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Wiley RL, Urbauer DL, Nugent E, Gallegos J, Ramondetta L. Endometrial cancer patients understanding and interest in weight loss surgery. Gynecol Oncol 2023; 175:88-92. [PMID: 37329873 DOI: 10.1016/j.ygyno.2023.05.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/18/2023] [Accepted: 05/26/2023] [Indexed: 06/19/2023]
Abstract
OBJECTIVE Obesity is a risk factor for endometrial hyperplasia (EH), endometrial intraepithelial neoplasia (EIN), and early type 1 endometrial cancer (EC) in 70%-90% of patients and is often a significant contributor to overall morbidity and mortality due to comorbidities. In 2011, bariatric surgery (BS) with lifestyle modification was identified as an intervention for reduction in overall mortality as well as risk for gynecologic cancers (Tsui et al., 2021). Our aim was to assess awareness of obesity as a risk factor and understanding of BS in an underinsured obese patient population with EC or EH. METHOD This IRB-approved survey was distributed to patients with type I EC or EH within the past 5 years and a BMI >30. Questions addressed demographics, health habits, cancer and obesity awareness, as well as benefits and concerns about undergoing BS. Information was provided about dietary requirements after BS, and then interest in BS was surveyed. RESULTS 61.2% of surveyed patients were interested in bariatric surgery for weight loss after receiving education about the procedure. Interest in bariatric surgery was correlated with higher BMI, higher ideal and comfortable weight loss in pounds and higher estimated weight loss that could be obtained with bariatric surgery. Additionally, patients who were interested in BS had better understanding of the risks of obesity with cancer overall. CONCLUSION Obese patients with history of EC/EIN/EH are aware of hazards associated with excess weight and understand the relationship between EC/EIN/EH diagnosis and obesity, and overall are very interested in BS as a modality to improve their health.
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Affiliation(s)
- R L Wiley
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Texas Health McGovern Medical School, 6431 Fannin St, JJL 304, Houston, TX 77030, United States of America.
| | - Diana L Urbauer
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77006, United States of America
| | - E Nugent
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Texas Health McGovern Medical School, 6431 Fannin St, JJL 304, Houston, TX 77030, United States of America
| | - J Gallegos
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77006, United States of America
| | - L Ramondetta
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77006, United States of America
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Parmekar S, Shah R, Gokulakrishnan G, Gowda S, Castillo D, Iniguez S, Gallegos J, Sisson A, Thammasitboon S, Pammi M. Components of interprofessional education programs in neonatal medicine: A focused BEME review: BEME Guide No. 73. Med Teach 2022; 44:823-835. [PMID: 35319316 DOI: 10.1080/0142159x.2022.2053086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
BACKGROUND Care delivery in neonatology is dependent on an interprofessional team. Collaborative learning and education amongst professionals can lead to successful management of critically ill patients. This focused BEME review synthesized the components, outcomes, and impact of such interprofessional education (IPE) programs in neonatal medicine. METHODS The authors systematically searched four online databases and hand-searched MedEdPublish up to 10 September 2020. Two authors independently screened titles, abstracts, full-texts, performed data extraction and risk of bias assessment related to study methodology and reporting. Discrepancies were resolved by a third author. We reported our findings based on BEME guidance and the STORIES (STructured apprOach to the Reporting in health education of Evidence Synthesis) statement. RESULTS We included 17 studies on IPE in neonatal medicine. Most studies were from North America with varying learners, objectives, instruction, and observed outcomes. Learners represented nurses, respiratory therapists, neonatal nurse practitioners, patient care technicians, parents, early interventionists, physicians, and medical trainees amongst others. Risk of bias assessment in reporting revealed poor reporting of resources and instructor training. Bias assessment for study methodology noted moderate quality evidence with validity evidence as the weakest domain. IPE instruction strategies included simulation with debriefing, didactics, and online instruction. Most studies reported level 1 Kirkpatrick outcomes (76%) and few reported level 3 or 4 outcomes (23%). Challenges include buy-in from leadership and the negative influence of hierarchy amongst learners. CONCLUSIONS This review highlights IPE program components within neonatal medicine and exemplary practices including a multimodal instructional approach, asynchronous instruction, an emphasis on teamwork, and elimination of hierarchy amongst learners. We identified a lack of reporting on program development and instructor training. Future work should address long term knowledge and skill retention and impact on patient outcomes and organizations.
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Affiliation(s)
- S Parmekar
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - R Shah
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - G Gokulakrishnan
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - S Gowda
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - D Castillo
- Texas Children's Hospital, Houston, TX, USA
| | - S Iniguez
- Texas Children's Hospital, Houston, TX, USA
| | - J Gallegos
- Texas Children's Hospital, Houston, TX, USA
| | - A Sisson
- The Texas Medical Center Library, Houston, TX, USA
| | - S Thammasitboon
- Section of Critical Care Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Center for Research, Innovation and Scholarship in medical Education, Texas Children's Hospital, Houston, TX, USA
| | - M Pammi
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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Swan AL, Schütt C, Rozman J, del Mar Muñiz Moreno M, Brandmaier S, Simon M, Leuchtenberger S, Griffiths M, Brommage R, Keskivali-Bond P, Grallert H, Werner T, Teperino R, Becker L, Miller G, Moshiri A, Seavitt JR, Cissell DD, Meehan TF, Acar EF, Lelliott CJ, Flenniken AM, Champy MF, Sorg T, Ayadi A, Braun RE, Cater H, Dickinson ME, Flicek P, Gallegos J, Ghirardello EJ, Heaney JD, Jacquot S, Lally C, Logan JG, Teboul L, Mason J, Spielmann N, McKerlie C, Murray SA, Nutter LMJ, Odfalk KF, Parkinson H, Prochazka J, Reynolds CL, Selloum M, Spoutil F, Svenson KL, Vales TS, Wells SE, White JK, Sedlacek R, Wurst W, Lloyd KCK, Croucher PI, Fuchs H, Williams GR, Bassett JHD, Gailus-Durner V, Herault Y, Mallon AM, Brown SDM, Mayer-Kuckuk P, Hrabe de Angelis M. Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density. PLoS Genet 2020; 16:e1009190. [PMID: 33370286 PMCID: PMC7822523 DOI: 10.1371/journal.pgen.1009190] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 01/22/2021] [Accepted: 10/13/2020] [Indexed: 12/18/2022] Open
Abstract
The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored data from 3,823 mutant mouse strains for BMD, a measure that is frequently altered in a range of bone pathologies, including osteoporosis. A total of 200 genes were found to significantly affect BMD. This pool of BMD genes comprised 141 genes with previously unknown functions in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 genes also caused skeletal abnormalities. Examination of the BMD genes in osteoclasts and osteoblasts underscored BMD pathways, including vesicle transport, in these cells and together with in silico bone turnover studies resulted in the prioritization of candidate genes for further investigation. Overall, the results add novel pathophysiological and molecular insight into bone health and disease. Patients affected by osteoporosis frequently present with decreased BMD and increased fracture risk. Genes are known to control the onset and progression of bone diseases such as osteoporosis. Therefore, we aimed to identify osteoporosis-related genes using BMD measures obtained from a large pool of mutant mice genetically modified for deletion of individual genes (knockout mice). In a collaborative endeavor involving several research sites world-wide, we generated and phenotyped 3,823 knockout mice and identified 200 genes which regulated BMD. Of the 200 BMD genes, 141 genes were previously not known to affect BMD. The discovery and study of novel BMD genes will help to better understand the causes and therapeutic options for patients with low BMD. In the long run, this will improve the clinical management of osteoporosis.
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Affiliation(s)
- Anna L. Swan
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Christine Schütt
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Jan Rozman
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | | | - Stefan Brandmaier
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michelle Simon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Stefanie Leuchtenberger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Mark Griffiths
- Mouse Informatics Group, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Robert Brommage
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Piia Keskivali-Bond
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Harald Grallert
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Thomas Werner
- Internal Medicine Nephrology and Center for Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Raffaele Teperino
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Gregor Miller
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Ala Moshiri
- University of California-Davis School of Medicine, Sacramento, California, United States of America
| | - John R. Seavitt
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Derek D. Cissell
- Department of Surgical & Radiological Sciences, University of California, Davis, California, United States of America
| | - Terrence F. Meehan
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Elif F. Acar
- The Center for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Department of Statistics, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Ann M. Flenniken
- The Center for Phenogenomics, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Marie-France Champy
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Abdel Ayadi
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Robert E. Braun
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Heather Cater
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Mary E. Dickinson
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Departments of Molecular Physiology & Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston,Texas, United States of America
| | - Paul Flicek
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Juan Gallegos
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, United States of America
| | - Elena J. Ghirardello
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Jason D. Heaney
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, United States of America
| | - Sylvie Jacquot
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Connor Lally
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - John G. Logan
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Lydia Teboul
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Jeremy Mason
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Nadine Spielmann
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Colin McKerlie
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Stephen A. Murray
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Lauryl M. J. Nutter
- The Center for Phenogenomics, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Kristian F. Odfalk
- Advanced Technologies Cores, Baylor College of Medicine, One Baylor Plaza, Houston Texas, United States of America
| | - Helen Parkinson
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Jan Prochazka
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | - Corey L. Reynolds
- Departments of Molecular Physiology & Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston,Texas, United States of America
| | - Mohammed Selloum
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Frantisek Spoutil
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | - Karen L. Svenson
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Taylor S. Vales
- Advanced Technologies Cores, Baylor College of Medicine, One Baylor Plaza, Houston Texas, United States of America
| | - Sara E. Wells
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Jacqueline K. White
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Radislav Sedlacek
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Chair of Developmental Genetics, TUM School of Life Sciences (SoLS), Technische Universität München, Freising, Germany
- Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Munich, Germany
| | - K. C. Kent Lloyd
- Department of Surgery, School of Medicine and Mouse Biology Program, University of California Davis
| | - Peter I. Croucher
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent’s Clinical School, Faculty of Medicine, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, New South Wales, Australia
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Graham R. Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - J. H. Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, IGBMC, Illkirch, France
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Ann-Marie Mallon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Steve D. M. Brown
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Philipp Mayer-Kuckuk
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences (SoLS), Technische Universität München, Freising, Germany
- * E-mail:
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Gallegos J, Underwood S, Katz E, Spalding R, Edelstein B. FACTORS INFLUENCING MEDICAL DECISON MAKING ROLE IN OLDER ADULTS. Innov Aging 2018. [DOI: 10.1093/geroni/igy031.3471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Lutz J, Katz E, Gallegos J, Spalding R, Edelstein B. A NEW MEASURE OF FEELINGS OF BURDEN FOR OLDER ADULTS. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.2545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H, Baker CN, Bower L, Brown JM, Caddle LB, Chiani F, Clary D, Cleak J, Daly MJ, Denegre JM, Doe B, Dolan ME, Edie Helmut Fuchs SM, Gailus-Durner V, Galli A, Gambadoro A, Gallegos J, Guo S, Horner NR, Hsu CW, Johnson SJ, Kalaga S, Keith LC, Lanoue L, Lawson TN, Lek M, Mark M, Marschall S, Mason J, McElwee ML, Nutter SNLMJ, Peterson KA, Ramirez-Solis R, Rowland DJ, Ryder E, Samocha KE, Seavitt JR, Selloum M, Szoke-Kovacs Z, Tamura M, Trainor AG, Tudose I, Wakana S, Warren J, Wendling O, West DB, Wong L, Yoshiki A, Wurst W, MacArthur DG, Tocchini-Valentini GP, Gao X, Flicek P, Bradley A, Skarnes WC, Justice MJ, Parkinson HE, Moore M, Wells S, Braun RE, Svenson KL, de Angelis MH, Herault Y, Mohun T, Mallon AM, Henkelman RM, Brown SDM, Adams DJ, Lloyd KCK, McKerlie C, Beaudet AL, Murray MBSA. Corrigendum: High-throughput discovery of novel developmental phenotypes. Nature 2017; 551:398. [PMID: 29144450 DOI: 10.1038/nature24643] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This corrects the article DOI: 10.1038/nature19356.
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Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, Chen CK, Tudose I, Relac M, Matthews P, Karp N, Santos L, Fiegel T, Ring N, Westerberg H, Greenaway S, Sneddon D, Morgan H, Codner GF, Stewart ME, Brown J, Horner N, Haendel M, Washington N, Mungall CJ, Reynolds CL, Gallegos J, Gailus-Durner V, Sorg T, Pavlovic G, Bower LR, Moore M, Morse I, Gao X, Tocchini-Valentini GP, Obata Y, Cho SY, Seong JK, Seavitt J, Beaudet AL, Dickinson ME, Herault Y, Wurst W, de Angelis MH, Lloyd KK, Flenniken AM, Nutter LMJ, Newbigging S, McKerlie C, Justice MJ, Murray SA, Svenson KL, Braun RE, White JK, Bradley A, Flicek P, Wells S, Skarnes WC, Adams DJ, Parkinson H, Mallon AM, Brown SD, Smedley D. Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium. Nat Genet 2017; 49:1231-1238. [PMID: 28650483 PMCID: PMC5546242 DOI: 10.1038/ng.3901] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 05/25/2017] [Indexed: 12/12/2022]
Abstract
Although next-generation sequencing has revolutionized the ability to associate variants with human diseases, diagnostic rates and development of new therapies are still limited by a lack of knowledge of the functions and pathobiological mechanisms of most genes. To address this challenge, the International Mouse Phenotyping Consortium is creating a genome- and phenome-wide catalog of gene function by characterizing new knockout-mouse strains across diverse biological systems through a broad set of standardized phenotyping tests. All mice will be readily available to the biomedical community. Analyzing the first 3,328 genes identified models for 360 diseases, including the first models, to our knowledge, for type C Bernard-Soulier, Bardet-Biedl-5 and Gordon Holmes syndromes. 90% of our phenotype annotations were novel, providing functional evidence for 1,092 genes and candidates in genetically uncharacterized diseases including arrhythmogenic right ventricular dysplasia 3. Finally, we describe our role in variant functional validation with The 100,000 Genomes Project and others.
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Affiliation(s)
- Terrence F. Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nathalie Conte
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David B. West
- Children’s Hospital Oakland Research Institute, Oakland, California 94609, USA
| | - Julius O. Jacobsen
- William Harvey Research Institute, Queen Mary University of London, London, E1 4NS, UK
| | - Jeremy Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan Warren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Chao-Kung Chen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ilinca Tudose
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mike Relac
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter Matthews
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Natasha Karp
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Luis Santos
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Tanja Fiegel
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Natalie Ring
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Henrik Westerberg
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Simon Greenaway
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Duncan Sneddon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Hugh Morgan
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Gemma F Codner
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Michelle E Stewart
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - James Brown
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Neil Horner
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | | | - Melissa Haendel
- Department of Medical Informatics and Clinical Epidemiology and OHSU Library, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Nicole Washington
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher J. Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Corey L Reynolds
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Juan Gallegos
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Valerie Gailus-Durner
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Neuherberg 85764, Germany
| | - Tania Sorg
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, F-67404 Illkirch-Graffenstaden, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
| | - Guillaume Pavlovic
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, F-67404 Illkirch-Graffenstaden, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
| | - Lynette R Bower
- Mouse Biology Program, University of California, Davis, California 95618, USA
| | - Mark Moore
- IMPC, San Anselmo, California 94960, USA
| | - Iva Morse
- Charles River Laboratories, Wilmington, Massachusetts 01887, USA
| | - Xiang Gao
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, Nanjing 210061, China
| | - Glauco P Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Monterotondo Scalo I-00015, Italy
| | - Yuichi Obata
- RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Soo Young Cho
- Korea Mouse Phenotyping Center, 08826, Republic of Korea
- National Cancer Center, Goyang, Gyeonggi, 10408, Republic of Korea
| | - Je Kyung Seong
- Korea Mouse Phenotyping Center, 08826, Republic of Korea
- Research Institute for Veterinary Science, Seoul National University, Republic of Korea
| | - John Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mary E. Dickinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yann Herault
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, F-67404 Illkirch-Graffenstaden, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
| | - Wolfgang Wurst
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Neuherberg 85764, Germany
| | - Martin Hrabe de Angelis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Neuherberg 85764, Germany
| | - K.C. Kent Lloyd
- Mouse Biology Program, University of California, Davis, California 95618, USA
| | - Ann M Flenniken
- The Centre for Phenogenomics, Toronto, Ontario M5T 3H7, Canada
| | | | | | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, Ontario M5T 3H7, Canada
| | - Monica J. Justice
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada
| | | | | | | | - Jacqueline K. White
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sara Wells
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - William C. Skarnes
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - David J. Adams
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ann-Marie Mallon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Steve D.M. Brown
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, E1 4NS, UK
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8
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Armano M, Audley H, Auger G, Baird JT, Binetruy P, Born M, Bortoluzzi D, Brandt N, Bursi A, Caleno M, Cavalleri A, Cesarini A, Cruise M, Danzmann K, de Deus Silva M, Diepholz I, Dolesi R, Dunbar N, Ferraioli L, Ferroni V, Fitzsimons ED, Flatscher R, Freschi M, Gallegos J, García Marirrodriga C, Gerndt R, Gesa L, Gibert F, Giardini D, Giusteri R, Grimani C, Grzymisch J, Harrison I, Heinzel G, Hewitson M, Hollington D, Hueller M, Huesler J, Inchauspé H, Jennrich O, Jetzer P, Johlander B, Karnesis N, Kaune B, Killow CJ, Korsakova N, Lloro I, Liu L, López-Zaragoza JP, Maarschalkerweerd R, Madden S, Mance D, Martín V, Martin-Polo L, Martino J, Martin-Porqueras F, Mateos I, McNamara PW, Mendes J, Mendes L, Moroni A, Nofrarias M, Paczkowski S, Perreur-Lloyd M, Petiteau A, Pivato P, Plagnol E, Prat P, Ragnit U, Ramos-Castro J, Reiche J, Romera Perez JA, Robertson DI, Rozemeijer H, Rivas F, Russano G, Sarra P, Schleicher A, Slutsky J, Sopuerta C, Sumner TJ, Texier D, Thorpe JI, Trenkel C, Vetrugno D, Vitale S, Wanner G, Ward H, Wass PJ, Wealthy D, Weber WJ, Wittchen A, Zanoni C, Ziegler T, Zweifel P. Charge-Induced Force Noise on Free-Falling Test Masses: Results from LISA Pathfinder. Phys Rev Lett 2017; 118:171101. [PMID: 28498710 DOI: 10.1103/physrevlett.118.171101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Indexed: 06/07/2023]
Abstract
We report on electrostatic measurements made on board the European Space Agency mission LISA Pathfinder. Detailed measurements of the charge-induced electrostatic forces exerted on free-falling test masses (TMs) inside the capacitive gravitational reference sensor are the first made in a relevant environment for a space-based gravitational wave detector. Employing a combination of charge control and electric-field compensation, we show that the level of charge-induced acceleration noise on a single TM can be maintained at a level close to 1.0 fm s^{-2} Hz^{-1/2} across the 0.1-100 mHz frequency band that is crucial to an observatory such as the Laser Interferometer Space Antenna (LISA). Using dedicated measurements that detect these effects in the differential acceleration between the two test masses, we resolve the stochastic nature of the TM charge buildup due to interplanetary cosmic rays and the TM charge-to-force coupling through stray electric fields in the sensor. All our measurements are in good agreement with predictions based on a relatively simple electrostatic model of the LISA Pathfinder instrument.
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Affiliation(s)
- M Armano
- European Space Astronomy Centre, European Space Agency, Villanueva de la Cañada, 28692 Madrid, Spain
| | - H Audley
- Albert-Einstein-Institut, Max-Planck-Institut für Gravitationsphysik und Universität Hannover, 30167 Hannover, Germany
| | - G Auger
- APC UMR7164, Université Paris Diderot, 10, rue Alice Domon et Léonie Duquet, 75205 Paris Cedex 13, France
| | - J T Baird
- High Energy Physics Group, Department of Physics, Imperial College London, Blackett Laboratory, Prince Consort Road, London SW7 2BW, United Kingdom
| | - P Binetruy
- APC UMR7164, Université Paris Diderot, 10, rue Alice Domon et Léonie Duquet, 75205 Paris Cedex 13, France
| | - M Born
- Albert-Einstein-Institut, Max-Planck-Institut für Gravitationsphysik und Universität Hannover, 30167 Hannover, Germany
| | - D Bortoluzzi
- Department of Industrial Engineering, University of Trento, via Sommarive 9, 38123 Trento, Italy and Trento Institute for Fundamental Physics and Application/INFN, Italy
| | - N Brandt
- Airbus Defence and Space, Claude-Dornier-Strasse, 88090 Immenstaad, Germany
| | - A Bursi
- CGS S.p.A, Compagnia Generale per lo Spazio, Via Gallarate, 150-20151 Milano, Italy
| | - M Caleno
- European Space Technology Centre, European Space Agency, Keplerlaan 1, 2200 AG Noordwijk, Netherlands
| | - A Cavalleri
- Dipartimento di Fisica, Università di Trento and Trento Institute for Fundamental Physics and Application/INFN, 38123 Povo, Trento, Italy
| | - A Cesarini
- Dipartimento di Fisica, Università di Trento and Trento Institute for Fundamental Physics and Application/INFN, 38123 Povo, Trento, Italy
| | - M Cruise
- Department of Physics and Astronomy, University of Birmingham, Birmingham, Edgbaston Park Road, Birmingham B15 2TT, United Kingdom
| | - K Danzmann
- Albert-Einstein-Institut, Max-Planck-Institut für Gravitationsphysik und Universität Hannover, 30167 Hannover, Germany
| | - M de Deus Silva
- European Space Astronomy Centre, European Space Agency, Villanueva de la Cañada, 28692 Madrid, Spain
| | - I Diepholz
- Albert-Einstein-Institut, Max-Planck-Institut für Gravitationsphysik und Universität Hannover, 30167 Hannover, Germany
| | - R Dolesi
- Dipartimento di Fisica, Università di Trento and Trento Institute for Fundamental Physics and Application/INFN, 38123 Povo, Trento, Italy
| | - N Dunbar
- Airbus Defence and Space, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2AS, United Kingdom
| | - L Ferraioli
- Institut für Geophysik, ETH Zürich, Sonneggstrasse 5, CH-8092, Zürich, Switzerland
| | - V Ferroni
- Dipartimento di Fisica, Università di Trento and Trento Institute for Fundamental Physics and Application/INFN, 38123 Povo, Trento, Italy
| | - E D Fitzsimons
- United Kingdom Astronomy Technology Centre, Royal Observatory, Edinburgh EH9 3HJ, United Kingdom
| | - R Flatscher
- Airbus Defence and Space, Claude-Dornier-Strasse, 88090 Immenstaad, Germany
| | - M Freschi
- European Space Astronomy Centre, European Space Agency, Villanueva de la Cañada, 28692 Madrid, Spain
| | - J Gallegos
- European Space Astronomy Centre, European Space Agency, Villanueva de la Cañada, 28692 Madrid, Spain
| | - C García Marirrodriga
- European Space Technology Centre, European Space Agency, Keplerlaan 1, 2200 AG Noordwijk, Netherlands
| | - R Gerndt
- Airbus Defence and Space, Claude-Dornier-Strasse, 88090 Immenstaad, Germany
| | - L Gesa
- Institut de Ciències de l'Espai (CSIC-IEEC), Campus UAB, Carrer de Can Magrans s/n, 08193 Cerdanyola del Vallès, Spain
| | - F Gibert
- Dipartimento di Fisica, Università di Trento and Trento Institute for Fundamental Physics and Application/INFN, 38123 Povo, Trento, Italy
| | - D Giardini
- Institut für Geophysik, ETH Zürich, Sonneggstrasse 5, CH-8092, Zürich, Switzerland
| | - R Giusteri
- Dipartimento di Fisica, Università di Trento and Trento Institute for Fundamental Physics and Application/INFN, 38123 Povo, Trento, Italy
| | - C Grimani
- DiSPeA, Università di Urbino "Carlo Bo", Via S. Chiara, 27 61029 Urbino/INFN, Italy
| | - J Grzymisch
- European Space Technology Centre, European Space Agency, Keplerlaan 1, 2200 AG Noordwijk, Netherlands
| | - I Harrison
- European Space Operations Centre, European Space Agency, 64293 Darmstadt, Germany
| | - G Heinzel
- Albert-Einstein-Institut, Max-Planck-Institut für Gravitationsphysik und Universität Hannover, 30167 Hannover, Germany
| | - M Hewitson
- Albert-Einstein-Institut, Max-Planck-Institut für Gravitationsphysik und Universität Hannover, 30167 Hannover, Germany
| | - D Hollington
- High Energy Physics Group, Department of Physics, Imperial College London, Blackett Laboratory, Prince Consort Road, London SW7 2BW, United Kingdom
| | - M Hueller
- Dipartimento di Fisica, Università di Trento and Trento Institute for Fundamental Physics and Application/INFN, 38123 Povo, Trento, Italy
| | - J Huesler
- European Space Technology Centre, European Space Agency, Keplerlaan 1, 2200 AG Noordwijk, Netherlands
| | - H Inchauspé
- APC UMR7164, Université Paris Diderot, 10, rue Alice Domon et Léonie Duquet, 75205 Paris Cedex 13, France
| | - O Jennrich
- European Space Technology Centre, European Space Agency, Keplerlaan 1, 2200 AG Noordwijk, Netherlands
| | - P Jetzer
- Physik Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - B Johlander
- European Space Technology Centre, European Space Agency, Keplerlaan 1, 2200 AG Noordwijk, Netherlands
| | - N Karnesis
- Albert-Einstein-Institut, Max-Planck-Institut für Gravitationsphysik und Universität Hannover, 30167 Hannover, Germany
| | - B Kaune
- Albert-Einstein-Institut, Max-Planck-Institut für Gravitationsphysik und Universität Hannover, 30167 Hannover, Germany
| | - C J Killow
- SUPA, Institute for Gravitational Research, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - N Korsakova
- SUPA, Institute for Gravitational Research, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - I Lloro
- Institut de Ciències de l'Espai (CSIC-IEEC), Campus UAB, Carrer de Can Magrans s/n, 08193 Cerdanyola del Vallès, Spain
| | - L Liu
- Dipartimento di Fisica, Università di Trento and Trento Institute for Fundamental Physics and Application/INFN, 38123 Povo, Trento, Italy
| | - J P López-Zaragoza
- Institut de Ciències de l'Espai (CSIC-IEEC), Campus UAB, Carrer de Can Magrans s/n, 08193 Cerdanyola del Vallès, Spain
| | - R Maarschalkerweerd
- European Space Operations Centre, European Space Agency, 64293 Darmstadt, Germany
| | - S Madden
- European Space Technology Centre, European Space Agency, Keplerlaan 1, 2200 AG Noordwijk, Netherlands
| | - D Mance
- Institut für Geophysik, ETH Zürich, Sonneggstrasse 5, CH-8092, Zürich, Switzerland
| | - V Martín
- Institut de Ciències de l'Espai (CSIC-IEEC), Campus UAB, Carrer de Can Magrans s/n, 08193 Cerdanyola del Vallès, Spain
| | - L Martin-Polo
- European Space Astronomy Centre, European Space Agency, Villanueva de la Cañada, 28692 Madrid, Spain
| | - J Martino
- APC UMR7164, Université Paris Diderot, 10, rue Alice Domon et Léonie Duquet, 75205 Paris Cedex 13, France
| | - F Martin-Porqueras
- European Space Astronomy Centre, European Space Agency, Villanueva de la Cañada, 28692 Madrid, Spain
| | - I Mateos
- Institut de Ciències de l'Espai (CSIC-IEEC), Campus UAB, Carrer de Can Magrans s/n, 08193 Cerdanyola del Vallès, Spain
| | - P W McNamara
- European Space Technology Centre, European Space Agency, Keplerlaan 1, 2200 AG Noordwijk, Netherlands
| | - J Mendes
- European Space Operations Centre, European Space Agency, 64293 Darmstadt, Germany
| | - L Mendes
- European Space Astronomy Centre, European Space Agency, Villanueva de la Cañada, 28692 Madrid, Spain
| | - A Moroni
- CGS S.p.A, Compagnia Generale per lo Spazio, Via Gallarate, 150-20151 Milano, Italy
| | - M Nofrarias
- Institut de Ciències de l'Espai (CSIC-IEEC), Campus UAB, Carrer de Can Magrans s/n, 08193 Cerdanyola del Vallès, Spain
| | - S Paczkowski
- Albert-Einstein-Institut, Max-Planck-Institut für Gravitationsphysik und Universität Hannover, 30167 Hannover, Germany
| | - M Perreur-Lloyd
- SUPA, Institute for Gravitational Research, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - A Petiteau
- APC UMR7164, Université Paris Diderot, 10, rue Alice Domon et Léonie Duquet, 75205 Paris Cedex 13, France
| | - P Pivato
- Dipartimento di Fisica, Università di Trento and Trento Institute for Fundamental Physics and Application/INFN, 38123 Povo, Trento, Italy
| | - E Plagnol
- APC UMR7164, Université Paris Diderot, 10, rue Alice Domon et Léonie Duquet, 75205 Paris Cedex 13, France
| | - P Prat
- APC UMR7164, Université Paris Diderot, 10, rue Alice Domon et Léonie Duquet, 75205 Paris Cedex 13, France
| | - U Ragnit
- European Space Technology Centre, European Space Agency, Keplerlaan 1, 2200 AG Noordwijk, Netherlands
| | - J Ramos-Castro
- Department d'Enginyeria Electrònica, Universitat Politècnica de Catalunya, 08034 Barcelona, Spain
- Institut d'Estudis Espacials de Catalunya (IEEC), C/ Gran Capità 2-4, 08034 Barcelona, Spain
| | - J Reiche
- Albert-Einstein-Institut, Max-Planck-Institut für Gravitationsphysik und Universität Hannover, 30167 Hannover, Germany
| | - J A Romera Perez
- European Space Technology Centre, European Space Agency, Keplerlaan 1, 2200 AG Noordwijk, Netherlands
| | - D I Robertson
- SUPA, Institute for Gravitational Research, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - H Rozemeijer
- European Space Technology Centre, European Space Agency, Keplerlaan 1, 2200 AG Noordwijk, Netherlands
| | - F Rivas
- Institut de Ciències de l'Espai (CSIC-IEEC), Campus UAB, Carrer de Can Magrans s/n, 08193 Cerdanyola del Vallès, Spain
| | - G Russano
- Dipartimento di Fisica, Università di Trento and Trento Institute for Fundamental Physics and Application/INFN, 38123 Povo, Trento, Italy
| | - P Sarra
- CGS S.p.A, Compagnia Generale per lo Spazio, Via Gallarate, 150-20151 Milano, Italy
| | - A Schleicher
- Airbus Defence and Space, Claude-Dornier-Strasse, 88090 Immenstaad, Germany
| | - J Slutsky
- NASA Goddard Space Flight Center, 8800 Greenbelt Road, Greenbelt, Maryland 20771, USA
| | - C Sopuerta
- Institut de Ciències de l'Espai (CSIC-IEEC), Campus UAB, Carrer de Can Magrans s/n, 08193 Cerdanyola del Vallès, Spain
| | - T J Sumner
- High Energy Physics Group, Department of Physics, Imperial College London, Blackett Laboratory, Prince Consort Road, London SW7 2BW, United Kingdom
| | - D Texier
- European Space Astronomy Centre, European Space Agency, Villanueva de la Cañada, 28692 Madrid, Spain
| | - J I Thorpe
- NASA Goddard Space Flight Center, 8800 Greenbelt Road, Greenbelt, Maryland 20771, USA
| | - C Trenkel
- Airbus Defence and Space, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2AS, United Kingdom
| | - D Vetrugno
- Dipartimento di Fisica, Università di Trento and Trento Institute for Fundamental Physics and Application/INFN, 38123 Povo, Trento, Italy
| | - S Vitale
- Dipartimento di Fisica, Università di Trento and Trento Institute for Fundamental Physics and Application/INFN, 38123 Povo, Trento, Italy
| | - G Wanner
- Albert-Einstein-Institut, Max-Planck-Institut für Gravitationsphysik und Universität Hannover, 30167 Hannover, Germany
| | - H Ward
- SUPA, Institute for Gravitational Research, School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - P J Wass
- High Energy Physics Group, Department of Physics, Imperial College London, Blackett Laboratory, Prince Consort Road, London SW7 2BW, United Kingdom
| | - D Wealthy
- Airbus Defence and Space, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2AS, United Kingdom
| | - W J Weber
- Dipartimento di Fisica, Università di Trento and Trento Institute for Fundamental Physics and Application/INFN, 38123 Povo, Trento, Italy
| | - A Wittchen
- Albert-Einstein-Institut, Max-Planck-Institut für Gravitationsphysik und Universität Hannover, 30167 Hannover, Germany
| | - C Zanoni
- Department of Industrial Engineering, University of Trento, via Sommarive 9, 38123 Trento, Italy and Trento Institute for Fundamental Physics and Application/INFN, Italy
| | - T Ziegler
- Airbus Defence and Space, Claude-Dornier-Strasse, 88090 Immenstaad, Germany
| | - P Zweifel
- Institut für Geophysik, ETH Zürich, Sonneggstrasse 5, CH-8092, Zürich, Switzerland
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9
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Peña A, Abarca K, Weitzel T, Gallegos J, Cerda J, García P, López J. One Health in Practice: A Pilot Project for Integrated Care of Zoonotic Infections in Immunocompromised Children and Their Pets in Chile. Zoonoses Public Health 2015; 63:403-9. [PMID: 26684576 DOI: 10.1111/zph.12241] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Indexed: 11/28/2022]
Abstract
Although pets provide physiological and psychological benefits to their owners, they are a potential source of zoonotic infections, especially for vulnerable individuals such as immunocompromised patients. During 1 year, we therefore performed a pilot project, which included 32 immunocompromised Chilean children and their family pets (35 dogs and 9 cats) with the aim of detecting, treating and preventing zoonotic infections. Children were examined by Infectious Diseases paediatricians and demographical and clinical information related to zoonotic infections were recorded. Pets were examined and sampled by veterinarians, who also administered missing routine vaccines and anti-parasitics. During family visits, all members were informed and educated about zoonoses and a satisfaction survey was performed. Visits also included vector control and indoor residual spraying with pyrethroids. Children were re-examined and re-tested according to the findings of their pets, and all detected zoonotic infections were treated both in children and pets. Physical examination revealed abnormalities in 18 dogs (51.4%) and three cats (33.3%). Twenty-eight (63.6%) of the pets were diagnosed with a zoonotic pathogen, and seven (15.9%) with a facultative pathogen. Most zoonotic agents were isolated from the pet's external ear and intestine. Bacteria with the highest pathogenic potential were Campylobacter jejuni and Brucella canis. In two children and their respective pets, the same zoonotic diseases were diagnosed (toxocariasis and giardiasis). Arthropods serving as potential vectors of zoonotic infections were found in 49% of dogs and 44% of cats. The pilot project was positively evaluated by the participating families. Our pilot project confirmed that pets are reservoir for various zoonotic agents in Chile and that the implementation of an integrated multidisciplinary programme was a valuable tool to prevent, diagnose and treat such zoonotic infections in vulnerable patients such as immunocompromised children.
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Affiliation(s)
- A Peña
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Hospital Dr. Sótero del Río, Santiago, Chile
| | - K Abarca
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - T Weitzel
- Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | | | - J Cerda
- División de Salud Pública y Medicina Familiar, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - P García
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - J López
- Hospital Veterinario Puente Alto, Santiago, Chile
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10
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Maier H, Schütt C, Steinkamp R, Hurt A, Schneltzer E, Gormanns P, Lengger C, Griffiths M, Melvin D, Agrawal N, Alcantara R, Evans A, Gannon D, Holroyd S, Kipp C, Raj NP, Richardson D, LeBlanc S, Vasseur L, Masuya H, Kobayashi K, Suzuki T, Tanaka N, Wakana S, Walling A, Clary D, Gallegos J, Fuchs H, de Angelis MH, Gailus-Durner V. Principles and application of LIMS in mouse clinics. Mamm Genome 2015. [PMID: 26208973 PMCID: PMC4602070 DOI: 10.1007/s00335-015-9586-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Large-scale systemic mouse phenotyping, as performed by mouse clinics for more than a decade, requires thousands of mice from a multitude of different mutant lines to be bred, individually tracked and subjected to phenotyping procedures according to a standardised schedule. All these efforts are typically organised in overlapping projects, running in parallel. In terms of logistics, data capture, data analysis, result visualisation and reporting, new challenges have emerged from such projects. These challenges could hardly be met with traditional methods such as pen & paper colony management, spreadsheet-based data management and manual data analysis. Hence, different Laboratory Information Management Systems (LIMS) have been developed in mouse clinics to facilitate or even enable mouse and data management in the described order of magnitude. This review shows that general principles of LIMS can be empirically deduced from LIMS used by different mouse clinics, although these have evolved differently. Supported by LIMS descriptions and lessons learned from seven mouse clinics, this review also shows that the unique LIMS environment in a particular facility strongly influences strategic LIMS decisions and LIMS development. As a major conclusion, this review states that there is no universal LIMS for the mouse research domain that fits all requirements. Still, empirically deduced general LIMS principles can serve as a master decision support template, which is provided as a hands-on tool for mouse research facilities looking for a LIMS.
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Affiliation(s)
- Holger Maier
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
| | - Christine Schütt
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Ralph Steinkamp
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Anja Hurt
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Elida Schneltzer
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Philipp Gormanns
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Christoph Lengger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Mark Griffiths
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - David Melvin
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Neha Agrawal
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Rafael Alcantara
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Arthur Evans
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - David Gannon
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Simon Holroyd
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Christian Kipp
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Navis Pretheeba Raj
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - David Richardson
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Sophie LeBlanc
- Institut Clinique de la Souris - ICS, 1 rue Laurent Fries, BP 10142, 67404, Illkirch Cedex, France
| | - Laurent Vasseur
- Institut Clinique de la Souris - ICS, 1 rue Laurent Fries, BP 10142, 67404, Illkirch Cedex, France
| | - Hiroshi Masuya
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Kimio Kobayashi
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Tomohiro Suzuki
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Nobuhiko Tanaka
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Shigeharu Wakana
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Alison Walling
- Mary Lyon Centre, Medical Research Council Harwell, Harwell Science and Innovation Campus, Harwell, Oxfordshire, OX11 0RD, UK
| | - David Clary
- Mouse Biology Program, University of California, Davis, 2795 2nd Street, Suite 400, Davis, CA, 95618, USA
| | - Juan Gallegos
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Chair for Experimental Genetics, Life and Food Science Center Weihenstephan, Technische Universität Munich, Freising-Weihenstephan, 85354, Munich, Germany. .,Member of German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany.
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
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Li H, Tong P, Gallegos J, Dimmer E, Cai G, Molldrem JJ, Liang S. PAND: A Distribution to Identify Functional Linkage from Networks with Preferential Attachment Property. PLoS One 2015; 10:e0127968. [PMID: 26158709 PMCID: PMC4497646 DOI: 10.1371/journal.pone.0127968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 04/22/2015] [Indexed: 12/28/2022] Open
Abstract
Technology advances have immensely accelerated large-scale mapping of biological networks, which necessitates the development of accurate and powerful network-based algorithms to make functional inferences. A prevailing approach is to leverage functions of neighboring nodes to predict unknown molecular function. However, existing neighbor-based algorithms have ignored the scale-free property hidden in many biological networks. By assuming that neighbor sharing is constrained by the preferential attachment property, we developed a Preferential Attachment based common Neighbor Distribution (PAND) to calculate the probability of the neighbor-sharing event between any two nodes in scale-free networks, which nearly perfectly matched the observed probability in simulations. By applying PAND to a human protein-protein interaction (PPI) network, we showed that smaller probabilities represented closer functional linkages between proteins. With the PAND-derive linkages, we were able to build new networks where the links are more functionally reliable than those of the human PPI network. We then applied simple annotation schemes to a PAND-derived network to make reliable functional predictions for proteins. We also developed an R package called PANDA (PAND-derived functional Associations) to implement the methods proposed in this study. In conclusion, PAND is a useful distribution to calculate the probability of the neighbor-sharing events in scale-free networks. With PAND, we are able to extract reliable functional linkages from real biological networks and builds new networks that are better bases for further functional inference.
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Affiliation(s)
- Hua Li
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, United States of America
- * E-mail: (HL); (SL)
| | - Pan Tong
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, United States of America
| | - Juan Gallegos
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, United States of America
| | - Emily Dimmer
- The EMBL Outstation-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Guoshuai Cai
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, United States of America
| | - Jeffrey J. Molldrem
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, United States of America
| | - Shoudan Liang
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, United States of America
- * E-mail: (HL); (SL)
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Resendiz C, Hernández O, Guerrero I, Gallegos J, Martínez P, Sánchez C. Engorda de corderos Pelibuey con diferente nivel de alfalfa en la dieta. Arch zootec 2013. [DOI: 10.4321/s0004-05922013000300014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Parke E, Hart J, Baldock D, Barchard K, Etcoff L, Allen D, Stolberg P, Nardi N, Cohen J, Jones W, Loe S, Etcoff L, Delgaty L, Tan A, Bunner M, Delgaty L, Tan A, Bunner M, Tan A, Delgaty L, Bunner M, Tan A, Delgaty L, Bunner M, Goodman G, Kim W, Nolty A, Marion S, Davis A, Finch W, Piehl J, Moss L, Nogin R, Dean R, Davis J, Lindstrom W, Poon M, Fonseca F, Bure-Reyes A, Stewart J, Golden C, Fonseca F, Bure-Reyes A, Stewart J, Golden C, Fields K, Hill B, Corley E, Russ K, Boettcher A, Musso M, Rohling M, Rowden A, Downing K, Benners M, Miller D, Maricle D, Dugbartey T, Anum A, Anderson J, Daniel M, Hoskins L, Gillis K, Khen S, Carter K, Ayers C, Neeland I, Cullum M, Weiner M, Rossetti H, Buddin W, Mahal S, Schroeder R, Baade L, Macaluso M, Phelps K, Evans C, Clark J, Vickery C, Chow J, Stokic D, Phelps K, Evans C, Watson S, Odom R, Clark J, Clark J, Odom R, Evans C, Vickery C, Thompson J, Noggle C, Kane C, Kecala N, Lane E, Raymond M, Woods S, Iudicello J, Dawson M, Ghias A, Choe M, Yudovin S, McArthur D, Asarnow R, Giza C, Babikian T, Tun S, O'Neil M, Ensley M, Storzbach D, Ellis R, O'Neil M, Carlson K, Storzbach D, Brenner L, Freeman M, Quinones A, Motu'apuaka M, Ensley M, Kansagara D, Brickell T, Grant I, Lange R, Kennedy J, Ivins B, Marshall K, Prokhorenko O, French L, Brickell T, Lange R, Bhagwat A, French L, Weber E, Nemeth D, Songy C, Gremillion A, Lange R, Brubacher J, Shewchuk J, Heran M, Jarrett M, Rauscher A, Iverson G, Woods S, Ukueberuwa D, Medaglia J, Hillary F, Meyer J, Vargas G, Rabinowitz A, Barwick F, Arnett P, Levan A, Gale S, Atkinson J, Boettcher A, Hill B, Rohling M, Stolberg P, Hart J, Allen D, Mayfield J, Ellis M, Marion SD, Houshyarnejad A, Grant I, Akarakian R, Kernan C, Babikian T, Asarnow R, Bens M, Fisher M, Garrett C, Vinogradov S, Walker K, Torstrick A, Uderman J, Wellington R, Zhao L, Fromm N, Dahdah M, Salisbury D, Monden K, Lande E, Wanlass R, Fong G, Smith K, Miele A, Novakovic-Agopian T, Chen A, Rome S, Rossi A, Abrams G, Murphy M, Binder D, Muir J, Carlin G, Loya F, Rabinovitz B, Bruhns M, Adler M, Schleicher-Dilks S, Messerly J, Babika C, Ukpabi C, Golden C, Schleicher-Dilks S, Coad S, Messerly J, Schaffer S, Babika C, Golden C, Cowad S, Paisley S, Fontanetta R, Messerly J, Golden C, Holder C, Kloezeman K, Henry B, Burns W, Patt V, Minassian A, Perry W, Cooper L, Allen D, Vogel S, Woolery H, Ciobanu C, Simone A, Bedard A, Olivier T, O'Neill S, Rajendran K, Halperin J, Rudd-Barnard A, Steenari M, Murry J, Le M, Becker T, Mucci G, Zupanc M, Shapiro E, Santos O, Cadavid N, Giese E, Londono N, Osmon D, Zamzow J, Culnan E, D'Argenio D, Mosti C, Spiers M, Schleicher-Dilks S, Kloss J, Curiel A, Miller K, Olmstead R, Gottuso A, Saucier C, Miller J, Dye R, Small G, Kent A, Andrews P, Puente N, Terry D, Faraco C, Brown C, Patel A, Siegel J, Miller L, Lee B, Joan M, Thaler N, Fontanetta R, Carla F, Allen D, Nguyen T, Glass L, Coles C, Julie K, May P, Sowell E, Jones K, Riley E, Demsky Y, Mattson S, Allart A, Freer B, Tiersky L, Sunderaraman P, Sylvester P, Ang J, Schultheis M, Newton S, Holland A, Burns K, Bunting J, Taylor J, Muetze H, Coe M, Harrison D, Putnam M, Tiersky L, Freer B, Holland A, Newton S, Sakamoto M, Bunting J, Taylor J, Coe M, Harrison D, Musso M, Hill B, Barker A, Pella R, Gouvier W, Davis J, Woods S, Wall J, Etherton J, Brand T, Hummer B, O'Shea C, Segovia J, Thomlinson S, Schulze E, Roskos P, Gfeller J, Loftis J, Fogel T, Barrera K, Sherzai A, Chappell A, Harrison A, Armstrong I, Flaro L, Pedersen H, Shultz LS, Roper B, Huckans M, Basso M, Silk-Eglit G, Stenclik J, Miele A, Lynch J, McCaffrey R, Silk-Eglit G, Stenclik J, Miele A, Lynch J, Musso M, McCaffrey R, Martin P, VonDran E, Baade L, Heinrichs R, Schroeder R, Hunter B, Calloway J, Rolin S, Akeson S, Westervelt H, Mohammed S, An K, Jeffay E, Zakzanis K, Lynch A, Drasnin D, Ikanga J, Graham O, Reid M, Cooper D, Long J, Lange R, Kennedy J, Hopewell C, Lukaszewska B, Pachalska M, Bidzan M, Lipowska M, McCutcheon L, Kaup A, Park J, Morgan E, Kenton J, Norman M, Martin P, Netson K, Woods S, Smith M, Paulsen J, Hahn-Ketter A, Paxton J, Fink J, Kelley K, Lee R, Pliskin N, Segala L, Vasilev G, Bozgunov K, Naslednikova R, Raynov I, Gonzalez R, Vassileva J, Bonilla X, Fedio A, Johnson K, Sexton J, Blackstone K, Weber E, Moore D, Grant I, Woods S, Pimental P, Welch M, Ring M, Stranks E, Crowe S, Jaehnert S, Ellis C, Prince C, Wheaton V, Schwartz D, Loftis J, Fuller B, Hoffman W, Huckans M, Turecka S, McKeever J, Morse C, Schultheis M, Dinishak D, Dasher N, Vik P, Hachey D, Bowman B, Van Ness E, Williams C, Zamzow J, Sunderaraman P, Kloss J, Spiers M, Swirsky-Sacchetti T, Alhassoon O, Taylor M, Sorg S, Schweinsburg B, Stricker N, Kimmel C, Grant I, Alhassoon O, Taylor M, Sorg S, Schweinsburg B, Stephan R, Stricker N, Grant I, Hertza J, Tyson K, Northington S, Loughan A, Perna R, Davis A, Collier M, Schroeder R, Buddin W, Schroeder R, Moore C, Andrew W, Ghelani A, Kim J, Curri M, Patel S, Denney D, Taylor S, Huberman S, Greenberg B, Lacritz L, Brown D, Hughes S, Greenberg B, Lacritz L, Vargas V, Upshaw N, Whigham K, Peery S, Casto B, Barker L, Otero T, La D, Nunan-Saah J, Phoong M, Gill S, Melville T, Harley A, Gomez R, Adler M, Tsou J, Schleicher-Dilks S, Golden C, Tsou J, Schleicher-Dilks S, Adler M, Golden C, Cowad S, Link J, Barker T, Gulliver K, Golden C, Young K, Moses J, Lum J, Vik P, Legarreta M, Van Ness E, Williams C, Dasher N, Williams C, Vik P, Dasher N, Van Ness E, Bowman B, Nakhutina L, Margolis S, Baek R, Gonzalez J, Hill F, England H, Horne-Moyer L, Stringer A, DeFilippis N, Lyon A, Giovannetti T, Fanning M, Heverly-Fitt S, Stambrook E, Price C, Selnes O, Floyd T, Vogt E, Thiruselvam I, Quasney E, Hoelzle J, Grant N, Moses J, Matevosyan A, Delano-Wood L, Alhassoon O, Hanson K, Lanni E, Luc N, Kim R, Schiehser D, Benners M, Downing K, Rowden A, Miller D, Maricle D, Kaminetskaya M, Moses J, Tai C, Kaminetskaya M, Melville T, Poole J, Scott R, Hays F, Walsh B, Mihailescu C, Douangratdy M, Scott B, Draffkorn C, Andrews P, Schmitt A, Waksmunski C, Brady K, Andrews A, Golden C, Olivier T, Espinoza K, Sterk V, Spengler K, Golden C, Olivier T, Spengler K, Sterk V, Espinoza K, Golden C, Gross J, DeFilippis N, Neiman-Kimel J, Romers C, Isaacs C, Soper H, Sordahl J, Tai C, Moses J, D'Orio V, Glukhovsky L, Beier M, Shuman M, Spat J, Foley F, Guatney L, Bott N, Moses J, Miranda C, Renteria MA, Rosario A, Sheynin J, Fuentes A, Byrd D, Mindt MR, Batchelor E, Meyers J, Patt V, Thomas M, Minassian A, Geyer M, Brown G, Perry W, Smith C, Kiefel J, Rooney A, Gouaux B, Ellis R, Grant I, Moore D, Graefe A, Wyman-Chick K, Daniel M, Beene K, Jaehnert S, Choi A, Moses J, Iudicello J, Henry B, Minassian A, Perry W, Marquine M, Morgan E, Letendre S, Ellis R, Woods S, Grant I, Heaton R, Constantine K, Fine J, Palewjala M, Macher R, Guatney L, Earleywine M, Draffkorn C, Scott B, Andrews P, Schmitt A, Dudley M, Silk-Eglit G, Stenclik J, Miele A, Lynch J, McCaffrey R, Scharaga E, Gomes W, McGinley J, Miles-Mason E, Colvin M, Carrion L, Romers C, Soper H, Zec R, Kohlrus S, Fritz S, Robbs R, Ala T, Zec R, Fritz S, Kohlrus S, Robbs R, Ala T, Edwards M, Hall J, O'Bryant S, Miller J, Dye R, Miller K, Baerresen K, Small G, Moskowitz J, Puente A, Ahmed F, Faraco C, Brown C, Evans S, Chu K, Miller L, Young-Bernier M, Tanguay A, Tremblay F, Davidson P, Duda B, Puente A, Terry D, Kent A, Patel A, Miller L, Junod A, Marion SD, Harrington M, Fonteh A, Gurnani A, John S, Gavett B, Diaz-Santos M, Mauro S, Beaute J, Cronin-Golomb A, Fazeli P, Gouaux B, Rosario D, Heaton R, Moore D, Puente A, Lindbergh C, Chu K, Evans S, Terry D, Duda B, Mackillop J, Miller S, Greco S, Klimik L, Cohen J, Robbins J, Lashley L, Schleicher-Dilks S, Golden C, Kunkes I, Culotta V, Kunkes I, Griffits K, Loughan A, Perna R, Hertza J, Cohen M, Northington S, Tyson K, Musielak K, Fine J, Kaczorowski J, Doty N, Braaten E, Shah S, Nemanim N, Singer E, Hinkin C, Levine A, Gold A, Evankovich K, Lotze T, Yoshida H, O'Bryan S, Roberg B, Glusman M, Ness A, Thelen J, Wilson L, Feaster T, Bruce J, Lobue C, Brown D, Hughes S, Greenberg B, Lacritz L, Bristow-Murray B, Andrews A, Bermudez C, Golden C, Moore R, Pulver A, Patterson T, Bowie C, Harvey P, Jeste D, Mausbach B, Wingo J, Fink J, Lee R, Pliskin N, Legenkaya A, Henry B, Minassian A, Perry W, McKeever J, Morse C, Thomas F, Schultheis M, Ruocco A, Daros A, Gill S, Grimm D, Saini G, Relova R, Hoblyn J, Lee T, Stasio C, Mahncke H, Drag L, Grimm D, Gill S, Saini G, Relova R, Hoblyn J, Lee T, Stasio C, Mahncke H, Drag L, Verbiest R, Ringdahl E, Thaler N, Sutton G, Vogel S, Reyes A, Ringdahl E, Vogel S, Freeman A, Call E, Allen D, March E, Salzberg M, Vogel S, Ringdahl E, Freeman A, Dadis F, Allen D, Sisk S, Ringdahl E, Vogel S, Freeman A, Allen D, DiGangi J, Silva L, Pliskin N, Thieme B, Daniel M, Jaehnert S, Noggle C, Thompson J, Kecala N, Lane E, Kane C, Noggle C, Thompson J, Lane E, Kecala N, Kane C, Palmer G, Happe M, Paxson J, Jurek B, Graca J, Olson S, Melville T, Harley A, La D, Phoong M, Gill S, Jocson VA, Nunan-Saah J, Keller J, Gomez R, Melville T, Kaminetskaya M, Poole J, Vernon A, Van Vleet T, DeGutis J, Chen A, Marini C, Dabit S, Gallegos J, Zomet A, Merzenich M, Thaler N, Linck J, Heyanka D, Pastorek N, Miller B, Romesser J, Sim A, Allen D, Zimmer A, Marcinak J, Hibyan S, Webbe F, Rainwater B, Francis J, Baum L, Sautter S, Donders J, Hui E, Barnes K, Walls G, Erikson S, Bailie J, Schwab K, Ivins B, Boyd C, Neff J, Cole W, Lewis S, Bailie J, Schwab K, Ivins B, Boyd C, Neff J, Cole W, Lewis S, Ramirez C, Oganes M, Gold S, Tanner S, Pina D, Merritt V, Arnett P, Heyanka D, Linck J, Thaler N, Pastorek N, Miller B, Romesser J, Sim A, Parks A, Roskos P, Gfeller J, Clark A, Isham K, Carter J, McLeod J, Romero R, Dahdah M, Barisa M, Schmidt K, Barnes S, Dubiel R, Dunklin C, Harper C, Callender L, Wilson A, Diaz-Arrastia R, Shafi S, Jacquin K, Bolshin L, Jacquin K, Romers C, Gutierrez E, Messerly J, Tsou J, Adler M, Golden C, Harmell A, Mausbach B, Moore R, Depp C, Jeste D, Palmer B, Hoadley R, Hill B, Rohling M, Mahdavi S, Fine J, daCruz K, Dinishak D, Richardson G, Vertinski M, Allen D, Mayfield J, Margolis S, Miele A, Rabinovitz B, Schaffer S, Kline J, Boettcher A, Hill B, Hoadley R, Rohling M, Eichstaedt K, Vale F, Benbadis S, Bozorg A, Rodgers-Neame N, Rinehardt E, Mattingly M, Schoenberg M, Fares R, Fares R, Carrasco R, Grups J, Evans B, Simco E, Mittenberg W, Carrasco R, Grups J, Evans B, Simco E, Mittenberg W, Rach A, Baughman B, Young C, Bene E, Irwin C, Li Y, Poulin R, Jerram M, Susmaras T, Gansler D, Ashendorf L, Miarmi L, Fazio R, Cantor J, Fernandez A, Godoy-Garcete G, Marchetti P, Harrison A, Armstrong I, Harrison L, Iverson G, Brinckman D, Ayaz H, Schultheis M, Heinly M, Vitelli K, Russler K, Sanchez I, Jones W, Loe S, Raines T, Hart J, Bene E, Li Y, Irwin C, Baughman B, Rach A, Bravo J, Schilling B, Weiss L, Lange R, Shewchuk J, Heran M, Rauscher A, Jarrett M, Brubacher J, Iverson G, Zink D, Barney S, Gilbert G, Allen D, Martin P, Schroeder R, Klas P, Jeffay E, Zakzanis K, Iverson G, Lanting S, Saffer B, Koehle M, Palmer B, Barrio C, Vergara R, Muniz M, Pinto L, Jeste D, Stenclik J, Lynch J, McCaffrey R, Shultz LS, Pedersen H, Roper B, Crouse E, Crucian G, Dezhkam N, Mulligan K, Singer R, Psihogios A, Davis A, Stephens B, Love C, Mulligan K, Webbe F, West S, McCue R, Goldin Y, Cicerone K, Ruchinskas R, Seidl JT, Massman P, Tam J, Schmitter-Edgecombe M, Baerresen K, Hanson E, Miller K, Miller J, Yeh D, Kim J, Ercoli L, Siddarth P, Small G, Noback M, Noback M, Baldock D, Mahmoud S, Munic-Miller D, Bonner-Jackson A, Banks S, Rabin L, Emerson J, Smith C, Roberts R, Hass S, Duhig A, Pankratz V, Petersen R, Leibson C, Harley A, Melville T, Phoong M, Gill S, Nunan-Saah J, La D, Gomez R, Lindbergh C, Puente A, Gray J, Chu K, Evans S, Sweet L, MacKillop J, Miller L, McAlister C, Schmitter-Edgecombe M, Baldassarre M, Kamm J, Wolff D, Dombrowski C, Bullard S, Edwards M, Hall J, Parsons T, O'Bryant S, Lawson R, Papadakis A, Higginson C, Barnett J, Wills M, Strang J, Dominska A, Wallace G, Kenworthy L, Bott N, Kletter H, Carrion V, Ward C, Getz G, Peer J, Baum C, Edner B, Mannarino A, Casnar C, Janke K, van der Fluit F, Natalie B, Haberman D, Solomon M, Hunter S, Klein-Tasman B, Starza-Smith A, Talbot E, Hart A, Hall M, Baker J, Kral M, Lally M, Zisk A, Lo T, Ross P, Cuevas M, Patel S, Lebby P, Mouanoutoua A, Harrison J, Pollock M, Mathiowetz C, Romero R, Boys C, Vekaria P, Vasserman M, MacAllister W, Stevens S, Van Hecke A, Carson A, Karst J, Schohl K, Dolan B, McKindles R, Remel R, Reveles A, Fritz N, McDonald G, Wasisco J, Kahne J, Hertza J, Tyson K, Northington S, Loughan A, Perna R, Newman A, Garmoe W, Clark J, Loughan A, Perna R, Hertza J, Cohen M, Northington S, Tyson K, Whithers K, Puente A, Dedmon A, Capps J, Lindsey H, Francis M, Weigand L, Steed A, Puente A, Edmed S, Sullivan K, Puente A, Lindsey H, Dedmon A, Capps J, Whithers K, Weigand L, Steed A, Kark S, Lafleche G, Brown T, Bogdanova Y, Strongin E, Spickler C, Drasnin D, Strongin C, Poreh A, Houshyarnejad A, Ellis M, Babikian T, Kernan C, Asarnow R, Didehbani N, Cullum M, Loneman L, Mansinghani S, Hart J, Fischer J. POSTER SESSIONS SCHEDULE. Arch Clin Neuropsychol 2013. [DOI: 10.1093/arclin/act054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Li H, Su X, Gallegos J, Lu Y, Ji Y, Molldrem JJ, Liang S. dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes. BMC Bioinformatics 2012; 13:271. [PMID: 23083219 PMCID: PMC3497615 DOI: 10.1186/1471-2105-13-271] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 09/28/2012] [Indexed: 12/01/2022] Open
Abstract
Background Dysregulation of imprinted genes, which are expressed in a parent-of-origin-specific manner, plays an important role in various human diseases, such as cancer and behavioral disorder. To date, however, fewer than 100 imprinted genes have been identified in the human genome. The recent availability of high-throughput technology makes it possible to have large-scale prediction of imprinted genes. Here we propose a Bayesian model (dsPIG) to predict imprinted genes on the basis of allelic expression observed in mRNA-Seq data of independent human tissues. Results Our model (dsPIG) was capable of identifying imprinted genes with high sensitivity and specificity and a low false discovery rate when the number of sequenced tissue samples was fairly large, according to simulations. By applying dsPIG to the mRNA-Seq data, we predicted 94 imprinted genes in 20 cerebellum samples and 57 imprinted genes in 9 diverse tissue samples with expected low false discovery rates. We also assessed dsPIG using previously validated imprinted and non-imprinted genes. With simulations, we further analyzed how imbalanced allelic expression of non-imprinted genes or different minor allele frequencies affected the predictions of dsPIG. Interestingly, we found that, among biallelically expressed genes, at least 18 genes expressed significantly more transcripts from one allele than the other among different individuals and tissues. Conclusion With the prevalence of the mRNA-Seq technology, dsPIG has become a useful tool for analysis of allelic expression and large-scale prediction of imprinted genes. For ease of use, we have set up a web service and also provided an R package for dsPIG at http://www.shoudanliang.com/dsPIG/.
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Affiliation(s)
- Hua Li
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
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Estécio MRH, Gallegos J, Dekmezian M, Lu Y, Liang S, Issa JPJ. SINE retrotransposons cause epigenetic reprogramming of adjacent gene promoters. Mol Cancer Res 2012; 10:1332-42. [PMID: 22952045 DOI: 10.1158/1541-7786.mcr-12-0351] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Almost half of the human genome and as much as 40% of the mouse genome is composed of repetitive DNA sequences. The majority of these repeats are retrotransposons of the SINE and LINE families, and such repeats are generally repressed by epigenetic mechanisms. It has been proposed that these elements can act as methylation centers from which DNA methylation spreads into gene promoters in cancer. Contradictory to a methylation center function, we have found that retrotransposons are enriched near promoter CpG islands that stay methylation-free in cancer. Clearly, it is important to determine which influence, if any, these repetitive elements have on nearby gene promoters. Using an in vitro system, we confirm here that SINE B1 elements can influence the activity of downstream gene promoters, with acquisition of DNA methylation and loss of activating histone marks, thus resulting in a repressed state. SINE sequences themselves did not immediately acquire DNA methylation but were marked by H3K9me2 and H3K27me3. Moreover, our bisulfite sequencing data did not support that gain of DNA methylation in gene promoters occurred by methylation spreading from SINE B1 repeats. Genome-wide analysis of SINE repeats distribution showed that their enrichment is directly correlated with the presence of USF1, USF2, and CTCF binding, proteins with insulator function. In summary, our work supports the concept that SINE repeats interfere negatively with gene expression and that their presence near gene promoters is counter-selected, except when the promoter is protected by an insulator element.
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Affiliation(s)
- Marcos R H Estécio
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA.
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16
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Resendiz CV, Hernández O, Guerrero I, Gallegos J, Martínez PA, Sánchez C. Engorda de corderos Pelibuey con diferente nivel de alfalfa en la dieta. ARCH ZOOTEC 2012. [DOI: 10.21071/az.v62i239.651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
El objetivo de este estudio fue evaluar el efecto de diferentes niveles de alfalfa (Medicago sativa L.) en la dieta de corderos sobre el comportamiento productivo, durante 11 semanas. Se utilizaron 36 corderos machos Pelibuey de 5 meses de edad, en estabulación, con peso inicial promedio de 22 kg, distribuidos homogéneamente en cuatro grupos de 3 animales cada uno, con 3 repeticiones por grupo. Los grupos fueron asignados al azar a cada uno de cuatro tratamientos evaluados: 0, 20, 30 y 40 % de alfalfa (base seca). Se utilizó un diseño completamente al azar, utilizando el Proc GLM (SAS, 1999) y cuando se observaron diferencias estadísticas, se realizó una comparación de medias utilizando la prueba de Tukey. Se determinó consumo de alimento, ganancia de peso, conversión, eficiencia alimenticia, rendimiento de canal en caliente y frio, y pH de la canal; además de la degradabilidad in situ de la MS de las dietas. El consumo de MS aumentó (p0,05), promediando 271 g animal-1 día-1. Tampoco hubo variación (p>0,05) en el peso final, conversión y eficiencia alimenticia, promediando 38,0 kg animal-1,4,74 y 0,212, respectivamente. El peso (19,3 y 18,8 kg) y rendimiento (54,4 y 53,0 %) de canal en caliente y fría, fueron similares entre tratamientos. Incluir alfalfa en la dieta de corderos, no ofrece ventajas en la ganancia de peso, sin embargo hasta 40 %, podría ser atractivo económicamente para el productor, además de promover mayor consumo de MS.
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Sun C, Jhingran A, Gallegos J, Bodurka D, Frumovitz M, Ramondetta L. Longitudinal quality of life in medically underserved women with locally advanced cervical cancer. Gynecol Oncol 2012. [DOI: 10.1016/j.ygyno.2011.12.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Estecio MR, Dekmezian M, Gallegos J, Liang S, Issa JP. Abstract 2791: SINE retrotransposons cause epigenetic reprogramming of adjacent gene promoters. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-2791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Retrotransposons of SINE and LINE classes have been extremely successful in colonizing mammalian genomes. Almost half of the human genome and as much as 40% of the mouse genome is composed of repetitive DNA sequences. The comparison of human and mouse genomes revealed a spatial concordance in positioning of SINE but not LINE repeats, indicating evolutionary pressure to maintain and/or exclude these repeats from orthologous regions. We hypothesized that this phenomenon is due to a negative influence of SINE repeats on gene expression and counter selection over evolution, resulting in exclusion of these repeats from vulnerable genomic environments. To test the capacity of SINE B1 elements in promoting gene silencing, we generated a system where the luciferase gene is under the control of three different mouse gene promoters (cdkn2a, p14arf and mlh1), and we inserted two and four copies of SINE B1 elements upstream to these promoters. Using this in vitro system, we found that SINE B1 elements can influence the activity of downstream gene promoters, with acquisition of DNA methylation and loss of activating histone marks, thus resulting in a repressed state. Interestingly, SINE sequences themselves do not immediately acquired DNA methylation, but became marked by H3K9me2 and H3K27me3. Moreover, gain of DNA methylation depended on cryptic genomic methylation centers rather than spreading from SINE B1 repeats. Since mouse SINE B1 elements caused transcriptional repression, we sought to investigate whether human SINE Alu repeats could have the same effect. The human E-cadherin gene has three SINE Alus adjacent to the 3’ region of its CpG island, and in reporter assays the removal of these repeats resulted in higher, stable promoter activity. Genome-wide analysis of SINE repeats distribution in the human and mouse genomes showed that they are excluded from proximal promoters and their enrichment is directly correlated with the presence of USF1, USF2 and CTCF binding, proteins with insulator function. In conclusion, our work supports the concept that SINE repeats interfere negatively with gene expression and that their presence near gene promoters is dependent on, and co-evolved with the presence of insulator elements.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2791. doi:10.1158/1538-7445.AM2011-2791
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Estécio MR, Gallegos J, Vallot C, Castoro RJ, Chung W, Maegawa S, Oki Y, Kondo Y, Jelinek J, Shen L, Hartung H, Aplan PD, Czerniak BA, Liang S, Issa JPJ. Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer. Genome Res 2010; 20:1369-82. [DOI: 10.1101/gr.107318.110] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Epigenetic silencing plays an important role in cancer development. An attractive hypothesis is that local DNA features may participate in differential predisposition to gene hypermethylation. We found that, compared with methylation-resistant genes, methylation-prone genes have a lower frequency of SINE and LINE retrotransposons near their transcription start site. In several large testing sets, this distribution was highly predictive of promoter methylation. Genome-wide analysis showed that 22% of human genes were predicted to be methylation-prone in cancer; these tended to be genes that are down-regulated in cancer and that function in developmental processes. Moreover, retrotransposon distribution marks a larger fraction of methylation-prone genes compared to Polycomb group protein (PcG) marking in embryonic stem cells; indeed, PcG marking and our predictive model based on retrotransposon frequency appear to be correlated but also complementary. In summary, our data indicate that retrotransposon elements, which are widespread in our genome, are strongly associated with gene promoter DNA methylation in cancer and may in fact play a role in influencing epigenetic regulation in normal and abnormal physiological states.
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Gunn GB, Anderson KE, Patel AJ, Gallegos J, Hallberg CK, Sood G, Hatch SS, Sanguineti G. Severe radiation therapy-related soft tissue toxicity in a patient with porphyria cutanea tarda: a literature review. Head Neck 2009; 32:1112-7. [PMID: 19536857 DOI: 10.1002/hed.21161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Some porphyrias are associated with cutaneous phototoxicity due to photoactivation of porphyrins, but whether ionizing radiation can have an additive effect is not clear. We report a case of severe radiation therapy-related toxicity in a patient with porphyria cutanea tarda and review the literature. METHODS A 50-year-old man with porphyria cutanea was treated for lower lip squamous cell carcinoma with definitive radiation therapy. During radiation therapy, acute toxicity was of an expected onset and severity. Six months after treatment completion, he developed skin hypopigmentation, soft tissue fibrosis, and areas of painful denuded skin and crusting within the previous treatment field. RESULTS Reports of 7 patients with porphyria receiving radiation therapy to at least 9 separate sites were reviewed, with only 1 previous report suggestive of increased radiation therapy-related toxicity. CONCLUSION Based on this and 1 other report, caution is warranted when considering radiation therapy in patients with active porphyria.
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Affiliation(s)
- G Brandon Gunn
- Department of Radiation Oncology, University of Texas Medical Branch, Galveston, Texas, USA.
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Shinn E, Le T, Gallegos J, Basen-Engquist K. A pilot analysis of multispectral digital colposcopy for women with high-grade squamous intraepithelial lesion (HGSIL) Pap smear results. Gynecol Oncol 2007; 107:S83-5. [PMID: 17822747 DOI: 10.1016/j.ygyno.2007.07.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Accepted: 07/06/2007] [Indexed: 11/29/2022]
Affiliation(s)
- E Shinn
- Department of Behavioral Science, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Blvd. Unit 193, Houston, TX 77030, USA.
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Zhu YT, Egeland GW, Li Y, Jia QX, Gallegos J, Serquis A, Liao XZ, Peterson DE, Dye RC, Roop BJ, Hoffbauer MA. Formation of pile networks by long carbon nanotubes from decomposition of CO on Co-Mo film. J Nanosci Nanotechnol 2004; 4:189-191. [PMID: 15112565 DOI: 10.1166/jnn.2004.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We report the formation of pile networks by long carbon nanotubes grown at 700 degrees C from a Co-Mo film on a quartz plate. Carbon monoxide (CO) was used as the carbon source. The networks were formed because the density of catalyst particles on the substrate was low, which resulted in low carbon nanotube density that did not support vertical growth. At the same time, the low carbon nanotube density makes it possible for CO to reach the catalysts on the substrate for continuous growth. No obvious amorphous carbon chunks were observed, suggesting that the pile networks consisted of fairly high-quality, long carbon nanotubes.
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Affiliation(s)
- Y T Zhu
- Materials Science and Technology Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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Jonsson CB, Gallegos J, Ferro P, Severson W, Xu X, Schmaljohn CS, Fero P. Purification and characterization of the Sin Nombre virus nucleocapsid protein expressed in Escherichia coli. Protein Expr Purif 2001; 23:134-41. [PMID: 11570855 DOI: 10.1006/prep.2001.1489] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sin Nombre virus is a member of the Hantavirus genus, family Bunyaviridae, and is an etiologic agent of hantavirus pulmonary syndrome. The hantavirus nucleocapsid (N) protein plays an important role in the encapsidation and assembly of the viral negative-sense genomic RNA. The Sin Nombre N protein was expressed as a C-terminal hexahistidine fusion in Escherichia coli and initially purified by nickel-affinity chromatography. We developed methods to extract the soluble fraction and to solubilize the remainder of the N protein using denaturants. Maximal expression of protein from native purification was observed after a 1.5-h induction with IPTG (2.4 mg/L). The zwitterionic detergent Chaps did not enhance the yield of native purifications, but increased the yield of protein obtained from insoluble purifications. Both soluble and insoluble materials, purified by nickel-affinity chromatography, were also subjected to Hi Trap SP Sepharose fast-flow (FF) chromatography. Both soluble and insoluble proteins had a similar A(280) profile on the Sepharose FF column, and both suggested the presence of a nucleic acid contaminant. The apparent dissociation constant of the N protein, purified by nickel-affinity and SP Sepharose FF chromatography, and the 5' end of the viral S-segment genome were measured using a filter binding assay. The N protein-vRNA complex had an apparent dissociation constant of 140 nM.
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Affiliation(s)
- C B Jonsson
- Department of Chemistry, New Mexico State University, Las Cruces 88003, USA.
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Valencia-Flores M, Orea A, Castaño VA, Resendiz M, Rosales M, Rebollar V, Santiago V, Gallegos J, Campos RM, González J, Oseguera J, García-Ramos G, Bliwise DL. Prevalence of sleep apnea and electrocardiographic disturbances in morbidly obese patients. Obes Res 2000; 8:262-9. [PMID: 10832770 DOI: 10.1038/oby.2000.31] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE To determine the prevalence of sleep apnea in morbidly obese patients and its relationship with cardiac arrhythmias. RESEARCH METHODS AND PROCEDURES Fifty-two consecutive morbidly obese (body mass index > or = 40 kg/m2) outpatients from the Obesity Clinic of the National Institute of Nutrition Salvador Zubirán underwent two nights of polysomnography with standard laboratory techniques. Electrocardiographic polysomnography signals (Lead II) were evaluated by two experienced cardiologists, and sleep complaints were measured with a standard sleep questionnaire (Sleep Disorders Questionnaire). In order to make comparisons between groups with different severities of sleep-disordered breathing, we classified the patients in four groups using the apnea-hypopnea index (AHI): Group 1, AHI 5 < 15 (n = 10); Group 2, AHI 15 < 30 (n = 10); Group 3, AHI 30 < 65 (n = 14); Group 4, AHI > or = 65 (n = 17). RESULTS A wide range of sleep-disordered breathing, ranging from AHI of 2.5 to 128.9 was found. Ninety-eight percent of the sample (n = 51) had an AHI > or = 5 (mean = 51 +/- 37), and 33% had severe sleep apnea with AHI > or = 65 with a mean nocturnal desaturation time of <65% over 135 minutes. Electrocardiographic abnormalities were present in 31% of the patients. Cardiac rhythm alterations showed an association with the level of sleep-disordered breathing and oxygen desaturation. DISCUSSION We conclude that there is a high prevalence of sleep apnea in morbidly obese patients and that the risk for cardiac arrhythmias increases in this population in the presence of a severe sleep apnea (AHI > or = 65) with severe oxygen desaturation (SaO2 < or = 65%).
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Affiliation(s)
- M Valencia-Flores
- Neurology Department, National Institute of Nutrition Salvador Zubirán, School of Psychology, National Autonomous University of México, Federal District.
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Restaino S, Dayton D, Browne S, Gonglewski J, Baker J, Rogers S, McDermott S, Gallegos J, Shilko M. On the use of dual frequency nematic material for adaptive optics systems: first results of a closed-loop experiment. Opt Express 2000; 6:2-6. [PMID: 19401740 DOI: 10.1364/oe.6.000002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The use of liquid crystal devices for wavefront control has been suggested and implemented by several authors. In this paper we report some preliminary results on the use of Nematic based liquid crystal devices. Several experimental efforts have been carried out in the past few months. One of the main aims was to characterize a new device that uses dual frequency nematic material in a closed loop arrangement.
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Affiliation(s)
- J Suazo-Barahona
- Department of Gastroenterology, Instituto Nacional de la Nutrición Salvador Zubirán, Mexico City, Mexico
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Wallace JE, Harris SC, Gallegos J, Foulds G, Chen TJ, Rinaldi MG. Assay of fluconazole by high-performance liquid chromatography with a mixed-phase column. Antimicrob Agents Chemother 1992; 36:603-6. [PMID: 1622169 PMCID: PMC190563 DOI: 10.1128/aac.36.3.603] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A mixed-phase liquid chromatographic column was used to assay fluconazole in plasma, serum, and cerebrospinal fluid. The assay was linear from 0.2 to 20 micrograms/ml, with an average coefficient of variation of less than 5%. The partitioning of the drug between serum and cerebrospinal fluid was determined for 34 patients. The method was demonstrated to be suitable for both pharmacokinetic studies and monitoring of patients receiving treatment with this antifungal agent.
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Affiliation(s)
- J E Wallace
- Department of Pathology, University of Texas Health Science Center, San Antonio 78284-7750
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Abstract
The purpose of this study was to investigate the effect of norfloxacin on theophylline elimination. Ten normal volunteers were studied. In a randomized crossover sequence, each subject received 6 mg of aminophylline per kg of body weight by a 30-min intravenous infusion on day 4 of taking norfloxacin (400 mg every 12 h) or while drug free. Mean theophylline clearance decreased and mean elimination half-life increased after norfloxacin administration (from 0.036 +/- 0.006 to 0.033 +/- 0.004 liter/h per kg and from 8.7 +/- 1.2 to 9.5 +/- 1.5 h, respectively; P less than 0.05, Wilcoxon signed-ranks test). We conclude that norfloxacin taken in recommended doses for 3 days has a small inhibitory effect on theophylline metabolism that would probably not cause clinically important elevations in theophylline concentrations in most patients.
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Affiliation(s)
- R L Davis
- College of Pharmacy, School of Medicine, University of New Mexico, Albuquerque 87131
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