Genetics and Genomics Commons^™

Identification Of Markers Associated With Sow Lifetime Productivity For Whole Genomic Selection, Daniel Ciobanu

Department of Animal Science: Faculty Publications

Sows are more productive today than ever before. However, concurrent with increased prolificacy, high sow death losses and replacement rates are serious economic and welfare issues facing producers. Reproductive failure is the most frequent reason for culling sows. Length of productive life is moderately heritable and has high variance; thus, substantial genetic variation is expected to exist in most populations. Genetic improvement in the swine industry occurs from selection in nucleus herds and is then transmitted through the breeding pyramid in the multiplication process. Thus, it is critical to identify selection methods that can be applied in nucleus herds that …

Error Correcting Codes And The Human Genome., Suzanne Mclean Lyle

Electronic Theses and Dissertations

In this work, we study error correcting codes and generalize the concepts with a view toward a novel application in the study of DNA sequences. The author investigates the possibility that an error correcting linear code could be included in the human genome through application and research. The author finds that while it is an accepted hypothesis that it is reasonable that some kind of error correcting code is used in DNA, no one has actually been able to identify one. The author uses the application to illustrate how the subject of coding theory can provide a teaching enrichment activity …

Natural Competence In Thermoanaerobacter And Thermoanaerobacterium Species, A Joe Shaw, David A. Hogsett, Lee R. Lynd

Dartmouth Scholarship

Low-G+C thermophilic obligate anaerobes in the class Clostridia are considered among the bacteria most resistant to genetic engineering due to the difficulty of introducing foreign DNA, thus limiting the ability to study and exploit their native hydrolytic and fermentative capabilities. Here, we report evidence of natural genetic competence in 13 Thermoanaerobacter and Thermoanaerobacterium strains previously believed to be difficult to transform or genetically recalcitrant.

In Thermoanaerobacterium saccharolyticum JW/SL-YS485, natural competence- mediated DNA incorporation occurs during the exponential growth phase with both replicating plasmid and homologous recombination-based integration, and circular or linear DNA. In T. saccharolyticum, disruptions of genes similar to …

Electrically Mediated Delivery Of Plasmid Dna To The Skin, Using A Multielectrode Array, Richard Heller, Yolmari Criz, Loree C. Heller, Richard A. Gilbert, Mark J. Jaroszeski

Bioelectrics Publications

The easy accessibility of skin makes it an excellent target for gene transfer protocols. To take full advantage of skin as a target for gene transfer, it is important to establish an efficient and reproducible delivery system. Electroporation is a strong candidate to meet this delivery criterion. Electroporation of the skin is a simple, direct, in vivo method to deliver genes for therapy. Previously, delivery to the skin was performed by means of applicators with relatively large distances between electrodes, resulting in significant muscle stimulation and pain. These applicators also had limitations in controlling the directionality of the applied field. …

Meiotic Dna Re-Replication And The Recombination Checkpoint, Nicole Ann Najor

Wayne State University Dissertations

Progression through meiosis occurs through a strict sequence of events, so that one round of DNA replication precedes programmed recombination and two nuclear divisions. Cyclin dependent kinase 1 (Cdk1) is required for meiosis, and any disruption in its activity leads to meiotic defects. The Cdk1 inhibitor, Sic1, regulates the G1-S transition in the mitotic cell cycle and the analogous transition in meiosis. We have employed a form of Sic1, Sic1deltaP^HA, that is mutated at multiple phosphorylation sites and resistant to degradation. Meiosis specific expression of Sic1deltaP^HA disrupts Cdk1 activity and leads to significant accumulation of over replicated …

Electroporation-Mediated Delivery Of A Naked Dna Plasmid Expressing Vegf To The Porcine Heart Enhances Protein Expression, W. G. Marshall Jr., B. A. Boone, J. D. Burgos, S. I. Gografe, M. K. Baldwin, M. L. Danielson, M. J. Larson, D. R. Caretto, Y. Cruz, B. Ferraro, L. C. Heller, K. E. Ugen, M. J. Jaroszeski, R. Heller

Bioelectrics Publications

Gene therapy is an attractive method for the treatment of cardiovascular disease. However, using current strategies, induction of gene expression at therapeutic levels is often inefficient. In this study, we show a novel electroporation (EP) method to enhance the delivery of a plasmid expressing an angiogenic growth factor (vascular endothelial growth factor, VEGF), which is a molecule previously documented to stimulate revascularization in coronary artery disease. DNA expression plasmids were delivered in vivo to the porcine heart with or without coadministered EP to determine the potential effect of electrically mediated delivery. The results showed that plasmid delivery through EP significantly …

Dna, Red Tide And The Sea: A New Exhibit At Mystic Aquarium & Ife, Margaret (Peg) A. Van_Patten

Wrack Lines

DNA, Red Tide and the Sea is a new exhibit at Mystic Aquarium & IFE. It was developed by UConn Marine Sciences Professor Senjie Lin, and Mystic Aquarium. Children can extract DNA from fruit and learn about genetic codes and red tides in the ocean.

Bridging Functional Genomics And Toxicogenomics Through Dna Microarrays In A Fish Model, Shuzhao Li

Dissertations

In a case study of finding gene expression signatures for environmental stressors in Cyprinodon variegatus, this dissertation examines several important issues of applying DNA microarray technology to fish toxicogenomics. The most relevant disciplines, fish toxicogenomics and computational systems biology are reviewed in Chapter 1. Chapter 2 reviews major aspects of DNA microarray technology.

On DNA microarrays, even for probes that target the same transcript, large variations are seen in the probe signals. These variations are partly dependent and partly independent on probe sequences. Chapter 3 estimates the sequence independent variation by combining experimental and computational approaches. Chapter 4 and …

Borrelia Burgdorferi Ebfc Defines A Newly-Identified, Widespread Family Of Bacterial Dna-Binding Proteins, Sean P. Riley, Tomasz Bykowski, Anne E. Cooley, Logan H. Burns, Kelly Babb, Catherine A. Brissette, Amy Bowman, Matthew L. Rotondi, M. Clarke Miller, Edward Demoll, Kap Lim, Michael G. Fried, Brian Stevenson

Microbiology, Immunology, and Molecular Genetics Faculty Publications

The Lyme disease spirochete, Borrelia burgdorferi, encodes a novel type of DNA-binding protein named EbfC. Orthologs of EbfC are encoded by a wide range of bacterial species, so characterization of the borrelial protein has implications that span the eubacterial kingdom. The present work defines the DNA sequence required for high-affinity binding by EbfC to be the 4 bp broken palindrome GTnAC, where ‘n’ can be any nucleotide. Two high-affinity EbfC-binding sites are located immediately 5′ of B. burgdorferi erp transcriptional promoters, and binding of EbfC was found to alter the conformation of erp promoter DNA. Consensus EbfC-binding …

Comparison Of Dna Pyrosequencing With Alternative Methods For Identification Of Mycobacteria, Loree C. Heller, Michael Jones, Ray H. Widen

Bioelectrics Publications

Identification of mycobacterial clinical isolates by pyrosequencing within the hypervariable A region of the 16S rRNA gene was compared to other identification methods. For >90% of isolates, these identifications correlated to the level of complex or species. For identification of many mycobacteria, pyrosequencing offers an inexpensive alternative to traditional sequencing.

Reverse Recruitment: Activation Of Yeast Genes At The Nuclear Periphery, Terry Marvin Haley

Dissertations

The regulation of genes at the nuclear periphery is an evolutionarily conserved phenomenon in eukaryotes. The reverse-recruitment model of transcriptional activation postulates that genes are activated by moving to and contacting transcription machinery located at subnuclear structures. In Saccharomyces cerevisiae it has been reported that this platform for gene regulation may reside at the nuclear periphery. To test this hypothesis, I utilized a GFP-gene tagging technique, which uses LacI-GFP to visualize a tandem array of its DNA-binding sequence, to monitor localization ofSUC2 and GALL I found that both genes preferentially localized to the nuclear periphery when transcriptionally active. By developing …

Intracellular Levels Of Centrin2, Xpc, & Hhr23b Increase After Dna Damage, Nicholas A. Rowland

Honors Capstones

Capstone submitted as a graduate requirement for the BSU Honors Program.

2c Dna Content Values In Amaranthus (Amaranthaceae) [Abstract], Donald B. Pratt, Shalini N. Jhangiani, Robert J. Wiggers

Faculty Publications

No abstract provided.

Single-Stranded Dna-Binding Proteins Regulate The Abundance Of Lim Domain And Lim Domain-Binding Proteins, Zhixiong Xu, Xianzhang Meng, Ying Cai, Hong Liang, Lalitha Nagarajan, Stephen J Brandt

Faculty, Staff and Student Publications

The LIM domain-binding protein Ldb1 is an essential cofactor of LIM-homeodomain (LIM-HD) and LIM-only (LMO) proteins in development. The stoichiometry of Ldb1, LIM-HD, and LMO proteins is tightly controlled in the cell and is likely a critical determinant of their biological actions. Single-stranded DNA-binding proteins (SSBPs) were recently shown to interact with Ldb1 and are also important in developmental programs. We establish here that two mammalian SSBPs, SSBP2 and SSBP3, contribute to an erythroid DNA-binding complex that contains the transcription factors Tal1 and GATA-1, the LIM domain protein Lmo2, and Ldb1 and binds a bipartite E-box-GATA DNA sequence motif. In …

Saccharomyces Cerevisiae-Based Molecular Tool Kit For Manipulation Of Genes From Gram-Negative Bacteria, Robert M. Q. Shanks, Nicky C. Caiazza, Shannon M. Hinsa, Christine M. Toutain, George A. O'Toole

Dartmouth Scholarship

A tool kit of vectors was designed to manipulate and express genes from a wide range of gram-negative species by using in vivo recombination. Saccharomyces cerevisiae can use its native recombination proteins to combine several amplicons in a single transformation step with high efficiency. We show that this technology is particularly useful for vector design. Shuttle, suicide, and expression vectors useful in a diverse group of bacteria are described and utilized. This report describes the use of these vectors to mutate clpX and clpP of the opportunistic pathogen Pseudomonas aeruginosa and to explore their roles in biofilm formation and surface …

Plasmid Probes For Screening Specific Genes In Large Fragment Dna Libraries, Leah Ferguson

Senior Honors Projects

Heliothis virescens, a member of the lepidopteran family, is of great importance to many people who rely on agriculture as a source of income because it is a pest of many important crops. Because H. virescens feeds on a broad array of hosts including cotton, tobacco, tomato, and soybean it has earned its place as a major nuisance in the United States. Heliothis subflexa is a close taxonomic relative of H. virescens, but the two species differ in that H. subflexa is a specialized herbivore that only feeds on plants in the genus Physalis. Studies have been performed to determine …

Federal Court Adjudication Of State Prisoner Claims For Post-Conviction Dna Testing: A Bifurcated Approach, Dylan Ruga

The University of New Hampshire Law Review

[Excerpt] “Undoubtedly, there are innocent people in prison. Moreover, it is probable that the wrongly convicted, if given a chance to conduct DNA testing on evidence used against them at trial, could establish their innocence. […]

Part II of this Comment will examine the reasoning behind recent circuit court decisions concerning prisoners’ rights to post-conviction genetic testing. I will explain that a bifurcated approach is the appropriate paradigm for reviewing these claims and demonstrate why three of the four circuit courts erred in their analyses. This part also will review the Supreme Court decisions cited by the circuit courts and …

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.

Consent To The Use Of Stored Dna For Genetics Research: A Survey Of Attitudes In The Jewish Population, Marc D. Schwartz, Karen H. Rothenberg, Linda Joseph, Judith Benkendorf, Caryn Lerman

Faculty Scholarship

No abstract provided.

Cationic Surfactant Mediated Hybridization And Hydrophobization Of Dna Molecules At The Liquid/Liquid Interface And Their Phase Transfer, Murali Sastry, Ashavani Kumar, Mrunalini Pattarkine, Vidya Ramakrishnan, Krishna N. Ganesh

Faculty Works

Hybridization of complementary oligonucleotides mediated by a cationic surfactant at the water/hexane interface leads to hydrophobic, double-helical DNA which may be readily phase transferred to the organic phase and cast into thin films on solid substrates.

Psychosocial Risks Of Storing And Using Human Tissues In Research, Jon F. Merz

RISK: Health, Safety & Environment (1990-2002)

Dr. Merz argues that genetics technology makes it more compelling that researchers plan more carefully for the collection and disposition of information derived from subjects' tissues and blood.

Genome-Wide High-Resolution Mapping By Recurrent Intermating Using Arabidopsis Thaliana As A Model, Sin-Chieh Liu, Stanley Kowalski, Tien-Hung Lan, Kenneth A. Feldmann, Andrew H. Patterson

Law Faculty Scholarship

We demonstrate a method for developing populations suitable for genome-wide high-resolution genetic linkage mapping, by recurrent intermating among F2 individuals derived from crosses between homozygous parents. Comparison of intermated progenies to F2 and “recombinant inbred” (RI) populations from the same pedigree corroborate theoretical expectations that progenies intermated for four generations harbor about threefold more information for estimating recombination fraction between closely linked markers than either RI-selfed or F2 individuals (which are, in fact, equivalent in this regard) . Although intermated populations are heterozygous, homozygous “intermated recombinant inbred” (IN) populations can readily be generated, combining additional information afforded by intermating with …

Biotechnology : Exposing The Myths & Realities, Sue Sutherland, Alan Lymbery

Journal of the Department of Agriculture, Western Australia, Series 4

Biotechnology has become one of the buzz words of the 1990s. Sounds impressive but what's it all about? Sue Sutherland and Alan Lymbery unravel some of the jargon and explore its potential for Western Australian agriculture.

Molecular Cloning And Rare Cleavage Mapping Of Human 2p, 6q, 8q, 12q, And 18q Telomeres, Roberto A. Macina, Ken Morii, Xue-Lan Hu, Dimitri G. Negorev, Chrysanthe Spais, Lisa A. Ruthig, Harold C. Riethman

School of Medical Diagnostics & Translational Sciences Publications

Large terminal fragments of human chromosomes 2p, 6q, 8q, 12q, and 18q were cloned using yeast artificial chromosomes (YACs). RecA-assisted restriction endonuclease (RARE) cleavage analysis of genomic DNA samples from 11 unrelated individuals using YAC-derived probes confirmed the telomeric localizations of the half-YACs studied. The cloned Fragments provide telomeric closure of maps for the respective chromosome arms and will supply the reagents needed for analyzing and sequencing these distal subtelomeric regions.

Review Of: The Genetic Frontier: Ethics, Law, And Policy (Mark S. Frankel & Albert Teich Eds., American Association For The Advancement Of Science 1994), Suzanne A. Sprunger

RISK: Health, Safety & Environment (1990-2002)

Review of: The Genetic Frontier: Ethics, Law, and Policy (Mark S. Frankel & Albert Teich eds., American Association for the Advancement of Science 1994). Acknowledgments, appendix, contributors, figures, index, introduction, notes, references, tables. LC 93-37230, ISBN 0-87168-526-4. [260 pp. Paper $22.95. 1333 H St., NW, Washington DC 20005.]

Technology Transfer: A View From The Trenches, Harvey Drucker

RISK: Health, Safety & Environment (1990-2002)

Dr. Drucker, who has lab-wide responsibility for technology transfer at Argonne National Laboratory, argues that transferring rights in discoveries made through tax supported research to private entities can contribute to public welfare in many ways.

Origins Of The Human Genome Project, Robert Mullan Cook-Deegan

RISK: Health, Safety & Environment (1990-2002)

Dr. Cook-Deegan recounts some of the scientific and political history leading to controversy about the proper mix of private and public roles in pursuing genome research and bringing its fruits to bear, e.g., in preventing and curing disease.

Overview Of Potential Intellectual Property Protection For Biotechnology, Kate H. Murashige

RISK: Health, Safety & Environment (1990-2002)

Dr. Murashige compares the function and value of copyright, patent and trade secret laws in recovering investments in developing genome-related biotechnology.

Comparative Mapping Of Arabidopsis Thaliana And Brassica Oleracea Chromosomes Reveals Islands Of Conserved Organization, Stanley P. Kowalski, Tien-Hung Lan, Kenneth A. Feldmann, Andrew H. Patterson

Law Faculty Scholarship

The chromosomes of Arabidopsis thaliana and Brassica oleracea have been extensively rearranged since the divergence of these species; however, conserved regions are evident. Eleven regions of conserved organization were detected, ranging from 3.7 to 49.6 cM in A. thaliana, spanning 158.2 cM (24.6%) of the A. thaliana genome, and 245 cM (29.9%) of the B. oleracea genome. At least 17 translocations and 9 inversions distinguish the genomes of A. thaliana and B. oleracea. In one case B. oleracea homoeologs show a common marker order, which is distinguished from the A. thaliana order by a rearrangement, indicating that the lineages of …

An Analysis Of Mitochondrial Dna In Rett Syndrome And Other Neurodegenerative Disorders, Catherine Erickson Burgess

Theses and Dissertations in Biomedical Sciences

Mitochondrial dysfunction resulting from mutations on mitochondrial DNA (mtDNA) is being recognized in a growing spectrum of diseases. These diseases, resulting from single base mutations, large deletions, or insertions, have been largely neuromuscular in origin. However, as an understanding of the effects of mtDNA mutations progresses, attention is now focusing on neurodegenerative diseases. Rett Syndrome (RS), a progressive neurodegenerative disease with predominantly female cases, demonstrates morphologic mitochondrial changes, mitochondrial enzyme deficiencies and maternal inheritance (characteristic of mtDNA diseases). No investigation of mtDNA involvement has been previously conducted and, to date, no biological marker exists for this disorder.

Our preliminary studies …