Genetics and Genomics Commons^™

Mitochondrial Dna And The Origins Of The Domestic Horse, Thomas Jansen, Peter Forster, Marsha Levine, Hardy Oelke, Matthew Hurles, Colin Renfrew, Jürgen Weber, Klaus Olek

Genetics Collection

The place and date of the domestication of the horse has long been a matter for debate among archaeologists. To determine whether horses were domesticated from one or several ancestral horse populations, we sequenced the mitochondrial D-loop for 318 horses from 25 oriental and European breeds, including American mustangs. Adding these sequences to previously published data, the total comes to 652, the largest currently available database. From these sequences, a phylogenetic network was constructed that showed that most of the 93 different mitochondrial (mt)DNA types grouped into 17 distinct phylogenetic clusters. Several of the clusters correspond to breeds and/or geographic …

Testing For Genetic Evidence Of Population Expansion And Contraction: An Empirical Analysis Of Microsatellite Dna Variation Using A Hierarchical Bayesian Model, Jay F. Storz, Mark Beaumont

Jay F. Storz Publications

The role of past climatic change in shaping the distributions of tropical rain forest vertebrates is central to long-standing hypotheses about the legacy of the Quaternary ice ages. One approach to testing such hypotheses is to use genetic data to infer the demographic history of codistributed species. Population genetic theory that relates the structure of allelic genealogies to historical changes in effective population size can be used to detect a past history of demographic expansion or contraction. The fruit bats Cynopterus sphinx and C. brachyotis (Chiroptera: Pteropodidae) exhibit markedly different distribution patterns across the Indomalayan region and therefore represent an …

Genetic Evidence For Long-Term Population Decline In A Savannah Dwelling Primate: Inferences From A Hierarchical Bayesian Model, Jay F. Storz, Mark A. Beaumont, Susan C. Alberts

Jay F. Storz Publications

The purpose of this study was to test for evidence that savannah baboons (Papio cynocephalus) underwent a population expansion in concert with a hypothesized expansion of African human and chimpanzee populations during the late Pleistocene. The rationale is that any type of environmental event sufficient to cause simultaneous population expansions in African humans and chimpanzees would also be expected to affect other codistributed mammals. To test for genetic evidence of population expansion or contraction, we performed a coalescent analysis of multilocus microsatellite data using a hierarchical Bayesian model. Markov chain Monte Carlo (MCMC) simulations were used to estimate …

Caudal Spotting In The Beacon Fish (Hemigrammus Ocellifer Characidae), Jack Frankel

Department of Biology Faculty Publications

The beacon fish (Hemigrammus ocellifer) exhibits two phenotypes associated with spotting at the base of the caudal fin, with fish either possessing (H. o. ocellifer) or lacking (H. o. falsus) a prominent red spot in this region. Segregation patterns observed from the progenies of 15 different crosses support a hypothesis that caudal spotting in this species is controlled by a single gene with two alleles, for which the caudal spotting allele is completely dominant.

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, …

Mechanisms Of Autoantigen Cleavage During Cell Death, Xiwei Wu

Loma Linda University Electronic Theses, Dissertations & Projects

Specific intracellular autoantigens targeted by autoantibodies in systemic autoimmune and chronic inflammatory diseases undergo posttranslational modifications, such as cleavage, during cell death that could potentially enhance their immunogenicity. In light of the increasing interest in the immunological consequences of defective clearance of apoptotic cells, we explored whether autoantigens cleaved during apoptosis undergo an additional wave of proteolysis as apoptosis progresses to secondary necrosis in the absence of phagocytosis. Jurkat T cells treated with different apoptosis inducers underwent a rapid apoptosis that gradually progressed to secondary necrosis. During the initial apoptotic stages, several nuclear autoantigens, including PARP, Topo I, and LEDGF/p75 …

Construction Of Rhas And Rhar Overexpression Plasmids And The Effects Of Crp Mutants On E.Coli L-Rhamnose Gene Expression, Amber Bromenshenkel, Susan Egan

Honors Capstones

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

Processes For The Allocation, Reallocation And Governance Of Resource Access In Connection With A Framework For The Future Management Of Fisheries In Western Australia, Government Of Western Australia Department Of Fisheries

Fisheries Management Papers

This paper outlines the issues associated with developing a framework to deal explicitly with the allocation, reallocation and the governance of access to the fisheries resources of Western Australia.

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 …

Comparative Genomic Hybridization Array Analysis, Annette M. Molinaro, Mark J. Van Der Laan, Dan H. Moore

U.C. Berkeley Division of Biostatistics Working Paper Series

At the present time, there is increasing evidence that cancer may be regulated by the number of copies of genes in tumor cells. Through microarray technology it is now possible to measure the number of copies of thousands of genes and gene segments in samples of chromosomal DNA. Microarray comparative genomic hybridization (array CGH) provides the opportunity to both measure DNA sequence copy number gains and losses and map these aberrations to the genomic sequence. Gains can signify the over-expression of oncogenes, genes which stimulate cell growth and have become hyperactive, while losses can signify under-expression of tumor suppressor genes, …

Use Of The Caulobacter Crescentus Genome Sequence To Develop A Method For Systematic Genetic Mapping, Craig Stephens, Lisandra West, Desiree Yang

Biology

The functional analysis of sequenced genomes will be facilitated by the development of tools for the rapid mapping of mutations. We have developed a systematic approach to genetic mapping in Caulobacter crescentus that is based on bacteriophage-mediated transduction of strategically placed antibiotic resistance markers. The genomic DNA sequence was used to identify sites distributed evenly around the chromosome at which plasmids could be nondisruptively integrated. DNA fragments from these sites were amplified by PCR and cloned into a kanamycin-resistant (Kanr) suicide vector. Delivery of these plasmids into C. crescentus resulted in integration via homologous recombination. A set of 41 strains …

Production Of A Monoclonal Antibody Against Benzo[Α]Pyrene Diol Epoxide Dna Adducts, Brian Peden Austin

Chemistry & Biochemistry Theses & Dissertations

Benzo[α]pyrene is a ubiquitous pollutant produced from the incomplete combustion of organic material such as fossil fuels. It is found in the workplace, urban air, drinking water, and the food supply. Recently, it has been proposed that benzo[α]pyrene may be the causative agent in the formation of lung adenocarcinomas among some Taiwanese women exposed to cooking oil fumes without adequate ventilation. In this study, calf thymus DNA was modified in vitro with benzo[α]pyrene-diol epoxide (BPDE) to a level consistent with that found in biological samples. This DNA of low modification was used as an immunogen in the production of a …

A Study Of Radiofrequency Effects On Gene Expression, Elizabeth A. Coln

Electrical & Computer Engineering Theses & Dissertations

Numerous studies have been completed over the past several years to look at the non-thermal effects of low-level radiofrequency exposure on biological systems. These studies were done to determine if exposure to radiofrequency fields are safe, or if they may lead to health problems or changes to any of the biological processes continually occurring within the human body. Responses measured include stress responses (I), gene expression (2), cell proliferation (3), cell morphology (4), and changes in DNA (5).

Dispersion is the most common model for explaining the electric behavior of biomaterials. It refers to the corresponding frequency domain concept of …

Genetic Testing: A Cautionary Tale Of Foster And Pre-Adoptive Children, Janet Farrell Smith

New England Journal of Public Policy

Genetic testing of children in the foster care and pre-adoptive stage may be thought to facilitate child placement and satisfy prospective parents’ need to know. But, the policy analysis in this paper recommends great caution, especially given eugenic attitudes in the history of adoption and the risk of creating a second tier of un-adoptable children. Testing should be done only when two conditions are satisfied: test information is medically useful for childhood onset diseases; test information supports and does not diminish the child’s access to present and future healthcare (or the child’s future insurability). Public policy needs to make a …

Editor's Note, Padraig O'Malley

New England Journal of Public Policy

This issue of the journal can be summed up in one word: provocative. At least two articles break new ground. Anthony Robbins and Phyllis Freeman explore the ways in which environmentally oriented public health is uniquely suited to help organized medical care in providing health and in restraining expenditures. Janet Farrell Smith challenges policymakers to look at what will soon become a hot issue — the medical use of genetic information. The genetic testing of children, now becoming prevalent in the foster care and pre-adoptive stage in order to facilitate placement and satisfy prospective parents’ “need to know,” is already …

Genomic Microsatellites As Evolutionary Chronometers: A Test In Wild Cats, Carlos A. Driscoll, Marilyn Menotti-Raymond, George Nelson, David Goldstein, Stephen J. O'Brien

Biology Faculty Articles

Nuclear microsatellite loci (2- to 5-bp tandem repeats) would seem to be ideal markers for population genetic monitoring because of their abundant polymorphism, wide dispersal in vertebrate genomes, near selective neutrality, and ease of assessment; however, questions about their mode of generation, mutation rates and ascertainment bias have limited interpretation considerably. We have assessed the patterns of genomic diversity for ninety feline microsatellite loci among previously characterized populations of cheetahs, lions and pumas in recapitulating demographic history. The results imply that the microsatellite diversity measures (heterozygosity, allele reconstitution and microsatellite allele variance) offer proportionate indicators, albeit with large variance, of …

A New Partitioning Around Medoids Algorithm, Mark J. Van Der Laan, Katherine S. Pollard, Jennifer Bryan

U.C. Berkeley Division of Biostatistics Working Paper Series

Kaufman & Rousseeuw (1990) proposed a clustering algorithm Partitioning Around Medoids (PAM) which maps a distance matrix into a specified number of clusters. A particularly nice property is that PAM allows clustering with respect to any specified distance metric. In addition, the medoids are robust representations of the cluster centers, which is particularly important in the common context that many elements do not belong well to any cluster. Based on our experience in clustering gene expression data, we have noticed that PAM does have problems recognizing relatively small clusters in situations where good partitions around medoids clearly exist. In this …

Neurospora Clock-Controlled Gene 9 (Ccg-9) Encodes Trehalose Synthase: Circadian Regulation Of Stress Responses And Development, Mari L. Shinohara, Alejandro Correa, Deborah Bell-Pedersen, Jay C. Dunlap, Jennifer J. Loros

Dartmouth Scholarship

The circadian clock of Neurospora crassa regulates the rhythmic expression of a number of genes encoding diverse functions which, as an ensemble, are adaptive to life in a rhythmic environment of alternating levels of light and dark, warmth and coolness, and dryness and humidity. Previous differential screens have identified a number of such genes based solely on their cycling expression, including clock-controlled gene 9 (ccg-9). Sequence analysis now shows the predicted CCG-9 polypeptide to be homologous to a novel form of trehalose synthase; as such it would catalyze the synthesis of the disaccharide trehalose, which plays an important …

The Unblazed Trail: Bioinformatics And The Protection Of Genetic Knowledge, Lawrence M. Sung

Faculty Scholarship

No abstract provided.

Methods And Compositions To Enhance Tenderness And Value Of Meat, Chris R. Calkins, Jesus Pablo Velazco De La Garcia, Nancy Coromoto Jerez-Timaure

Department of Animal Science: Faculty Publications

A method of enhancing the tenderness of meat for animal or human consumption by treatment of pre-rigor muscle with the compositions of the invention. It has been found that other quality meat traits can also be enhanced with the method of the invention.

Rapid Communication: Mapping Of The Beta Tropomyosin (Tpm2) Gene To Pig Chromosome 1, J. Sherwood, Daniel C. Gill, M. F. Rothschild

Department of Animal Science: Faculty Publications

Locus. Pig Tropomyosin beta (TPM2) gene.

Genus and Species. Sus Scrofa.

Source and Description of Primers. Primers were derived by using well-conserved regions of published human and mouse sequence (GenBank accession nos. AF209746 and NM_009416). The primers were used to amplify a 1.4-kp fragment of the porcine TPM2 gene covering exons 3 through 8. The porcine cDNA sequence (GenBank accession no. AF420022) showed 95% exonic identity (325 bp) at the nucleotide level to the human skeletal muscle beta tropomyosin (GenBank accession no. X06825). Additionally, pig specific primers were designed to amplify a 246-bp piece that spans exons 3 to …

Rapid Communication: Mapping Of The Ca2+ Atpase Of Fast Twitch 1 Skeletal Muscle Sarcoplasmic Reticulum (Atp2a1) Gene To Porcine Chromosome 3, Daniel C. Ciobanu, Y. Ciobanu, M. F. Rothschild

Department of Animal Science: Faculty Publications

Locus Name. Ca²⁺ ATPase of fast twitch 1 skeletal muscle sarcoplasmic reticulum.

Species. Sus scrofa.

Locus Symbol. ATP2A1.

Source of Primers. Two sets of PCR primers were designed based on human ATP2A1 sequences (Gen- Bank accession numbers U96773 and U96777) available in the GenBank database. Using pig genomic DNA as a template we used set A primers to amplify approximately 1,100 bp spanning exon 1 to exon 2 and set B primers to amplify 1,200 bp gene segment covering some of exon 8 through part of exon 9. These sequences were deposited in GenBank, accession number AY027797-AY027799.

Compensation For Herbivory In Wild Sunflower: Response To Simulated Damage By The Head-Clipping Weevil, Diana Pilson, Karin L. Decker

Diana Pilson Publications

Herbivore damage is generally detrimental to plant fitness, and the evolutionary response of plant populations to damage can involve either increased resistance or increased tolerance. While characters that contribute to resistance, such as secondary chemicals and trichomes, are relatively well understood, characters that contribute to a plant’s ability to tolerate damage have received much less attention. Using Helianthus annuus (wild sunflower) and simulated damage of Haplorhynchites aeneus (head-clipping weevil) as a model system, we examined morphological characters and developmental processes that contribute to compensatory ability. We performed a factorial experiment that included three levels of damage (none, the first two, …

Application Of Fuzzy-Neural Network In Classification Of Soils Using Ground-Penetrating Radar Imagery, Lameck O. Odhiambo, Robert S. Freeland, Ronald E. Yoder, J. Wesley Hines

Department of Animal Science: Faculty Publications

Errors associated with visual inspection and interpretation of radargrams often inhibits the intensive surveying of widespread areas using ground-penetrating radar (GPR). To automate the interpretive process, this paper presents an application of a fuzzy-neural network (F-NN) classifier for unsupervised clustering and classification of soil profile using GPR imagery. The classifier clusters and classifies soil profiles strips along a traverse based on common pattern similarities that can relate to physical features of the soil (e.g., number of horizons; depth, texture and structure of the horizons; and relative arrangement of the horizons, etc). This paper illustrates this classification procedure by its application …

Rapid Communication: Physical And Linkage Mapping Of The Porcine Calcitonin (Calc) Gene, J. E. Neil, S. E. Zhang, J. M. Helm, Daniel C. Ciobanu, M. F. Rothschild

Department of Animal Science: Faculty Publications

Genus and Species. Sus scrofa.

Locus. Porcine calcitonin (CALC) gene.

Source and Description of Primers. Primers, CCA1F and CCA1R, were designed from canine calcitonin sequence (GenBank Accession no. AJ271090) to amplify genomic porcine DNA. Using sequence obtained from the amplified PCR product, additional pig-specific primers (CIPBF, CIPBR, CIPCF, CIPCR) were designed.

Primer Sequences. CCA1F: 5′-CAC TTT GGA TTG GCC GCG C-3′; CCA1R: 5′-ACC AGG GCA GCC AGC AGG A-3′; CIPBF: 5′-AAC TTC CCA CTC TGC ACA CT-3′; CIPBR: 5′-AGA CCA AAC TTC AGC AGG AT- 3′; CIPCF: 5′-TTC TCC TTC CTC TGC TTC TG-3′; CIPCR: 5′-GCA AAC CCA ATA …

A Broad Survey Of Web-Based Bioinformatics Research And Data Mining Using Blast, Wooi Keng Tan

Student Works (2000-2009)

This research covers a broad survey of bioinformatics resources and data mining tools available on the web. Bioinformatics is the field of science in which biology, computer science, and information technology merge to form a single discipline. The three main public domain bioinformatics resources covered here includes NCBI (National Center for Biotechnology Information), EBI (European Bioinformatics Institute) and Genome Net (Japanese Bioinfom1atics Servers). The technology now has enabled researchers to gain global access to these databases and software. These databases and tools will provide the research community with a wealth of information and computing tools followed with the vast data …

Il-12 Plasmid Delivery By In Vivo Electroporation For The Successful Treatment Of Established Subcutaneous B16.F10 Melanoma, M. Lee Lucus, Loree Heller, Domenico Coppola, Richard Heller

Bioelectrics Publications

Interleukin-12 (IL-12) has been used in numerous immunotherapy protocols against melanoma. However, delivery of IL-12 in the form of recombinant protein can result in severe toxicity, and gene therapy has had limited success against B16.F10 murine melanoma. The purpose of this study was to examine the effectiveness of in vivo electroporation for the delivery of plasmid DNA encoding IL-12 as an antitumor agent against B16.F10 melanoma. We treated mice bearing established B16.F10 melanoma tumors with intratumoral (i.t.) or intramuscular (i.m.) injections of a plasmid encoding IL-12, followed by in vivo electroporation. For i.t. treatments, we used an applicator containing six …

Phylogeography And Genetic Diversity Of The Seal Salamander (Desmognathus Monticola), Erin D. Casey

Masters Theses

Phylogeography is defined as the spatial distribution of taxa with respect to geologic and geographic events. It is well documented that the distributions of many taxa have been affected by glacial events during the Pleistocene Era. The patterns generated can be very complex and result from shifts in climate and/or vegetation.

The Seal salamander, (Desmognathus monticola), is one species that still has questions pertaining to its phylogeography. The range of this species extends from southwestern Pennsylvania to northern Alabama and Georgia, with a highly disjunct, state-endangered population in the Red Hills of Alabama. The main goal of this study …

Mitochondrial Dna And Microsatellite Genetic Variation Of Dollar Sunfish (Lepomis Marginatus), Nancy A. Schable

Masters Theses

Dollar sunfish (Lepomis marginatus) at the Savannah River Site were sampled from two radiocesium contaminated ponds with a history of thermal elevation and from reference ponds with no history of radioactive or thermal contamination. Fluorescent sequencing of a portion of the mitochondrial control region showed no genetic variation within or between populations. Centrarchidae microsatellite loci Lma 120 (6 alleles, N=124 from 5 populations), Lma 20 (10 alleles, N=37 from 3 populations) and Rb 7 (14 alleles. N=17 from 2 populations) were variable for dollar sunfish. An additional 9 microsatellite primer pairs were designed for dollar sunfish. Testing of the designed …

Positive And Negative Roles Of Cd72 In B Cell Function., Hsin-Jung Wu, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Regulation of B cell activation depends on integration of signals transmitted by the B cell receptor (BCR) and a variety of co-receptors. CD72 is a B cell co-receptor that is expressed in all stages of B cell development except plasma cells. Ligation of CD72 enhances B cell growth and differentiation. Recently, the class IV semaphoring, CD100, has been identified as the natural ligand for CD72. Cytoplasmic domain of CD72 has been shown to be associated with SHP-1 leading to the proposal that the positive effects of CD72 on B cell response may result from sequestration of negative signals from BCR. …