Genomics Commons^™

Inference, Orthology, And Inundation: Addressing Current Challenges In The Field Of Metagenomics, Gregory Detlev Alexander Vey

Theses and Dissertations (Comprehensive)

The vast increase in the number of sequenced genomes has irreversibly changed the landscape of the biological sciences and has spawned the current post-genomic era of research. Genomic data have illuminated many adaptation and survival strategies between species and their habitats. Moreover, the analysis of prokaryotic genomic sequences is indispensible for understanding the mechanisms of bacterial pathogens and for subsequently developing effective diagnostics, drugs, and vaccines. Computational strategies for the annotation of genomic sequences are driven by the inference of function from reference genomes. However, the effectiveness of such methods is bounded by the fractional diversity of known genomes. Although …

Choosing The Right Path: Enhancement Of Biologically Relevant Sets Of Genes Or Proteins Using Pathway Structure, Reuben Thomas, Julia M. Gohlke, Geffrey F. Stopper, Frederick M. Parham, Christopher J. Portier

Biology Faculty Publications

A method is proposed that finds enriched pathways relevant to a studied condition using the measured molecular data and also the structural information of the pathway viewed as a network of nodes and edges. Tests are performed using simulated data and genomic data sets and the method is compared to two existing approaches. The analysis provided demonstrates the method proposed is very competitive with the current approaches and also provides biologically relevant results.

Micrornas And The Advent Of Vertebrate Morphological Complexity, Alysha M. Heimberg, Lorenzo F. Sempere, Vanessa N. Moy, Phillip C. J. Donoghue, Kevin J. Peterson

Dartmouth Scholarship

The causal basis of vertebrate complexity has been sought in genome duplication events (GDEs) that occurred during the emergence of vertebrates, but evidence beyond coincidence is wanting. MicroRNAs (miRNAs) have recently been identified as a viable causal factor in increasing organismal complexity through the action of these ≈22-nt noncoding RNAs in regulating gene expression. Because miRNAs are continuously being added to animalian genomes, and, once integrated into a gene regulatory network, are strongly conserved in primary sequence and rarely secondarily lost, their evolutionary history can be accurately reconstructed. Here, using a combination of Northern analyses and genomic searches, we show …

Effect Of Thyroid Hormone Concentration On The Transcriptional Response Underlying Induced Metamorphosis In The Mexican Axolotl (Ambystoma), Robert B. Page, Stephen R. Voss, Amy K. Samuels, Jeramiah J. Smith, Srikrishna Putta, Christopher K. Beachy

Biology Faculty Publications

BACKGROUND: Thyroid hormones (TH) induce gene expression programs that orchestrate amphibian metamorphosis. In contrast to anurans, many salamanders do not undergo metamorphosis in nature. However, they can be induced to undergo metamorphosis via exposure to thyroxine (T4). We induced metamorphosis in juvenile Mexican axolotls (Ambystoma mexicanum) using 5 and 50 nM T4, collected epidermal tissue from the head at four time points (Days 0, 2, 12, 28), and used microarray analysis to quantify mRNA abundances.

RESULTS: Individuals reared in the higher T4 concentration initiated morphological and transcriptional changes earlier and completed metamorphosis by Day 28. In contrast, initiation of metamorphosis …

High-Throughput Genotyping With The Goldengate Assay In The Complex Genome Of Soybean, David L. Hyten, Qijian Song, Ik-Young Choi, Mun-Sup Yoon, James E. Specht, Lakshimi Matukumalli, Randall L. Nelson, Randy C. Shoemaker, Nevin D. Young, Perry B. Cregan

Department of Agronomy and Horticulture: Faculty Publications

Large numbers of single nucleotide polymorphism (SNP) markers are now available for a number of crop species. However, the high-throughput methods for multiplexing SNP assays are untested in complex genomes, such as soybean, that have a high proportion of paralogous genes. The Illumina GoldenGate assay is capable of multiplexing from 96 to 1,536 SNPs in a single reaction over a 3-day period. We tested the GoldenGate assay in soybean to determine the success rate of converting verified SNPs into working assays. A custom 384-SNP GoldenGate assay was designed using SNPs that had been discovered through the resequencing of five diverse …

High Rate Of Recent Transposable Element–Induced Adaptation In Drosophila Melanogaster, Josefa Gonzalez, Kapa Lenkov, Mikhail Lipatov, J. Michael Macpherson, Dmitri A. Petrov

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Although transposable elements (TEs) are known to be potent sources of mutation, their contribution to the generation of recent adaptive changes has never been systematically assessed. In this work, we conduct a genome-wide screen for adaptive TE insertions in Drosophila melanogaster that have taken place during or after the spread of this species out of Africa. We determine population frequencies of 902 of the 1,572 TEs in Release 3 of the D. melanogaster genome and identify a set of 13 putatively adaptive TEs. These 13 TEs increased in population frequency sharply after the spread out of Africa. We argue that …

Transcriptional Profiling Of Aphid Resistant And Susceptible Melon (Cucumis Melo) Following Cotton -Melon Aphid (Aphis Gossypii) Feeding, Preethi Samuel

Theses and Dissertations

The interaction between phloem feeding aphids Aphis gossypii (cotton-melon aphid) and Cucumis melo (melon) provides an opportunity to elucidate the means by which a host plant defends itself against aphid attack. The relationship is of scientific as well as economic importance since A. gossypii is among the most destructive insects to agriculture in the U.S. and abroad. The resistance to A. gossypii in melon is controlled at the Vat (Virus aphid transmission) locus by a major dominant gene, Vat that has the unique feature of conferring resistance to A. gossypii and resistance to transmission of non-persistent viruses by A. gossypii …

United States Regulation Of Stem Cell Research: Recasting Government's Role And Questions To Be Resolved, Owen C. B. Hughes, Alan L. Jakimo, Michael J. Malinowski

Journal Articles

This article directly addresses the stem cell controversy, but also the broader history and norms regarding the roles of federal and state government in U.S. science research funding.

Ecological Genomics: Understanding Gene And Genome Function In The Natural Environment, M. C. Ungerer, L. C. Johnson, M. A. Herman

School of Biological Sciences: Faculty Publications

The field of ecological genomics seeks to understand the genetic mechanisms underlying responses of organisms to their natural environments. This is being achieved through the application of functional genomic approaches to identify and characterize genes with ecological and evolutionary relevance. By its very nature, ecological genomics is an interdisciplinary field. In this review, we consider the significance of this new area of study from both an ecological and genomic perspective using examples from the recent literature. We submit that by considering more fully an ecological context, researchers may gain additional insights into the underlying genetic basis of ecologically relevant phenotypic …

Gene Response Profiles For Daphnia Pulex Exposed To The Environmental Stressor Cadmium Reveals Novel Crustacean Metallothioneins, Joseph R. Shaw, John K. Colbourne, Jennifer C. Davey, Stephen P. Glaholt, Thomas H. Hampton, Celia Y. Chen, Carol L. Folt, Joshua W. Hamilton

Dartmouth Scholarship

Genomic research tools such as microarrays are proving to be important resources to study the complex regulation of genes that respond to environmental perturbations. A first generation cDNA microarray was developed for the environmental indicator species Daphnia pulex, to identify genes whose regulation is modulated following exposure to the metal stressor cadmium. Our experiments revealed interesting changes in gene transcription that suggest their biological roles and their potentially toxicological features in responding to this important environmental contaminant.

A Regulator Of Dscam Mutually Exclusive Splicing Fidelity, Sara Olson, Yiannis Savva, Jung Park, Brenton R. Graveley

UCHC Articles - Research

The Down syndrome cell adhesion molecule (Dscam) gene has essential roles in neural wiring and pathogen recognition in Drosophila melanogaster. Dscam encodes 38,016 distinct isoforms via extensive alternative splicing. The 95 alternative exons in Dscam are organized into clusters that are spliced in a mutually exclusive manner. The exon 6 cluster contains 48 variable exons and uses a complex system of competing RNA structures to ensure that only one variable exon is included. Here we show that the heterogeneous nuclear ribonucleoprotein hrp36 acts specifically within, and throughout, the exon 6 cluster to prevent the inclusion of multiple exons. Moreover, hrp36 …

Sampling Daphnia's Expressed Genes: Preservation, Expansion And Invention Of Crustacean Genes With Reference To Insect Genomes, John K. Colbourne, Brian D. Eads, Joseph Shaw, Elizabeth Bohuski, Darren Bauer, Justen Andrews

Dartmouth Scholarship

Functional and comparative studies of insect genomes have shed light on the complement of genes, which in part, account for shared morphologies, developmental programs and life-histories. Contrasting the gene inventories of insects to those of the nematodes provides insight into the genomic changes responsible for their diversification. However, nematodes have weak relationships to insects, as each belongs to separate animal phyla. A better outgroup to distinguish lineage specific novelties would include other members of Arthropoda. For example, crustaceans are close allies to the insects (together forming Pancrustacea) and their fascinating aquatic lifestyle provides an important comparison for understanding the genetic …

Comparative Chloroplast Genomics: Analyses Including New Sequences From The Angiosperms Nuphar Advena And Ranunculus Macranthus, Linda A. Raubeson, Rhiannon Peery, Timothy W. Chumley, Chris Dziubek, H. Matthew Fourcade, Jeffrey L. Boore, Robert K. Jansen

All Faculty Scholarship for the College of the Sciences

Background

The number of completely sequenced plastid genomes available is growing rapidly. This array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is often useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the genomes reported here: Nuphar advena (from a basal-most lineage) and Ranunculus macranthus (a basal eudicot). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution …

Maptogenome: A Comparative Genomic Tool That Aligns Transcript Maps To Sequenced Genomes, Srikrishna Putta, Jeramiah J. Smith, Chuck Staben, S. Randal Voss

Biology Faculty Publications

Efforts to generate whole genome assemblies and dense genetic maps have provided a wealth of gene positional information for several vertebrate species. Comparing the relative location of orthologous genes among these genomes provides perspective on genome evolution and can aid in translating genetic information between distantly related organisms. However, large-scale comparisons between genetic maps and genome assemblies can prove challenging because genetic markers are commonly derived from transcribed sequences that are incompletely and variably annotated. We developed the program MapToGenome as a tool for comparing transcript maps and genome assemblies. MapToGenome processes sequence alignments between mapped transcripts and whole genome …

Sensory Genes And Mate Choice: Evidence That Duplications, Mutations, And Adaptive Evolution Alter Variation In Mating Cue Genes And Their Receptors, Lisa Horth

Biological Sciences Faculty Publications

Fascinating new data, revealed through gene sequencing, comparative genomics, and genetic engineering, precisely establish which genes are involved in mate choice and mating activity—behaviors that are surprisingly understudied from a genetic perspective. Discussed here are some of the recently identified visual and chemosensory genes that are involved in mate choice and mating behavior. These genes’ products are involved in the production, transmission, and receipt of crucial sensory mate-choice cues that affect fitness. This review exposes newfound evidence that alternative splicing, gene-expression pattern changes, and molecular genetic variation in sensory genes are crucial for both intra- and interspecific mate choice and …

The Plant Structure Ontology, A Unified Vocabulary Of Anatomy And Morphology Of A Flowering Plant, Katica Ilic, Elizabeth Kellogg, Pankaj Jaiswal, Felipe Zapata, Peter Stevens, Leszek Vincent, Shulamit Avraham, Leonore Reiser, Anuradha Pujar, Martin Sachs, Noah Whitman, Susan Mccouch, Mary Schaeffer, Doreen Ware, Lincoln Stein, Seung Rhee

Biology Department Faculty Works

Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species comparative studies and quantitative comparison of phenotypes and expression patterns. A major drawback is variable terminology that is used to describe plant anatomy and morphology in publications and genomic databases for different species. The same terms are sometimes applied to different plant structures in different taxonomic groups. Conversely, similar structures are named by their species-specific terms. To address this problem, we created the Plant Structure Ontology (PSO), the first generic ontological …

Genomeblast: A Web Tool For Small Genome Comparison, Guoqing Lu, Liying Jiang, Resa M. K. Helikar, Thaine W. Rowley, Luwen Zhang, Xianfeng Chen, Etsuko N. Moriyama

Biology Faculty Publications

Background: Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inference of phylogenetic relationships in a given set of genomes.

Results: GenomeBlast is a Web tool developed for comparative analysis of multiple small genomes. A new parameter called "coverage" was introduced and used along with sequence identity to evaluate global similarity between genes. With GenomeBlast, the following results can be obtained: (1) unique genes in each …

Gene Order Data From A Model Amphibian (Ambystoma): New Perspectives On Vertebrate Genome Structure And Evolution, Jeramiah J. Smith, S. Randal Voss

Biology Faculty Publications

BACKGROUND: Because amphibians arise from a branch of the vertebrate evolutionary tree that is juxtaposed between fishes and amniotes, they provide important comparative perspective for reconstructing character changes that have occurred during vertebrate evolution. Here, we report the first comparative study of vertebrate genome structure that includes a representative amphibian. We used 491 transcribed sequences from a salamander (Ambystoma) genetic map and whole genome assemblies for human, mouse, rat, dog, chicken, zebrafish, and the freshwater pufferfish Tetraodon nigroviridis to compare gene orders and rearrangement rates.

RESULTS: Ambystoma has experienced a rate of genome rearrangement that is substantially lower than mammalian …

Shelling Out For Genomics, Timothy S. Mcclintock, Charles D. Derby

Physiology Faculty Publications

A report on the symposium 'Genomic and Proteomic Approaches to Crustacean Biology' held as part of the Society for Integrative and Comparative Biology 2006 Annual Meeting, Orlando, USA, 4-8 January 2006.

Tannerella Forsythia, A Periodontal Pathogen Entering The Genomic Era, Anne C. R. Tanner, Jacques Izard

Department of Food Science and Technology: Faculty Publications

Several questions need to be addressed to evaluate whether Tannerella forsythia is to be considered a periodontal pathogen. T. forsythia has been detected in periodontal health and disease, so could it be a pathogen? The species was not detected in many studies despite finding other putative pathogens, so could it be important in pathogenicity? The challenges of working with T. forsythia include its fastidious and anaerobic growth requirements for cultural detection. Thus, studies associating T. forsythia with periodontal and other oral infections have used noncultural approaches (immunoassays and DNA-based assays) in addition to cultural approaches. We feel …

Characterization Of The Yeast Ionome: A Genome-Wide Analysis Of Nutrient Mineral And Trace Element Homeostasis In Saccharomyces Cerevisiae, David J. Eide, Suzanne Clark, T . Murlidharan Nair, Mathias Gehl, Michael Gribskov, Mary Lou Guerinot, Jeffrey Harper

Dartmouth Scholarship

Nutrient minerals are essential yet potentially toxic, and homeostatic mechanisms are required to regulate their intracellular levels. We describe here a genome-wide screen for genes involved in the homeostasis of minerals in Saccharomyces cerevisiae. Using inductively coupled plasma-atomic emission spectroscopy (ICP-AES), we assayed 4,385 mutant strains for the accumulation of 13 elements (calcium, cobalt, copper, iron, potassium, magnesium, manganese, nickel, phosphorus, selenium, sodium, sulfur, and zinc). We refer to the resulting accumulation profile as the yeast 'ionome'.

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, …

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 …

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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Analysis Of Genotypic And Phenotypic Differences In Desmognathus Quadramaculatus Across The Southern Appalachians, Deborah Susan Merritt

Theses, Dissertations and Capstones

Populations of Desmognathus quadramaculatus were compared for genotypic and phenotypic differences across 5 states in the Southern Appalachians. Series consisting of 10 salamanders each were collected from West Virginia, Virginia, Tennessee, North Carolina and Georgia. Salamanders were assessed for genotypic differences by using allozyme (proteins with polymorphic loci) electrophoresis staining for 13 loci of the muscle, liver and stomach tissue. Nei’s genetic distance was used to score genetic variation between populations. Phenotypic differences were assessed by comparing 10 external morphological measurements between populations. Mahalanobis’ distance was used to score morphological differences between populations. Both genetic and morphological differences were correlated …

Multiple Kh Domains Of Poly C Binding Protein Are Required For Its Trans-Activation On The Proximal Promoter Of The Mu-Opioid Receptor Gene, Adnan K. Malik

Seton Hall University Dissertations and Theses (ETDs)

The mu-opioid receptor (MOR) has been shown to mediate morphine induced analgesia, addiction, and tolerance. The expression of the major product of the MOR (MOR-1) gene has been found to be driven by two promoters, a distal promoter and a proximal promoter. The proximal promoter region has been shown in previous studies to be the major promoter for the regulation of MOR gene transcription in the adult mouse brain and embryonic development. Recent studies have shown that single-stranded DNA binding proteins (such as Poly C Binding Protein) are involved in transcriptional regulation of mouse MOR gene. Poly C binding protein …

Chemical Genomics In Yeast, Charles Brenner

Dartmouth Scholarship

Four recent 'chemical genomic' studies, using genome-scale collections of yeast gene deletions, have presented complementary approaches to identifying gene-drug and pathway-drug interactions.Many drugs have unknown, controversial or multiple mechanisms of action. Four recent 'chemical genomic' studies, using genome-scale collections of yeast gene deletions that were either arrayed or barcoded, have presented complementary approaches to identifying gene-drug and pathway-drug interactions.

Chloroplast Dna Rearrangements In Campanulaceae: Phylogenetic Utility Of Highly Rearranged Genomes, Mary E. Cosner, Linda A. Raubeson, Robert K. Jansen

All Faculty Scholarship for the College of the Sciences

Background

The Campanulaceae (the "hare bell" or "bellflower" family) is a derived angiosperm family comprised of about 600 species treated in 35 to 55 genera. Taxonomic treatments vary widely and little phylogenetic work has been done in the family. Gene order in the chloroplast genome usually varies little among vascular plants. However, chloroplast genomes of Campanulaceae represent an exception and phylogenetic analyses solely based on chloroplast rearrangement characters support a reasonably well-resolved tree.

Results

Chloroplast DNA physical maps were constructed for eighteen representatives of the family. So many gene order changes have occurred among the genomes that characterizing individual mutational …

A Role For Tbx5 In Proepicardial Cell Migration During Cardiogenesis, Cathy J. Hatcher, Nata Diman, Minsu Kim, David Pennisi, Yan Song, Marsha M. Goldstien, Takashi Mikawa, Craig T. Basson

PCOM Scholarly Works

Transcriptional regulatory cascades during epicardial and coronary vascular development from proepicardial progenitor cells remain to be defined. We have used immunohistochemistry of human embryonic tissues to demonstrate that the TBX5 transcription factor is expressed not only in the myocardium, but also throughout the embryonic epicardium and coronary vasculature. TBX5 is not expressed in other human fetal vascular beds. Furthermore, immunohistochemical analyses of human embryonic tissues reveals that unlike their epicardial counterparts, delaminating epicardial-derived cells do not express TBX5 as they migrate through the subepicardium before undergoing epithelial-mesenchymal transformation required for coronary vasculogenesis. In the chick, Tbx5 is expressed in the …

Bioethics: Everything You Wanted To Know About Life Or Death, But Were Afraid To Ask, St Mary's University

President's Peace Commission - Programs

The President’s Peace Commission existed from 1984 to 2013 at St. Mary's University. The Commission fostered an ethical commitment to participate in the establishment of world peace and social justice.

This program is about genetic technologies, ethical issues in human and animal experimentation and physician assisted suicide.