Genomes and Genes
Douglas M Ruden
Affiliation: Wayne State University
- Evidence for an epigenetic mechanism by which Hsp90 acts as a capacitor for morphological evolutionVincent Sollars
Kimmel Cancer Institute, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
Nat Genet 33:70-4. 2003..These findings suggest that Hsp90 acts as a capacitor for morphological evolution through epigenetic and genetic mechanisms...
- Hsp90 inhibitors and the reduction of anti-cancer drug resistance by non-genetic and genetic mechanismsXiangyi Lu
Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA
Pharmaceuticals (Basel) 5:890-8. 2012..We believe that inhibition of these processes can increase the efficacy of Hsp90 inhibitors with other anti-cancer drugs. ..
- Hsp90 affecting chromatin remodeling might explain transgenerational epigenetic inheritance in DrosophilaDouglas M Ruden
Wayne State University, Institute for Environmental Health Sciences, 2727 2 Ave, Room 4000, Detroit, MI 48201, USA
Curr Genomics 9:500-8. 2008....
- Drosophila melanogaster as a model for lead neurotoxicology and toxicogenomics researchHelmut V B Hirsch
Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
Front Genet 3:68. 2012..Studying the effects of lead on Drosophila nervous system development will give us a better understanding of the mechanisms of Pb neurotoxicity in the developing human nervous system...
- Intronic non-CG DNA hydroxymethylation and alternative mRNA splicing in honey beesPablo Cingolani
Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA
BMC Genomics 14:666. 2013..By doing this, we have performed the first whole genome analyses of DNA modifications at non-CG sites in honey bees and correlated the effects of these DNA modifications on gene expression and alternative mRNA splicing...
- CloudAligner: A fast and full-featured MapReduce based tool for sequence mappingTung Nguyen
Computer Science Department, Wayne State University, US
BMC Res Notes 4:171. 2011..Last, it is difficult for a majority of biologists untrained in programming skills to use these tools because most were developed on Linux with a command line interface...
- Potential long-term consequences of fad diets on health, cancer, and longevity: lessons learned from model organism studiesDouglas M Ruden
Institute for Environmental, Health Sciences, 2727 2nd Avenue, Room 4000, Wayne State University, Detroit, MI 48201, USA
Technol Cancer Res Treat 6:247-54. 2007....
- Genetical toxicogenomics in Drosophila identifies master-modulatory loci that are regulated by developmental exposure to leadDouglas M Ruden
Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201 2654, USA
Neurotoxicology 30:898-914. 2009..For these 33 genes, rather than allelic variation at one locus exerting differential effects in two environments, we found that variation at two different loci are required for optimal effects on lead-induced expression...
- The EDGE hypothesis: epigenetically directed genetic errors in repeat-containing proteins (RCPs) involved in evolution, neuroendocrine signaling, and cancerDouglas M Ruden
Institute of Environmental Health Sciences, Wayne State University, Room 4000, 2727 2nd Avenue, Detroit, MI 48201, USA
Front Neuroendocrinol 29:428-44. 2008..In the model, "epigenetic assimilation" of metastable epialleles of RCPs over many generations can lead to mutations directed to those genes, thereby permanently stabilizing the adaptive phenotype...
- Multigenerational epigenetic inheritance in humans: DNA methylation changes associated with maternal exposure to lead can be transmitted to the grandchildrenArko Sen
Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201
Sci Rep 5:14466. 2015..This is the first demonstration that an environmental exposure in pregnant mothers can have an epigenetic effect on the DNA methylation pattern in the grandchildren. ..
- A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3Pablo Cingolani
Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
Fly (Austin) 6:80-92. 2012..As genome sequencing is becoming inexpensive and routine, SnpEff enables rapid analyses of whole-genome sequencing data to be performed by an individual laboratory...
- Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSiftPablo Cingolani
Institute of Environmental Health Sciences, Wayne State University Detroit, MI, USA
Front Genet 3:35. 2012..This technique can also be used to characterize the variety of mutations generated by genotoxic chemicals...
- Massively parallel resequencing of the isogenic Drosophila melanogaster strain w(1118); iso-2; iso-3 identifies hotspots for mutations in sensory perception genesAdrian E Platts
The Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
Fly (Austin) 3:192-203. 2009..Because of the dramatic increase in power in using isogenic lines rather than outbred individuals, the SNP information should be valuable as a test bed for understanding genotype-by-environment interactions in human population studies...
- Lead exposure induces changes in 5-hydroxymethylcytosine clusters in CpG islands in human embryonic stem cells and umbilical cord bloodArko Sen
a Institute of Environmental Health Sciences Wayne State University Detroit, MI, USA
Epigenetics 10:607-21. 2015..In this study we identified several 5hmC and 5mC genomic loci, which we believe might have some potential as early biomarkers of prenatal Pb exposure...
- Hypothesis: environmental regulation of 5-hydroxymethylcytosine by oxidative stressNancy Chia
Institute of Environmental Health Sciences, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
Epigenetics 6:853-6. 2011..We will also discuss how 5-hmC and 5-mC levels at the promoters of specific genes might be a useful biomarker for exposure to environmental toxins...
- Variations at a quantitative trait locus (QTL) affect development of behavior in lead-exposed Drosophila melanogasterHelmut V B Hirsch
Department of Biology, University at Albany, SUNY, Albany, NY 12222, USA
Neurotoxicology 30:305-11. 2009..Drosophila are thus a useful, underutilized model for studying behavioral, synaptic and genetic changes following chronic exposure to lead or other neurotoxins during development...
- Size-Dependent Toxicity of Gold Nanoparticles on Human Embryonic Stem Cells and Their Neural DerivativesMarie Claude Senut
Institute of Environmental Health Sciences, Wayne State University, 275 East Hancock Road, Detroit, MI, 48201, USA
Small 12:631-46. 2016..This work identifies a type of AuNPs highly toxic to hESCs and demonstrates the potential of hESCs in predicting nanotoxicity and characterizing their ability to alter the DNA methylation and hydroxymethylation patterns in the cells...
- Early life lead exposure causes gender-specific changes in the DNA methylation profile of DNA extracted from dried blood spotsArko Sen
Institute of Environmental Health Sciences, Wayne State University, 2727 Second Avenue, Detroit, MI 48201, USA
Epigenomics 7:379-93. 2015..In this paper, we tested the hypothesis that early life lead (Pb) exposure associated DNA methylation (5 mC) changes are dependent on the sex of the child and can serve as biomarkers for Pb exposure...
- Hsp90 inhibitors and drug resistance in cancer: the potential benefits of combination therapies of Hsp90 inhibitors and other anti-cancer drugsXiangyi Lu
Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, United States
Biochem Pharmacol 83:995-1004. 2012..We also discuss recent results from yeast focused on the genetics of drug resistance when Hsp90 is inhibited and the implications that this might have in understanding the effects of genetic variation in treating cancer in humans...
- Lead exposure disrupts global DNA methylation in human embryonic stem cells and alters their neuronal differentiationMarie Claude Senut
Institute of Environmental Health Sciences, C S Mott Center for Human Health and Development, Detroit, Michigan 48201
Toxicol Sci 139:142-61. 2014....
- Hsp90 and environmental impacts on epigenetic states: a model for the trans-generational effects of diethylstibesterol on uterine development and cancerDouglas M Ruden
Department of Environmental Health Sciences, University of Alabama at Birmingham, 35294 0022, USA
Hum Mol Genet 14:R149-55. 2005..This model suggests that inhibitors of Hsp90, WNT signaling and chromatin-remodeling enzymes might function as anticancer agents by interfering with epigenetic reprogramming and canalization in cancer stem cells...
- Methods for nutrigenomics and longevity studies in Drosophila: effects of diets high in sucrose, palmitic acid, soy, or beefJiatao Ye
Department of Environmental Health Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
Methods Mol Biol 371:111-41. 2007..The significance of these results and other types of nutrigenomics and longevity analyses is discussed...
- Possible effects of early treatments of hsp90 inhibitors on preventing the evolution of drug resistance to other anti-cancer drugsLi Xiao
Department of Environmental Health Sciences, University of Alabama at Birmingham, Birmingham, AL 35294 0022, USA
Curr Med Chem 14:223-32. 2007....
- Effectiveness of hsp90 inhibitors as anti-cancer drugsLi Xiao
Department of Environmental Health Sciences, 1530 Ryals Public Health Building, University of Alabama at Birmingham, Birmingham, AL 35294, USA
Mini Rev Med Chem 6:1137-43. 2006..In this mini-review, we present hypothetical mechanisms for Hsp90 inhibitors in treating cancers, preliminary studies in early clinical trials, and potential tumor-killing and tumor-promoting activities of Hsp90 inhibitors...
- Drosophila nutrigenomics can provide clues to human gene-nutrient interactionsDouglas M Ruden
Department of Environmental Health Sciences, University of Alabama at Birmingham, Alabama 35294, USA
Annu Rev Nutr 25:499-522. 2005..This review summarizes what has already been learned in Drosophila nutrigenomics (with an emphasis on lipids and sterols), critically evaluates the data, and discusses fruitful areas for future research...
- Multigenerational selection and detection of altered histone acetylation and methylation patterns: toward a quantitative epigenetics in DrosophilaMark D Garfinkel
Department of Environmental Health Sciences, University of Alabama, Birmingham, USA
Methods Mol Biol 287:151-68. 2004..In this chapter, we present a case study for QE analysis-epigenetic mapping of enhancers of the KrIf-1 ectopic eye bristle phenotype in an isogenic strain of Drosophila melanogaster...
- Waddington's widget: Hsp90 and the inheritance of acquired charactersDouglas M Ruden
Department of Environmental Health Sciences, University of Alabama at Birmingham, Ryals Public Health Building, 1665 University Boulevard, Birmingham, AL 35294 0022, USA
Semin Cell Dev Biol 14:301-10. 2003..This review will discuss evidence for, and arguments against, the role of Hsp90 as a capacitor for morphological evolution, and as a key component of what we call "Waddington's widget."..
- Chromatin effects in nutrition, cancer, and obesityMark D Garfinkel
Department of Environmental Health Sciences, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
Nutrition 20:56-62. 2004
- PKD2 cation channel is required for directional sperm movement and male fertilityZhiqian Gao
Department of Environmental Health Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA
Curr Biol 13:2175-8. 2003..Our data demonstrate that the Drosophila PKD2 cation channel operates in sperm for directional movement inside the female reproductive tract...
- Toxicogenomics of Lead, Mercury, and CadmiumDouglas Ruden; Fiscal Year: 2003....
- Dominant Mutation that Affect EGF-R Signal TransductionDouglas Ruden; Fiscal Year: 2003..It is important to understand regulators of RTK signaling because Ras-Raf dependent neoplasia accounts for as many as one-fifth of all human cancers. ..
- GLUTAMATE BIOSYNTHESIS MUTANTS AND ALCOHOL SENSITIVITYDouglas Ruden; Fiscal Year: 2003..This genetic approach would eventually lead to a better understanding to a better understanding of the genetic influences that underlie risk for alcoholism. ..
- Epigenetics of Dietary and Body Fat in DrosophilaDouglas Ruden; Fiscal Year: 2006..abstract_text> ..