Polymorphism of Paraoxonase-2 Gene Is Associated With
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Transcriptome Analysis of Alzheimer's Disease Identifies Links to Cardiovascular Disease
Washington University in St. Louis Washington University Open Scholarship All Computer Science and Engineering Research Computer Science and Engineering Report Number: WUCSE-2008-6 2008-01-01 Transcriptome analysis of Alzheimer's disease identifies links ot cardiovascular disease Monika Ray, Jianhua Ruan, and Weixiong Zhang Follow this and additional works at: https://openscholarship.wustl.edu/cse_research Part of the Computer Engineering Commons, and the Computer Sciences Commons Recommended Citation Ray, Monika; Ruan, Jianhua; and Zhang, Weixiong, "Transcriptome analysis of Alzheimer's disease identifies links ot cardiovascular disease" Report Number: WUCSE-2008-6 (2008). All Computer Science and Engineering Research. https://openscholarship.wustl.edu/cse_research/237 Department of Computer Science & Engineering - Washington University in St. Louis Campus Box 1045 - St. Louis, MO - 63130 - ph: (314) 935-6160. Department of Computer Science & Engineering 2008-6 Transcriptome analysis of Alzheimer's disease identifies links to cardiovascular disease Authors: Monika Ray, Jianhua Ruan, Weixiong Zhang Corresponding Author: [email protected] Type of Report: Other Department of Computer Science & Engineering - Washington University in St. Louis Campus Box 1045 - St. Louis, MO - 63130 - ph: (314) 935-6160 Transcriptome analysis of Alzheimer’s disease identifies links to cardiovascular disease Monika Ray1¤, Jianhua Ruan2¤, Weixiong Zhang1;3 1Washington University School of Engineering, Dept. of Computer Science and Engineering, St. Louis, MO 63130 2University of Texas at San Antonio, Dept. of Computer Science, San Antonio, TX 78249 3Washington University School of Medicine, Dept. of Genetics, St. Louis, MO 63110 Correspondence Email: [email protected] ¤ Co-first authors Abstract Understanding the pathogenesis in the early stages of late-onset Alzheimer’s disease (AD) can help in gaining important mechanistic insights into this devastating neurode- generative disorder. -
Screening and Functional Pathway Analysis of Pulmonary Genes
Hindawi Stem Cells International Volume 2020, Article ID 5684250, 11 pages https://doi.org/10.1155/2020/5684250 Research Article Screening and Functional Pathway Analysis of Pulmonary Genes Associated with Suppression of Allergic Airway Inflammation by Adipose Stem Cell-Derived Extracellular Vesicles Sung-Dong Kim,1 Shin Ae Kang,2 Yong-Wan Kim,3 Hak Sun Yu,2 Kyu-Sup Cho ,1 and Hwan-Jung Roh 4 1Department of Otorhinolaryngology and Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea 2Department of Parasitology and Tropical Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea 3Department of Otorhinolaryngology, Inje University Haeundae Paik Hospital, Republic of Korea 4Department of Otorhinolaryngology and Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea Correspondence should be addressed to Hwan-Jung Roh; [email protected] Received 5 February 2020; Revised 19 May 2020; Accepted 2 June 2020; Published 27 June 2020 Academic Editor: Kar Wey Yong Copyright © 2020 Sung-Dong Kim et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background. Although mesenchymal stem cell- (MSC-) derived extracellular vesicles (EVs) are as effective as MSCs in the suppression of allergic airway inflammation, few studies have explored the molecular mechanisms of MSC-derived EVs in allergic airway diseases. The objective of this study was to evaluate differentially expressed genes (DEGs) in the lung associated with the suppression of allergic airway inflammation using adipose stem cell- (ASC-) derived EVs. -
Association of Paraoxonase-2 Genetic Variation with Serum
ASSOCIATION OF PARAOXONASE-2 GENETIC VARIATION WITH SERUM PARAOXONASE ACTIVITY AND SYSTEMIC LUPUS ERYTHEMATOSUS by Sudeshna Dasgupta B.S., University of Calcutta, India, 2001 M.S., University of Calcutta, India, 2003 Submitted to the Graduate Faculty of Graduate School of Public Health in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Pittsburgh 2008 UNIVERSITY OF PITTSBURGH Graduate School of Public Health This dissertation was presented by Sudeshna Dasgupta It was defended on November 3rd, 2008 and approved by F. Yesim Demirci M.D., Research Assistant Professor, Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh Susan M. Manzi, MD, MPH, Associate Professor, Department of Medicine, School of Medicine and Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh Candace M. Kammerer, Ph.D. Associate Professor, Department of Human Genetics Graduate School of Public Health, University of Pittsburgh Committee Chair Person Robert E. Ferrell, Ph.D. Professor, Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh Dissertation Advisor, M. Ilyas Kamboh, Ph.D. Professor and Chair, Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh ii Dedicated to my mother Mrs. Susmita Dasgupta and my father Dr. Gautam Dasgupta iii Copyright © by Sudeshna Dasgupta 2008 iv M. Ilyas Kamboh PhD ASSOCIATION OF PARAOXONASE-2 GENETIC VARIATION WITH SERUM PARAOXONASE ACTIVITY AND SYSTEMIC LUPUS ERYTHEMATOSUS Sudeshna Dasgupta, PhD University of Pittsburgh, 2008 SLE, a severe autoimmune disease is of major public health relevance since it predominantly affects women at child bearing age and even though immunosuppressives have increased the life span of SLE patients, lack of absolute cure is still troubling. -
PON1) Polymorphisms with Osteoporotic Fracture Risk in Postmenopausal Korean Women
EXPERIMENTAL and MOLECULAR MEDICINE, Vol. 43, No. 2, 71-81, February 2011 Association of Paraoxonase 1 (PON1) polymorphisms with osteoporotic fracture risk in postmenopausal Korean women Beom-Jun Kim1,2*, Shin-Yoon Kim2,6*, PON1 to ascertain its contribution to osteoporotic frac- Yoon Shin Cho3, Bon-Jo Kim3, Bok-Ghee Han3, tures (OFs) and bone mineral density (BMD). We di- Eui Kyun Park2,4, Seung Hun Lee1,2, Ha Young Kim5, rectly sequenced the PON1 gene in 24 Korean in- Ghi Su Kim1,2, Jong-Young Lee3,7 dividuals and identified 26 sequence variants. A large population of Korean postmenopausal women (n = and Jung-Min Koh1,2,7 1,329) was then genotyped for eight selected PON1 polymorphisms. BMD at the lumbar spine and femoral 1Division of Endocrinology and Metabolism neck was measured using dual-energy X-ray ab- Asan Medical Center, University of Ulsan College of Medicine sorptiometry. Lateral thoracolumbar (T4-L4) radio- Seoul 138-736, Korea 2 graphs were obtained for vertebral fracture assess- Skeletal Diseases Genome Research Center Kyungpook National University Hospital ment, and the occurrence of non-vertebral fractures Daegu 700-412, Korea (i.e., wrist, hip, forearm, humerus, rib, and pelvis) was 3The Center for Genome Science examined using self-reported data. Multivariate analy- National Institute of Health ses showed that none of the polymorphisms was asso- Seoul 122-701, Korea ciated with BMD at either site. However, +5989A>G 4Department of Pathology and Regenerative Medicine and +26080T>C polymorphisms were significantly School of Dentistry, Kyungpook National University associated with non-vertebral and vertebral fractures, Daegu 700-412, Korea respectively, after adjustment for covariates. -
Comparative Genome Mapping in the Sequence-Based Era: Early Experience with Human Chromosome 7
Downloaded from genome.cshlp.org on May 28, 2019 - Published by Cold Spring Harbor Laboratory Press First Glimpses/Report Comparative Genome Mapping in the Sequence-based Era: Early Experience with Human Chromosome 7 James W. Thomas,1 Tyrone J. Summers,1 Shih-Queen Lee-Lin,1 Valerie V. Braden Maduro,1 Jacquelyn R. Idol,1 Stephen D. Mastrian,1 Joseph F. Ryan,1 D. Curtis Jamison,1 and Eric D. Green1,2 1Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892 USA The success of the ongoing Human Genome Project has resulted in accelerated plans for completing the human genome sequence and the earlier-than-anticipated initiation of efforts to sequence the mouse genome. As a complement to these efforts, we are utilizing the available human sequence to refine human-mouse comparative maps and to assemble sequence-ready mouse physical maps. Here we describe how the first glimpses of genomic sequence from human chromosome 7 are directly facilitating these activities. Specifically, we are actively enhancing the available human-mouse comparative map by analyzing human chromosome 7 sequence for the presence of orthologs of mapped mouse genes. Such orthologs can then be precisely positioned relative to mapped human STSs and other genes. The chromosome 7 sequence generated to date has allowed us to more than double the number of genes that can be placed on the comparative map. The latter effort reveals that human chromosome 7 is represented by at least 20 orthologous segments of DNA in the mouse genome. A second component of our program involves systematically analyzing the evolving human chromosome 7 sequence for the presence of matching mouse genes and expressed-sequence tags (ESTs). -
Serendipitous Discovery and X-Ray Structure of a Human Phosphate Binding Apolipoprotein
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Structure 14, 601–609, March 2006 ª2006 Elsevier Ltd All rights reserved DOI 10.1016/j.str.2005.12.012 Serendipitous Discovery and X-Ray Structure of a Human Phosphate Binding Apolipoprotein Renaud Morales,1 Anne Berna,2 Philippe Carpentier,1 is the only known transporter capable of binding phos- Carlos Contreras-Martel,1 Fre´de´rique Renault,3 phate ions in human plasma and may become a new Murielle Nicodeme,4 Marie-Laure Chesne-Seck,6 predictor of or a potential therapeutic agent for phos- Franc¸ois Bernier,2 Je´roˆ me Dupuy,1 phate-related diseases such as atherosclerosis. Christine Schaeffer,7 He´le`ne Diemer,7 Alain Van-Dorsselaer,7 Juan C. Fontecilla-Camps,1 Introduction Patrick Masson,3 Daniel Rochu,3 and Eric Chabriere3,5,* Both cholesterol and HDL (high-density lipoprotein) 1 Laboratoire de Cristallogene` se et Cristallographie levels are commonly used as risk predictors of cardio- des Prote´ ines vascular disease (Gordon and Rifkind, 1989; Amann Institut de Biologie Structurale JP EBEL et al., 2003). HDL protects against atherosclerosis 38027 Grenoble mainly through the reverse cholesterol transport pro- France cess in which excess cholesterol is transferred from 2 Institut de Biologie Mole´ culaire des Plantes du CNRS peripheral tissues to the liver by the ATP binding cas- Universite´ Louis Pasteur sette ABCA1 transporter, which is defective in Tangier 67083 Strasbourg Cedex disease (Brooks-Wilson et al., 1999). Although HDLs France have been extensively studied, their metabolic role 3 Unite´ d’Enzymologie has not been completely elucidated yet. -
Paraoxonase Role in Human Neurodegenerative Diseases
antioxidants Review Paraoxonase Role in Human Neurodegenerative Diseases Cadiele Oliana Reichert 1, Debora Levy 1 and Sergio P. Bydlowski 1,2,* 1 Lipids, Oxidation, and Cell Biology Group, Laboratory of Immunology (LIM19), Heart Institute (InCor), Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-900, Brazil; [email protected] (C.O.R.); [email protected] (D.L.) 2 Instituto Nacional de Ciencia e Tecnologia em Medicina Regenerativa (INCT-Regenera), CNPq, Rio de Janeiro 21941-902, Brazil * Correspondence: [email protected] Abstract: The human body has biological redox systems capable of preventing or mitigating the damage caused by increased oxidative stress throughout life. One of them are the paraoxonase (PON) enzymes. The PONs genetic cluster is made up of three members (PON1, PON2, PON3) that share a structural homology, located adjacent to chromosome seven. The most studied enzyme is PON1, which is associated with high density lipoprotein (HDL), having paraoxonase, arylesterase and lactonase activities. Due to these characteristics, the enzyme PON1 has been associated with the development of neurodegenerative diseases. Here we update the knowledge about the association of PON enzymes and their polymorphisms and the development of multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), Alzheimer’s disease (AD) and Parkinson’s disease (PD). Keywords: paraoxonases; oxidative stress; multiple sclerosis; amyotrophic lateral sclerosis; Alzhei- mer’s disease; Parkinson’s disease 1. Introduction Over the years, biotechnological changes and advances have guaranteed the popula- tion a significant increase in life expectancy that does not necessarily involve an increase in quality of life and/or having a healthy old age. -
Mclean, Chelsea.Pdf
COMPUTATIONAL PREDICTION AND EXPERIMENTAL VALIDATION OF NOVEL MOUSE IMPRINTED GENES A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Chelsea Marie McLean August 2009 © 2009 Chelsea Marie McLean COMPUTATIONAL PREDICTION AND EXPERIMENTAL VALIDATION OF NOVEL MOUSE IMPRINTED GENES Chelsea Marie McLean, Ph.D. Cornell University 2009 Epigenetic modifications, including DNA methylation and covalent modifications to histone tails, are major contributors to the regulation of gene expression. These changes are reversible, yet can be stably inherited, and may last for multiple generations without change to the underlying DNA sequence. Genomic imprinting results in expression from one of the two parental alleles and is one example of epigenetic control of gene expression. So far, 60 to 100 imprinted genes have been identified in the human and mouse genomes, respectively. Identification of additional imprinted genes has become increasingly important with the realization that imprinting defects are associated with complex disorders ranging from obesity to diabetes and behavioral disorders. Despite the importance imprinted genes play in human health, few studies have undertaken genome-wide searches for new imprinted genes. These have used empirical approaches, with some success. However, computational prediction of novel imprinted genes has recently come to the forefront. I have developed generalized linear models using data on a variety of sequence and epigenetic features within a training set of known imprinted genes. The resulting models were used to predict novel imprinted genes in the mouse genome. After imposing a stringency threshold, I compiled an initial candidate list of 155 genes. -
Genome-Wide DNA Methylation Dynamics During Epigenetic
Gómez‑Redondo et al. Clin Epigenet (2021) 13:27 https://doi.org/10.1186/s13148‑021‑01003‑x RESEARCH Open Access Genome‑wide DNA methylation dynamics during epigenetic reprogramming in the porcine germline Isabel Gómez‑Redondo1*† , Benjamín Planells1†, Sebastián Cánovas2,3, Elena Ivanova4, Gavin Kelsey4,5 and Alfonso Gutiérrez‑Adán1 Abstract Background: Prior work in mice has shown that some retrotransposed elements remain substantially methylated during DNA methylation reprogramming of germ cells. In the pig, however, information about this process is scarce. The present study was designed to examine the methylation profles of porcine germ cells during the time course of epigenetic reprogramming. Results: Sows were artifcially inseminated, and their fetuses were collected 28, 32, 36, 39, and 42 days later. At each time point, genital ridges were dissected from the mesonephros and germ cells were isolated through magnetic‑ activated cell sorting using an anti‑SSEA‑1 antibody, and recovered germ cells were subjected to whole‑genome bisulphite sequencing. Methylation levels were quantifed using SeqMonk software by performing an unbiased analysis, and persistently methylated regions (PMRs) in each sex were determined to extract those regions showing 50% or more methylation. Most genomic elements underwent a dramatic loss of methylation from day 28 to day 36, when the lowest levels were shown. By day 42, there was evidence for the initiation of genomic re‑methylation. We identifed a total of 1456 and 1122 PMRs in male and female germ cells, respectively, and large numbers of transpos‑ able elements (SINEs, LINEs, and LTRs) were found to be located within these PMRs. Twenty‑one percent of the introns located in these PMRs were found to be the frst introns of a gene, suggesting their regulatory role in the expression of these genes. -
1471-2105-8-217.Pdf
BMC Bioinformatics BioMed Central Software Open Access GenMAPP 2: new features and resources for pathway analysis Nathan Salomonis1,2, Kristina Hanspers1, Alexander C Zambon1, Karen Vranizan1,3, Steven C Lawlor1, Kam D Dahlquist4, Scott W Doniger5, Josh Stuart6, Bruce R Conklin1,2,7,8 and Alexander R Pico*1 Address: 1Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, CA 94158 USA, 2Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA, 3Functional Genomics Laboratory, University of California, Berkeley, CA 94720 USA, 4Department of Biology, Loyola Marymount University, 1 LMU Drive, MS 8220, Los Angeles, CA 90045 USA, 5Computational Biology Graduate Program, Washington University School of Medicine, St. Louis, MO 63108 USA, 6Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064 USA, 7Department of Medicine, University of California, San Francisco, CA 94143 USA and 8Department of Molecular and Cellular Pharmacology, University of California, San Francisco, CA 94143 USA Email: Nathan Salomonis - [email protected]; Kristina Hanspers - [email protected]; Alexander C Zambon - [email protected]; Karen Vranizan - [email protected]; Steven C Lawlor - [email protected]; Kam D Dahlquist - [email protected]; Scott W Doniger - [email protected]; Josh Stuart - [email protected]; Bruce R Conklin - [email protected]; Alexander R Pico* - [email protected] * Corresponding author Published: 24 June 2007 Received: 16 November 2006 Accepted: 24 June 2007 BMC Bioinformatics 2007, 8:217 doi:10.1186/1471-2105-8-217 This article is available from: http://www.biomedcentral.com/1471-2105/8/217 © 2007 Salomonis et al; licensee BioMed Central Ltd. -
Comparative Genome Mapping in the Sequence-Based Era: Early Experience with Human Chromosome 7
Downloaded from genome.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press First Glimpses/Report Comparative Genome Mapping in the Sequence-based Era: Early Experience with Human Chromosome 7 James W. Thomas,1 Tyrone J. Summers,1 Shih-Queen Lee-Lin,1 Valerie V. Braden Maduro,1 Jacquelyn R. Idol,1 Stephen D. Mastrian,1 Joseph F. Ryan,1 D. Curtis Jamison,1 and Eric D. Green1,2 1Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892 USA The success of the ongoing Human Genome Project has resulted in accelerated plans for completing the human genome sequence and the earlier-than-anticipated initiation of efforts to sequence the mouse genome. As a complement to these efforts, we are utilizing the available human sequence to refine human-mouse comparative maps and to assemble sequence-ready mouse physical maps. Here we describe how the first glimpses of genomic sequence from human chromosome 7 are directly facilitating these activities. Specifically, we are actively enhancing the available human-mouse comparative map by analyzing human chromosome 7 sequence for the presence of orthologs of mapped mouse genes. Such orthologs can then be precisely positioned relative to mapped human STSs and other genes. The chromosome 7 sequence generated to date has allowed us to more than double the number of genes that can be placed on the comparative map. The latter effort reveals that human chromosome 7 is represented by at least 20 orthologous segments of DNA in the mouse genome. A second component of our program involves systematically analyzing the evolving human chromosome 7 sequence for the presence of matching mouse genes and expressed-sequence tags (ESTs). -
PON1 Status of Farmworker Mothers and Children As a Predictor of Organophosphate Sensitivity Clement E
Original article 183 PON1 status of farmworker mothers and children as a predictor of organophosphate sensitivity Clement E. Furlonga,*, Nina Hollandb,*, Rebecca J. Richtera, Asa Bradmanb, Alan Hob and Brenda Eskenazib The objective was to determine PON1 status as a predictor the mothers in this cohort would be more susceptible for organophosphorus insecticide sensitivity in a cohort of to the adverse effects of specific organophosphorus Latina mothers and newborns from the Salinas Valley, pesticide exposure due to their PON1 status. Of particular California, an area with high levels of organophosphorus concern are exposures of pregnant mothers and newborns insecticide use. PON1 status was established for 130 with low PON1 status. Pharmacogenetics and Genomics pregnant Latina women and their newborns using a high- 16:183–190 c 2006 Lippincott Williams & Wilkins. throughput two substrate activity/analysis method which plots rates of diazoxon (DZO) hydrolysis against rates of Pharmacogenetics and Genomics 2006, 16:183–190 paraoxon (PO) hydrolysis. Arylesterase activity (AREase) Keywords: children, chlorpyrifos, diazinon, Latino cohort, paraoxonase 1 was determined using phenylacetate as a substrate, (PON1), PON1 status, pregnancy allowing comparison of PON1 levels across PON1192 genotypes in mothers and children. Phenylacetate hydro- aDepartments of Genome Sciences and Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington and bCenter for Children’s lysis is not affected by the Q192R polymorphism. Among Environmental Health, School of Public Health, University of California, Berkeley, newborns, levels of PON1 (AREase) varied by 26-fold California, USA (4.3–110.7 U/ml) and among mothers by 14-fold Correspondence and requests for reprints to Clement Furlong, University (19.8–281.4 U/ml).