Genome Sequence Of Strain Himb55, A Novel Marine Gammaproteobacterium Of The Om60/Nor5 Clade, 2012 Edith Cowan University
Genome Sequence Of Strain Himb55, A Novel Marine Gammaproteobacterium Of The Om60/Nor5 Clade, Megan Huggett, Michael Rappe
Research outputs 2012
Strain HIMB55 is a phylogenetically unique member of the OM60/NOR5 clade of the Gammaproteobacteria isolated from coastal seawater of Kaneohe Bay on the northeastern shore of Oahu, Hawaii, by extinction culturing in seawater-based oligotrophic medium. Here we present the genome sequence of strain HIMB55, including genes for bacteriochlorophyll-based phototrophy.
Oxygenation Properties And Oxidation Rates Of Mouse Hemoglobins That Differ In Reactive Cysteine Content, 2012 University of Nebraska-Lincoln
Oxygenation Properties And Oxidation Rates Of Mouse Hemoglobins That Differ In Reactive Cysteine Content, Jay F. Storz, Roy E. Weber, Angela Fago
Jay F. Storz Publications
House mice (genus Mus) harbor extensive allelic variation at two tandemly duplicated genes that encode the β-chain subunits of adult hemoglobin (Hb). Alternative haplotypes differ in the level of sequence divergence between the two β-globin gene duplicates: the Hbbd and Hbbp haplotypes harbor two structurally distinct β-globin genes, whereas the Hbbs haplotype harbors two β-globin duplicates that are identical in sequence. One especially salient difference between the s-type Hbs relative to the d- and p-type Hbs relates to the number of reactive β-chain cysteine residues. In addition to the highly conserved cysteine residue …
Regulatory Changes Contribute To The Adaptive Enhancement Of Thermogenic Capacity In High-Altitude Deer Mice, 2012 University of Nebraska-Lincoln
Regulatory Changes Contribute To The Adaptive Enhancement Of Thermogenic Capacity In High-Altitude Deer Mice, Zachary A. Cheviron, Gwendolyn C. Bachman, Alex D. Connaty, Jay F. Storz
Jay F. Storz Publications
In response to hypoxic stress, many animals compensate for a reduced cellular O2 supply by suppressing total metabolism, thereby reducing O2 demand. For small endotherms that are native to high-altitude environments, this is not always a viable strategy, as the capacity for sustained aerobic thermogenesis is critical for survival during periods of prolonged cold stress. For example, survivorship studies of deer mice (Peromyscus maniculatus) have demonstrated that thermogenic capacity is under strong directional selection at high altitude. Here, we integrate measures of whole-organism thermogenic performance with measures of metabolic enzyme activities and genomic transcriptional profiles to …
Genetic Diversity Of Neotropical Myotis (Chiroptera: Vespertilionidae) With An Emphasis On South American Species, 2012 Texas Tech University
Genetic Diversity Of Neotropical Myotis (Chiroptera: Vespertilionidae) With An Emphasis On South American Species, Roxanne J. Larsen, Michelle C. Knapp, Hugh H. Genoways, Faisal Ali Anwarali Khan, Peter A. Larsen, Don E. Wilson, Robert J. Baker
University of Nebraska State Museum: Mammalogy Papers
Background: Cryptic morphological variation in the Chiropteran genus Myotis limits the understanding of species boundaries and species richness within the genus. Several authors have suggested that it is likely there are unrecognized species-level lineages of Myotis in the Neotropics. This study provides an assessment of the diversity in New World Myotis by analyzing cytochrome-b gene variation from an expansive sample ranging throughout North, Central, and South America. We provide baseline genetic data for researchers investigating phylogeographic and phylogenetic patterns of Myotis in these regions, with an emphasis on South America.
Methodology and Principal Findings: Cytochrome-b sequences were …
Widespread Triploidy In Western North American Aspen (Populus Tremuloides), 2012 Utah State University
Widespread Triploidy In Western North American Aspen (Populus Tremuloides), Karen E. Mock, Colin M. Callahan, M. Nurul Islam-Faridi, John D. Shaw, Hardeep S. Rai, Stewart C. Sanderson, Carol A. Rowe, Ronald J. Ryel, Michael D. Madritch, Richard S. Gardner, Paul G. Wolf
Aspen Bibliography
No abstract provided.
In Silico Prediction Of Protein-Protein Interactions Between Cronobacter Sakazakii And Human Host, 2012 Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland.
In Silico Prediction Of Protein-Protein Interactions Between Cronobacter Sakazakii And Human Host, Sean Held
Theses
The genus Cronobacter accommodates 16 biogroups of the emerging opportunistic pathogen known formerly as Enterobacter sakazakii. Cronobacter are occasional contaminants of milk powder and, consequently, powdered infant formula (PIT). Since it is a pathogen that is transmitted in infant formula it represents a significant health risk to neonates. These bacteria are opportunistic pathogens (can only cause disease when the host's resistance is low) and are linked with life-threatening infections in neonates. Some of the clinical symptoms of Cronohacter infection include necrotizing enterocolitis, bacteremia, and meningitis, with case fatality rates of 50-80% being reported (Healy et al. 2010). Infant formula manufacturers …
Design Of A Distributed Hadoop Solution For The Multiple Sequence Alignment Algorithm: Clustal Omega, 2012 Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland,
Design Of A Distributed Hadoop Solution For The Multiple Sequence Alignment Algorithm: Clustal Omega, Jurate Daugelaite
Theses
Multiple Sequence Alignment (MSA) of DNA and protein sequences is one of the most essential techniques in the fields of molecular biology, computational biology and bioinformatics. It aids the identification and prediction of three dimensional structures, primary functions and evolutionary relatedness amongst groups of species, organisms, and genes. Since as the completion of the Human Genome Project and with the advent of sequencing initiatives such as the Genome 10K project, the rate of genome sequencing has increased exponentially, producing vast amounts of DNA and protein sequences. MSA algorithms, when applied to such sequence data, can identify common homology, structure and …
Dynamic Herbal Monographs For A Digital World, 2012 School of Science and Informatics, Cork Institute of Technology, Cork, Ireland.
Dynamic Herbal Monographs For A Digital World, Niamh O'Brien
Theses
Post analysis of a worldwide survey of Medical Herbalists, 93% of respondents were in favour of an online system which could update monographs dynamically. 63% of respondents suggested that some current monographs are out of date and lack certain practicalities in areas such as : Interactions, Dosage and Safety. Research into gaining optimal responses from surveys led to a 78% response rate. Survey analysis resulted in a modem up-to-date monograph template being created and each of the aforementioned information systems tested against same. Testing involved the generation of XML, HTML, PHP and OWL languages for encoding documents to allow for …
Successful Genotyping Of Microsatellites In The Woolly Mammoth, 2012 Old Dominion University
Successful Genotyping Of Microsatellites In The Woolly Mammoth, Yasuko Ishida, Alfred L. Roca, Stephen Fratpietro, Alex D. Greenwood
Biological Sciences Faculty Publications
Genetic analyses using ancient DNA from Pleistocene and early Holocene fossils have largely relied on mitochondrial DNA (mtDNA) sequences. Among woolly mammoths, Mammuthus primigenius, mtDNA analyses have identified 2 distinct clades (I and II) that diverged 1-2 Ma. Here, we establish that microsatellite markers can be effective on Pleistocene samples, successfully genotyping woolly mammoth specimens at 2 loci. Although significant differentiation at the 2 microsatellite loci was not detected between 16 clade I and 4 clade II woolly mammoths, our results demonstrate that the nuclear population structure of Pleistocene species can be examined using fast-evolving nuclear microsatellite markers.
Identification Of Cellular Functions Of Cardiolipin As Physiological Modifiers Of Barth Syndrome, 2012 Wayne State University
Identification Of Cellular Functions Of Cardiolipin As Physiological Modifiers Of Barth Syndrome, Amit Shridhar Joshi
Wayne State University Dissertations
Cardiolipin (CL) is an anionic phospholipid synthesized in the mitochondrial inner membrane. Perturbation of CL metabolism leads to Barth syndrome (BTHS), a life threatening genetic disorder. I utilized genetic, biochemical and cell biological approaches in yeast to elucidate the cellular functions of CL. Understanding the functions of CL is expected to shed light on the pathology and possible treatments for BTHS.
BTHS is caused by mutations in TAZ1, which encodes a CL remodeling enzyme called tafazzin. BTHS patients exhibit a wide range of clinical presentations, indicating that physiological modifiers influence the BTHS phenotype. A targeted synthetic lethality screen was performed …
Development And Application Of Methods Used To Source Prehistoric Southwestern Maize: A Review, 2012 U.S. Geological Survey
Development And Application Of Methods Used To Source Prehistoric Southwestern Maize: A Review, Larry Benson
United States Geological Survey: Staff Publications
Archaeological cobs free of mineral contaminants should be used to source the soils in which they were grown. Mineral contaminants often contain much higher concentrations of metals than vegetal materials and can alter a cob’s apparent metal and heavy-isotope content. Cleaning a cob via immersion in an acid solution for more than a few minutes will result in the incongruent and sometimes complete leaching of metals, including strontium (Sr), from the cob. When using 87Sr/86Sr to determine the location of potential agriculture fields, it is best to either integrate several depth-integrated soil samples or to integrate several …
Patterns Of Population Structure And Historical Dispersal In Squaloid Sharks: A Species-Level Approach Using Molecular Markers, 2012 College of William and Mary - Virginia Institute of Marine Science
Patterns Of Population Structure And Historical Dispersal In Squaloid Sharks: A Species-Level Approach Using Molecular Markers, Ana Christina Pimenta Verissimo
Dissertations, Theses, and Masters Projects
Squaloids (Order Squaliformes) are a highle diverse group of mostly deepwater habitats (> 200 m). Many species are regularly caught in commercial fisheries worldwide but their low productivity and correspondingly low intrinsic rebound potentials make them particularly vulnerable to population depletion and overexploitation. of special concern to fisheries management and conservation efforts are the spiny dogfish Squalus acanthias, the leafscale gulper shark Centrophorus squamosus and the Portuguese dogfish Centroscymnus coelolepis. These taxa have recently been declared overfished in several parts of each species' distribution but management efforts have been made to recover the "stocks" without a good understanding of the …
Pando Clone (World's Largest Living Organism?) History And Evaluation : Case Study For Revalidation, 2012 Utah State University
Pando Clone (World's Largest Living Organism?) History And Evaluation : Case Study For Revalidation, Allen V. Henningson
Aspen Bibliography
No abstract provided.
Inheritance Of Humeral Spotting In The Croaking Gourami (Osphronemidae: Trichopsis Vittatus), 2012 Howard University
Inheritance Of Humeral Spotting In The Croaking Gourami (Osphronemidae: Trichopsis Vittatus), Jack Frankel, Lisa Alder-Golden, Andre Porter
Department of Biology Faculty Publications
The croaking gourami (Trichopsis vittatus) exhibits two phenotypes associated with humeral spotting. Fish possess a prominent, dark humeral patch or spot located behind the operculum or lack this spotting pattern. Segregation patterns observed from the progenies of eleven different crosses support the hypothesis that the inheritance of humeral spotting in T. vittatus is controlled by the action of a single autosomal locus, with complete dominance of the allele controlling the spotted phenotype.
Decision Memo: Pando Aspen Clone Restoration Project, 2012 Utah State University
Decision Memo: Pando Aspen Clone Restoration Project, Kurt Robins
Aspen Bibliography
The Pando Clone is located in Township 26 South, Range 1 East, Sections 24 and 25 about 1 mile southwest of the Lakeside Resort on State Highway 25 and about 1 mile due east of Mallard Bay at the southwest corner of Fish Lake (see map). The Pando Clone is the largest aspen clone in the world and the largest (most massive) single living organism in existence that has been discovered to date (Grant, 1993; DeWoody et al, 2008). It encompasses approximately 106 acres and is estimated to weigh in excess of 13 million pounds (Grant, 1993). This clone is …
Causes And Consequences Of Mitochondrial Variation In Caenorhabditid Nematodes, 2012 Portland State University
Causes And Consequences Of Mitochondrial Variation In Caenorhabditid Nematodes, Kiley Ann Hicks
Dissertations and Theses
Mitochondria are dynamic organelles that harbor their own stream-lined genome and generate much of the ATP necessary to sustain eukaryotic life via an electron transport chain (ETC). Because of the central role for mitochondria in organismal physiology, mitochondrial genetic and phenotypic variation can alter organismal fitness and affect population genetic and evolutionary outcomes. Despite the far-reaching relevance of mitochondria to evolutionary processes and human health, we lack a basic understanding of the causes and consequences of mitochondrial genetic and phenotypic variation. In this thesis, I quantified mitochondrial reactive oxygen species (ROS), membrane potential (δΨM), and mitochondrial morphological traits within Caenorhabditis …
Dna Secondary Structures And Their Contribution To Mutagenesis In B. Subtilis Stationary Phase Cells, 2012 University of Nevada, Las Vegas
Dna Secondary Structures And Their Contribution To Mutagenesis In B. Subtilis Stationary Phase Cells, Carmen Vallin, Holly Anne Martin, Christian Ross, Ronald Yasbin, Eduardo Robleto
McNair Poster Presentations
It is widely known and accepted that the cause of many mutations in cells are generated during the replication process of actively dividing cells, however more recent research has shown that mutations also arise in non growing conditions, a phenomenon known as stationary phase mutagenesis. Much of what is known come from studies in eukaryotic and bacterial models. It has been proposed that in non-growing cells, the process of transcription plays an important role in mutagenesis. We test the hypothesis that DNA secondary structures, formed during transcription, promote mutagenesis. The transcription-generated structures are speculated to be prone to by blocking …
The Role Of Chromatin And Cofactors In The Transcriptional Memory Effect Exerted In Saccharomyces Cerevisiae, 2012 University at Albany, State University of New York
The Role Of Chromatin And Cofactors In The Transcriptional Memory Effect Exerted In Saccharomyces Cerevisiae, Emily Leigh Paul
Legacy Theses & Dissertations (2009 - 2024)
Abf1 and Rap1 are functionally similar general regulatory factors (GRFs) found in Saccharomyces cerevisiae . Abf1, in its role as a transcriptional activator, exerts a memory effect on some genes under its control. This effect results in transcription levels remaining steady when Abf1 dissociates from its binding site in a conditional mutant. In contrast, Rap1 fails to elicit the same effect on its regulatory targets. Transcriptional memory effects have been observed in many fields of study, including immunology, cancer, and stem cells, and conservation of transcription machinery will allow studies in yeast to be applied to higher organisms.
The Role Of Ess1 In Survival, Morphogenetic Switching And Transcription In The Fungal Pathogen Candida Albicans, 2012 University at Albany, State University of New York
The Role Of Ess1 In Survival, Morphogenetic Switching And Transcription In The Fungal Pathogen Candida Albicans, Dhanushki Poornima Samaranayake
Legacy Theses & Dissertations (2009 - 2024)
Candida albicans is a fungal pathogen that causes serious infections among immune-compromised patients and premature infants. C. albicans can become drug resistant, therefore, identifying new antifungal drug targets is an important goal. Here, we study a peptidyl-prolyl cis/trans isomerase called Ess1 as a potential drug target. Ess1 is conserved among pathogenic fungi, and therefore, potential inhibitors of Ess1 should display a broad spectrum of activity. We confirm that Ess1 is essential for growth in Candida albicans, but unlike the previously published find, deleting one copy of the C. albicans ESS1 gene did not affect morphogenetic switching. However, further reducing activity …
Protein Structure Networks, 2012 Old Dominion University
Protein Structure Networks, Lesley H. Greene
Chemistry & Biochemistry Faculty Publications
The application of the field of network science to the scientific disciplines of structural biology and biochemistry, have yielded important new insights into the nature and determinants of protein structures, function, dynamics and the folding process. Advancements in further understanding protein relationships through network science have also reshaped the way we view the connectivity of proteins in the protein universe. The canonical hierarchical classification can now be visualized for example, as a protein fold continuum. This review will survey several key advances in the expanding area of research being conducted to study protein structures and folding using network approaches.