Genetics and Genomics Commons^™

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 …

Shar-Pei Mediates Cell Proliferation Arrest During Imaginal Disc Growth In Drosophila, Madhuri Kango-Singh, Riitta Nolo, Chunyao Tao, Patrik Verstreken, P. Robin Hiesinger, Hugo J. Bellen, Georg Halder

Biology Faculty Publications

During animal development, organ size is determined primarily by the amount of cell proliferation, which must be tightly regulated to ensure the generation of properly proportioned organs. However, little is known about the molecular pathways that direct cells to stop proliferating when an organ has attained its proper size. We have identified mutations in a novel gene, shar-pei, that is required for proper termination of cell proliferation during Drosophila imaginal disc development. Clones of shar-pei mutant cells in imaginal discs produce enlarged tissues containing more cells of normal size. We show that this phenotype is the result of both …

Contrasting Patterns Of Divergence In Quantitative Traits And Neutral Dna Markers: Analysis Of Clinal Variation, Jay F. Storz

Jay F. Storz Publications

Clinal variation in quantitative traits is often attributed to the effects of spatially varying selection. However, identical patterns can be produced by the interplay between purely stochastic processes (i.e. drift in combination with spatially restricted gene flow). One means of distinguishing between adaptive and nonadaptive causes of geographical variation is to compare relative levels of between population divergence in quantitative traits and neutral DNA markers. Such comparisons can be used to test whether levels of trait divergence attributable to additive genetic effects (as measured by Q_ST) exceed null expectations based on the level of divergence at neutral marker …

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.

Workshop On Sustainable Development Of Marine Fish Farming In Wa, Peter Rogers, R Fletcher

Fisheries management papers

The purpose of this paper is twofold. First to provide an overview of the role of government and more particularly the Department of Fisheries and second to outline government expectations for aquaculture development agencies in the implementation of sustainable development initiatives and the effect this could have on the management of aquaculture within WA.

Sequencing The Genome Of The Domestic Cat Felis Catus, Stephen J. O'Brien, Eric S. Lander, M. E. Haskins, Urs Giger, Niels C. Pederson, David E. Wildt, William J. Murphy, Naoya Yuhki, Marilyn Menotti-Raymond

Biology Faculty Articles

No abstract provided.

An Afternoon With Dr. Freeman Dyson, Freeman Dyson

IMSA Great Minds Program ®

Dyson will speak with IMSA students and faculty on a variety of topics including space, origins of the universe, and how science and technology change society. Learn how three burgeoning technologies – solar energy, genetic engineering and the Internet could narrow the gap between rich and poor in this century. Dyson’s visions for the future include forests of genetically enhanced trees oozing high-octane fuel from their roots and laser-launched earthlings colonizing the comets of the Kuiper Belt. Are his visions convincing? You can decide by joining us at IMSA’s website.

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 …

The Meowplex: A New Dna Test Using Tetranucleotide Str Markers For The Domestic Cat, John M. Butler, Victor A. David, Stephen J. O'Brien, Marilyn Menotti-Raymond

Biology Faculty Articles

No abstract provided.

The Tadpole Of Proceratophrys Avelinoi (Anura: Leptodactylidae), Rafael O. De Sá, José A. Langone

Biology Faculty Publications

The genus Proceratoprhrys is poorly known. It consists of 14 currently recognized species (Frost, 2000) of medium-sized frogs distributed from northeastern Argentina and Paraguay to southeast Amazonia (Rondonia State), eastern and southern Brazil. Proceratophrys avelinoi was described from Misiones, Argentina (Mercadal de Barrio and Barrio, 1993). The larval stage of this species is unknown. Herein, we describe the tadpole and the characteristics of the internal oral anatomy of P avelinoi using scanning electron micros- copy (SEM).

Eye Suppression, A Novel Function Of Teashirt, Requires Wingless Signaling, Amit Singh, Madhuri Kango-Singh, Y. Henry Sun

Biology Faculty Publications

Teashirt (tsh) encodes a Drosophila zinc-finger protein. Misexpression of tsh has been shown to induce ectopic eye formation in the antenna. We report that tsh can suppress eye development. This novel function of tsh is due to the induction of homothorax (hth), a known repressor of eye development, and requires Wingless (WG) signaling. Interestingly, tsh has different functions in the dorsal and ventral eye, suppressing eye development close to the ventral margin, while promoting eye development near the dorsal margin. It affects both growth of eye disc and retinal cell differentiation.

Genetic Effective Size Of A Wild Primate Population: Influence Of Current And Historical Demography, Jay F. Storz, Uma Ramakrishnan, Susan C. Alberts

Jay F. Storz Publications

A comprehensive assessment of the determinants of effective population size (N_e) requires estimates of variance in lifetime reproductive success and past changes in census numbers. For natural populations, such information can be best obtained by combining longitudinal data on individual life histories and genetic marker-based inferences of demographic history. Independent estimates of the variance effective size (N_eV, obtained from life-history data) and the inbreeding effective size (N_eI, obtained from genetic data) provide a means of disentangling the effects of current and historical demography. The purpose of this study was to assess …

Fine Mapping In Tomato Using Microsynteny With The Arabidopsis Genome: The Diageotropica (Dgt) Locus, Kwangchul Oh, Kristine Hardeman, Maria G. Ivanchenko, Mary Ellard-Ivey, Andreas Nebenfüh, Tj White, Terri L. Lomax

Faculty Publications and Other Works -- General Biology

Background

The Arabidopsis thaliana genome sequence provides a catalog of reference genes applicable to comparative microsynteny analysis of other species, facilitating map-based cloning in economically important crops. We have applied such an analysis to the tomato expressed sequence tag (EST) database to expedite high-resolution mapping of the Diageotropica (Dgt) gene within the distal end of chromosome 1 in tomato (Lycopersicon esculentum).

Results

A BLAST search of the Arabidopsis database with nucleotide sequences of markers that flank the tomato dgt locus revealed regions of microsynteny between the distal end of chromosome 1 in tomato, two regions of …

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 …

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, …

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.

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 …

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 …

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 …

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 …

An Equity Paradigm For Preventing Genetic Discrimination, Anita Silvers, Michael Ashley Stein

Faculty Publications

No abstract provided.

Registration Of N547 Maize Germplasm Line, Nora E. D'Croz-Mason, John E. Foster, Stephen C. Mason

Department of Entomology: Faculty Publications

N547 germplasm line (Reg. no. GP-367, PI 615526) was released by the Agriculture Research Division, Institute of Agriculture and Natural Resources, University of Nebraska, on 24 Aug. 1999. N547 is a yellow endosperm maize inbred germplasm with resistance to stalk and shank tunneling damage caused by the second generation of the European corn borer (ECB) Ostrinia nubilalis (Hubner).

N547 was derived by selfing a selected full-sib family from MBITA, a tropical population developed by CIMMYT, Mexico. MBITA was created to recombine sources of resistance to temperate and subtropical stalk borers. These insects included ECB, southwestern corn borer (SWCB) Diatraea grandiosella …

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: 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: 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 …