Genetics and Genomics Commons^™

Accuracy Of Msi Testing In Predicting Germline Mutations Of Msh2 And Mlh1: A Case Study In Bayesian Meta-Analysis Of Diagnostic Tests Without A Gold Standard, Sining Chen, Patrice Watson, Giovanni Parmigiani

Johns Hopkins University, Dept. of Biostatistics Working Papers

Microsatellite instability (MSI) testing is a common screening procedure used to identify families that may harbor mutations of a mismatch repair gene and therefore may be at high risk for hereditary colorectal cancer. A reliable estimate of sensitivity and specificity of MSI for detecting germline mutations of mismatch repair genes is critical in genetic counseling and colorectal cancer prevention. Several studies published results of both MSI and mutation analysis on the same subjects. In this article we perform a meta-analysis of these studies and obtain estimates that can be directly used in counseling and screening. In particular we estimate the …

The Recombinant Adeno-Associated Virus Vector (Raav2)-Mediated Apolipoprotein B Mrna-Specific Hammerhead Ribozyme: A Self-Complementary Aav2 Vector Improves The Gene Expression, Shumei Zhong, Shihua Sun, Ba-Bie Teng

Faculty, Staff and Student Publications

BACKGROUND: In humans, overproduction of apolipoprotein B (apoB) is positively associated with premature coronary artery diseases. To reduce the levels of apoB mRNA, we have designed an apoB mRNA-specific hammerhead ribozyme targeted at nucleotide sequences GUA6679 (RB15) mediated by adenovirus, which efficiently cleaves and decreases apoB mRNA by 80% in mouse liver and attenuates the hyperlipidemic condition. In the current study, we used an adeno-associated virus vector, serotype 2 (AAV2) and a self-complementary AAV2 vector (scAAV2) to demonstrate the effect of long-term tissue-specific gene expression of RB15 on the regulation apoB mRNA in vivo. METHODS: We constructed a hammerhead ribozyme …

Ionizing Radiation And Endostatin Gene Therapy Against Lung Tumor, Xian Luo

Loma Linda University Electronic Theses, Dissertations & Projects

Although many advances have been made in radiotherapy, tumor radioresistance and normal tissue damage continue to always be important issues for radiation oncologists. Numerous reports have also documented that radiation exposure increases the risk for malignancy and suppresses immune mechanisms. However, increasing evidence has suggested that anti-angiogenic therapy that targets tumor blood supply may alter abnormal tumor vasculature, thus synergizing radiotherapy. The governing hypothesis of the present study was that modification of tumor vasculature by antiangiogenic gene therapy can increase the efficacy of radiotherapy and that radiation can also improve DNA transfection efficiency by increasing expression of the administered gene. …

Conversion Of Myoblasts To Physiologically Active Neuronal Phenotype, Yumi Watanabe, Sei Kameoka, Vidya Gopalakrishnan, Kenneth D Aldape, Zhizhong Z Pan, Frederick F Lang, Sadhan Majumder

Faculty, Staff and Student Publications

Repressor element 1 (RE1)-silencing transcription factor (REST)/neuron-restrictive silencer factor (NRSF) can repress several terminal neuronal differentiation genes by binding to a specific DNA sequence (RE1/neuron-restrictive silencer element [NRSE]) present in their regulatory regions. REST-VP16 binds to the same RE1/NRSE, but activates these REST/NRSF target genes. However, it is unclear whether REST-VP16 expression is sufficient to cause formation of functional neurons either from neural stem cells or from heterologous stem cells. Here we show that the expression of REST-VP16 in myoblasts grown under muscle differentiation conditions blocked entry into the muscle differentiation pathway, countered endogenous REST/NRSF-dependent repression, activated the REST/NRSF target …

Genomically Intact Endogenous Feline Leukemia Viruses Of Recent Origin, Alfred L. Roca, Jill Pecon-Slattery, Stephen J. O'Brien

Biology Faculty Articles

We isolated and sequenced two complete endogenous feline leukemia viruses (enFeLVs), designated enFeLV-AGTT and enFeLV-GGAG. In enFeLV-AGTT, the open reading frames are reminiscent of a functioning FeLV genome, and the 5′ and 3′ long terminal repeat sequences are identical. Neither endogenous provirus is genetically fixed in cats but polymorphic, with 8.9 and 15.2% prevalence for enFeLV-AGTT and enFeLV-GGAG, respectively, among a survey of domestic cats. Neither provirus was found in the genomes of related species of the Felis genus, previously shown to harbor enFeLVs. The absence of mutational divergence, polymorphic incidence in cats, and absence in related species suggest that …

Phylogenetic Analyses Of Texas Isolates Indicate An Evolving Subtype Of The Clade B Feline Immunodeficiency Viruses, Eric A. Weaver, Ellen W. Collisson, Margaret Slater, Guan Zhu

Nebraska Center for Virology: Faculty Publications

Rigorous phylogenetic analyses were used to compare the nucleotide sequences of feline immunodeficiency virus strains isolated from Texas and throughout the world. The envelope V3-V4 sequences and capsid gene of the Texas isolates formed a cluster between subtypes B and E. Statistical comparisons with other published sequences confirmed that the Texas group is a unique cluster, possibly a new subtype, arising from subtype B.

Feline immunodeficiency virus (FIV) was initially isolated in 1987 from a cat in California with severe immunodeficiency and has been recognized as a common worldwide feline pathogen (11, 14, 19, 20, 33). FIV-infected cats exhibit a …

Glycosyltransferases Encoded By Viruses, Nicolas Markine-Goriaynoff, Laurent Gillet, James L. Van Etten, Haralambos Korres, Naresh Verma, Alain Vanderplasschen

James Van Etten Publications

Studies of cellular biology in recent decades have highlighted the crucial roles of glycans in numerous important biological processes, raising the concept of glycomics that is now considered as important as genomics, transcriptomics and proteomics. For millions of years, viruses have been co-evolving with their hosts. Consequently, during this co-evolution process, viruses have acquired mechanisms to mimic, hijack or sabotage host processes that favour their replication, including mechanisms to modify the glycome. The importance of the glycome in the regulation of host–virus interactions has recently led to a new concept called ‘glycovirology’. One fascinating aspect of glycovirology is the study …

Cd46-Mediated Transduction Of A Species D Adenovirus Vaccine Improves Mucosal Vaccine Efficacy, Zenaido T. Camacho, Mallory A. Turner, Michael A. Barry, Eric A. Weaver

Nebraska Center for Virology: Faculty Publications

The high levels of preexisting immunity against Adenovirus type 5 (Ad5) have deemed Ad5 unusable for translation as a human vaccine vector. Low seroprevalent alternative viral vectors may be less impacted by preexisting immunity, but they may also have significantly different phenotypes from that of Ad5. In this study we compare species D Ads (26, 28, and 48) to the species C Ad5. In vitro transduction studies show striking differences between the species C and D viruses. Most notably, Ad26 transduced human dendritic cells much more effectively than Ad5. In vivo imaging studies showed strikingly different transgene expression profiles. The …

Phylogenetic Analyses Of Texas Isolates Indicate An Evolving Subtype Of The Clade B Feline Immunodeficiency Viruses, Eric A. Weaver, Ellen W. Collisson, Margaret Slater, Guan Zhu

Nebraska Center for Virology: Faculty Publications

Rigorous phylogenetic analyses were used to compare the nucleotide sequences of feline immunodeficiency virus strains isolated from Texas and throughout the world. The envelope V3-V4 sequences and capsid gene of the Texas isolates formed a cluster between subtypes B and E. Statistical comparisons with other published sequences confirmed that the Texas group is a unique cluster, possibly a new subtype, arising from subtype B.

Impaired Antigen Receptor Induced Calcium Mobilization In A Phospholipase C-Gamma1 Deficient B Cell Line., Natarajan Muthusamy, Do Joon Park, Hei-Won Rho, Sue Goo Rhee, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

B lymphocytes express phospholipase C-gamma(1) (PLC-gamma(1)) and phospholipase C-gamma(2) (PLC-gamma(2)) isozymes. However, the relative importance of these two isozymes in B cell signaling is not known. We report here the identification and analysis of a B cell line deficient in PLC-gamma(1). Mature splenic B lymphocytes and a panel of cell lines representing pre-B, immature and mature B cell stages expressed phospholipase C-gamma (PLC-gamma), but not the beta or delta isoforms of phospholipase C (PLC). While all the tested B cell lines and primary splenic B cells expressed PLC-gamma(1) and PLC-gamma(2) isozymes, the L1.2 B cell line exclusively expressed PLC-gamma(2), but …

Determination Of The Optimal Form Of A Dna Vaccine To Induce An Effective Immune Response Against A Murine B-Cell Lymphoma, Deepti Aurora

All-Inclusive List of Electronic Theses and Dissertations

Tumor vaccines are a promising alternative to chemotherapy for the treatment of cancer. To be effective and safe, a cancer vaccine should specifically target antigens expressed only on tumor cells. The B-cell tumor-derived Ig receptor may be considered a model tumor antigen for cancer vaccine development. Specifically the immunoglobulin idiotype (ld) encoded by the variable region genes (VH and VL) provides a target antigen. Promising results have been obtained in clinical studies of ld vaccination using ld proteins. However, ld protein is laborious and time-consuming to produce. Gene-based vaccines, on the other hand, are inexpensive and offer ease of manipulation …

Reconstructing The Genomic Architecture Of Mammalian Ancestors Using Multispecies Comparative Maps, William J. Murphy, Guillaume Bourque, Glenn Tesler, Pavel Pevzner, Stephen J. O'Brien

Biology Faculty Articles

Rapidly developing comparative gene maps in selected mammal species are providing an opportunity to reconstruct the genomic architecture of mammalian ancestors and study rearrangements that transformed this ancestral genome into existing mammalian genomes. Here, the recently developed Multiple Genome Rearrangement (MGR) algorithm is applied to human, mouse, cat and cattle comparative maps (with 311-470 shared markers) to impute the ancestral mammalian genome. Reconstructed ancestors consist of 70-100 conserved segments shared across the genomes that have been exchanged by rearrangement events along the ordinal lineages leading to modern species genomes. Genomic distances between species, dominated by inversions (reversals) and translocations, are …

Bioethics: Everything You Wanted To Know About Life Or Death, But Were Afraid To Ask, St Mary's University

President's Peace Commission - Programs

The President’s Peace Commission existed from 1984 to 2013 at St. Mary's University. The Commission fostered an ethical commitment to participate in the establishment of world peace and social justice.

This program is about genetic technologies, ethical issues in human and animal experimentation and physician assisted suicide.

Sheep Updates 2003 - Husbandry, Paul Barrett, Kevin Bell, J Greeff, L. Butler, S. Brown, K. Hart, A. Gray, John Karlsson, Paula Coombe, Ron Mctarrart, David Scobie, Sandy White

Sheep Updates

This session covers seven papers from different authors:1. Setting up a successful, low input feedlot Paul Barrett, ‘Bimberdong’ Jerramungup 2. Effective mineral supplementation of sheep Kevin Bell, Sheep Management and Production Consultants, Kojonup, WA 3. Genetic benchmarking for WA sheep producers J. Greeff, L. Butler, S. Brown, K. Hart and A. Gray Department of Agriculture Western Australia 4. Does selecting sheep for low WEC reduce scouring? John Karlsson, Johan Greeff and Paula Coombe, Department of Agriculture Western Australia 5. Summer quarters for sheep - stubbles Ron McTaggart, Department of Agriculture Western Australia, Albany 6. Thinking about breeding Easy Care Sheep? …

Sheep Updates 2003 - Plenaries, Ashley Mercy, David Scobie, Neil Buchanan, Kevin Bell, John Milton, Graeme Martin, Bob Hall, Maurie Stephen, Rob Woodgate

Sheep Updates

This session covers eight papers from different authors:1. Biosecurity in the sheep industry will improve production and profits Ashley Mercy, Department of Agriculture, Western Australia 2. Easy care sheep David Scobie, AgResearch, PO Box 60 Lincoln, 8152, New Zealand 3. Targeting the market’s requirements - live sheep exports Neil Buchanan, Manager Animal Health Operations, Primary Industries & Resources, South Australia 4. Setting flock breeding objectives Kevin Bell, Sheep Management and Production Consultants, Kojonup WA 5. Future feeding of sheep in Western Australia John Milton and Graeme Martin, The University of Western Australia 6. Recipe for getting back into Sheep Bob …

Potential Mechanisms Explaining The Antitumor Effect Of Total-Body Irradiation, Glen Michael Miller

Loma Linda University Electronic Theses, Dissertations & Projects

While numerous reports have documented that radiation exposure increases the risk for malignancy and suppresses immune mechanisms, increasing evidence has suggested that low-dose total-body irradiation (TBI) may alter leukocyte composition and function leading to heightened immune responsiveness and long-term remission of certain cancers. Having observed that moderate-dose TBI produces an antitumor effect in the Lewis lung carcinoma (EEC) model, the major goal of this study was to determine whether changes in tumor growth could be correlated with radiation-induced alterations of immune system parameters. The governing hypothesis was that selective immune augmentation, i.e. upregulation of specific leukocyte subsets, is primarily responsible …

Expression Of Glutathione-S-Transferase Mu 1 (Gstm1) And Glutathione-S-Transferase Theta 1 (Gstt1) In Patients With Aplastic Anemia And Myelodysplastic Syndromes, Aaron Conrad Spivey

Theses and Dissertations in Biomedical Sciences

Aplastic Anemia is a disorder of the hematopoietic bone marrow stem cells that is frequently associated with drug or chemical exposures. Reduced ability to detoxify drugs or chemicals may result in an increased risk of disease. Glutathione S-transferases are Phase II enzymes, which help detoxify xenobiotics. Many patients who have developed aplastic anemia and myelodysplastic syndrome have the null genotype for GSTMI and/or GSTTI. For patients with GSTMI and GSTTI positive genotypes, non-expression of these enzymes may cause an increased risk in developing aplastic anemia or myelodysplastic syndrome. To test whether genotype positive patients have GSTMI or GSTTI null …

Comparison Of Methods For Dna Isolation From Food Samples For Detection Of Shiga Toxin-Producing Escherichia Coli By Real-Time Pcr, Loree C. Heller, Carisa R. Davis, K. Kealy Peak, David Wingfield, Andrew C. Cannons, Philip T. Amuso, Jacqueline Cattani

Bioelectrics Publications

In this study, food samples were intentionally contaminated with Escherichia coli O157:H7, and then DNA was isolated by using four commercial kits. The isolated DNA samples were compared by using real-time PCR detection of the Shiga toxin genes. The four kits tested worked similarly.

Selecting Differentially Expressed Genes From Microarray Experiments, Margaret S. Pepe, Gary M. Longton, Garnet L. Anderson, Michel Schummer

UW Biostatistics Working Paper Series

High throughput technologies, such as gene expression arrays and protein mass spectrometry, allow one to simultaneously evaluate thousands of potential biomarkers that distinguish different tissue types. Of particular interest here is cancer versus normal organ tissues. We consider statistical methods to rank genes (or proteins) in regards to differential expression between tissues. Various statistical measures are considered and we argue that two measures related to the Receiver Operating Characteristic Curve are particularly suitable for this purpose. We also propose that sampling variability in the gene rankings be quantified and suggest using the “selection probability function”, the probability distribution of rankings …

Structural Analyses Of Phycodnaviridae And Iridoviridae, Alan A. Simpson, Narayanasamy Nandhagopal, James L. Van Etten, Michael G. Rossmann

Nebraska Center for Virology: Faculty Publications

The Phycodnaviridae, Iridoviridae and related viruses, with diameters of 1500±2000 A Ê , are formed from large trigonal arrays of hexagonally close-packed capsomers forming the faces of icosahedra [Yan et al. (2000), Nature Struct. Biol. 7, 101-103; Nandhagopal et al. (2002), Proc. Natl Acad. Sci. USA, 99, 14758-14763]. Caspar and Klug predicted that such structures could be assembled from hexameric capsomers [Caspar & Klug (1962), Cold Spring Harbor. Symp. Quant. Biol. 27, 1-24], as was subsequently found in numerous icosahedral viruses. During the course of evolution, some viruses, including the virus families …

Development Of An Automated Thiopurine Methyltransferase (Tpmt) Genotyping Assay, Mary Corcoran

Theses

Thiopurine methyltransferase (TPMT) is a cytosolic enzyme that catalyses the S- methylation of aromatic and sulphydryl compounds known as the thiopurines. These therapeutic agents are used in the treatment of acute lymphoblastic leukemia, autoimmune disorders, inflammatory bowel disease and organ transplant recipients.

Erythrocyte TPMT activity is polymorphic and patients with intermediate or deficient TPMT are at significant risk for excessive toxicity after receiving ‘standard’ doses of thiopurine medications. The activity of TPMT is inherited as an autosomal co-dominant trait. Several mutations in the TPMT gene have been described that correlate with a low activity phenotype. Three mutations G238C, G460A and …

Functional Implications In Apoptosis By Interferon Inducible Gene Product 1-8d, The Binding Protein To Adenovirus Preterminal Protein, Insil Joung, Peter C. Angeletti, Jeffrey A. Engler

Nebraska Center for Virology: Faculty Publications

Adenovirus (Ad) precursor to the terminal protein (pTP) plays an essential roles in the viral DNA

replication. Ad pTP serves as a primer for the synthesis of a new DNA strand during the initiation

step of replication. In addition, Ad pTP forms organized spherical replication foci on the nuclear

matrix (NM) and anchors the viral genome to the NM. Here we identified the interferon inducible

gene product 1-8D (Inid) as a pTP binding protein by using a two-hybrid screen of a HeLa cDNA

library. Of the clones obtained in this assay, nine were identical to the Inid, a 13-kDa polypeptide …

Animal Anti-Apoptotic Genes Ameliorate The Loss Of Turgor In Water-Stressed Transgenic Tobacco, Tala Awada, D. D. Dunigan, M. B. Dickman

Nebraska Center for Virology: Faculty Publications

Nicotiana tabacum L. ‘Glurk’ plants were transformed with antiapoptotic animal genes [chicken Bcl-xl; nematode CED-9; chicken Bcl-xl(GA) a mutant of Bcl-xl; and a 3’ non-coding region of human Bcl-2, referred to as 161-1]. Our objectives were to determine whether plant transformation with anti-apoptotic genes ameliorates drought tolerance in tobacco plants by subjecting the plants to a dry-down period. The non-transformed Glurk and the transgenic Glurk harboring G115, which expresses β-glucuronidase, served as controls. Transformation of tobacco plants with animal anti-apoptotic genes significantly impacted the rates of photosynthesis (A) and stomatal conductance (g_s), but not to the same extent …

Identification Of Novel Domains Within Sox-2 And Sox-11 Involved In Autoinhibition Of Dna Binding And Partnership Specificity, Matthew S. Wiebe, Tamara K. Nowling, Angie Rizzino

Nebraska Center for Virology: Faculty Publications

Sox transcription factors play key regulatory roles throughout development, binding DNA through a consensus (A/T)(A/T)CAA(A/T)G sequence. Although many different Sox proteins bind to this se-quence, it has been observed that gene regulatory elements are commonly responsive to only a small subset of the entire family, implying that regulatory mechanisms exist to permit selective DNA bind-ing and/or transactivation by Sox family members. To identify and explore the mechanisms modu-lating gene activation by Sox proteins further, we compared the function of Sox-2 and Sox-11. This led to the discovery that Sox proteins are regulated differentially at multiple levels, including trans-activation, protein partnerships …

Feline Immunodeficiency Virus Integration In B-Cell Lymphoma Identifies A Candidate Tumor Suppressor Gene On Human Chromosome 15q151, Julia Beatty, Anne Terry, Julie Macdonald, Elizabeth Gault, Stanley Cevario, Stephen J. O'Brien, Ewan Cameron, James C. Neil

Biology Faculty Articles

Infection with immunosuppressive lentiviruses is associated with increased cancer risk,but most studies have implicated indirect mechanisms as the tumor cells generally lack integrated viral sequences.An exception wasfound in a B-cell lymphoma (Q254) where the tumor cells contained a single integrated feline immunodeficiency virus genome. Additional analysis now indicates that feline immunodeficiency virus integration in lymphoma Q254 resulted in promoter insertion and truncation of a conserved gene on feline chromosome B3, whereas the unaffected allele of the gene appeared to be transcriptionally down-regulated. The orthologous human gene (FLJ12973), is expressed ubiquitously and encodes a WD-repeat protein with structural similarity …

Mining Of Correlated Rules In Genome Sequences, L. Lin, L. Wong, Tze-Yun Leong, P. S. Lai

Research Collection School Of Computing and Information Systems

With the huge amount of data collected by scientists in the molecular genetics community in recent years, there exists a need to develop some novel algorithms based on existing data mining techniques to discover useful information from genome databases. We propose an algorithm that integrates the statistical method, association rule mining, and classification rule mining in the discovery of allelic combinations of genes that are peculiar to certain phenotypes of diseased patients.

Electrically Mediated Delivery Of Vector Plasmid Dna Elicits An Antitumor Effect, L. Heller, D. Coppola

Bioelectrics Publications

In vivo electroporation is an efficient means of increasing plasmid DNA delivery to normal tissues, such as skin and muscle, as well as directly to tumors. In the experiments described here, plasmid DNA was delivered by in vivo electroporation to B16 mouse melanomas using two very different pulsing protocols. Reporter expression increased 21- or 42-fold, respectively with electroporation over injection alone. The growth of experimental melanomas with an approximate diameter of 4 mm on the day of treatment was monitored after electroporation delivery of reporter plasmid DNA. Remarkably, short-term complete regressions using one of these pulsing protocols occurred in up …

Defective Cd19-Dependent Signaling In B-1a And B-1b B Lymphocyte Subpopulations., Goutam Sen, Hsin-Jung Wu, Gabriel Bikah, Chandrasekar Venkataraman, Darrell A Robertson, E Charles Snow, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Peritoneal and pleural cavities in mice and humans contain a unique population of B-lymphocytes called B-1 cells that are defective in B cell antigen receptor (BCR) signaling but have an increased propensity to produce autoantibodies. Several molecules such as Btk, Vav, and CD19 known to be important for BCR signaling have been shown to be critical for the development of B-1 cells from undefined precursors. Here we demonstrate that B-1 cell unresponsiveness to BCR cross-linking is in part due to defective signaling through CD19, a molecule known to modulate signaling thresholds in B cells. The defective CD19 signaling is manifested …

Effect Of Electrically Mediated Intratumor And Intramuscular Delivery Of A Plasmid Encoding Ifn Α On Visible B16 Mouse Melanomas, Loree C. Heller, Stephanie F. Ingram, M. Lee Lucas, Richard A. Gilbert, Richard Heller

Bioelectrics Publications

Interferon α may be used as a single agent therapy for metastatic malignant melanoma or as an adjuvant to chemotherapy. Delivery of interferon α by gene therapy offers an alternative to recombinant protein therapy. Electrically mediated delivery enhances plasmid expression in a number of tissues, for instance skin, liver, muscle and tumors including melanomas. Here we compare the effect of delivery of a plasmid encoding mouse interferon α on growth of visible B16 mouse melanomas following electrically mediated delivery to muscle or directly to the tumor. Intratumoral delivery of interferon α plasmid not only slows melanoma growth, but induces complete, …

Hla-Cw*04 And Hepatitis C Virus Persistence, Chloe L. Thio, Xiaojiang Gao, James J. Goedert, David Vlahov, Kenrad E. Nelson, Margaret Hilgartner, Stephen J. O'Brien, Peter Karacki, Jacquie Astemborski, Mary Carrington, David L. Thomas

Biology Faculty Articles

In studies of acute hepatitis C virus (HCV) infection, the early host immune response is one of the determinants of viral persistence. The class I human leukocyte antigens (HLA), which present foreign antigen to cytolytic T cells, are integral components of this response. We hypothesized that the highly polymorphic HLA genes affect the outcome of an HCV infection. To test this hypothesis, we molecularly typed 231 persons with well-documented clearance of an HCV infection and 444 matched persistently infected persons. HLA-A*1101 (odds ratio [OR], 0.49; 95% confidence interval [95% CI], 0.27 to 0.89), HLA-B*57 (OR, 0.62; 95% CI, 0.39 to …