DNA and RNA viruses was practically nonexistent. The discovery of the "RNA-DNA Hybrid Virus" (RDHV) genome in a metavirome from a hightemperature acidic lake changed this view (Diemer and Stedman, 2012). We, and others, have discovered multiple examples of this recombination "hiding in plain sight" in multiple both published and unpublished metagenomes from many different environments and recent publications (Rosario et al., 2012 a Tae Woong Whon et al, 2012, Mitsuhiro Yoshida et al., 2013, and several others through personal communication). Comparing the proteins within these hybrid viruses against each other …

Section Abstracts: Biology With Microbiology And Molecular Biology

Virginia Journal of Science

Abstracts of the Biology with Microbiology and Molecular Biology Section for the 91st Annual Virginia Journal of Science Meeting, May 2013

Analysis Of The Chondroitinase Operon Of Flavobacterium Columnare, Erin L. Sorlien

Senior Honors Projects

Analysis of the chondroitinase operon of Flavobacterium columnare

Erin Sorlien

Major

Cell and Molecular Biology, Chemistry

Advisor

Dr. David R. Nelson

Date

May 2, 2013

Keywords

Flavobacterium columnare, columnaris disease, chondroitin AC lyase, complementation, csl operon

Abstract
Flavobacterium columnare, an opportunistic bacterial pathogen of fish, is the causative agent of columnaris disease (CD). The bacterium is a Gram-negative rod that exhibits gliding motility and avidly forms biofilms. CD affects both wild and cultured freshwater fish, and continues to cause large economic losses to the fish farming industry. According to an investigation conducted by the National Animal Health Monitoring System, CD …

Manipulating Aktivated Metabolism Via Mtorc1, Ivan Von Hack Prestinary

HIM 1990-2015

Although poorly understood, normal cells and cancerous cells of the same type exhibit different patterns of nutrient consumption, processing and utility of metabolic substrates. Differences in substrate uptake, preference, and alternately emphasized metabolic pathways offer opportunities for selective targeting of cancer versus stroma. This may be accomplished by using a sequential approach of nutrient deprivation and pharmaceutical perturbation of metabolic pathways to inhibit cellular proliferation. The purpose of this study was to investigate the effects of restricting glucose and glutamine concentrations, in vitro, to levels that resemble a potential human fasting state. The mammalian target of rapamycin (mTOR), a mediator …

Mechanisms Underlying The Heterogeneous Sensitivities Of Cancer Cells To Proteasome Inhibitors, Matthew C. White

Dissertations and Theses (Open Access)

The mechanisms underlying cellular response to proteasome inhibitors have not been clearly elucidated in solid tumor models. Evidence suggests that the ability of a cell to manage the amount of proteotoxic stress following proteasome inhibition dictates survival. In this study using the FDA-approved proteasome inhibitor bortezomib (Velcade®) in solid tumor cells, we demonstrated that perhaps the most critical response to proteasome inhibition is repression of global protein synthesis by phosphorylation of the eukaryotic initiation factor 2-α subunit (eIF2α). In a panel of 10 distinct human pancreatic cancer cells, we showed marked heterogeneity in the ability of cancer cells to induce …

Molecular Diagnosis Of Metabolic Fast Growth Related Diseases In Broiler, Adnan Ali Khalaf Al-Rubaye

Graduate Theses and Dissertations

Pulmonary Hypertension Syndrome (PHS) and lameness are important metabolic diseases that affect rapidly growing broilers. The research reported in the first section of this dissertation focused on developing qPCR assays to identify differences in the expression levels of four candidate genes possibly associated with PHS: angiotensin II type 1 receptor (AGTR1): urotensin receptor 2D (UTS2D); serotonin receptor/transporter type 2Bn (HTR2B); and angiotensinogen cleaving enzyme (ACE). Expression levels of these candidate genes were examined in four different tissues. We established ribosomal protein S14 (RPS14) and RNA polymerase subunit 2B (RP2B) as suitable reference genes because they showed the most consistent deltaCt …

Dynamics And Model Of The Pore-Forming Protein Lysenin, Eric Krueger

Graduate Theses and Dissertations

Membrane transporters are a class of membrane proteins that function to provide a pathway across a cell membrane for the movement of ions and biomolecules. Investigations into the regulatory mechanism of these systems are hindered by their extensive preparation requirements compounded by their fragility and instability. However, lysenin, a pore-forming protein extracted from the earthworm Eisenia foetida, provided a unique opportunity to study a protein which is stable in both a soluble and membrane phase. Lysenin channels possess several important properties characteristic of ion channels without the inherent difficulties that plague investigations with biologically vital membrane transporters like voltage-gated ion …

Characterizing The Role Of Cortactin In Actin Pedestal Assembly By Enterohemorrhagic Escherichia Coli (Ehec), Sarah E. Grout

Honors Scholar Theses

Enterohemorrhagic Escherichia coli (EHEC) is a major foodborne cause of bloody diarrhea and renal failure. During colonization of the intestine, EHEC injects the transmembrane receptor protein Tir and the cytoplasmic effector protein EspFU into host cells to reorganize the actin cytoskeleton into adhesion “pedestals.” EspFU has been shown to bind and activate the actin nucleation factor N-WASP to drive actin polymerization into pedestals. However, EspFU can still assemble pedestals in cells lacking N-WASP, suggesting that this effector protein is able to also trigger N-WASP-independent pathways of actin polymerization during infection. Cortactin is an atypical nucleation factor that localizes to pedestals, …

The Role Of Oswrky71 And Its Interacting Proteins In Seed Germination And Early Growth Of Cereal Grains, Margaret Ja Shin

UNLV Theses, Dissertations, Professional Papers, and Capstones

During seed germination and early seedling growth, complex molecular and physiological events occur in rice (Oryza sativa) and other cereal grains. As the seed transitions to vegetative tissue, it responds to both favorable and unfavorable environmental conditions and is vulnerable to attack by predation and disease. Although seeds are relatively small and tender in size, extensive and sophisticated molecular networks enables the immobile seed to grow, survive and adapt in its environment. One of the networks I am interested in is in the crosstalk between the gibberellin (GA) and abscisic acid (ABA) signaling pathways. These pathways are interesting because they …

Genome-Wide Profiling Unveils Criticial Functions Of P53 In Human Embryonic Stem Cells, Kadir C. Akdemir

Dissertations and Theses (Open Access)

Embryonic stem cells (ESCs) possess two unique characteristics: infinite self-renewal and the potential to differentiate into almost every cell type (pluripotency). Recently, global expression analyses of metastatic breast and lung cancers revealed an ESC-like expression program or signature, specifically for cancers that are mutant for p53 function. Surprisingly, although p53 is widely recognized as the guardian of the genome, due to its roles in cell cycle checkpoints, programmed cell death or senescence, relatively little is known about p53 functions in normal cells, especially in ESCs. My hypothesis is that p53 has specific transcription regulatory functions in human ESCs (hESCs) that …

Interaction Between Brk And Her2 In Breast Cancer, Midan Ai

Dissertations and Theses (Open Access)

INTERACTION BETWEEN BRK AND HER2 IN BREAST CANCER

Midan Ai, Ph.D.

Supervisory Professor: Zhen Fan, M.D.

Breast tumor kinase (Brk) is a nonreceptor protein-tyrosine kinase that is highly expressed in approximately two thirds of breast cancers but is not detectable or is expressed at very low levels in normal mammary epithelium. Brk plays important roles in promoting proliferation, survival, invasion, and metastasis of breast cancer cells, but the mechanism(s) of which remain largely unknown. Recent studies showed that Brk is frequently co-overexpressed with human epidermal growth factor receptor-2 (HER2) and is physically associated with HER2 in breast cancer. The mechanism …

Structure-Function Analysis Of Human Integrator Subunit-4, Anupama Sataluri

Dissertations and Theses (Open Access)

Structure-function analysis of human Integrator subunit 4

Anupama Sataluri

Advisor: Eric. J. Wagner, Ph.D.

Uridine-rich small nuclear RNAs (U snRNA) are RNA Polymerase-II (RNAPII) transcripts that are ubiquitously expressed and are known to be essential for gene expression. snRNAs play a key role in mRNA splicing and in histone mRNA expression. Inaccurate snRNA biosynthesis can lead to diseases related to defective splicing and histone mRNA expression. Although the 3′ end formation mechanism and processing machinery of other RNAPII transcripts such as mRNA has been well studied, the mechanism of snRNA 3′ end processing has remained a mystery until the recent …

Bio-Separation Process Improvement Via Genomic Manipulation: Development Of Novel Strains For Use In Immobilized Metal Affinity Chromatography (Imac), Ryan Curtis Haley

Graduate Theses and Dissertations

The dissertation is comprised of three parts. Part I describes proteomic analysis of native bacterial proteins from Escherichia coli (E.coli) that bind during Immobilized Metal Affinity Chromatography (IMAC). Part II describes the value in exploiting proteome based data as a tool toward the design an E. coli expression strain that is particularly useful when Immobilized Metal Affinity Chromatography is employed as the initial capture step of a homologous protein purification process. Part III describes a methodology of chromosomal mapping of all contaminant gene products.

The objective of Part I was to identify all E. coli proteins that bind to Co(II), …

Using Rnai In C. Elegans To Demonstrate Gene Knockdown Phenotypes In The Undergraduate Biology Lab Setting, Nicole M. Roy

Biology Faculty Publications

RNA interference (RNAi) is a powerful technology used to knock down genes in basic research and medicine. In 2006 RNAi technology using Caenorhabditis elegans (C. elegans) was awarded the Nobel Prize in medicine and thus students graduating in the biological sciences should have experience with this technology. However, students struggle conceptually with the molecular biology behind the RNAi technology and find the technology difficult to grasp. To this end, we have provided a simple, streamlined and inexpensive RNAi procedure using C. elegans that can be adopted in upper level biology classes. By using an unknown RNAi-producing bacteria, students perform novel …

Evaluation Of The Tgf-Ss Inhibitor Repsox On The Expression Of Pluripotency Pathways In Murine And Bovine Cells, Davin M. Larsen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Embryonic stem cells are cells which are isolated from early stage embryos and have the theoretical ability to become any adult cell type in the body. In the past few years much research has focused on the use of embryonic stem cells for clinical applications in the treatment of degenerative diseases. Consequently they are a promising tool in the treatment of diseases such as Diabetes and Parkinson’s disease, and could potentially be used in the repair of permanently damaged tissue. However, since these cells are isolated from early stage embryos their successful isolation often results in the destruction of the …

Characterization And Potential Utility Of Porcine Trophoblast-Derived Stem-Like Cells, Edison A. Suasnavas

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In mammalian pregnancy, the placenta is a very important organ which helps to establish a healthy pregnancy. Its functions could be described in four points: 1) It allows the fetus to receive gases and nutrients from the mother in a safe way; 2) it lets the fetus get rid of waste through the mother's kidneys; 3) it releases essential pregnancy-related hormones and growth factors that let the uterus hold the fetus; 4) it secretes immune response regulators to give the fetus immune protection against the mother. Abnormalities in the placenta can be the cause of death to the fetus. Mammalian …

Divergent Protein Motifs Direct Ef-P Mediated Translational Regulation In Salmonella And Escherichia Coli, Steven J. Hersch, Mengchi Wang, S. Betty Zou, Kyung-Mee Moon, Leonard J. Foster, Michael Ibba, William Wiley Navarre

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Elongation factor P (EF-P) is a universally conserved bacterial translation factor homologous to eukaryotic/archaeal initiation factor 5A. In Salmonella, deletion of the efp gene results in pleiotropic phenotypes, including increased susceptibility to numerous cellular stressors. Only a limited number of proteins are affected by the loss of EF-P, and it has recently been determined that EF-P plays a critical role in rescuing ribosomes stalled at PPP and PPG peptide sequences. Here we present an unbiased in vivo investigation of the specific targets of EF-P by employing stable isotope labeling of amino acids in cell culture (SILAC) to compare the …

Effects Of Beta Amyloid On The Dna Methylation Status Of An In Vitro Model Of Alzheimer’S Disease, Noor Taher

Senior Honors Theses

Available evidence points toward an epigenetic process in Alzheimer’s disease. This thesis describes the research that was done to investigate changes in DNA methylation using an in vitro model of the disease. Although the results indicated no global changes in methylation levels after treating differentiated IMR-32 cells with beta amyloid, there were several regions of the genome that changed their methylation status. Gene ontology studies revealed that these regions are associated with neuronal differentiation and cell fate genes, thus providing a possible model for the contribution of beta amyloid to the development of Alzheimer’s disease. This study provides incentive to …

Investigations Of Substrate Channeling In The Proline Oxidative Pathway, Nikhilesh Sanyal

Department of Biochemistry: Dissertations, Theses, and Student Research

In cell metabolism, substrate channeling is a phenomenon where the product of one reaction is transported to a second enzyme active site without equilibrating into bulk solvent. Chapter 1 reviews the rationale and evidence for substrate channeling with the specific example of proline metabolism. Oxidation of proline to glutamate is catalyzed in consecutive reactions by proline dehydrogenase (PRODH) and pyrroline-5-carboxylate dehydrogenase (P5CDH). The intermediate Δ¹-pyrroline-5-carboxylate reportedly tends to be labile and inhibitory towards several metabolic pathways.

One of the main objectives of this dissertation was to investigate substrate channeling between independent proline oxidative enzymes from Thermus thermophilus- …

Adenovirus Type 5 Virions Asymmetrically Lose Icosahedral Structure At Low Phs Of Endosomes, Jennifer Marie Jarboe

Honors Theses

After receptor mediated endocytosis into an endosome, human Adenovirus Type 5 (Ad5) undergoes structural changes that allow the virus to release a viral protein, pVI, that lyses the endosome and releases the virus core into the cytosol, where it travels to the nucleus to insert its genome. Structural studies of Ad5 at a range of pHs typical of endosomes (7.5-4.5) using a transmission electron microscope show that Ad5 undergoes asymmetrical loss of proteins from vertex regions at the pH of the late endosome (pH5.15). Following further acidification, Ad5 ejects core material preferentially through one vertex—indicating an asymmetry at one vertex …

The Inner Workings Of The Dna Copying Nanomachine : Kinetic Studies Of Dna Polymerase I From The Thermophilic Bacterium Rhodothermus Marinus, Emily P. Kornberg

Honors Theses

DNA polymerase I from Rhodothermus marinus is a high-fidelity DNA polymerase capable of operating at high temperatures and incorporating 2´,3´-dideoxynucleotides. The R. marinus DNA Polymerase I active site contains an unusual proline in the middle of a mobile “O helix.” This proline residue is hypothesized to decrease the relative free energy of a kinetic checkpoint termed the ajar conformation, and thereby slow the incorporation of incorrect nucleotides. We aim to test the accuracy of a newly developed nucleotide incorporation model, in which the enzyme allows the template to interact with the bound dNTP in the ajar conformation, whether correct or …

Trimethylsilyl Trifluoromethanesulfonate-Mediated Additions To Acetals, Nitrones, And Aminals, Chelsea Safran

Honors Theses

One-pot reactions were studied in order to develop procedures for the formation of important carbon-carbon and carbon-nitrogen bonds that are easily reproducible. In the presence of trimethylsilyl triflouromethanesulfonate (TMSOTf), Mukaiyama-aldol and aldol-like reactions occur in one-pot due to TMSOTf acting as a Lewis acid and silylating agent. A variety of reactions, including methoxyalkylation, were performed to form carbon-nitrogen bonds. Here, research involving TMSOTf-mediated additions to acetals, nitrones, and aminals will be discussed.

Bayesian Reconstruction Of P(R) Directly From Two-Dimensional Detector Images Via A Markov Chain Monte Carlo Method, Sudeshna Paul, Alan M. Friedman, Chris Bailey-Kellogg, Bruce Craig

Dartmouth Scholarship

The interatomic distance distribution, P(r), is a valuable tool for evaluating the structure of a molecule in solution and represents the maximum structural information that can be derived from solution scattering data without further assumptions. Most current instrumentation for scattering experiments (typically CCD detectors) generates a finely pixelated two-dimensional image. In contin­uation of the standard practice with earlier one-dimensional detectors, these images are typically reduced to a one-dimensional profile of scattering inten­sities, I(q), by circular averaging of the two-dimensional image. Indirect Fourier transformation methods are then used to reconstruct P(r) from …

Novel Architecture Of Costal Cartilage And Implications In Chest Wall Deformities, Anthony J. Asmar

Biological Sciences Theses & Dissertations

Costal cartilage is a type of hyaline cartilage that forms rod-like structures that connect the ribs to the sternum. Deformation of costal cartilage is observed in the chest wall deformities, pectus excavatum and pectus carinatum. Pectus excavatum involves a sternal displacement causing a depression of the chest while pectus carinatum causes a protrusion of the chest. As costal cartilage is not a widely studied tissue, this leaves little knowledge into possible factors involved in the pathogenesis of pectus deformities. Costal cartilage in these deformities has been described as being weakened and may implicate proteoglycans which play an important role in …

Expansion Of Breast Cancer Stem Cells With Fibrous Scaffolds, Sheng Feng, Pang-Kuo Lo, Shou Liu, Xinfeng Liu, Hexin Chen, Qian Wang

Faculty Publications

Cancer stem cells (CSCs) are hypothesized as tumor-initiating cells within tumors and main contributors of tumor growth, metastasis and recurrence. Mammary cancer cells, MCF-7 cells, were cultured on 3D polycaprolactone (PCL) fibrous scaffolds, showing an increased proportion of CSCs. The expression of stem cell markers, including OCT3/4 and SOX2, and breast CSC-specific markers, SOX4 and CD49f, was significantly upregulated, and the mammosphere-forming capability in cells cultured on PCL fibrous scaffolds increased. The fibrous scaffolds also induced the elongation of MCF-7 cells and extended cell proliferation. The increase of CSC properties after being cultured on fibrous scaffolds was further confirmed with …

Bed Bugs Evolved Unique Adaptive Strategy To Resist Pyrethroid Insecticides, Fang Zhu, Hemant Gujar, Jennifer R. Gordon, Kenneth F. Haynes, Michael F. Potter, Subba R. Palli

Entomology Faculty Publications

Recent advances in genomic and post-genomic technologies have facilitated a genome-wide analysis of the insecticide resistance-associated genes in insects. Through bed bug, Cimex lectularius transcriptome analysis, we identified 14 molecular markers associated with pyrethroid resistance. Our studies revealed that most of the resistance-associated genes functioning in diverse mechanisms are expressed in the epidermal layer of the integument, which could prevent or slow down the toxin from reaching the target sites on nerve cells, where an additional layer of resistance (kdr) is possible. This strategy evolved in bed bugs is based on their unique morphological, physiological and behavioral characteristics …

Broad Vision: The Art & Science Of Looking, Heather Barnett, John R. A. Smith

The Transdisciplinary STEAM+ Journal

Undergraduate students and academic staff from diverse disciplines in the arts and sciences investigated questions of mediated vision through a year-long interdisciplinary research project at the University of Westminster, London, United Kingdom. The Broad Vision project explored the perception and interpretation of microscopic worlds, and investigated the benefits and challenges of working across disciplinary divides in a university setting. This article describes the three-phase model for interdisciplinary learning and research developed through the project, providing a valuable case study for inquiry based art/science education.

Identification Of The Interaction Between Rack1-Pcbp1 And Characterization Of The Novel Functional Effect Of The Interaction, Pranjal Nahar-Gohad

Seton Hall University Dissertations and Theses (ETDs)

No abstract provided.

Characterization Of Myxococcus Xanthus Mazf And Implications For A New Point Of Regulation, Tye O. Boynton, Jonathan L. Mcmurry, Lawrence J. Shimkets

Faculty Articles

During development, Myxococcus xanthus cells undergo programmed cell death (PCD) whereby 80% of vegetative cells die. Previously, the MazF RNA interferase has been implicated in this role. Recently, it was shown that deletion of the mazF gene does not eliminate PCD in wild-type strain DK1622 as originally seen in DZF1. To clarify the role of MazF, recombinant enzyme was characterized using a highly sensitive assay in the presence and absence of the proposed antitoxin MrpC. In contrast to previous reports that MrpC inhibits MazF activity, the hydrolysis rate was enhanced in a concentration-dependent manner with MrpC or MrpC2, an N-terminally …

Dna Damage Repair Genes Controlling Human Papillomavirus (Hpv) Episome Levels Under Conditions Of Stability And Extreme Instability, Terri Edwards, Thomas Vidmar, Kevin Koeller, James Bashkin, Chris Fisher

Chemistry & Biochemistry Faculty Works

DNA damage response (DDR) genes and pathways controlling the stability of HPV episomal DNA are reported here. We set out to understand the mechanism by which a DNA-binding, N-methylpyrrole-imidazole hairpin polyamide (PA25) acts to cause the dramatic loss of HPV DNA from cells. Southern blots revealed that PA25 alters HPV episomes within 5 hours of treatment. Gene expression arrays identified numerous DDR genes that were specifically altered in HPV16 episome-containing cells (W12E) by PA25, but not in HPV-negative (C33A) cells or in cells with integrated HPV16 (SiHa). A siRNA screen of 240 DDR genes was then conducted to identify enhancers …