Screening of Key Genes Associated with R‑CHOP Immunochemotherapy and Construction of a Prognostic Risk Model in Diffuse Large B‑Cell Lymphoma
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Sex-Specific Hippocampal 5-Hydroxymethylcytosine Is Disrupted in Response to Acute Stress Ligia A
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications, Department of Statistics Statistics, Department of 2016 Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress Ligia A. Papale University of Wisconsin, [email protected] Sisi Li University of Wisconsin, [email protected] Andy Madrid University of Wisconsin, [email protected] Qi Zhang University of Nebraska-Lincoln, [email protected] Li Chen Emory University See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/statisticsfacpub Part of the Other Statistics and Probability Commons Papale, Ligia A.; Li, Sisi; Madrid, Andy; Zhang, Qi; Chen, Li; Chopra, Pankaj; Jin, Peng; Keles, Sunduz; and Alisch, Reid S., "Sex- specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress" (2016). Faculty Publications, Department of Statistics. 62. https://digitalcommons.unl.edu/statisticsfacpub/62 This Article is brought to you for free and open access by the Statistics, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications, Department of Statistics by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Ligia A. Papale, Sisi Li, Andy Madrid, Qi Zhang, Li Chen, Pankaj Chopra, Peng Jin, Sunduz Keles, and Reid S. Alisch This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/statisticsfacpub/62 Neurobiology of Disease 96 (2016) 54–66 Contents lists available at ScienceDirect Neurobiology of Disease journal homepage: www.elsevier.com/locate/ynbdi Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress Ligia A. Papale a,1,SisiLia,c,1, Andy Madrid a,c,QiZhangd,LiChene,PankajChoprae,PengJine, Sündüz Keleş b, Reid S. -
Toxicogenomics Applications of New Functional Genomics Technologies in Toxicology
\-\w j Toxicogenomics Applications of new functional genomics technologies in toxicology Wilbert H.M. Heijne Proefschrift ter verkrijging vand egraa dva n doctor opgeza gva nd e rector magnificus vanWageninge n Universiteit, Prof.dr.ir. L. Speelman, in netopenbaa r te verdedigen op maandag6 decembe r200 4 des namiddagst e half twee ind eAul a - Table of contents Abstract Chapter I. page 1 General introduction [1] Chapter II page 21 Toxicogenomics of bromobenzene hepatotoxicity: a combined transcriptomics and proteomics approach[2] Chapter III page 48 Bromobenzene-induced hepatotoxicity atth etranscriptom e level PI Chapter IV page 67 Profiles of metabolites and gene expression in rats with chemically induced hepatic necrosis[4] Chapter V page 88 Liver gene expression profiles in relation to subacute toxicity in rats exposed to benzene[5] Chapter VI page 115 Toxicogenomics analysis of liver gene expression in relation to subacute toxicity in rats exposed totrichloroethylen e [6] Chapter VII page 135 Toxicogenomics analysis ofjoin t effects of benzene and trichloroethylene mixtures in rats m Chapter VII page 159 Discussion and conclusions References page 171 Appendices page 187 Samenvatting page 199 Dankwoord About the author Glossary Abbreviations List of genes Chapter I General introduction Parts of this introduction were publishedin : Molecular Biology in Medicinal Chemistry, Heijne etal., 2003 m NATO Advanced Research Workshop proceedings, Heijne eral., 2003 81 Chapter I 1. General introduction 1.1 Background /.1.1 Toxicologicalrisk -
Baboon JMP CES Paper
Baboon carboxylesterases 1 and 2: sequences, structures and phylogenetic relationships with human and other primate carboxylesterases Author Holmes, Roger S, Glenn, Jeremy P, VandeBerg, John L, Cox, Laura A Published 2009 Journal Title Journal of Medical Primatology DOI https://doi.org/10.1111/j.1600-0684.2008.00315.x Copyright Statement © 2009 John Wiley & Sons A/S. This is the author-manuscript version of the paper. Reproduced in accordance with the copyright policy of the publisher.The definitive version is available at www.interscience.wiley.com Downloaded from http://hdl.handle.net/10072/29362 Griffith Research Online https://research-repository.griffith.edu.au Baboon Carboxylesterases 1 and 2: Sequences, Structures and Phylogenetic Relationships with Human and other Primate Carboxylesterases Roger S. Holmes 1,2,3 , Jeremy P. Glenn 1, John L. VandeBerg 1,2 , Laura A. Cox 1,2,4 1. Department of Genetics and 2. Southwest National Primate Research Center, Southwest Foundation for Biomedical Research, San Antonio, TX, USA, and 3. School of Biomolecular and Physical Sciences, Griffith University, Nathan. Queensland, Australia 4. Corresponding Author: Laura A. Cox, Ph.D. Department of Genetics Southwest National Primate Research Center Southwest Foundation for Biomedical Research San Antonio, TX, USA 78227 Email: [email protected] Phone: 210-258-9687 Fax: 210-258-9600 Keywords: cDNA sequence; amino acid sequence; 3-D structure Running Head: Carboxylesterases: sequences and phylogeny Published in Journal of Medical Primatology (2009) 38: 27-38. Abstract Background Carboxylesterase (CES) is predominantly responsible for the detoxification of a wide range of drugs and narcotics, and catalyze several reactions in cholesterol and fatty acid metabolism. -
NIH Public Access Author Manuscript Mamm Genome
NIH Public Access Author Manuscript Mamm Genome. Author manuscript; available in PMC 2011 October 8. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Mamm Genome. 2010 October ; 21(9-10): 427±441. doi:10.1007/s00335-010-9284-4. Recommended nomenclature for five mammalian carboxylesterase gene families: human, mouse, and rat genes and proteins Roger S. Holmes Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX 78227-5301, USA Southwest National Primate Research Center, Southwest Foundation for Biomedical Research, San Antonio, TX, USA School of Biomolecular and Physical Sciences, Griffith University, Brisbane, QLD, Australia Matthew W. Wright European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK Stanley J. F. Laulederkind Rat Genome Database, Human Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA Laura A. Cox Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX 78227-5301, USA Southwest National Primate Research Center, Southwest Foundation for Biomedical Research, San Antonio, TX, USA Masakiyo Hosokawa Laboratory of Drug Metabolism and Biopharmaceutics, Chiba Institute of Science, Choshi, Chiba, Japan Teruko Imai Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan Shun Ishibashi Department of Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan Richard Lehner CIHR Group on Molecular and Cell Biology of Lipids, University of Alberta, Edmonton, AB, Canada Masao Miyazaki The Institute of Glycoscience, Tokai University, Kanagawa, Japan Everett J. Perkins Department of Drug Disposition, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA Phillip M. Potter © Springer Science+Business Media, LLC 2010 [email protected] . Holmes et al. -
Proteomic Signatures of Brain Regions Affected by Tau Pathology in Early and Late Stages of Alzheimer's Disease
Neurobiology of Disease 130 (2019) 104509 Contents lists available at ScienceDirect Neurobiology of Disease journal homepage: www.elsevier.com/locate/ynbdi Proteomic signatures of brain regions affected by tau pathology in early and T late stages of Alzheimer's disease Clarissa Ferolla Mendonçaa,b, Magdalena Kurasc, Fábio César Sousa Nogueiraa,d, Indira Plác, Tibor Hortobágyie,f,g, László Csibae,h, Miklós Palkovitsi, Éva Renneri, Péter Dömej,k, ⁎ ⁎ György Marko-Vargac, Gilberto B. Domonta, , Melinda Rezelic, a Proteomics Unit, Department of Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil b Gladstone Institute of Neurological Disease, San Francisco, USA c Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering, Lund University, Lund, Sweden d Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil e MTA-DE Cerebrovascular and Neurodegenerative Research Group, University of Debrecen, Debrecen, Hungary f Institute of Pathology, Faculty of Medicine, University of Szeged, Szeged, Hungary g Centre for Age-Related Medicine, SESAM, Stavanger University Hospital, Stavanger, Norway h Department of Neurology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary i SE-NAP – Human Brain Tissue Bank Microdissection Laboratory, Semmelweis University, Budapest, Hungary j Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary k National Institute of Psychiatry and Addictions, Nyírő Gyula Hospital, Budapest, Hungary ARTICLE INFO ABSTRACT Keywords: Background: Alzheimer's disease (AD) is the most common neurodegenerative disorder. Depositions of amyloid β Alzheimer's disease peptide (Aβ) and tau protein are among the major pathological hallmarks of AD. Aβ and tau burden follows Proteomics predictable spatial patterns during the progression of AD. -
Carboxylesterases in Lipid Metabolism: from Mouse to Human
Protein Cell DOI 10.1007/s13238-017-0437-z Protein & Cell REVIEW Carboxylesterases in lipid metabolism: from mouse to human & Jihong Lian1,2 , Randal Nelson1,2, Richard Lehner1,2,3 1 Group on Molecular and Cell Biology of Lipids, University of Alberta, Edmonton, Alberta, Canada 2 Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada 3 Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada & Correspondence: [email protected] (J. Lian) Received March 2, 2017 Accepted May 31, 2017 Cell & ABSTRACT Hatfield et al., 2016; Fukami et al., 2015; Laizure et al., 2013; Staudinger et al., 2010; Sanghani et al., 2009; Imai, 2006). Mammalian carboxylesterases hydrolyze a wide range However, carboxylesterases have also been demonstrated of xenobiotic and endogenous compounds, including to hydrolyze endogenous esters and thioesters including lipid esters. Physiological functions of car- lipids and some of these enzymes have been shown to play Protein boxylesterases in lipid metabolism and energy home- important physiological functions in lipid metabolism and ostasis in vivo have been demonstrated by genetic energy homeostasis. Recent research endeavors have manipulations and chemical inhibition in mice, and provided more insight into the roles of human car- in vitro through (over)expression, knockdown of boxylesterases in metabolic diseases. expression, and chemical inhibition in a variety of cells. Genes encoding six human carboxylesterases and twenty Recent research advances have revealed the relevance mouse carboxylesterases have been classified. However, of carboxylesterases to metabolic diseases such as given the interspecies diversity of carboxylesterases both in obesity and fatty liver disease, suggesting these the number and primary amino acid sequences there is a enzymes might be potential targets for treatment of need to define functional mouse and human orthologs. -
393LN V 393P 344SQ V 393P Probe Set Entrez Gene
393LN v 393P 344SQ v 393P Entrez fold fold probe set Gene Gene Symbol Gene cluster Gene Title p-value change p-value change chemokine (C-C motif) ligand 21b /// chemokine (C-C motif) ligand 21a /// chemokine (C-C motif) ligand 21c 1419426_s_at 18829 /// Ccl21b /// Ccl2 1 - up 393 LN only (leucine) 0.0047 9.199837 0.45212 6.847887 nuclear factor of activated T-cells, cytoplasmic, calcineurin- 1447085_s_at 18018 Nfatc1 1 - up 393 LN only dependent 1 0.009048 12.065 0.13718 4.81 RIKEN cDNA 1453647_at 78668 9530059J11Rik1 - up 393 LN only 9530059J11 gene 0.002208 5.482897 0.27642 3.45171 transient receptor potential cation channel, subfamily 1457164_at 277328 Trpa1 1 - up 393 LN only A, member 1 0.000111 9.180344 0.01771 3.048114 regulating synaptic membrane 1422809_at 116838 Rims2 1 - up 393 LN only exocytosis 2 0.001891 8.560424 0.13159 2.980501 glial cell line derived neurotrophic factor family receptor alpha 1433716_x_at 14586 Gfra2 1 - up 393 LN only 2 0.006868 30.88736 0.01066 2.811211 1446936_at --- --- 1 - up 393 LN only --- 0.007695 6.373955 0.11733 2.480287 zinc finger protein 1438742_at 320683 Zfp629 1 - up 393 LN only 629 0.002644 5.231855 0.38124 2.377016 phospholipase A2, 1426019_at 18786 Plaa 1 - up 393 LN only activating protein 0.008657 6.2364 0.12336 2.262117 1445314_at 14009 Etv1 1 - up 393 LN only ets variant gene 1 0.007224 3.643646 0.36434 2.01989 ciliary rootlet coiled- 1427338_at 230872 Crocc 1 - up 393 LN only coil, rootletin 0.002482 7.783242 0.49977 1.794171 expressed sequence 1436585_at 99463 BB182297 1 - up 393 -
Age-Dependent Absolute Abundance of Hepatic Carboxylesterases
Supplemental material to this article can be found at: http://dmd.aspetjournals.org/content/suppl/2016/11/28/dmd.116.072652.DC1 1521-009X/45/2/216–223$25.00 http://dx.doi.org/10.1124/dmd.116.072652 DRUG METABOLISM AND DISPOSITION Drug Metab Dispos 45:216–223, February 2017 Copyright ª 2017 by The American Society for Pharmacology and Experimental Therapeutics Age-Dependent Absolute Abundance of Hepatic Carboxylesterases (CES1 and CES2) by LC-MS/MS Proteomics: Application to PBPK Modeling of Oseltamivir In Vivo Pharmacokinetics in Infants s Mikael Boberg, Marc Vrana, Aanchal Mehrotra, Robin E. Pearce, Andrea Gaedigk, Deepak Kumar Bhatt, J. Steven Leeder, and Bhagwat Prasad Department of Pharmaceutics, University of Washington, Seattle, Washington (M.B., M.V., A.M., D.K.B., B.P.); Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden (M.B.); Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children’s Mercy Kansas City, Kansas City, Missouri (R.E.P., A.G., J.S.L.); and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri (R.E.P., A.G., J.S.L.) Received July 22, 2016; accepted November 22, 2016 Downloaded from ABSTRACT The age-dependent absolute protein abundance of carboxylester- milligram total protein) increased approximately 5-fold (315.2 vs. ase (CES) 1 and CES2 in human liver was investigated and ap- 1664.4) and approximately 3-fold (59.8 vs. 174.1) from neonates to plied to predict infant pharmacokinetics (PK) of oseltamivir. The adults, respectively. CES1 protein abundance in liver cytosol also CES absolute protein abundance was determined by liquid showed age-dependent maturation. -
Identification and Characterization of Carboxylesterase Variants
Identification and characterization of Carboxylesterase variants Master thesis for the degree Master of Pharmacy Kathleen Nanding School of Pharmacy The Faculty of Mathematics and Natural Sciences UNIVERSITY OF OSLO Department of Pharmacology OSLO UNIVERSITY HOSPITAL, ULLEVÅL April, 2016 I II III IV Copyright © Kathleen Nanding 2016 Identification and characterization of carboxylesterase variants Kathleen Nanding http://www.duo.uio.no Printed Reprosentralen, University of Oslo V VI Preface This thesis is made as a completion of the master education in Pharmacy and it took place at the Department of Pharmacology, Oslo University Hospital, Ullevål during the period of August 2015 to April 2016. First of all, I would like to express my deep gratitude to my external supervisors Marianne K. Kringen and Kari Bente Foss Haug for all the guidance and support through the entire study. I have learnt so much and I am truely insipired. I would also like to thank Hege Gilbø Bakke for helping me with all the practical problems I had, and for her kindness and patience. Furthermore I would like to thank all the colleagues at the department for their help and for a delightful and warm working atomsphere. I am grateful to my internal supervisor Hege Thoresen for following the progress of my study and for her constructive comments on the thesis. My thanks also go to the Class 2016 and my friends for all the support and for joyful memories through the years of my education. Finally I would like to thank my parents for all the love and encouragement, I would have never completed my education without your support. -
De Novo Transcriptome Assembly and Annotation of Liver and Brain
G C A T T A C G G C A T genes Communication De Novo Transcriptome Assembly and Annotation of Liver and Brain Tissues of Common Brushtail Possums (Trichosurus vulpecula) in New Zealand: Transcriptome Diversity after Decades of Population Control Arsalan Emami-Khoyi 1,2 , Shilpa Pradeep Parbhu 1 , James G. Ross 2 , Elaine C. Murphy 2, Jennifer Bothwell 2 , Daniela M. Monsanto 1 , Bettine Jansen van Vuuren 1 , Peter R. Teske 1 and Adrian M. Paterson 2,* 1 Center for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa; [email protected] (A.E.-K.); [email protected] (S.P.P.); [email protected] (D.M.M.); [email protected] (B.J.v.V.); [email protected] (P.R.T.) 2 Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; [email protected] (J.G.R.); [email protected] (E.C.M.); [email protected] (J.B.) * Correspondence: [email protected] Received: 27 February 2020; Accepted: 10 April 2020; Published: 17 April 2020 Abstract: The common brushtail possum (Trichosurus vulpecula), introduced from Australia in the mid-nineteenth century, is an invasive species in New Zealand where it is widespread and forms the largest self-sustained reservoir of bovine tuberculosis (Mycobacterium bovis) among wild populations. Conservation and agricultural authorities regularly apply a series of population control measures to suppress brushtail possum populations. The evolutionary consequence of more than half a century of intensive population control operations on the species’ genomic diversity and population structure is hindered by a paucity of available genomic resources. -
Report on Research and Other Activities of National Institute of Genetics (During 2014~2018)
Report on Research and Other Activities of National Institute of Genetics (During 2014~2018) ᅜ❧㑇ఏᏛ◊✲ᡤ⮬ᕫホ౯ሗ࿌᭩ National Institute of Genetics October 2019 ᅜ❧㑇ఏᏛ◊✲ᡤ 2019 ᖺ 10 ᭶ CONTENTS 1. Preface 2. Overview of National Institute of Genetics 2 z Our Mission 2 z History 3 z Organization 5 z Outline of Departments and Centers for Research Infrastructures 6 3. Research Achievements and Self Evaluation 7 z Department of Informatics 7 z Department of Genomics and Evolutionary Biology 10 z Department of Gene Function and Phenomics 13 z Department of Chromosome Science 18 z Center for Frontier Research 21 4. Intellectual Infrastructure Center 22 z Bioinformation and DDBJ Center 22 z Advanced Genomics Center 29 z Genetic Resource Center 32 5. Joint Research and Research Meeting (NIG-JOINT), and International Symposium 41 6. Education and Outreach 42 z Graduate Education 42 z Education: Outreach 47 7. Activities to Promote International Interaction and Cooperation 51 8. Office for Research Development 53 9. NIG INNOVATION 55 10. Office for Gender Equality56 11. Publication Lists 57 Preface Director-General: Fumio Hanaoka The National Institute of Genetics (NIG) recently celebrated its 70th anniversary since its founding and continues to strive for excellence in research, service and education. To pursue our commitment to future development, we have initiated an evaluation by an external review committee and have compiled this report which summarizes the activity of NIG during the 5 years from January 2014 to December 2018. NIG was established in 1949 by the Japanese Ministry of Education for comprehensive studies of genetics. In 1984, it was reorganized into an Inter-University Research Institute, and the new designation established an additional official role of NIG: collaboration with researchers at universities. -
Interplay of Placental DNA Methylation and Maternal Insulin Sensitivity in Pregnancy Short Title
Page 1 of 53 Diabetes Title: Interplay of placental DNA methylation and maternal insulin sensitivity in pregnancy Short title: Placental epigenetics of insulin sensitivity Authors: Marie-France Hivert1,2,3; Andres Cardenas4; Catherine Allard5; Myriam Doyon5; Camille E Powe2; Patrick M Catalano6; Patrice Perron3,5; Luigi Bouchard5,7,8 Affiliations 1- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA 2- Diabetes Unit, Massachusetts General Hospital, and Harvard Medical School, Boston, MA USA 3- Department of Medicine, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada 4- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA 5- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada 6- Mother Infant Research Institute, Department of Obstetrics and Gynecology, Tufts Medical Center, Tufts University School of Medicine and Friedman School of Nutrition and Science Policy, Boston, MA, USA 7- Department of Biochemistry, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada 8- Department of Medical Biology, CIUSSS Saguenay-Lac-Saint-Jean — Hôpital de Chicoutimi, Saguenay, QC, Canada *Corresponding Author: Marie-France Hivert, MD Department of Population Medicine Harvard Medical School and Harvard Pilgrim Health Care Institute 401 Park Drive, Suite 401 Boston, MA 02215 Phone: (617) 867-4505; Fax: (617) 867-4845 Email: [email protected] Word count: 3,996 Number of tables: 1 Number of figures: 2 Supplementary Tables: 11 Supplementary Figures 3 Diabetes Publish Ahead of Print, published online December 27, 2019 Diabetes Page 2 of 53 Abstract: The placenta participates in maternal insulin sensitivity changes during pregnancy, however mechanisms remain unclear.