Genomics Commons^™

The Hyperthermophilic Archaeon Sulfolobus: From Exploration To Exploitation, Stan J.J. Brouns, Thijs J.G. Ettema, Kenneth M. Stedman, Jasper Walther, Hauke Smith, Ambrosius P.L. Snijders, Mark Young, Rolf Bernander, Phillip C. Wright, Betina Siebers, John Van Der Oost

Biology Faculty Publications and Presentations

In the early 1970s, Sulfolobus was first isolated by Thomas Brock and co-workers from sulfur-rich acidic hot springs in Yellowstone National Park. Sulfolobus became one of the model organisms of Archaea in general, and of Crenarchaea in particular. Many of its unusual physiological characteristics have been investigated, and several of its thermostable enzymes have been studied in considerable detail. For fundamental reasons, and because of its potential for industrial applications, Sulfolobus has been selected for a genome sequence project. The recent completion of the Sulfolobus solfataricus genome has set the stage for a series of postgenome research lines that will …

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.

Mappfinder: Using Gene Ontology And Genmapp To Create A Global Gene-Expression Profile From Microarray Data, Scott W. Doniger, Nathan Salomonis, Kam D. Dahlquist, Karen Vranizan, Steven C. Lawlor, Bruce R. Conklin

Biology Faculty Works

MAPPFinder is a tool that creates a global gene-expression profile across all areas of biology by integrating the annotations of the Gene Ontology (GO) Project with the free software package GenMAPP (http://www.GenMAPP.org). The results are displayed in a searchable browser, allowing the user to rapidly identify GO terms with over-represented numbers of geneexpression changes. Clicking on GO terms generates GenMAPP graphical files where gene relationships can be explored, annotated, and files can be freely exchanged.

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).

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 …

The Taxonomic Rank Of Spizella Taverneri: A Response To Mayr And Johnson, John Klicka, Robert M. Zink, Jon C. Barlow, W. Bruce Mcgillivray, Terry J. Doyle

Ornithology Program (HRC)

Mayr and Johnson suggest that Spizella taverneri should be a subspecies of the biological species S. breweri, because it is possibly not reproductively isolated. We originally concluded that evidence from mitochondrial DNA sequences, habitat preferences, timing of breeding, vocalizations, and morphology supported the recognition of S. taverneri as a phylogenetic and biological species. Nothing in the commentary by Mayr and Johnson causes us to change that conclusion. We believe that it is probable that these two allopatric taxa are isolated. Contrary to Mayr and Johnson, we believe that more information is given by ranking S. taverneri as a species, because …

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 …

Recolonization Of The Flicker And Other Notes From Isla Guadalupe, Mexico, Paul R. Sweet, George F. Barrrowclough, John Klicka, Liliana Montanez-Godoy, Patricia Escalante

Ornithology Program (HRC)

During a visit to Isla Guadalupe from 31 May to 3 June 1996, we documented three species new to the island, the Barn Owl, Swainson's Thrush, and Hooded Oriole, and established first breeding records for the European Starling and Western Meadowlark. Red-shafted Flickers are now breeding on the island, representing a recent recolonization from the mainland following the extinction of the endemic population. We investigated the validity of Colaptes auratus rufipileus and concluded that it doesn’t meet the standard for phylogenetic species but differs from C. a. collaris at the 75% level usually associated with subspecific rank. Damage to the …

Molecular Evolution Of Insecticidal Spore-Forming Bacteria, John Pool

Honors Theses

Molecular methods are increasingly being used to determine the phylogeny of microorganisms. This research was intended to determine phylogenetic relationships for bacteria of the species Bacillus thuringiensis and other members of the Bacillus cereus group. Each strain was analyzed by its sasp-B gene sequence to determine its species classification and relation to other strains studied. Results of this study indicated that according to the sasp-B gene tree, the species Bacillus thuringiensis is a paraphyletic with respect to both Bacillus cereus and Bacillus anthracis. Some unexpected results and implications for species designations are also discussed.

Evolutionary Patterns Of Morphometrics, Allozymes And Mitochondrial Dna In Thrashers (Genus Toxostoma), Robert M. Zink, Donna L. Dittmann, John Klicka, Rachelle C. Blackwell-Rago

Ornithology Program (HRC)

We examined patterns of variation in skeletal morphometrics (29 characters), allozymes (34 loci), mitochondrial DNA (mtDNA) restriction sites (n = 74) and fragments (n = 395), and mtDNA sequences (1,739 bp from cytochrome b, ND2, ND6, and the control region) among all species of Toxostoma. The phenetic pattern of variation in skeletal morphometrics generally matched traditional taxonomic groupings (based on plumage patterns) with the exceptions of T. redivivum, which because of its large size clusters outside of its proper evolutionary group (lecontei), and T. occelatum, which did not cluster with T. curvirostre. Skull characters contributed highly to species discrimination, suggesting …

Transcriptional Regulation Of The Bmp2 Gene: Retinoic Acid Induction In F9 Embryonal Carcinoma Cells And Saccharomyces Cerevisiae, Loree C. Heller, Yong Li, Kevin L. Abrams, Melissa B. Rogers

Bioelectrics Publications

Bmp2, a highly conserved member of the transforming growth factor-beta gene family, is crucial for normal development. Retinoic acid, combined with cAMP analogs, sharply induces the Bmp2 mRNA during the differentiation of F9 embryonal carcinoma cells into parietal endoderm. Retinoic acid (RA) also induces the Bmp2 gene in chick limb buds. Since normal Bmp2 expression may require an endogenous retinoid signal and aberrant Bmp2 expression may cause some aspects of RA-induced teratogenesis, we studied the mechanism underlying the induction of Bmp2. Measurements of the Bmp2 mRNA half-life and nuclear run-on assays …

Characterization Of Metal-Regulated Genes In Pseudomonas Fluorescens, Melanie Pearson

Honors Theses

One side effect of today's industrialized world is increased levels of heavy metals in the environment. Many of these metals are necessary for biological function as trace elements, but at higher concentrations are toxic. Other metals, such as cadmium, are not beneficial at any level, and have only deleterious effects on living organisms. Cadmium is primarily thought to interfere with normal biological function of proteins. Human exposure to cadmium appears to primarily damage the kidneys, but may also affect the liver, lungs, immune system, and central nervous system. Bacteria, however, have developed several methods for handling toxic heavy metals: cation …

Multiple Members Of A Third Subfamily Of P-Type Atpases Identified By Genomic Sequences And Ests, Margaret S. Halleck, Deepti Pradhan, Christie Blackman, Charlotte A. Berkes, Partrick Williamson, Robert A. Schlegel

Biology Faculty Publications

The Saccharomyces cerevisiae genome contains five P-type ATPases divergent from both of the well-known subfamilies of these membrane ion transporters. This newly recognized third subfamily can be further divided into four classes of genes with nearly equal relatedness to each other. Genes of this new subfamily are also present and expressed in multicellular organisms such as Caenorhabditis elegans and mammals; some, but not all, can be assigned to the classes identified in yeast. Different classes of genes and different genes within a class are expressed differentially in tissues of the mouse. The recently cloned gene for the mammalian aminophospholipid translocase …

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 …

1: "To Know Ourselves", The U.S. Department Of Energy, The Human Genome Project

Genomics: Past & Future

AT THE END OF THE ROAD in Little Cottonwood Canyon, near Salt Lake City, Alta is a place of near-mythic renown among skiers. In time it may well assume similar status among molecular geneticists. In December 1984, a conference there, co-sponsored by the U.S. Department of Energy, pondered a single question: Does modern DNA research offer a way of detecting tiny genetic mutations—and, in particular, of observing any increase in the mutation rate among the survivors of the Hiroshima and Nagasaki bombings and their descendants? In short the answer was, Not yet. But in an atmosphere of rare intellectual fertility, …

Mapping The Transcriptional Start Site(S) Of The Cannabinoid Receptor Gene, Jordana Baden

MUSC Theses and Dissertations

The cannabinoid receptor gene has recently been cloned. Comparisons of cDNA clones with genomic DNA show that the gene consists of a coding region and at least two untranslated 5' exons (A and B). Two alternative transcripts, differing in their 5' untranslated sequence, have been found that code for identical receptors. Primer extension for transcript A reveal that its most 5' transcriptional start site corresponds to nucleotide -548. Additional transcripts initiated 3' of -548 may exist. Ribonuclease protection assay and primer extension for transcript B reveal that its most 5' transcriptional start site corresponds to nucleotide -406. It is possible …

Molecular Cloning And Rare Cleavage Mapping Of Human 2p, 6q, 8q, 12q, And 18q Telomeres, Roberto A. Macina, Ken Morii, Xue-Lan Hu, Dimitri G. Negorev, Chrysanthe Spais, Lisa A. Ruthig, Harold C. Riethman

School of Medical Diagnostics & Translational Sciences Publications

Large terminal fragments of human chromosomes 2p, 6q, 8q, 12q, and 18q were cloned using yeast artificial chromosomes (YACs). RecA-assisted restriction endonuclease (RARE) cleavage analysis of genomic DNA samples from 11 unrelated individuals using YAC-derived probes confirmed the telomeric localizations of the half-YACs studied. The cloned Fragments provide telomeric closure of maps for the respective chromosome arms and will supply the reagents needed for analyzing and sequencing these distal subtelomeric regions.

A Physical Map Of The Klebsiella Pneumoniae M5a1 Genome, Alexandrine Randriamahefa

Loma Linda University Electronic Theses, Dissertations & Projects

Klebsiella pneumoniae is an enteric opportunistic pathogen which commonly causes pulmonary, urinary tract and kidney infections. It has also been widely used for the study of nitrogen fixation. In this study, a macrorestriction map of K. pneumoniae M5a1 chromosomal DNA was constructed using pulsed field gel electrophoresis (PFGE) and Southern hybridization techniques. The genome DNA was digested with two rare cutting restriction enzymes (XbaI and BlnI) and the genome size was estimated from the sum of the fragment sizes as 5,121 Kb (+2.8%). A tentative order of fragments was deduced using Southern hybridization with purified restriction fragments. …

2: "The Mapping Of Chromosome 16", Norman A. Doggett, Raymond L. Stallings, Carl E. Hildebrand, Robert K. Moyzis

Genomics: Past & Future

Human chromosome 16 is the main focus of the mapping efforts at Los Alamos. The large photomicrograph on these opening pages illustrates the starting point for those mapping efforts, the evaluation of our chromosome-16-specific library of cloned fragments. Among the 23 pairs of human chromosomes, one pair, chromosome 16, is identified by fluorescence in-situ hybridization. Thousands of yellow fluorescent probes derived from the clone library have hybridized to both copies of chromosome 16. The high density and uniform coverage of the fluorescent signals were a strong indication that we could use the library to construct a map of overlapping cloned …

Characterization Of Chemical And Radiation-Induced Dna Damage In The Mdbk Cell Culture System, Jeffrey R. Hincks

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

A mechanism common to many carcinogens and mutagens is the interaction with cellular DNA. Alkaline elution is a sensitive and commonly used technique to detect cellular DNA damage in the form of DNA single-strand breaks (SSB), DNA-protein cross-links (DPC), and DNA interstrand cross-links (ISC). In the present study, gravity-flow alkaline elution was developed and validated to rapidly detect DNA damage in the MDBK cell culture system by genotoxic agents.

The system was first validated by detecting a dose dependent induction of DNA SSB in cells exposed to 25-1500 rad of X-ray. The assay reliably detected the DNA damage of seven …

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 …

Cytogenetic Test Of Captan And Triethylenemelamine In Mouse Bone Marrow, Stephen M. Fry

Honors Theses

Following a single non-toxic i.p. injection with 0.5 or 1.0 mg triethylenemelamine/kig a significant increase in chromosome aberrations in mouse bone marrow was observed 6, 12, 30, but not 54 h after treatment. A single i.p. injection with 250 mg captan/kig caused up to 68% lethality above controls, but no significant increase in chromosome aberrations after the same time intervals. One metacentric chromosome was observed 6, 30, and 54 h after captan treatment among 300, 300, and 101 metaphase spreads respectively, whereas none appeared in 1495 control spreads.

A Cytological Study Of The Salivary Gland Chromosomes Of The Attached-X Variety Of Drosophila Melanogaster, Jack Schull

Bachelors’ Theses

The detailed study of -the salivary chromosomes of the Diptera has been of great importance in substantiating cytologically the theories of genetics. A noteworthy example of the importance of cytological study is the non-disjunctive phenomenon which has occurred on at least several occasions in the strain of Drosophila melanogaster. Bridges (1913) was the first to report nondisjunction of sex chromosomes which was an important confirmation of the chromosome theory. L. V. Morgan (1922) used the cytological study of the germ cells of Drosophila melanogaster to prove that there was no disjunction of the sex chromosomes in the attached-X strain.