Whole Genome Sequence of a Turkish Individual
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Function and Gene Expression of Circulating Neutrophils in Dairy Cows: Impact of Micronutrient Supplementation
FUNCTION AND GENE EXPRESSION OF CIRCULATING NEUTROPHILS IN DAIRY COWS: IMPACT OF MICRONUTRIENT SUPPLEMENTATION A Dissertation Presented to The Faculty of the Graduate School At The University of Missouri In Partial Fulfillment Of the Requirements for the Degree Doctor of Philosophy By Xavier S. Revelo Dr. Matthew R. Waldron, Dissertation Supervisor July, 2012 ©Copyright by Xavier S. Revelo 2012 All rights reserved The undersigned, appointed by the dean of the Graduate School, have examined the dissertation entitled: FUNCTION AND GENE EXPRESSION OF CIRCULATING NEUTROPHILS IN DAIRY COWS: IMPACT OF MICRONUTRIENT SUPPLEMENTATION Presented by Xavier Revelo A candidate for the degree of Doctor of Philosophy in Animal Sciences And hereby certify that, in their opinion, it is worthy of acceptance. Dissertation Examination Committee: ________________________ Advisor Matthew R. Waldron, Ph.D. ________________________ Kevin L. Fritsche, Ph.D. ________________________ Matthew C. Lucy, Ph.D. ________________________ James W. Perfield, Ph.D. ACKNOWLEDGEMENTS First of all, I would like to thank my family for their patience, love and inseparable support even after all the years that I have been away from home. Thanks to my mother Sonia for dedicating her life to the guidance, inspiration, and nurturance of our family. I have been blessed with a loving and devoted family who gave me the motivation I needed to pursue my professional goals. I would also like to offer my sincerest gratitude to the friends I made while pursuing my doctorate degree at the University of Missouri. Special thanks to Daniel Mathew, Brad Scharf, Ky Pohler, Eric Coate, and Emma Jinks for sharing their time and friendship. -
A Single-Cell Transcriptomic Landscape of Primate Arterial Aging
ARTICLE https://doi.org/10.1038/s41467-020-15997-0 OPEN A single-cell transcriptomic landscape of primate arterial aging Weiqi Zhang 1,2,3,4,5,13, Shu Zhang6,7,13, Pengze Yan3,8,13, Jie Ren7,9,13, Moshi Song3,5,8, Jingyi Li2,3,8, Jinghui Lei4, Huize Pan2,3, Si Wang3,5,8, Xibo Ma3,10, Shuai Ma2,3,8, Hongyu Li2,3, Fei Sun2,3, Haifeng Wan3,5,11, ✉ ✉ ✉ Wei Li 3,5,11, Piu Chan4, Qi Zhou3,5,11, Guang-Hui Liu 2,3,4,5,8 , Fuchou Tang 6,7,9,12 & Jing Qu 3,5,11 Our understanding of how aging affects the cellular and molecular components of the vas- 1234567890():,; culature and contributes to cardiovascular diseases is still limited. Here we report a single-cell transcriptomic survey of aortas and coronary arteries in young and old cynomolgus monkeys. Our data define the molecular signatures of specialized arteries and identify eight markers discriminating aortic and coronary vasculatures. Gene network analyses characterize tran- scriptional landmarks that regulate vascular senility and position FOXO3A, a longevity- associated transcription factor, as a master regulator gene that is downregulated in six subtypes of monkey vascular cells during aging. Targeted inactivation of FOXO3A in human vascular endothelial cells recapitulates the major phenotypic defects observed in aged monkey arteries, verifying FOXO3A loss as a key driver for arterial endothelial aging. Our study provides a critical resource for understanding the principles underlying primate arterial aging and contributes important clues to future treatment of age-associated vascular disorders. 1 CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. -
5' Untranslated Region Elements Show High Abundance and Great
International Journal of Molecular Sciences Article 0 5 Untranslated Region Elements Show High Abundance and Great Variability in Homologous ABCA Subfamily Genes Pavel Dvorak 1,2,* , Viktor Hlavac 2,3 and Pavel Soucek 2,3 1 Department of Biology, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic 2 Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; [email protected] (V.H.); [email protected] (P.S.) 3 Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic * Correspondence: [email protected]; Tel.: +420-377593263 Received: 7 October 2020; Accepted: 20 November 2020; Published: 23 November 2020 Abstract: The 12 members of the ABCA subfamily in humans are known for their ability to transport cholesterol and its derivatives, vitamins, and xenobiotics across biomembranes. Several ABCA genes are causatively linked to inborn diseases, and the role in cancer progression and metastasis is studied intensively. The regulation of translation initiation is implicated as the major mechanism in the processes of post-transcriptional modifications determining final protein levels. In the current bioinformatics study, we mapped the features of the 50 untranslated regions (50UTR) known to have the potential to regulate translation, such as the length of 50UTRs, upstream ATG codons, upstream open-reading frames, introns, RNA G-quadruplex-forming sequences, stem loops, and Kozak consensus motifs, in the DNA sequences of all members of the subfamily. Subsequently, the conservation of the features, correlations among them, ribosome profiling data as well as protein levels in normal human tissues were examined. The 50UTRs of ABCA genes contain above-average numbers of upstream ATGs, open-reading frames and introns, as well as conserved ones, and these elements probably play important biological roles in this subfamily, unlike RG4s. -
Molecular Structure of a Novel Cholesterol-Responsive a Subclass ABC Transporter, ABCA9
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Regensburg Publication Server BBRC Biochemical and Biophysical Research Communications 295 (2002) 408–416 www.academicpress.com Molecular structure of a novel cholesterol-responsive A subclass ABC transporter, ABCA9 Armin Piehler,1 Wolfgang E. Kaminski,1 Juurgen€ J. Wenzel, Thomas Langmann, and Gerd Schmitz* Institute for Clinical Chemistry and Laboratory Medicine, University of Regensburg, Franz-Josef-Strauß-Allee 11, D-93042, Regensburg, Germany Received 25 May 2002 Abstract We recently identified a novel ABC A subclass transporter, ABCA6, in human macrophages. Here, we report the molecular cloning of an additional ABC A subfamily transporter from macrophages denoted ABCA9. The identified coding sequence is 4.9 kb in size and codes for a 1624 amino acid protein product. In accordance with the proposed nomenclature, the novel transporter was designated ABCA9. The putative full-length ABC transporter polypeptide consists of two transmembrane domains and two nu- cleotide binding folds and thus conforms to the group of full-size ABC transporters. We identified alternative ABCA9 mRNA variants in human macrophages that predict the existence of three truncated forms of the novel transporter. Among the human ABC A subfamily transporters, ABCA9 exhibits the highest amino acid sequence homology with ABCA8 (72%) and ABCA6 (60%), respectively. The striking amino acid sequence similarity between these transporter molecules supports the notion that they represent an evolutionary more recently emerged subgroup within the family of ABC A transporters, which we refer to as ‘‘ABCA6-like transporters.’’ ABCA9 mRNA is ubiquitously expressed with the highest mRNA levels in heart, brain, and fetal tissues. -
Transcriptional and Post-Transcriptional Regulation of ATP-Binding Cassette Transporter Expression
Transcriptional and Post-transcriptional Regulation of ATP-binding Cassette Transporter Expression by Aparna Chhibber DISSERTATION Submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Pharmaceutical Sciences and Pbarmacogenomies in the Copyright 2014 by Aparna Chhibber ii Acknowledgements First and foremost, I would like to thank my advisor, Dr. Deanna Kroetz. More than just a research advisor, Deanna has clearly made it a priority to guide her students to become better scientists, and I am grateful for the countless hours she has spent editing papers, developing presentations, discussing research, and so much more. I would not have made it this far without her support and guidance. My thesis committee has provided valuable advice through the years. Dr. Nadav Ahituv in particular has been a source of support from my first year in the graduate program as my academic advisor, qualifying exam committee chair, and finally thesis committee member. Dr. Kathy Giacomini graciously stepped in as a member of my thesis committee in my 3rd year, and Dr. Steven Brenner provided valuable input as thesis committee member in my 2nd year. My labmates over the past five years have been incredible colleagues and friends. Dr. Svetlana Markova first welcomed me into the lab and taught me numerous laboratory techniques, and has always been willing to act as a sounding board. Michael Martin has been my partner-in-crime in the lab from the beginning, and has made my days in lab fly by. Dr. Yingmei Lui has made the lab run smoothly, and has always been willing to jump in to help me at a moment’s notice. -
Interindividual Differences in the Expression of ATP-Binding
Supplemental material to this article can be found at: http://dmd.aspetjournals.org/content/suppl/2018/02/02/dmd.117.079061.DC1 1521-009X/46/5/628–635$35.00 https://doi.org/10.1124/dmd.117.079061 DRUG METABOLISM AND DISPOSITION Drug Metab Dispos 46:628–635, May 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Special Section on Transporters in Drug Disposition and Pharmacokinetic Prediction Interindividual Differences in the Expression of ATP-Binding Cassette and Solute Carrier Family Transporters in Human Skin: DNA Methylation Regulates Transcriptional Activity of the Human ABCC3 Gene s Tomoki Takechi, Takeshi Hirota, Tatsuya Sakai, Natsumi Maeda, Daisuke Kobayashi, and Ichiro Ieiri Downloaded from Department of Clinical Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan (T.T., T.H., T.S., N.M., I.I.); Drug Development Research Laboratories, Kyoto R&D Center, Maruho Co., Ltd., Kyoto, Japan (T.T.); and Department of Clinical Pharmacy and Pharmaceutical Care, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan (D.K.) Received October 19, 2017; accepted January 30, 2018 dmd.aspetjournals.org ABSTRACT The identification of drug transporters expressed in human skin and levels. ABCC3 expression levels negatively correlated with the methylation interindividual differences in gene expression is important for understanding status of the CpG island (CGI) located approximately 10 kilobase pairs the role of drug transporters in human skin. In the present study, we upstream of ABCC3 (Rs: 20.323, P < 0.05). The reporter gene assay revealed evaluated the expression of ATP-binding cassette (ABC) and solute carrier a significant increase in transcriptional activity in the presence of CGI. -
1 Fibrillar Αβ Triggers Microglial Proteome Alterations and Dysfunction in Alzheimer Mouse 1 Models 2 3 4 Laura Sebastian
bioRxiv preprint doi: https://doi.org/10.1101/861146; this version posted December 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Fibrillar triggers microglial proteome alterations and dysfunction in Alzheimer mouse 2 models 3 4 5 Laura Sebastian Monasor1,10*, Stephan A. Müller1*, Alessio Colombo1, Jasmin König1,2, Stefan 6 Roth3, Arthur Liesz3,4, Anna Berghofer5, Takashi Saito6,7, Takaomi C. Saido6, Jochen Herms1,4,8, 7 Michael Willem9, Christian Haass1,4,9, Stefan F. Lichtenthaler 1,4,5# & Sabina Tahirovic1# 8 9 1 German Center for Neurodegenerative Diseases (DZNE) Munich, 81377 Munich, Germany 10 2 Faculty of Chemistry, Technical University of Munich, Garching, Germany 11 3 Institute for Stroke and Dementia Research (ISD), Ludwig-Maximilians Universität München, 12 81377 Munich, Germany 13 4 Munich Cluster for Systems Neurology (SyNergy), Munich, Germany 14 5 Neuroproteomics, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, 15 Munich, Germany 16 6 Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science Institute, Wako, 17 Saitama 351-0198, Japan 18 7 Department of Neurocognitive Science, Nagoya City University Graduate School of Medical 19 Science, Nagoya, Aichi 467-8601, Japan 20 8 Center for Neuropathology and Prion Research, Ludwig-Maximilians-Universität München, 81377 21 Munich, Germany 22 9 Biomedical Center (BMC), Ludwig-Maximilians Universität München, 81377 Munich, Germany 23 10 Graduate School of Systemic Neuroscience, Ludwig-Maximilians-University Munich, Munich, 24 Germany. 25 *Contributed equally 26 #Correspondence: [email protected] and [email protected] 27 28 Running title: 29 Microglial proteomic signatures of AD 30 Keywords: Alzheimer’s disease / microglia / proteomic signatures / neuroinflammation / 31 phagocytosis 32 1 bioRxiv preprint doi: https://doi.org/10.1101/861146; this version posted December 2, 2019. -
Role of Genetic Variation in ABC Transporters in Breast Cancer Prognosis and Therapy Response
International Journal of Molecular Sciences Article Role of Genetic Variation in ABC Transporters in Breast Cancer Prognosis and Therapy Response Viktor Hlaváˇc 1,2 , Radka Václavíková 1,2, Veronika Brynychová 1,2, Renata Koževnikovová 3, Katerina Kopeˇcková 4, David Vrána 5 , Jiˇrí Gatˇek 6 and Pavel Souˇcek 1,2,* 1 Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic; [email protected] (V.H.); [email protected] (R.V.); [email protected] (V.B.) 2 Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00 Pilsen, Czech Republic 3 Department of Oncosurgery, Medicon Services, 140 00 Prague, Czech Republic; [email protected] 4 Department of Oncology, Second Faculty of Medicine, Charles University and Motol University Hospital, 150 06 Prague, Czech Republic; [email protected] 5 Department of Oncology, Medical School and Teaching Hospital, Palacky University, 779 00 Olomouc, Czech Republic; [email protected] 6 Department of Surgery, EUC Hospital and University of Tomas Bata in Zlin, 760 01 Zlin, Czech Republic; [email protected] * Correspondence: [email protected]; Tel.: +420-267-082-711 Received: 19 November 2020; Accepted: 11 December 2020; Published: 15 December 2020 Abstract: Breast cancer is the most common cancer in women in the world. The role of germline genetic variability in ATP-binding cassette (ABC) transporters in cancer chemoresistance and prognosis still needs to be elucidated. We used next-generation sequencing to assess associations of germline variants in coding and regulatory sequences of all human ABC genes with response of the patients to the neoadjuvant cytotoxic chemotherapy and disease-free survival (n = 105). -
ATP‑Binding Cassette Transporter A1: a Promising Therapy Target for Prostate Cancer (Review)
MOLECULAR AND CLINICAL ONCOLOGY 8: 9-14, 2018 ATP‑binding cassette transporter A1: A promising therapy target for prostate cancer (Review) TING XIONG1, GANG XU2, XUE-LONG HUANG1, KAI-QIANG LU1, WEI-QUAN XIE1, KAI YIN2 and JIAN TU1 1Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, and 2Department of Diagnostics Teaching and Research, University of South China, Hengyang, Hunan 421001, P.R. China Received May 6, 2017; Accepted November 10, 2017 DOI: 10.3892/mco.2017.1506 Abstract. ATP-binding cassette transporter A1 (ABCA1) Contents has been found to mediate the transfer of cellular cholesterol across the plasma membrane to apolipoprotein A-I (apoA-I), 1. Introduction and is essential for the synthesis of high-density lipoprotein. 2. Effect of ABCA1 on the progression of prostate cancer Mutations of the ABCA1 gene may induce Tangier disease 3. Association of ABCA1 with apoptosis and autophagy in and familial hypoalphalipoproteinemia; they may also prostate cancer lead to loss of cellular cholesterol homeostasis in prostate 4. ABCA1 and multidrug resistance (MDR) cancer, and increased intracellular cholesterol levels are frequently found in prostate cancer cells. Recent studies have demonstrated that ABCA1 may exert anticancer effects 1. Introduction through cellular cholesterol efflux, which has been attracting increasing attention in association with prostate cancer. The Prostate cancer is a common malignancy among men in aim of the present review was to focus on the current views Western countries; however, a sharp increase in its morbidity on prostate cancer progression and the various functions and mortality was recently observed in several Asian countries, of ABCA1, in order to provide new therapeutic targets for including China (1). -
UK Lipoedema’ Cohort
medRxiv preprint doi: https://doi.org/10.1101/2021.06.15.21258988; this version posted June 18, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license . Investigation of clinical characteristics and genome associations in the ‘UK Lipoedema’ cohort Authors Dionysios Grigoriadis1*, Ege Sackey1*, Katie Riches2**, Malou van Zanten1**, Glen Brice3, Ruth England2, Mike Mills1, Sara E Dobbins1, Lipoedema Consortium, Genomics England Research Consortium4, Steve Jeffery1, Liang Dong5, David B. Savage5, Peter S. Mortimer1,6, Vaughan Keeley2,7, Alan Pittman1, Kristiana Gordon1,6 ‡, Pia Ostergaard1 ‡ Affiliations 1. Molecular and Clinical Sciences Institute, St George’s University of London, London, UK 2. University Hospitals of Derby and Burton NHS Foundation Trust, Derby, UK 3. South West Thames Regional Genetics Unit, St George's University of London, London, UK 4. Genomics England, London, UK 5. Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK 6. Dermatology & Lymphovascular Medicine, St George's Universities NHS Foundation trust, London, UK 7. University of Nottingham Medical School, Nottingham, UK *These two authors contributed equally; ** These two authors contributed equally ‡Clinical correspondence to Kristiana Gordon [email protected] and research- related correspondence to Pia Ostergaard, [email protected] NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. 1 medRxiv preprint doi: https://doi.org/10.1101/2021.06.15.21258988; this version posted June 18, 2021. -
13Q Deletion Syndrome Involving RB1: Characterization of a New Minimal Critical Region for Psychomotor Delay
G C A T T A C G G C A T genes Article 13q Deletion Syndrome Involving RB1: Characterization of a New Minimal Critical Region for Psychomotor Delay Flavia Privitera 1,2, Arianna Calonaci 3, Gabriella Doddato 1,2, Filomena Tiziana Papa 1,2, Margherita Baldassarri 1,2 , Anna Maria Pinto 4, Francesca Mari 1,2,4, Ilaria Longo 4, Mauro Caini 3, Daniela Galimberti 3, Theodora Hadjistilianou 5, Sonia De Francesco 5, Alessandra Renieri 1,2,4 and Francesca Ariani 1,2,4,* 1 Medical Genetics, University of Siena, 53100 Siena, Italy; fl[email protected] (F.P.); [email protected] (G.D.); fi[email protected] (F.T.P.); [email protected] (M.B.); [email protected] (F.M.); [email protected] (A.R.) 2 Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy 3 Unit of Pediatrics, Department of Maternal, Newborn and Child Health, Azienda Ospedaliera Universitaria Senese, Policlinico ‘Santa Maria alle Scotte’, 53100 Siena, Italy; [email protected] (A.C.); [email protected] (M.C.); [email protected] (D.G.) 4 Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; [email protected] (A.M.P.); [email protected] (I.L.) 5 Unit of Ophthalmology and Retinoblastoma Referral Center, Department of Surgery, University of Siena, Policlinico ‘Santa Maria alle Scotte’, 53100 Siena, Italy; [email protected] (T.H.); [email protected] (S.D.F.) * Correspondence: [email protected]; Tel.: +39-057-723-3303 Citation: Privitera, F.; Calonaci, A.; Abstract: Retinoblastoma (RB) is an ocular tumor of the pediatric age caused by biallelic inactivation Doddato, G.; Papa, F.T.; Baldassarri, of the RB1 gene (13q14). -
Tests to Predict Responsiveness of Cancer Patients to Chemotherapy Treatment Options
(19) TZZ _5B_T (11) EP 2 294 215 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12Q 1/68 (2006.01) G01N 33/53 (2006.01) 16.01.2013 Bulletin 2013/03 G01N 33/574 (2006.01) (21) Application number: 09747388.8 (86) International application number: PCT/US2009/043667 (22) Date of filing: 12.05.2009 (87) International publication number: WO 2009/140304 (19.11.2009 Gazette 2009/47) (54) TESTS TO PREDICT RESPONSIVENESS OF CANCER PATIENTS TO CHEMOTHERAPY TREATMENT OPTIONS TESTS ZUR VORHERSAGE DER ANSPRECHRATE VON KREBSPATIENTEN AUF CHEMOTHERAPEUTISCHE BEHANDLUNGSOPTIONEN TESTSPOUR PRÉDIRE UNE SENSIBILITÉ DE PATIENTS ATTEINTS DE CANCER ÀDES OPTIONS DE TRAITEMENT DE CHIMIOTHÉRAPIE (84) Designated Contracting States: (74) Representative: Ellis, Katherine Elizabeth Sleigh AT BE BG CH CY CZ DE DK EE ES FI FR GB GR Williams Powell HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL Staple Court PT RO SE SI SK TR 11 Staple Inn Buildings London, WC1V 7QH (GB) (30) Priority: 12.05.2008 US 52573 P 29.05.2008 US 57182 P (56) References cited: WO-A1-2006/052862 WO-A2-2005/100606 (43) Date of publication of application: WO-A2-2007/085497 US-A1- 2006 275 810 16.03.2011 Bulletin 2011/11 US-A1- 2007 105 133 US-A1- 2007 134 669 US-A1- 2008 085 519 (60) Divisional application: 12195318.6 • IVANOV OLGA ET AL: "alpha B-crystallin is a novel predictor of resistance to neoadjuvant (73) Proprietors: chemotherapy in breast cancer", BREAST • Genomic Health, Inc.