Open Access. Powered by Scholars. Published by Universities.®

Life Sciences Commons

Open Access. Powered by Scholars. Published by Universities.®

Evolution

2009

Discipline
Institution
Publication
Publication Type

Articles 1 - 26 of 26

Full-Text Articles in Life Sciences

Evolution Of Genome-Wide Gene Regulation In The Budding Yeast Cell-Division Cycle, Daniel F. Simola Dec 2009

Evolution Of Genome-Wide Gene Regulation In The Budding Yeast Cell-Division Cycle, Daniel F. Simola

Publicly Accessible Penn Dissertations

Genome-wide regulation of gene expression involves a dynamic epigenetic structure which generates an organism's life-cycle. Although changes in gene expression during development have broad effects on many basic phenomena including cell growth, differentiation, morphogenesis, and disease progression, the evolutionary forces influencing gene expression dynamics and gene regulation remain largely unknown, due to the nature of gene expression as a polygenic, quantitative trait. Moreover, gene expression is regulated differentially over time, so evolutionary forces may be influenced by developmental context. To advance the understanding of evolution in the context of the life-cycle, the architecture of gene expression timing control and ...


Modular Organization And Composability Of Rna, Miler T. Lee Dec 2009

Modular Organization And Composability Of Rna, Miler T. Lee

Publicly Accessible Penn Dissertations

Life is organized. Organization is largely achieved via composability -- that at some level of abstraction, a system consists of smaller parts that serve as building blocks -- and modularity -- the tendency for these blocks to be independent units that recombine to form functionally different systems. Here, we explore the organization, composition, and modularity of ribonucleic acid (RNA) molecules, biopolymers that adopt three-dimensional structures according to their specific nucleotide sequence. We address three themes: the efficacy of specific sequences to function as modules or as the context in which modules are inserted; the sources of novel modules in modern genomes; and the ...


Microbial Nad Metabolism: Lessons From Comparative Genomics, Francesca Gazzaniga, Rebecca Stebbins, Sheila Z. Chang, Mark A. Mcpeek, Charles Brenner Sep 2009

Microbial Nad Metabolism: Lessons From Comparative Genomics, Francesca Gazzaniga, Rebecca Stebbins, Sheila Z. Chang, Mark A. Mcpeek, Charles Brenner

Open Dartmouth: Faculty Open Access Scholarship

NAD is a coenzyme for redox reactions and a substrate of NAD-consuming enzymes, including ADP-ribose transferases, Sir2-related protein lysine deacetylases, and bacterial DNA ligases. Microorganisms that synthesize NAD from as few as one to as many as five of the six identified biosynthetic precursors have been identified. De novo NAD synthesis from aspartate or tryptophan is neither universal nor strictly aerobic. Salvage NAD synthesis from nicotinamide, nicotinic acid, nicotinamide riboside, and nicotinic acid riboside occurs via modules of different genes. Nicotinamide salvage genes nadV and pncA, found in distinct bacteria, appear to have spread throughout the tree of life via ...


Evolution Of A Subtilisin-Like Protease Gene Family In The Grass Endophytic Fungus Epichloë Festucae, Michelle K. Bryant, Christopher L. Schardl, Uljana Hesse, Barry Scott Jul 2009

Evolution Of A Subtilisin-Like Protease Gene Family In The Grass Endophytic Fungus Epichloë Festucae, Michelle K. Bryant, Christopher L. Schardl, Uljana Hesse, Barry Scott

Plant Pathology Faculty Publications

BACKGROUND: Subtilisin-like proteases (SLPs) form a superfamily of enzymes that act to degrade protein substrates. In fungi, SLPs can play either a general nutritive role, or may play specific roles in cell metabolism, or as pathogenicity or virulence factors.

RESULTS: Fifteen different genes encoding SLPs were identified in the genome of the grass endophytic fungus Epichloë festucae. Phylogenetic analysis indicated that these SLPs belong to four different subtilisin families: proteinase K, kexin, pyrolysin and subtilisin. The pattern of intron loss and gain is consistent with this phylogeny. E. festucae is exceptional in that it contains two kexin-like genes. Phylogenetic analysis ...


The Role Of Chromosomal Rearrangements In Adaptation In Drosophila Americana, Paulina Alejandra Mena Jul 2009

The Role Of Chromosomal Rearrangements In Adaptation In Drosophila Americana, Paulina Alejandra Mena

Theses and Dissertations

Natural environments expose organisms to multifarious selective pressures involving numerous aspects of the overall phenotype, therefore eliciting a response from multiple correlated loci. It has been hypothesized that chromosomal rearrangements can play a role in facilitating local adaptation by establishing new linkage relationships and modifying the recombination patterns between the different chromosomal forms, allowing coordinated adaptation of several loci. The central aim of the work presented here is to test this hypothesis using Drosophila americana as a model system. This species segregates several inversions and an X-4 centromeric fusion which makes it an excellent model to study the role of ...


Conservation Of The Glucan Phosphatase Laforin Is Linked To Rates Of Molecular Evolution And The Glucan Metabolism Of The Organism, Matthew S. Gentry, Rachel M. Pace Jun 2009

Conservation Of The Glucan Phosphatase Laforin Is Linked To Rates Of Molecular Evolution And The Glucan Metabolism Of The Organism, Matthew S. Gentry, Rachel M. Pace

Molecular and Cellular Biochemistry Faculty Publications

BACKGROUND: Lafora disease (LD) is a fatal autosomal recessive neurodegenerative disease. A hallmark of LD is cytoplasmic accumulation of insoluble glucans, called Lafora bodies (LBs). Mutations in the gene encoding the phosphatase laforin account for approximately 50% of LD cases, and this gene is conserved in all vertebrates. We recently demonstrated that laforin is the founding member of a unique class of phosphatases that dephosphorylate glucans.

RESULTS: Herein, we identify laforin orthologs in a protist and two invertebrate genomes, and report that laforin is absent in the vast majority of protozoan genomes and it is lacking in all other invertebrate ...


Descriptive Anatomy And Evolutionary Patterns Of Anatomical Diversification In Adenia (Passifloraceae), David J. Hearn May 2009

Descriptive Anatomy And Evolutionary Patterns Of Anatomical Diversification In Adenia (Passifloraceae), David J. Hearn

Aliso: A Journal of Systematic and Evolutionary Botany

To understand evolutionary patterns and processes that account for anatomical diversity in relation to ecology and life form diversity, anatomy of storage roots and stems of the genus Adenia (Passifloraceae) were analyzed using an explicit phylogenetic context. Over 65,000 measurements are reported for 47 quantitative and qualitative traits from 58 species in the genus. Vestiges of lianous ancestry were apparent throughout the group, as treelets and lianous taxa alike share relatively short, often wide, vessel elements with simple, transverse perforation plates, and alternate lateral wall pitting; fibriform vessel elements, tracheids associated with vessels, and libriform fibers as additional tracheary ...


Characterization Of Conserved Properties Of Hemagglutinin Of H5n1 And Human Influenza Viruses: Possible Consequences For Therapy And Infection Control, Veljko Veljkovic, Nevena Veljkovic, Claude P. Muller, Sybille Müller, Sanja Glisic, Vladimir Perovic, Heinz Köhler Apr 2009

Characterization Of Conserved Properties Of Hemagglutinin Of H5n1 And Human Influenza Viruses: Possible Consequences For Therapy And Infection Control, Veljko Veljkovic, Nevena Veljkovic, Claude P. Muller, Sybille Müller, Sanja Glisic, Vladimir Perovic, Heinz Köhler

Microbiology, Immunology, and Molecular Genetics Faculty Publications

BACKGROUND: Epidemics caused by highly pathogenic avian influenza virus (HPAIV) are a continuing threat to human health and to the world's economy. The development of approaches, which help to understand the significance of structural changes resulting from the alarming mutational propensity for human-to-human transmission of HPAIV, is of particularly interest. Here we compare informational and structural properties of the hemagglutinin (HA) of H5N1 virus and human influenza virus subtypes, which are important for the receptor/virus interaction.

RESULTS: Presented results revealed that HA proteins encode highly conserved information that differ between influenza virus subtypes H5N1, H1N1, H3N2, H7N7 and ...


Historical Information On Bird Distributions Indicates That Mute Swans Were Introduced To North America, Robert A. Askins Mar 2009

Historical Information On Bird Distributions Indicates That Mute Swans Were Introduced To North America, Robert A. Askins

Biology Faculty Publications

No abstract provided.


Celebrating Darwin's Legacy: Evolution In The Galapagos Islands And The Great Plains, Paul A. Johnsgard Feb 2009

Celebrating Darwin's Legacy: Evolution In The Galapagos Islands And The Great Plains, Paul A. Johnsgard

Papers in Ornithology

An exhibition of photographs by Linda R. Brown, Josef Kren, Paul A. Johnsgard, Allison Johnson, and Stephen Johnson; paintings by Allison Johnson; drawings by Paul A. Johnsgard; and related Darwiniana. Sponsored by the Center for Great Plains Studies, James Stubbendieck, director, and the Great Plains Art Museum, Amber Mohr, curator, in honor of the bicentennial of Charles Darwin's birth (1809-2009) and the 150th anniversary of The Origin of Species (1859).

EXHlBlTORS
Linda R. Brown, Lincoln, Nebraska. B.S. (Pharmacy) University of Nebraska-Lincoln, Lincoln, NE, 1965.
Paul A. Johnsgard, Lincoln, Nebraska. Foundation Professor Emeritus, University of Nebraska-Lincoln. B.S. (Zoology ...


Species Delimitation In Lemurs: Multiple Genetic Loci Reveal Low Levels Of Species Diversity In The Genus Cheirogaleus, Linn F. Groeneveld, David W. Weisrock, Rodin M. Rasoloarison, Anne D. Yoder, Peter M. Kappeler Feb 2009

Species Delimitation In Lemurs: Multiple Genetic Loci Reveal Low Levels Of Species Diversity In The Genus Cheirogaleus, Linn F. Groeneveld, David W. Weisrock, Rodin M. Rasoloarison, Anne D. Yoder, Peter M. Kappeler

Biology Faculty Publications

BACKGROUND: Species are viewed as the fundamental unit in most subdisciplines of biology. To conservationists this unit represents the currency for global biodiversity assessments. Even though Madagascar belongs to one of the top eight biodiversity hotspots of the world, the taxonomy of its charismatic lemuriform primates is not stable. Within the last 25 years, the number of described lemur species has more than doubled, with many newly described species identified among the nocturnal and small-bodied cheirogaleids. Here, we characterize the diversity of the dwarf lemurs (genus Cheirogaleus) and assess the status of the seven described species, based on phylogenetic and ...


Genes, Gene Flow And Adaptation Of Diabrotica Virgifera Virgifera, Nicholas J. Miller, Thomas Guillemaud, Rosanna Giordano, Blair D. Siegfried, Michael E. Gray, Lance J. Meinke, Thomas W. Sappington Feb 2009

Genes, Gene Flow And Adaptation Of Diabrotica Virgifera Virgifera, Nicholas J. Miller, Thomas Guillemaud, Rosanna Giordano, Blair D. Siegfried, Michael E. Gray, Lance J. Meinke, Thomas W. Sappington

Entomology Publications

Diabrotica virgifera virgifera has emerged as a major pest of cultivated maize, due to a combination of its high capacity to inflict economic damage, adaptability to pest management techniques and invasiveness. This review presents a survey of the current state of knowledge about the genetics of D. v. virgifera. In addition, the tools and resources currently available to Diabrotica geneticists are identified, as are areas where knowledge is lacking and research should be prioritized. A substantial amount of information has been published concerning the molecular phylogenetic relationships of D. v. virgifera to other chrysomelids. There is a growing literature focused ...


Xarx2: An Aristaless Homolog That Regulates Brain Regionalization During Development In Xenopus Laevis, Marian Wolanski, Farhad Khosrowshahian, Le Kelly, Michael J. Crawford Jan 2009

Xarx2: An Aristaless Homolog That Regulates Brain Regionalization During Development In Xenopus Laevis, Marian Wolanski, Farhad Khosrowshahian, Le Kelly, Michael J. Crawford

Biological Sciences Publications

The aristaless-related gene, Arx, plays a fundamental role in patterning the brain in humans and mice. Arx mutants exhibit lissencephaly among other anomalies. We have cloned a Xenopus aristaless homolog that appears to define specific regions of the developing forebrain. xArx2 is transcribed in blastula through neurula stages, and comes to be restricted to the ventra and lateral telencephalon, lateral diencephalon, neural floor plate of the anterior spinal cord, and somites. In this respect, Arx2 expresses in regions similar to Arx with the exception of the somites. Overexpression enlarges the telencephalon, and interference by means of antisense morpholino-mediated translation knockdown ...


The Evolution Of Reduced Microbial Killing, Jan A.C. Vriezen Dr., Michael Valliere, Margaret A. Riley Dr. Jan 2009

The Evolution Of Reduced Microbial Killing, Jan A.C. Vriezen Dr., Michael Valliere, Margaret A. Riley Dr.

Jan A.C. Vriezen Dr.

Bacteria engage in a never-ending arms race in which they compete for limited resources and niche space. The outcome of this intense interaction is the evolution of a powerful arsenal of biological weapons. Perhaps the most studied of these are colicins, plasmid-based toxins produced by and active against Escherichia coli. The present study was designed to explore the molecular responses of a colicin-producing strain during serial transfer evolution. What evolutionary changes occur when colicins are produced with no target present? Can killing ability be maintained in the absence of a target? To address these, and other, questions, colicinogenic strains and ...


On The Tendency Of Varieties To Depart Indefinitely From The Original Type (1858), Alfred Russel Wallace Jan 2009

On The Tendency Of Varieties To Depart Indefinitely From The Original Type (1858), Alfred Russel Wallace

Alfred Russel Wallace Classic Writings

No abstract provided.


On The Law Which Has Regulated The Introduction Of New Species (1855), Alfred Russel Wallace Jan 2009

On The Law Which Has Regulated The Introduction Of New Species (1855), Alfred Russel Wallace

Alfred Russel Wallace Classic Writings

No abstract provided.


A Phylogenetic Analysis Of Armored Scale Insects, Based Upon Nuclear, Mitochondrial, And Endosymbiont Gene Sequences, Jeremy C. Andersen Jan 2009

A Phylogenetic Analysis Of Armored Scale Insects, Based Upon Nuclear, Mitochondrial, And Endosymbiont Gene Sequences, Jeremy C. Andersen

Masters Theses 1911 - February 2014

Armored scale insects (Hemiptera: Diaspididae) are among the most invasive insects in the world. They have unusual genetic systems, including diverse types of paternal genome elimination (PGE) and parthenogenesis. Intimate relationships with their host plants and bacterial endosymbionts make them potentially important subjects for the study of co- evolution. Also, in some groups, the adult female never sheds the second instars cuticle, and remains within its confines, a habit referred to as the pupillarial habit. Here we expand upon recent phylogenetic work (Morse and Normark 2006) by analyzing a partitioned dataset including armored scale and endoysmbiont DNA from one hundred ...


The Evolution Of Food Preferences In Coccinellidae, José Adriano Giorgi, Natalia J. Vandenberg, Joseph V. Mchugh, Juanita A. Forrester, S. Adam Ślipiński, Kelly B. Miller, Lori R. Shapiro, Michael F. Whiting Jan 2009

The Evolution Of Food Preferences In Coccinellidae, José Adriano Giorgi, Natalia J. Vandenberg, Joseph V. Mchugh, Juanita A. Forrester, S. Adam Ślipiński, Kelly B. Miller, Lori R. Shapiro, Michael F. Whiting

USDA Systematic Entomology Laboratory

Despite the familiarity and economic significance of Coccinellidae, the family has thus far escaped analysis by rigorous phylogenetic methods. As a result, the internal classification remains unstable and there is no framework with which to interpret evolutionary events within the family. Coccinellids exhibit a wide range of preferred food types spanning kingdoms, and trophic levels. To provide an evolutionary perspective on coccinellid feeding preferences, we performed a phylogenetic analysis of 62 taxa based on the ribosomal nuclear genes 18S and 28S. The entire dataset consists of 3957 aligned nucleotide sites, 787 of which are parsimony informative. Bayesian and parsimony analyses ...


Evolution And Pleiotropy Of Trithorax Function In Arabidopsis, Zoya Avramova Jan 2009

Evolution And Pleiotropy Of Trithorax Function In Arabidopsis, Zoya Avramova

Faculty Publications in the Biological Sciences

The SET domain-containing genes of the TRITHORAX family encode epigenetic factors that maintain the expression of targeted genes. Trithorax homologs have been found in both animals and plants. Since these are thought to have evolved multicellularity independently, common mechanisms of epigenetic regulation must be evolutionarily ancient and derived from a common ancestor. In addition, each lineage has evolved unique mechanisms to expand the original repertoire of epigenetic functions. Phylogenetic analysis of SET domain proteins has outlined some intriguing evolutionary trends. In plants, epigenetic gene silencing mechanisms have been aggressively pursued. In contrast, studies of epigenetic mechanisms maintaining active gene expression ...


Dragon's Paradise Lost: Palaeobiogeography, Evolution And Extinction Of The Largest-Ever Terrestrial Lizards (Varanidae), Scott A. Hocknull, Michael J. Morwood, Rokus Awe, Gerrit D. Van Den Bergh, P Piper, I Kurniawan Jan 2009

Dragon's Paradise Lost: Palaeobiogeography, Evolution And Extinction Of The Largest-Ever Terrestrial Lizards (Varanidae), Scott A. Hocknull, Michael J. Morwood, Rokus Awe, Gerrit D. Van Den Bergh, P Piper, I Kurniawan

Faculty of Science - Papers (Archive)

Background The largest living lizard species, Varanus komodoensis Ouwens 1912, is vulnerable to extinction, being restricted to a few isolated islands in eastern Indonesia, between Java and Australia, where it is the dominant terrestrial carnivore. Understanding how large-bodied varanids responded to past environmental change underpins long-term management of V. komodoensis populations. Methodology/Principal Findings We reconstruct the palaeobiogeography of Neogene giant varanids and identify a new (unnamed) species from the island of Timor. Our data reject the long-held perception that V. komodoensis became a giant because of insular evolution or as a specialist hunter of pygmy Stegodon. Phyletic giantism, coupled ...


Sandy Creek Gorge; Humans, Palaeofloods And Landscape Evolution, John D. Jansen, Derek Fabel Jan 2009

Sandy Creek Gorge; Humans, Palaeofloods And Landscape Evolution, John D. Jansen, Derek Fabel

Faculty of Science - Papers (Archive)

No abstract provided.


Assessment Of Biology Majors’ Versus Nonmajors’ Views On Evolution, Creationism, And Intelligent Design, Guillermo Paz-Y-Mino C., Avelina Espinosa Jan 2009

Assessment Of Biology Majors’ Versus Nonmajors’ Views On Evolution, Creationism, And Intelligent Design, Guillermo Paz-Y-Mino C., Avelina Espinosa

Arts & Sciences Faculty Publications

The controversy around evolution, creationism, and intelligent design resides in a historical struggle between scientific knowledge and popular belief. Four hundred seventy-six students (biology majors n=237, nonmajors n=239) at a secular liberal arts private university in Northeastern United States responded to a five-question survey to assess their views about: (1) evolution, creationism, and intelligent design in the science class; (2) students’ attitudes toward evolution; (3) students’ position about the teaching of human evolution; (4) evolution in science exams; and (5) students’ willingness to discuss evolution openly. There were 60.6% of biology majors and 42% of nonmajors supported ...


Genome-Wide Transcriptional Changes Associated With Allopolyploidy And Fiber Domestication In Cotton (Gossypium Spp. L.), Ryan Adam Rapp Jan 2009

Genome-Wide Transcriptional Changes Associated With Allopolyploidy And Fiber Domestication In Cotton (Gossypium Spp. L.), Ryan Adam Rapp

Graduate Theses and Dissertations

Interspecific hybridization and subsequent genome doubling (allopolyploidy) is a common phenomenon in flowering plant lineages. Within the cotton genus, Gossypium L., two diploid species merged 1-2 mya to form an allopolyploid species that would eventually give rise to 5 distinct species; two of which would be domesticated and dominate world cotton commerce. This series of experiments examines two facets of the human-entwined evolution of the Gossypium genus: one, genome-wide expression alterations associated with the formation of nascent allopolyploids and two, the transcriptome-wide changes in fiber, concomitant with domestication.

To better understand the genome-wide transcriptional changes that occur during the formation ...


Gene Expression Evolution Following Hybridization And Genome Duplication In Cotton (Genus Gossypium), Lex Flagel Jan 2009

Gene Expression Evolution Following Hybridization And Genome Duplication In Cotton (Genus Gossypium), Lex Flagel

Graduate Theses and Dissertations

Polyploidy, or whole genome duplication, is a common feature among plants, occurring in possibly more than half of all angiosperm species. Decades of research has revealed that polyploidy can have profound impacts on phenotypic, genomic, and epigenetic traits. Some changes associated with polyploidy arise immediately from the "genomic shock" caused by duplicating and combining genomes, while other changes result from long-term evolutionary processes that operate on duplicated and redundant genes and genomes. Within this context, this dissertation specifically explores allopolyploidy (polyploidy involving divergent genomes) and its effects on members of the cotton genus (Gossypium). The work in this dissertation focuses ...


Modeling, Simulation, Synthesis, And Optimization Of Biochemical Networks, Kent Allan Vander Velden Jan 2009

Modeling, Simulation, Synthesis, And Optimization Of Biochemical Networks, Kent Allan Vander Velden

Graduate Theses and Dissertations

The benefits of modeling are well recognized throughout engineering. Most systems constructed by people today are simply too complex to fully understand in all situations. The disciplines of systems biology, genetic engineering, and synthetic biology have been influenced by the engineering approach, and as such, as they mature these fields will also benefit from modeling. However, biological systems may prove to be more complicated and so there is an urgent need for advancement of methods for modeling biological systems.

This dissertation chronicles one group's attempt to apply modeling methods to improve their understanding of genotype to phenotype mapping as ...


Molecular Systematics And Phylogeography Of The Genus Richardsonius, Derek Dee Houston Jan 2009

Molecular Systematics And Phylogeography Of The Genus Richardsonius, Derek Dee Houston

UNLV Theses, Dissertations, Professional Papers, and Capstones

The complex geological and climatic events that significantly altered the landscape throughout the Cenozoic Era impacted the diversification of many North American taxa, including freshwater fishes. Here, I employ an array of phylogenetic analyses using a multiple gene tree approach to address several questions regarding the phylogenetic relationships of the North American cyprinid genus Richardsonius and two other closely related genera, Clinostomus and Iotichthys. I also use divergence time estimates generated using fossil calibrations to qualitatively assess the phylogeographic implications of evolution within and among these three genera. Mitochondrial and nuclear DNA sequences show a sister relationship between Iotichthys and ...