Works Published in 2009
Displaying works 61 - 80 of 165 in total
Sorted by most recent date added to the index first, which may not be the same as publication date order.
2009 journal article
Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics
Proceedings of the National Academy of Sciences of the United States of America, 106(44), 18644–18649.
Contributors: J. Decker, J. Pires, G. Conant* , S. McKay, M. Heaton *, K. Chen *, A. Cooper *, J. Vilkki *
author keywords: ancient DNA; Pecorans; domestication
MeSH headings : Animals; Biological Evolution; Breeding; Cattle; DNA / analysis; DNA / genetics; Extinction, Biological; Fossils; Genomics / methods; Genotype; Phylogeny; Ruminants / genetics
TL;DR:
It is demonstrated that a genome-wide single nucleotide polymorphism (SNP) genotyping platform designed for one species can be used to genotype ancient DNA from an extinct species and DNA from species diverged up to 29 million years ago and that the produced genotypes can beused to resolve the phylogeny for this rapidly radiated infraorder.
(via Semantic Scholar)
www.pnas.org (publisher PDF)
Source: ORCID
Added: September 12, 2019
2009 journal article
Solvent exposure imparts similar selective pressures across a range of yeast proteins
Molecular Biology and Evolution, 26(5), 1155–1161.
Contributors: G. Conant* & P. Stadler *
author keywords: amino acid substitution; evolutionary models; protein structure
MeSH headings : Amino Acid Substitution / genetics; Amino Acids; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae Proteins / chemistry; Saccharomyces cerevisiae Proteins / genetics; Selection, Genetic; Solvents / chemistry; Structural Homology, Protein; Surface Properties
TL;DR:
It is shown that although residue volume and hydropathy are strongly conserved across most alignments, there is little variation in interior versus surface conservation for these two properties.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: September 12, 2019
2009 journal article
Neutral evolution on mammalian protein surfaces
Trends in Genetics, 25(9), 377–381.
Contributors: G. Conant*
MeSH headings : Amino Acid Substitution / genetics; Animals; Evolution, Molecular; Genetic Variation; Humans; Membrane Proteins / chemistry; Membrane Proteins / genetics; Models, Genetic; Mutation; Selection, Genetic
TL;DR:
It is suggested that natural selection can function to preserve protein interactions without requiring strict conservation of the individual residue contacts that impart those interactions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: September 12, 2019
2009 journal article
Up-Regulation of Soluble Axl and Mer Receptor Tyrosine Kinases Negatively Correlates with Gas6 in Established Multiple Sclerosis Lesions
The American Journal of Pathology, 175(1), 283–293.
MeSH headings : ADAM Proteins / metabolism; ADAM10 Protein; ADAM17 Protein; Adult; Aged; Aged, 80 and over; Amyloid Precursor Protein Secretases / metabolism; Blotting, Western; Brain / metabolism; Female; Furin / metabolism; Gene Expression; Humans; Immunohistochemistry; Intercellular Signaling Peptides and Proteins / metabolism; Male; Membrane Proteins / metabolism; Middle Aged; Multiple Sclerosis / genetics; Multiple Sclerosis / metabolism; Neuroglia / metabolism; Oncogene Proteins / metabolism; Proto-Oncogene Proteins / metabolism; Receptor Protein-Tyrosine Kinases / metabolism; Up-Regulation; c-Mer Tyrosine Kinase; Axl Receptor Tyrosine Kinase
TL;DR:
Levels of membrane-bound Mer, soluble Mer, and soluble Axl were all significantly elevated in homogenates from established multiple sclerosis lesions comprised of both chronic active and chronic silent lesions, and dysregulation of protective Gas6 receptor signaling may prolong lesion activity.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2009 journal article
The location of the jaw adductor resultant vector in strepsirrhines
American Journal of Physical Anthropology, 209. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000263442701153&KeyUID=WOS:000263442701153
Contributors: J. Perry & A. Hartstone-Rose
Source: ORCID
Added: September 12, 2019
2009 journal article
Primate Dental Enamel: What It Says about Diet
Comparative Dental Morphology, 13, 44–48. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000276396500009&KeyUID=WOS:000276396500009
Contributors: P. Lucas, P. Constantino, J. Lee, A. Hartstone-Rose , H. Chai, W. Lee, N. Dominy, T. Koppe
Source: ORCID
Added: September 12, 2019
2009 journal article
Demographic history, geographical distribution and reproductive isolation of distinct lineages of blue rockfish (Sebastes mystinus), a marine fish with a high dispersal potential
Journal of Evolutionary Biology, 22(7), 1471–1486.
author keywords: admixture; assignment test; microsatellite loci; mismatch distribution; mtDNA control region; population expansion; reproductive isolation; speciation
MeSH headings : Animals; Fishes / classification; Fishes / genetics; Genetic Speciation; Genetics, Population; Geography; Microsatellite Repeats; Phylogeny
TL;DR:
The spatial distribution, demographic history and degree of genetic distinctiveness found from the genetic analysis, despite the high potential for dispersal in S. mystinus, suggest both lineages diverged in allopatry.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: September 11, 2019
2009 journal article
Long-term effects of environmental endocrine disruptors on reproductive physiology and behavior
Frontiers in Behavioral Neuroscience, 3, 10.
author keywords: bisphenol; genistein; soy; estrogen receptors; development; sexual differentiation
TL;DR:
An overview of how exposure to EDCs, particularly those that interfere with estrogen action, impacts reproductive physiology and behaviors in vertebrates is provided.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Crossref, ORCID
Added: August 25, 2019
2009 journal article
Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD)
BMC Bioinformatics, 10(1).
MeSH headings : Computational Biology / methods; Databases, Factual; Gene Regulatory Networks; Information Storage and Retrieval / methods; Toxicogenetics
TL;DR:
This text-mining project is unique in its integration of existing tools into a single workflow with direct application to CTD, which allowed us to measure the potential of these integrated tools to improve prioritization of journal articles for manual curation.
(via Semantic Scholar)
Sources: Crossref, ORCID
Added: August 10, 2019
2009 journal article
Perturbation of Defense Pathways by Low-Dose Arsenic Exposure in Zebrafish Embryos
Environmental Health Perspectives, 117(6), 981–987.
Contributors: C. Mattingly* , T. Hampton, K. Brothers, N. Griffin & A. Planchart*
author keywords: arsenic; Comparative Toxicogenomics Database; embryonic development; gene regulatory networks; immunity; microarray; toxicogenomics; transcriptional profiling; zebrafish
MeSH headings : Animals; Arsenic / toxicity; Embryo, Nonmammalian; Gene Expression / drug effects; Oligonucleotide Array Sequence Analysis; Reverse Transcriptase Polymerase Chain Reaction; Water Pollutants, Chemical / toxicity; Zebrafish / metabolism
TL;DR:
It is demonstrated that arsenic significantly down-regulates expression levels of multiple genes potentially critical for regulating the establishment of an immune response, and provides molecular evidence consistent with phenotypic observations reported in other model systems.
(via Semantic Scholar)
Sources: Crossref, ORCID
Added: August 10, 2019
2009 journal article
Chemical databases for environmental health and clinical research
Toxicology Letters, 186(1), 62–65.
author keywords: Chemical; Drug; Database; Toxicogenomics
MeSH headings : Animals; Databases, Factual; Drug-Related Side Effects and Adverse Reactions; Environmental Exposure; Environmental Health; Environmental Medicine; Environmental Pollutants / toxicity; Humans; Toxicogenetics
TL;DR:
These databases and their associated resources are incrementally strengthening the expanding field of toxicogenomics-based research by providing centralized sources of manually and computationally curated datasets and highly sophisticated tools for the meta-analysis of continually increasing environmental chemical, drug and small-molecule datasets.
(via Semantic Scholar)
Sources: Crossref, ORCID
Added: August 10, 2019
2009 journal article
Genetic and environmental pathways to complex diseases
BMC Systems Biology, 3(1), 46.
MeSH headings : Databases, Genetic; Disease / genetics; Environment; Evolution, Molecular; Gene Expression Regulation; Genome-Wide Association Study; Genotype; Humans; Mental Disorders / etiology; Mental Disorders / genetics; Mental Disorders / metabolism; Mental Disorders / pathology; Metabolic Diseases / etiology; Metabolic Diseases / genetics; Metabolic Diseases / metabolism; Metabolic Diseases / pathology; Phenotype; Transcription, Genetic
TL;DR:
This analysis identifies natural and synthetic retinoids, antipsychotic medications, Omega 3 fatty acids, and pyrethroid pesticides as potential environmental modulators of metabolic syndrome phenotypes through PPAR and adipocytokine signaling and organophosphate pesticides as potential environmental modulators of neuropsychiatric phenotypes.
(via Semantic Scholar)
Sources: Crossref, ORCID
Added: August 10, 2019
2009 journal article
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks
Nucleic Acids Research, 37(Database), D786–D792.
MeSH headings : Databases, Factual; Disease / etiology; Disease / genetics; Environmental Exposure; Genes; Genomics; Hazardous Substances / toxicity; Humans; Models, Biological; Proteins / drug effects; Proteins / genetics; Systems Integration; Toxicogenetics
TL;DR:
The Comparative Toxicogenomics Database is a curated database that promotes understanding about the effects of environmental chemicals on human health by integrating data to be integrated to construct chemical–gene–disease networks.
(via Semantic Scholar)
Sources: Crossref, ORCID
Added: August 10, 2019
2009 journal article
GeneComps and ChemComps: a new CTD metric to identify genes and chemicals with shared toxicogenomic profiles
Bioinformation, 4(4), 173–174.
author keywords: gene; chemical; toxicogenomic; database; curation
TL;DR:
GeneComps and ChemComps are now provided for every curated gene and chemical in CTD and provide a novel way to view and classify genes and chemicals and will help advance testable hypotheses about environmental chemical-genedisease networks.
(via Semantic Scholar)
Sources: Crossref, ORCID
Added: August 10, 2019
2009 journal article
Profiling Chemicals Based on Chronic Toxicity Results from the U.S. EPA ToxRef Database
Environ Health Perspect, 117(3), 392â399.
Contributors: M. Martin*, R. Judson *, D. Reif* , R. Kavlock* & D. Dix*
author keywords: cancer; chronic toxicity; pesticides; relational database; toxicity profile
MeSH headings : Computational Biology / methods; Databases, Factual; Ecotoxicology / methods; Environmental Pollutants / classification; Environmental Pollutants / toxicity; Pesticides / classification; Pesticides / toxicity; United States; United States Environmental Protection Agency
TL;DR:
The resulting toxicity profile classifications demonstrate the utility of structuring legacy toxicity information and facilitating the computation of these data within ToxRefDB for ToxCast and other applications.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2009 journal article
In Vitro Screening of Environmental Chemicals for Targeted Testing Prioritization: The ToxCast Project
Environ Health Perspect, 118(4), 485â492.
author keywords: in vitro screening; liver proliferative lesions; liver tumors; pathways; ToxCast
MeSH headings : Animals; Cell Line; Cells, Cultured; Computer Simulation; Environmental Pollutants / toxicity; Humans; Rats; Toxicity Tests / methods; United States; United States Environmental Protection Agency
TL;DR:
A statistically significant inverse association between the number of pathways perturbed by a chemical at low in vitro concentrations and the lowest in vivo dose at which a chemical causes toxicity is found.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2009 journal article
A comparison of analytical methods for genetic association studies
Genet. Epidemiol., 33(8), 751â751.
Contributors: A. Motsinger-Reif n, D. Reif* , T. Fanelli* & M. Ritchie*
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: May 14, 2019
2009 journal article
Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination.
Genes and Immunity, 10(2), 112–119.
Contributors: D. Reif* , A. Motsinger-Reif n, B. McKinney *, M. Rock*, J. Crowe Jr. & J. Moore *
author keywords: smallpox; Random Forests; integrated analysis; genetic; proteomic; interactions
MeSH headings : Biomarkers / blood; Cytokines / blood; Cytokines / genetics; Decision Making, Computer-Assisted; Female; Humans; Inflammation / blood; Inflammation / chemically induced; Inflammation / genetics; Intercellular Adhesion Molecule-1 / blood; Intercellular Adhesion Molecule-1 / genetics; Male; Models, Biological; Polymorphism, Single Nucleotide; Proteomics / methods; Smallpox Vaccine / administration & dosage; Smallpox Vaccine / adverse effects; Vaccination
TL;DR:
This study built a comprehensive model of AE development that includes the cytokines intercellular adhesion molecule-1 (ICAM-1 or CD54), interleukin-10 (IL-10), and colony stimulating factor-3 (CSF-3 or G-CSF) and a genetic polymorphism in the cyokine gene interleUKin-4 (IL4).
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: May 14, 2019
2009 journal article
Comparative microarray analysis and pulmonary changes in Brown Norway rats exposed to ovalbumin and concentrated air particulates.
Toxicological Sciences, 108(1), 207–221.
Contributors: B. Heidenfelder*, D. Reif* , J. Harkema*, E. Cohen Hubal *, E. Hudgens*, L. Bramble*, J. Wagner*, M. Morishita*
author keywords: ovalbumin; allergen; asthma; particulate matter; remodeling; inflammation; microarray
MeSH headings : Air Pollutants / toxicity; Allergens / administration & dosage; Allergens / immunology; Analysis of Variance; Animals; Bronchoalveolar Lavage Fluid / chemistry; Bronchoalveolar Lavage Fluid / immunology; Bronchopneumonia / metabolism; Bronchopneumonia / pathology; Gene Expression / drug effects; Inflammation / immunology; Lung / drug effects; Lung / immunology; Lung / metabolism; Lung / pathology; Male; Oligonucleotide Array Sequence Analysis; Ovalbumin / administration & dosage; Ovalbumin / immunology; Particulate Matter / administration & dosage; Particulate Matter / toxicity; Principal Component Analysis; Rats; Respiratory Hypersensitivity / metabolism; Respiratory Hypersensitivity / pathology; Respiratory Mucosa / drug effects; Respiratory Mucosa / immunology; Respiratory Mucosa / metabolism; Respiratory Mucosa / pathology
TL;DR:
The broad-based histopathology and functional genomic analyses demonstrate that exposure to CAPs exacerbates rodents with allergic inflammation induced by an allergen and suggests that asthmatics may be at increased risk for air pollution effects.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2009 journal article
Interspecific adoption of orphaned nests by polistes paper wasps (Hymenoptera: Vespidae)
Journal of Hymenoptera Research, 18(2), 136–139.
Source: NC State University Libraries
Added: August 6, 2018
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