Genetics Commons^™

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 …

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 …

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 …

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 …

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 …

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 …

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 Diversity Of Pseudomonas Aeruginosa In Cystic Fibrosis, Nathaniel Edwards Head

Theses, Dissertations and Capstones

Pseudomonas aeruginosa is a common environmental microorganism. However, it has the genetic capacity to cause diseases in patients with compromised host defense systems. Cystic fibrosis (CF) is one of the major hereditary diseases among Caucasian populations. CF patients are born with a defective chloride channel that is responsible for maintaining fluid and electrolyte balance across the lumen of the lung. This imbalance leads to the production of an abnormal dehydrated viscous mucous, prohibiting the patient from normally clearing the respiratory airway. Chronic pulmonary infections with P. aeruginosa are the major causes of high morbidity and mortality in CF. Two of …

Achievements In Wool 1997, Agriculture Western Australia

Animal production and livestock published reports

The Wool Strategy Group, which I initiated in 1993, and Agriculture Western Australia's Wool Program are strategic partners working together with industry to develop and market this State's wool industry.

Wool is Western Australia's second most important agricultural industry, with a current export value of $643 million. It has the potential to return to a billion dollar industry in the next five years and the industry needs to be strongly focused on producing what the market requires to take advantage of this.

The Wool Strategy Group, led by Chairman Mr Philip Gardiner, and the Wool Program, have established an international …

Conservation And Variation Of Nucleotide Sequences In Escherichia Coli Strains Isolated From Nature, Lawrence G. Harshman, Monica Riley

Lawrence G. Harshman Publications

A group of Escherichia coli isolates from nature were compared with one another and with laboratory strains of E. coli with respect to size distribution of chromosomal restriction endonuclease fragments and differences in nucleotide sequences in selected small portions of the genomes. The estimated frequency of base substitutions in nucleotide sequences in and near the trp operons of 26 of the 28 E. coli strains examined ranged from 0.008 to 0.066. Nucleotide sequences in or near λ prophage homologs were significantly more variable than the sequences in or near trp, tnaA, and thyA genes. Thus, the λ-homologous regions …