Genetics and Genomics Commons^™

Sheep Updates 2003 - Posters, Maxine Brown, Gaye Krebs, Diana Fredorenko, Kathryn Edgerton-Warburton, Evan Burt, Nazrul Islam, Roy Butler, L. G. Butler, S. R. Brown, M. F. D'Antuono, J. C. Greeff, Ken Hart, Tanya Kilminster, Rachel Kirby, M. E. Ladyman, A. C. Schlink, I. H. Williams, P. E. Vercoe, Anyou Lui, Karen Smith, Martin Bent, Matthew Young

Sheep Updates

This session covers eleven papers from different authors:1 Sheep production on annual stubbles/pastures vs lucerne Maxine Brown Gaye Krebs Muresk Institute, Curtin University Diana Fedorenko Kathryn Egerton-Warburton Centre for Cropping Systems, Department of Agriculture Western Australia 2. The value chain of the Lake Grace livestock industry Evan Burt Nazrul Islam Department of Agriculture Western Australia 3. Native pastures, Dorper sheep and the 2002 drought Roy Butler Department of Agriculture Western Australia 4. Commercial sheep breeders can improve their sheep breeding program using wether trials L.G. Butler, S.R. Brown, M.F. D’Antuono, J.C. Greeff Department of Agriculture 5. Western Australia Linked ewe …

Aphytophagy In The Miletinae (Lycaenidae): Phylogeny, Ecology, And Conservation, John Mathew

Biological Sciences Theses & Dissertations

Less than 1% of all Lepidoptera are aphytophagous; of these, a considerable proportion is found in the family Lycaenidae. The aphytophagous Lycaenidae are believed to have arisen from a mutualistic template involving ant attendance. With this association firmly in place, it is a relatively simple shift to exploitation, either of the ants themselves, through active carnivory on the brood/trophallactic feeding from adults, or by carnivory on ant-tended homopterans, with little to no interference by the ants. Among lycaenids, aphytophagy has arisen several times; most spectacularly in the subfamily Miletinae, where all of the approximately 150 species are presumed or known …

Some Environmental Relationships Of Undergrowth Species In Aspen Communities Of The Intermountain West, W F. Mueggler

Aspen Bibliography

This analysis results from an opportunity to explore plant-environmental relationships from data collected for a different purpose. Origin of the data is a study designed to develop an aspen community-type classification for southern Idaho, western Wyoming, Utah, and Nevada which resulted in the publication "Aspen Community Types of the Intermountain Region" GTR INT-250 by W.F. Mueggler (1988).

Cluster Stability Scores For Microarray Data In Cancer Studies, Mark Smolkin, Debashis Ghosh

The University of Michigan Department of Biostatistics Working Paper Series

A potential benefit of profiling of tissue samples using microarrays is the generation of molecular fingerprints that will define subtypes of disease. Hierarchical clustering has been the primary analytical tool used to define disease subtypes from microarray experiments in cancer settings. Assessing cluster reliability poses a major complication in analyzing output from these procedures. While much work has been done on assessing the global question of number of clusters in a dataset, relatively little research exists on assessing stability of individual clusters. A potential benefit of profiling of tissue samples using microarrays is the generation of molecular fingerprints that will …

Life Cycle Of A Torrenticolous Hawaiian Chironomid (Telmatogeton Torrenticola): Stream Flow And Microhabitat Effects, M. Eric Benbow, Albert J. Burky, Carl M. Way

Biology Faculty Publications

In this study we documented the instar densities and life cycle of Telmatogeton torrenticola Terry (Chironomidae : Telmatogetoninae) from Kinihapai Stream, Maui, Hawaii. Greatest larval densities of this midge are found on substrates of high velocity, shallow flows of cascades, and splash zones of waterfalls, with lower densities in riffles. In the summer of 1994 we compared the effects of two microhabitats (termed optimal and suboptimal) on inter-instar density and relative abundance. In a second year (1995), we evaluated the effect of long-term reduced stream flow on these variables only in optimal microhabitats. A significant reduction in stream flow from …

Comparative Genome Organization Of Human, Murine, And Feline Mhc Class Ii Region, Naoya Yuhki, Thomas W. Beck, Robert M. Stephens, Yoko Nishigaki, Kymberly Newmann, Stephen J. O'Brien

Biology Faculty Articles

To study comparative molecular dynamics in the genesis of the major histocompatibility complex (MHC), we determined a complete nucleotide sequence spanning 758,291 bp of the domestic cat (Felis catus) extended and classical class II region. The feline class II MHC includes 44 genes (31 predicted to be expressed) which display DNA sequence homology and ordered gene synteny with human HLA and mouse H2, in extended class II and centromere proximal regions (DM to DO) of the classical class II region. However, remarkable genomic alterations including gene gain and loss plus size differentials of 250 kb are …

A Novel Method To Detect Bacterial Restriction-Modification (R-M) Systems, Julie Kay Armantrout Kasarjian

Loma Linda University Electronic Theses, Dissertations & Projects

Analysis of recently sequenced microbial genomes has revealed many DNA sequences that code for previously unknown restriction endonucleases and their corresponding methyltransferases. These findings show that numerous restriction enzymes abundant in bacteria have yet to be discovered. Traditionally, restriction enzymes have been discovered by the classical restriction and modification (R-M) phenomena of bacteriophages (type I and III enzymes), or by direct enzyme assays (type II enzymes). To avoid the limitations of these traditional approaches, a quantitative R-M test based on plasmid transformation efficiency (Plasmid R-M Test) was established using DNA fragments derived from the E. coli bacteriophage lambda. This test …

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 …

Natural Selection On Protein Polymorphism In The Rodent Genus Peromyscus: Evidence From Interlocus Contrasts, Jay F. Storz, Michael W. Nachman

Jay F. Storz Publications

The effects of natural selection are generally locus-specific, whereas migration, drift, and inbreeding are expected to have relatively uniform effects across the entire genome. This suggests that multilocus surveys of multiple populations can be used to distinguish selection from demographic effects. The purpose of this study was to test for evidence of selection on protein polymorphism in natural populations of mice in the genus Peromyscus. We analyzed published data from geographic surveys of allozyme variation and used a coalescent- based simulation model to identify specific loci that deviated from neutral expectations. Observed F_ST values generally exhibited a remarkably …

Supervised Detection Of Regulatory Motifs In Dna Sequences, Sunduz Keles, Mark J. Van Der Laan, Sandrine Dudoit, Biao Xing, Michael B. Eisen

U.C. Berkeley Division of Biostatistics Working Paper Series

Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology. We propose a new likelihood based method, COMODE, for identifying structural motifs in DNA sequences. Commonly used methods (e.g. MEME, Gibbs sampler) model binding sites as families of sequences described by a position weight matrix (PWM) and identify PWMs that maximize the likelihood of observed sequence data under a simple multinomial mixture model. This model assumes that the positions of the PWM correspond to independent multinomial distributions with four cell probabilities. We address supervising the search for DNA binding sites using the information derived from …

Phylogenetic Position Of Pterocommatinae And Cavariella, And Implications For The Origins Of Host Alternation In Aphids, Carol A. Rowe

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Aphids are morphologically simple. Their numerous hypothesized convergent reductions, such as reduced siphunculi length in association with ant attendance, have made it difficult to define morphological synapomorphies that are necessary for phylogenetic studies. Thus, I used molecular characters both to reexamine the phylogenetic relationships of Cavariella and Pterocommatinae within Aphididae, and to further map host associations and life cycles onto these phylogenies to better understand the evolutionary lability of host alternation within Aphididae. Independent and combined analyses were performed under unweighted parsimony and maximum likelihood criteria for sequences of mitochondrial cytochrome oxidase II plus tRNA-Leucine plus partial cytochrome oxidase I …

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 …

A Bt Transgene Reduces Herbivory And Enhances Fecundity In Wild Sunflowers, A. A. Snow, Diana Pilson, L. H. Rieseberg, M. J. Paulsen, N. Pleskac, M. R. Reagon, D. E. Wolf, S. M. Selbo

Diana Pilson Publications

Gene flow from transgenic crops can introduce novel traits into related species, but the ecological importance of this process is unknown. Here, we report the first empirical evidence that wild plants can benefit from a bacterial transgene under uncaged, natural conditions. Cultivated sunflower (Helianthus annuus) is known to hybridize frequently with wild sunflower (H. annuus) in the western and midwestern United States. We studied a crop-developed Bacillus thuringiensis (Bt) transgene, cry1Ac, in backcrossed wild sunflower populations. Lepidopteran damage on transgenic plants was strongly reduced relative to control plants at our two study sites, while damage …

Blackwell Publishing Ltd. Chondrocranial, Hyobranchial And Internal Oral Morphology In Larvae Of The Basal Bufonid Genus Melanophryniscus (Amphibia: Anura), Peter M. Larson, Rafael O. De Sá, Diego Arrieta

Biology Faculty Publications

Melanophryniscus is a genus of small toads inhabiting the southern portion of South America. This genus is considered basal within the family Bufonidae. Data on larval chondrocranial morphology do not exist for the genus and larval internal oral anatomy has only been described for a single species. Here, we describe chondrocranial and internal oral morphology in Melanophryniscus montevidensis, M. orejasmirandai and M. sanmartini. Chondrocranial morphology is similar among the species examined. Comparisons with other bufonids and with outgroup taxa suggest that the following chondrocranial characters may represent synapomorphies for the Bufonidae: free (or absent) ceratobranchial IV, a reduced …

Simple Parallel Statistical Computing In R, Anthony Rossini, Luke Tierney, Na Li

UW Biostatistics Working Paper Series

Theoretically, many modern statistical procedures are trivial to parallelize. However, practical deployment of a parallelized implementation which is robust and reliably runs on different computational cluster configurations and environments is far from trivial. We present a framework for the R statistical computing language that provides a simple yet powerful programming interface to a computational cluster. This interface allows the development of R functions that distribute independent computations across the nodes of the computational cluster. The resulting framework allows statisticians to obtain significant speed-ups for some computations at little additional development cost. The particular implementation can be deployed in heterogeneous computing …

Literate Statistical Practice, Anthony Rossini, Friedrich Leisch

UW Biostatistics Working Paper Series

Literate Statistical Practice (LSP, Rossini, 2001) describes an approach for creating self-documenting statistical results. It applies literate programming (Knuth, 1992) and related techniques in a natural fashion to the practice of statistics. In particular, documentation, specification, and descriptions of results are written concurrently with writing and evaluation of statistical programs. We discuss how and where LSP can be integrated into practice and illustrate this with an example derived from an actual statistical consulting project. The approach is simplified through the use of a comprehensive, open source toolset incorporating Noweb, Emacs Speaks Statistics (ESS), Sweave (Ramsey, 1994; Rossini, et al, 2002; …

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.

Ibd Configuration Transition Matrices And Linkage Score Tests For Unilineal Relative Pairs, Sandrine Dudoit

U.C. Berkeley Division of Biostatistics Working Paper Series

Properties of transition matrices between IBD configurations are derived for four general classes of unilineal relative pairs obtained from the grand-parent/ grand-child, half-sib, avuncular, and cousin relationships. In this setting, IBD configurations are defined as orbits of groups acting on a set of inheritance vectors. Properties of the transition matrix between IBD configurations at two linked loci are derived by relating its infinitesimal generator to the adjacency matrix of a quotient graph. The second largest eigenvalue of the infinitesimal generator and its multiplicity are key in determining the form of the transition matrix and of likelihood-based linkage tests such as …

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 …

Microbial Genomics: Tropical Treasure?, Craig Stephens

Biology

A Brazilian consortium has unveiled the genomic DNA sequence of the purple-pigmented bacterium Chromobacterium violaceum, a dominant component of the tropical soil microbiota. The sequence provides insight into the abundant potential of this organism for biotechnological and pharmaceutical applications.

An Analysis Of Diversity In Freshwater Mussels (Bivalvia: Unionidae) Of The Cuyahoga And Rocky River Watersheds (Ohio, Usa) Based On The 16s Rrna Gene, Robert A. Krebs, Roxana N. Vlasceanu, Michael J.S. Tevesz

Biological, Geological, and Environmental Faculty Publications

The continued loss of freshwater unionid mussel species in the Great Lakes region, and particularly from Lake Erie, raises the question of how much phylogenetic and genetic variation remain in the watershed. The introduction of molecular markers into population biology offers one reproducible technique for assessing this variation. A fragment of the 16S rRNA gene of mitochondrial DNA has previously been used to infer phylogenetic relationships in the family Unionidae. Therefore, we reanalyzed these published molecular data with the addition of 12 species from the Cuyahoga and Rocky rivers in northeast Ohio. Both rivers drain to Lake Erie. The species …

Conservation And Restoration Of Pine Forest Genetic Resources In México, C. Sáenz-Romero, Amy E. Snively, R. Lindig-Cisneros

Student Published Works

Deforestation rates in México are about 670,000 ha/year. This threatens the richness of forest genetic resources in México, causing the disappearance of locally adapted populations and rare and endangered pine species. México is one of the six megadiverse countries in the world, with half of the world’s Pinus species. Pinus is one of the most economically and ecologically important forest genera in México. We suggest that delineation of seed zones and the establishment of a network of Forest Genetic Resource Conservation Units (FGRCUs), linked with forest management and ecological restoration programs will protect this valuable resource. We estimate that FGRCUs …

Growth And Carcass Characteristics In Wether Lambs Of A Crossbred Dam Line, A. M. Van Heelsum, R. M. Lewis, M. H. Davies, W. Haresign

Department of Animal Science: Faculty Publications

While crossing of specialized sire and dam breeds can be biologically efficient overall, a by-product is produced in the form of (crossbred) males of the dam line that are unwanted for breeding. In the UK sheep indusiru, most commercial females are first crosses between males of 'longwool' crossing sire breeds, predominantly the Biuefaced Leicester, and females of hill breeds. Genetic improvement of carcass quality in longwool breeds would benefit the surplus F₁males as well asfilter through to tile terminal sire cross lambs produced by the F₁ewes. As afirst step, this paper aims to describe thegrowth and …

Dna Sequence Of Melanocortin 1-Receptor Gene In Coturnix Japonica: Correlation With Three E Locus Alleles, E, E+, Erh, Rupali B. Ugrankar

Inquiry: The University of Arkansas Undergraduate Research Journal

The melanocortin 1-receptor (MC1-R) gene plays a key role in the expression of fur and feather color in mammals and birds by regulating the distribution of two melanin pigments: eumelanin (black/brown) and pheomelanin (red/yellow). MC1-R corresponds to the classical Extension (E) locus in mice, pigs, dogs, horses, and chickens. Three E locus alleles, the wild-type (e + ), brown (E), and redhead (e rh) have been identified in Japanese quail (Coturnix japonica). To determine if the quail E locus phenotypes were due to variation in the MC1-R gene, the coding region of the MC1-R gene was PCR amplified and DNA …

Lack Of Proopiomelanocortin Peptides Results In Obesity And Defective Adrenal Function But Normal Melanocyte Pigmentation In The Murine C57bl/6 Genetic Background, James L. Smart, Malcolm J. Low

Faculty Publications - Department of Biological & Molecular Science

No abstract provided.

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 …

The Ability Of The N-Alkane Technique To Estimate Intake And Diet Choice Of Sheep, R. M. Lewis, A. M. Magadlela, N. S. Jessop, G. C. Emmans

Department of Animal Science: Faculty Publications

This study assessed the efficacy of the n-alkane technique to estimate intake and diet composition in animals given single foods or a choice of two. In thefirst experiment intakes of pelleted ryegrassand lucerne, given eitheralone or as a choice, were measured in lambshoused indoors in individual pens. Each of the three feeding treatments was given to 12 lambs at two degrees of maturity (0.30 and 0·45 of estimated mature sizes). The 12 lambs were constituted as three replicates of the two sexes of each of two breeds. The measured intakes werecompared with those estimated using the n-alkanes C31 andC33, found …

Estrogen Receptor-Α Populations Change With Age In Commercial Laying Hens, K.K. Hansen, R.J. Kittok, G. Sarath, C.F. Toombs, N. Caceres, M.M. Beck

Department of Animal Science: Faculty Publications

Older hens in production lay larger but fewer eggs than younger birds, and the incidence of soft and broken shells is greater in older hens than younger. These changes are attributable at least in part to changing hormone profiles and diminished ability of the hen to transport calcium at the duodenum. In further exploration of this relationship, a study was conducted with three ages of Hy-Line W-36 birds: prelay pullets (PL; 19 wk, 0% production), peak-production hens (PP; 29 wk, ∼93% production), and late-stage hens (LS; 71 wk, ∼80% production). Hens from the PP and LS groups were palpated for …

Investigation Of Matrilineal Relationships Via Mitochondrial Dna In The Southeastern Yellowjacket (Vespula Squamosa), Anthony Deets

Masters Theses

The question of whether and how apparently "altruistic" behaviors can evolve in social animals has received an enormous amount of attention from evolutionary biologists and has been termed "the central theoretical problem of sociobiology". Thus, recent interest is eusocial species with coexisting multiple queens stems from the realization that the genetic relatedness of individuals in such colonies presents additional theoretical challenges beyond those addressed by the Hamiltonian model of kin selection and lengthens the potential list of reproductive conflicts of interest.

The Southeastern Yellowjacket (Vespula squamosa) exhibits two social forms sympatrically in the southern parts of its range. These two …

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 …