Genetics and Genomics Commons^™

Species Limits Within The Mexican Garter Snakes Of The Thamnophis Godmani Complex, Douglas A. Rossman, Frank T. Burbrink

Occasional Papers of the Museum of Natural Science, Louisiana State University

The highly variable Thamniphis godmani complex of southern Mexico, comprised of four apparently allopatric populations, was examined by using 28 morphological characters scored on 214 specimens. Character values were tested with univariate and multivariate statistics to determine if populations are morphologically distinct. The results suggest that the four populations represent independently evolving lineages. Four species, three previously undescribed, are recognized in the T. godmani complex. A lectotype is designated for T. godmani. For each species, a diagnosis description of holotype or lectotype, summary of interspecific variation, and statement of distribution are provided. Comparisons are made with T. errans, alleged to …

Sheep Updates 2005 - Part 7, S. M. Liu, A. C. Schlink, J. R. Williams, M. E. Dowling, J. C. Greeff, Roy Butler, Keith Croker, L. G. Butler, Rob Davidson, Ken Hart, Doug Harrington, Mario D'Antuono, Julian Gardner, Geoff Duddy, R. G. Woodgate, A. Le Feuvre, A Bailey, R. B. Besier, N. Campbell, I. Carmichael, S. Love, Richard Stovold

Sheep Updates

This session covers eight papers from different authors:

POSTERS

1. Sulpher in wool and its implications for fleece weight and sheep health, SM Liu, AC Schlink, JR Williams, CSIRO Livestock Industries Wembley WA, ME Dowling,JCGreef, Department of Agriculture Western Australia.

2. Stubbles for sheep: a reality check, Roy Butler, Keith Croker, Department of Agriculture Western Australia.

3. Genetic benchmarking using artificial insemination, LC Butler, JC Greeff, Department of Agriculture Western Australia.

4. The potential lambing performances of ewes in mixed age flocks, Kieth Croker, Department of Agriculture Western Australia, Rob Davidson, WAMMCO International, formally University of Western Australia, Ken Hart, …

Sheep Updates 2005 - Part 1, R. W. Kelly, R. Kingwell, A. R. Bray, Chris Oldham, Graeme Martin, D. Blanche, D. Ferguson, Keith Crocker, Di Evans

Sheep Updates

This session covers seven papers from different authors: Boosting lambing percentages of WA sheep flocks. R.W. Kelly CSIRO Livestock Industries, Floreat WA , R. Kingwell Department of Agriculture WA,

Kiwis can fly - 30% higher lambing in 15 years, AR Bray, Meat and Wool New Zealand, Wellington, New Zealand

Rams are not a trivial expense, so what can you do to maximise on your investment? Chri Oldham, Department of Agriculture Western Australia, Graeme Martin, University of West Australia.

Care for mun - fetal programming, lamb survival and lifetime performance. RW Kelly CSIRO Livestock Industries, Floreat WA

Boost lamb survival - …

Sheep Updates 2005 - Part 4, Lucy Anderton, John Young, Rob Davidson, Keith Croker, Ken Hart, Tim Wiese, B. M. Thomson, I Williams, J. R. Briegel, J. C. Greeff, N. R. Adams, E. N. Bermingham, Sue Hatcher, Gordon Refshauge, Emma Kopke, Ross Kingwell, K. E. Kemper, M. L. Hebart, F. D. Brien, K. S. Jaensch, R. J. Grimson, D. H. Smith, Melanie Dowling, A. (Tony) Schlink, John Karlsson

Sheep Updates

This session covers twelve papers from different authors:

REPRODUCTION

1. Is it worth increasing investment to increase lambing percentages? Lucy Anderton Department of Agriculture Western Australia.

2. What value is a lamb? John Young, Farming Systems Analysis Service, Kojonup, WA

3. Providing twin-bearing ewes with extra energy at lambing produces heavier lambs at marking. Rob Davidson WAMMCO International,, formerly University of Western Australia; Keith Croker, Ken Hart, Department of Agriculture Western Australia, Tim Wiese, "Chuckem", Highbury, Western Australia.

GENETICS

4. Underlying biological cause of trade-off between meat and wool. Part 1. Wool and muscle glycogen, BM Thomson, I Williams, University …

Seroprevalence And Genomic Divergence Of Circulating Strains Of Feline Immunodeficiency Virus Among Felidae And Hyaenidae Species, Jennifer L. Troyer, Jill Pecon-Slattery, Melody E. Roelke, Warren E. Johnson, Sue Vandewoude, Nuria Vazquez-Salat, Meredith Brown, Laurence Frank, Rosie Woodroffe, Christiaan Winterbach, Hanlie Winterbach, Graham Hemson, Mitchell Bush, Kathleen A. Alexander, Eloy Revilla, Stephen J. O'Brien

Biology Faculty Articles

Feline immunodeficiency virus (FIV) infects numerous wild and domestic feline species and is closely related to human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV). Species-specific strains of FIV have been described for domestic cat (Felis catus), puma (Puma concolor), lion (Panthera leo), leopard (Panthera pardus), and Pallas' cat (Otocolobus manul). Here, we employ a three-antigen Western blot screening (domestic cat, puma, and lion FIV antigens) and PCR analysis to survey worldwide prevalence, distribution, and genomic differentiation of FIV based on 3,055 specimens from 35 Felidae and 3 Hyaenidae species. …

Mannose Binding Lectin Genotypes Influence Recovery From Hepatitis B Virus Infection, Chloe L. Thio, Timothy L. Mosbruger, Jacquie Astemborski, Spencer Greer, Gregory D. Kirk, Stephen J. O'Brien, David L. Thomas

Biology Faculty Articles

Mannose binding lectin (MBL) is a central component of the innate immune response and thus may be important for determining hepatitis B virus (HBV) persistence. Since single-nucleotide polymorphisms (SNPs) in the gene encoding MBL (mbl2) alter the level of functional MBL, we hypothesized that mbl2 genotypes are a determinant of HBV persistence or recovery from viral infection. We tested this hypothesis by using a nested case control design with 189 persons with HBV persistence matched to 338 individuals who had naturally recovered from HBV infection. We determined genotypes of two promoter and three exon 1 SNPs in mbl2 …

Variation In The Fluorescence Of Green Fluorescent Protein In Various Strains Of Escherichia Coli, Paul R. Letellier Jr.

Biological Sciences Theses & Dissertations

Green fluorescent protein (GFP) was first identified in the jellyfish Aequorea victoria and generated interest due to its ability to noninvasively tag and visualize cells, cellular structures, and cellular proteins. Furthermore, the expression of green fluorescent protein in Esherichia coli cells as a tool for reporting gene expression and promotor activity has become important in the understanding of gene regulation. Expression of the gfp gene was found to vary depending on the strain of E. coli possessing the gfp gene. As a result of this fluctuation in fluorescence, gene expression and hence promotor activity may be difficult to detect or …

The Cell Cycle–Regulated Genes Of Schizosaccharomyces Pombe, Anna Oliva, Adan Rosebrock, Francisco Ferrezuelo, Haiying Chen, Saumyadipta Pyne, Steve Skiena, Bruce Futcher, Janet Leatherwood

Department of Molecular Genetics and Microbiology Faculty Publications

Many genes are regulated as an innate part of the eukaryotic cell cycle, and a complex transcriptional network helps enable the cyclic behavior of dividing cells. This transcriptional network has been studied in Saccharomyces cerevisiae (budding yeast) and elsewhere. To provide more perspective on these regulatory mechanisms, we have used microarrays to measure gene expression through the cell cycle of Schizosaccharomyces pombe (fission yeast). The 750 genes with the most significant oscillations were identified and analyzed. There were two broad waves of cell cycle transcription, one in early/mid G2 phase, and the other near the G2/M transition. The early/mid G2 …

A Bac-Based Physical Map Of The Nile Tilapia Genome, Takayuki Katagiri, Celeste Kidd, Elizabeth Tomasino, Jesse T. Davis, Cassandra Wishon, Justin E. Stern, Karen L. Carleton, Aimee E. Howe, Thomas D. Kocher

Hubbard Center for Genome Studies (HCGS)

Background

Cichlid fishes, particularly tilapias, are an important source of animal protein in tropical countries around the world. To support selective breeding of these species we are constructing genetic and physical maps of the tilapia genome. Physical maps linking collections of BAC clones are a critical resource for both positional cloning and assembly of whole genome sequences.

Results

We constructed a genome-wide physical map of the tilapia genome by restriction fingerprinting 35,245 bacterial artificial chromosome (BAC) clones using high-resolution capillary polyacrylamide gel electrophoresis. The map consists of 3,621 contigs and is estimated to span 1.752 Gb in physical length. An …

Mechanisms Of Virulence Regulation In Porphyromonas Gingivalis W83, Elaine Ann-Marie Vanterpool

Loma Linda University Electronic Theses, Dissertations & Projects

The expression of extracellular proteolytic activities is highly regulated in both prokaryotic and eukaryotic systems. This regulation can occur at multiple levels including expression of the protease genes, secretion, processing of an inactive secreted precursor to its active form and/or the posttranslational glycosylation of the proteins. These regulatory mechanisms are vital to ensure that expression is tightly controlled. Porphyromonas gingivalis has been associated with adult periodontitis and in the development of many systematic diseases. The major virulence factors of P. gingivalis, the gingipains, are responsible for pathogenesis including degradation of complement and immunoglobulin, inactivation of cytokines and their receptors, …

Oxygen Sensing By The Aer And Tsr Receptors Of Escherichia Coli, Jessica Claire Edwards

Loma Linda University Electronic Theses, Dissertations & Projects

Escherichia coli senses the oxygen concentration of its environment via the Aer and Tsr receptors, and swims to an oxygen concentration that provides optimal energy generation. Aer and Tsr do not sense oxygen per se but, sense the internal energy state via the electron transport system (ETS) in a previously unidentified mechanism. Proton motive force (PMF) and electron flow were proposed as possible sensory signals but, distinguishing between the two was not possible, previously, in live, motile cells. I differentiated PMF from electron flow by creating a series of ETS mutant strains that express ternary combinations of i) aerotaxis receptors, …

Nonrandom Dispersal And Local Adaptation, Jay F. Storz

Jay F. Storz Publications

Two recent studies of wild bird populations provide new insights into mechanisms of microevolutionary change by revealing how variation in fitness-related traits may be maintained over very small spatial scales.
When a population is distributed across a heterogeneous environment, the prospects for local adaptation depend on the spatial scale of fitness variation relative to the spatial scale of dispersal. If the patchiness of environmental conditions is too “fine-grained,” the spatial acuity of natural selection may be severely diminished by the homogenizing effects of gene flow (García-Ramos and Kirkpatrick, 1997; Lenormand, 2002). For example, habitat variation over a scale of several …

New Statistical Paradigms Leading To Web-Based Tools For Clinical/Translational Science, Knut M. Wittkowski

COBRA Preprint Series

As the field of functional genetics and genomics is beginning to mature, we become confronted with new challenges. The constant drop in price for sequencing and gene expression profiling as well as the increasing number of genetic and genomic variables that can be measured makes it feasible to address more complex questions. The success with rare diseases caused by single loci or genes has provided us with a proof-of-concept that new therapies can be developed based on functional genomics and genetics.

Common diseases, however, typically involve genetic epistasis, genomic pathways, and proteomic pattern. Moreover, to better understand the underlying biologi-cal …

Using Domination To Analyze Rna Structures., Travis Reves Coake

Electronic Theses and Dissertations

Understanding RNA molecules is important to genomics research. Recently researchers at the Courant Institute of Mathematical Sciences used graph theory to model RNA molecules and provided a database of trees representing possible secondary RNA structures. In this thesis we use domination parameters to predict which trees are more likely to exist in nature as RNA structures. This approach appears to have promise in graph theory applications in genomics research.

Myod Targets Chromatin Remodeling Complexes To The Myogenin Locus Prior To Forming A Stable Dna-Bound Complex, Ivana L. De La Serna, Yasuyuki Ohkawa, Charlotte A. Berkes, Donald A. Bergstrom, Caroline S. Dacwag, Stephen J. Tapscott Fred Hutchinson Cancer Research Center, Anthony N. Imbalzano

Biology Faculty Publications

The activation of muscle-specific gene expression requires the coordinated action of muscle regulatory proteins and chromatin-remodeling enzymes. Microarray analysis performed in the presence or absence of a dominant-negative BRG1 ATPase demonstrated that approximately one-third of MyoD-induced genes were highly dependent on SWI/SNF enzymes. To understand the mechanism of activation, we performed chromatin immunoprecipitations analyzing the myogenin promoter. We found that H4 hyperacetylation preceded Brg1 binding in a MyoD-dependent manner but that MyoD binding occurred subsequent to H4 modification and Brg1 interaction. In the absence of functional SWI/SNF enzymes, muscle regulatory proteins did not bind to the myogenin promoter, thereby providing …

Composite Genome Map And Recombination Parameters Derived From Three Archetypal Lineages Of Toxoplasma Gondii, Asis Khan, Sonya Taylor, Chunlei Su, Aaron J. Mackey, Jon Boyle, Robert Cole, Darius Glover, Keliang Tang, Ian T. Paulsen, Matt Berriman, John C. Boothroyd, Elmer K. Pfefferkorn, J P. Dubey, James W. Ajioka, David S. Roos, John C. Wootton, David Sibley

Dartmouth Scholarship

Toxoplasma gondii is a highly successful protozoan parasite in the phylum Apicomplexa, which contains numerous animal and human pathogens. T.gondii is amenable to cellular, biochemical, molecular and genetic studies, making it a model for the biology of this important group of parasites. To facilitate forward genetic analysis, we have developed a high-resolution genetic linkage map for T.gondii . The genetic map was used to assemble the scaffolds from a 10X shotgun whole genome sequence, thus defining 14 chromosomes with markers spaced at ∼300 kb intervals across the genome. Fourteen chromosomes were identified comprising a total genetic size of ∼592 cM …

The Effect Of Rooibos Tea (Aspalathus Linearis) On The Survival And Transformation Of C3h-Bt1 Mouse Fibroblasts, Krista M. Beach, Paul J. Smith

Honors Capstones

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

Methods For Obtaining And Analyzing Whole Chloroplast Genome Sequences, Robert K. Jansen, Linda A. Raubeson, Jeffrey L. Boore, Claude W. Depamphilis, Timothy W. Chumley, Rosemarie C. Haberle, Stacia K. Wyman, Andrew J. Alverson, Riannon Peery, Sallie J. Herman, H. Matthew Fourcade, Jennifer V. Kuehl, Joel R. Mcneal, James Leebens-Mack, Liying Cui

All Faculty Scholarship for the College of the Sciences

During the past decade there has been a rapid increase in our understanding of plastid genome organization and evolution due to the availability of many new completely sequenced genomes. Currently there are 43 complete genomes published and ongoing projects are likely to increase this sampling to nearly 200 genomes during the next five years. Several groups of researchers including ours have been developing new techniques for gathering and analyzing entire plastid genome sequences and details of these developments are summarized in this chapter. The most important recent developments that enhance our ability to generate whole chloroplast genome sequences involve the …

Insertional Polymorphisms Of Endogenous Feline Leukemia Viruses, Alfred L. Roca, William G. Nash, Joan C. Menninger, William J. Murphy, Stephen J. O'Brien

Biology Faculty Articles

The number, chromosomal distribution, and insertional polymorphisms of endogenous feline leukemia viruses (enFeLVs) were determined in four domestic cats (Burmese, Egyptian Mau, Persian, and nonbreed) using fluorescent in situ hybridization and radiation hybrid mapping. Twenty-nine distinct enFeLV loci were detected across 12 of the 18 autosomes. Each cat carried enFeLV at only 9 to 16 of the loci, and many loci were heterozygous for presence of the provirus. Thus, an average of 19 autosomal copies of enFeLV were present per cat diploid genome. Only five of the autosomal enFeLV sites were present in all four cats, and at only one …

The Linkage Disequilibrium Maps Of Three Human Chromosomes Across Four Populations Reflect Their Demographic History And A Common Underlying Recombination Pattern, Francisco M. De La Vega, Hadar Isaac, Andrew Collins, Charles R. Scafe, Bjarni V. Halldorsson, Xiaoping Su, Ross A. Lippert, Yu Wang, Marion Laig-Webster, Ryan T. Koehler, Janet S. Ziegle, Lewis T. Wogan, Junko F. Stevens, Kyle M. Leinen, Sheri J. Olson, Karl J. Guegler, Xiaoqing You, Lily H. Xu, Heinz G. Hemken, Francis Kalush, Mitsuo Itakura, Yi Zheng, Guy De The, Stephen J. O'Brien, Andrew G. Clark, Sorin Istrail, Michael W. Hunkapiller, Eugene G. Spier, Dennis A. Gilbert

Biology Faculty Articles

The extent and patterns of linkage disequilibrium (LD) determine the feasibility of association studies to map genes that underlie complex traits. Here we present a comparison of the patterns of LD across four major human populations (African-American, Caucasian, Chinese, and Japanese) with a high-resolution single-nucleotide polymorphism (SNP) map covering almost the entire length of chromosomes 6, 21, and 22. We constructed metric LD maps formulated such that the units measure the extent of useful LD for association mapping. LD reaches almost twice as far in chromosome 6 as in chromosomes 21 or 22, in agreement with their differences in recombination …

Developing And Optimizing Conditions For Single Cell Genetic Analysis, Susan Adele Gitlin

Theses and Dissertations in Biomedical Sciences

Preimplantation Genetic Diagnosis (PGD) allows for couples to obtain genetic information at the embryo stage, therefore preventing lethal genetic diseases in their offspring. A recent multi-center study determined a 17% amplification failure rate overall and a 3.4% misdiagnosis rate (ESHRE PGD consortium steering committee, 2002). Experiments presented here were conducted to decrease those rates by optimizing single cell sensitivity and specificity of PGD techniques. Primer extension preamplification (PEP) was used after initial amplification failure, followed by gene specific PCR. Reamplification experiments yielded 54% amplification rates using blastomeres that previously failed amplification. In the clinical trial, four of six blastomeres were …

Searching For Differentially Expressed Gene Combinations, Marcel Dettling, Edward Gabrielson, Giovanni Parmigiani

Johns Hopkins University, Dept. of Biostatistics Working Papers

Background: Comparison of mRNA expression levels across biological samples is a widely used approach in genomics. Available data-analytic tools for deriving comprehensive lists of differentially expressed genes rely on data summaries formed using each gene in isolation from others. These approaches ignore biological relationships among genes and may miss important biological insight provided by genomics data.

Methods: We propose a fast, easily interpretable and scalable approach for identifying pairs of genes that are differentially expressed across phenotypes or experimental conditions. These are defined as pairs for which there is detectable phenotype discrimination using the joint distribution, but not from either …

A Gene Expression Fingerprint Of C. Elegans Embryonic Motor Neurons, Rebecca M. Fox, Stephen E. Von Stetina, Susan J. Barlow, Christian Shaffer, Kellen L. Olszewski, Jason H. Moore

Dartmouth Scholarship

Differential gene expression specifies the highly diverse cell types that constitute the nervous system. With its sequenced genome and simple, well-defined neuroanatomy, the nematode C. elegans is a useful model system in which to correlate gene expression with neuron identity. The UNC-4 transcription factor is expressed in thirteen embryonic motor neurons where it specifies axonal morphology and synaptic function. These cells can be marked with an unc-4::GFP reporter transgene. Here we describe a powerful strategy, Micro-Array Profiling of C. elegans cells (MAPCeL), and confirm that this approach provides a comprehensive gene expression profile of unc-4::GFP motor neurons in vivo.

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Extrapair Fertilization And Genetic Similarity Of Social Mates In The Mexican Jay, John Eimes, Patricia Parker, Jerram Brown, Esther Brown

Biology Department Faculty Works

Inbreeding depression should favor the ability of females to avoid inbreeding or minimize its effects. We tested for a relationship between genetic similarity of social pairs and the occurrence of extrapair fertilization (EPF) in the Mexican jay (Aphelocoma ultramarina). Multilocus minisatellite and microsatellite DNA fingerprinting was used to detect extrapair young and measure genetic similarity between social parents. We found that 12 of 31 (39%) nests had at least one EPF and 15 of 93 (16%) young were the result of EPF. The mean DNA fingerprinting band sharing score between social mates who had at least one EPF was significantly …

Using Genome Scans Of Dna Polymorphism To Infer Adaptive Population Divergence, Jay F. Storz

Jay F. Storz Publications

Elucidating the genetic basis of adaptive population divergence is a goal of central importance in evolutionary biology. In principle, it should be possible to identify chromosomal regions involved in adaptive divergence by screening genome-wide patterns of DNA polymorphism to detect the locus-specific signature of positive directional selection. In the case of spatially separated populations that inhabit different environments or sympatric populations that exploit different ecological niches, it is possible to identify loci that underlie divergently selected traits by comparing relative levels of differentiation among large numbers of unlinked markers. In this review I first address the question of whether diversifying …

From The Cover: Assignment Of An Essential Role For The Neurospora Frequency Gene In Circadian Entrainment To Temperature Cycles, Antonio M. Pregueiro, Nathan Price-Lloyd, Deborah Bell-Pedersen, Christian Heintzen, Jennifer J. Loros, Jay C. Dunlap

Dartmouth Scholarship

Circadian systems include slave oscillators and central pacemakers, and the cores of eukaryotic circadian clocks described to date are composed of transcription and translation feedback loops (TTFLs). In the model system Neurospora, normal circadian rhythmicity requires a TTFL in which a White Collar complex (WCC) activates expression of the frequency (frq) gene, and the FRQ protein feeds back to attenuate that activation. To further test the centrality of this TTFL to the circadian mechanism in Neurospora, we used low-amplitude temperature cycles to compare WT and frq-null strains under conditions in which a banding rhythm was elicited. WT cultures were entrained …

A Monkey’S Tale: The Origin Of Plasmodium Vivax As A Human Malaria Parasite, Ananias A. Escalante, Omar E. Cornejo, Denise E. Freeland, Amanda C. Poe, Ester Durrego, William E. Collins, Altaf A. Lal

Harold W. Manter Laboratory of Parasitology: Library Materials

The high prevalence of Duffy negativity (lack of the Duffy blood group antigen) among human populations in sub-Saharan Africa has been used to argue that Plasmodium vivax originated on that continent. Here, we investigate the phylogenetic relationships among 10 species of Plasmodium that infect primates by using three genes, two nuclear (β-tubulin and cell division cycle 2) and a gene from the plastid genome (the elongation factor Tu). We find compelling evidence that P. vivax is derived from a species that inhabited macaques in Southeast Asia. Specifically, those phylogenies that include P. vivax as an ancient lineage from …

Relationship Among Genes Conferring Partial Resistance To Leaf Rust (Puccinia Triticina) In Wheat Lines Ci 13227 And L-574-1., Jeffery S. Lehman, Karin A. Hanson, Gregory Shaner

Biology and Earth Science Faculty Scholarship

This study describes the segregation of genes for resistance to the fungus Puccinia triticinain a cross between partially resistant wheat lines L-574-1 and CI 13227 with two and four genes for resistance, respectively. The objectives of this study were to use parental, F1, F2, and backcross populations to quantify maternal effects, degree of dominance, and transgressive segregation, and to determine whether CI 13227 and L-574-1 share any resistance genes for long latent period or small uredinia. In two experiments conducted in the greenhouse, the uppermost leaf of adult wheat plants was inoculated prior to heading with P. triticina. On days …

The Clustering Of Regression Models Method With Applications In Gene Expression Data, Li-Xuan Qin, Steven G. Self

UW Biostatistics Working Paper Series

Identification of differentially expressed genes and clustering of genes are two important and complementary objectives addressed with gene expression data. For the differential expression question, many "per-gene" analytic methods have been proposed. These methods can generally be characterized as using a regression function to independently model the observations for each gene; various adjustments for multiplicity are then used to interpret the statistical significance of these per-gene regression models over the collection of genes analyzed. Motivated by this common structure of per-gene models, we propose a new model-based clustering method -- the clustering of regression models method, which groups genes that …

Cluster Analysis Of Genomic Data With Applications In R, Katherine S. Pollard, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

In this paper, we provide an overview of existing partitioning and hierarchical clustering algorithms in R. We discuss statistical issues and methods in choosing the number of clusters, the choice of clustering algorithm, and the choice of dissimilarity matrix. In particular, we illustrate how the bootstrap can be employed as a statistical method in cluster analysis to establish the reproducibility of the clusters and the overall variability of the followed procedure. We also show how to visualize a clustering result by plotting ordered dissimilarity matrices in R. We present a new R package, hopach, which implements the hybrid clustering method, …