View and Standard Neuropathological Analysis of Brain Sections from Affected Pedigree Members
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Genomic Correlates of Relationship QTL Involved in Fore- Versus Hind Limb Divergence in Mice
Loyola University Chicago Loyola eCommons Biology: Faculty Publications and Other Works Faculty Publications 2013 Genomic Correlates of Relationship QTL Involved in Fore- Versus Hind Limb Divergence in Mice Mihaela Palicev Gunter P. Wagner James P. Noonan Benedikt Hallgrimsson James M. Cheverud Loyola University Chicago, [email protected] Follow this and additional works at: https://ecommons.luc.edu/biology_facpubs Part of the Biology Commons Recommended Citation Palicev, M, GP Wagner, JP Noonan, B Hallgrimsson, and JM Cheverud. "Genomic Correlates of Relationship QTL Involved in Fore- Versus Hind Limb Divergence in Mice." Genome Biology and Evolution 5(10), 2013. This Article is brought to you for free and open access by the Faculty Publications at Loyola eCommons. It has been accepted for inclusion in Biology: Faculty Publications and Other Works by an authorized administrator of Loyola eCommons. For more information, please contact [email protected]. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License. © Palicev et al., 2013. GBE Genomic Correlates of Relationship QTL Involved in Fore- versus Hind Limb Divergence in Mice Mihaela Pavlicev1,2,*, Gu¨ nter P. Wagner3, James P. Noonan4, Benedikt Hallgrı´msson5,and James M. Cheverud6 1Konrad Lorenz Institute for Evolution and Cognition Research, Altenberg, Austria 2Department of Pediatrics, Cincinnati Children‘s Hospital Medical Center, Cincinnati, Ohio 3Yale Systems Biology Institute and Department of Ecology and Evolutionary Biology, Yale University 4Department of Genetics, Yale University School of Medicine 5Department of Cell Biology and Anatomy, The McCaig Institute for Bone and Joint Health and the Alberta Children’s Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Canada 6Department of Anatomy and Neurobiology, Washington University *Corresponding author: E-mail: [email protected]. -
Smu1 and RED Are Required for Activation of Spliceosomal B Complexes Assembled on Short Introns
ARTICLE https://doi.org/10.1038/s41467-019-11293-8 OPEN Smu1 and RED are required for activation of spliceosomal B complexes assembled on short introns Sandra Keiper 1, Panagiotis Papasaikas 2,4,5, Cindy L. Will1, Juan Valcárcel2,3, Cyrille Girard1 & Reinhard Lührmann1 1234567890():,; Human pre-catalytic spliceosomes contain several proteins that associate transiently just prior to spliceosome activation and are absent in yeast, suggesting that this critical step is more complex in higher eukaryotes. We demonstrate via RNAi coupled with RNA-Seq that two of these human-specific proteins, Smu1 and RED, function both as alternative splicing regulators and as general splicing factors and are required predominantly for efficient splicing of short introns. In vitro splicing assays reveal that Smu1 and RED promote spliceosome activation, and are essential for this step when the distance between the pre-mRNA’s5′ splice site (SS) and branch site (BS) is sufficiently short. This Smu1-RED requirement can be bypassed when the 5′ and 3′ regions of short introns are physically separated. Our obser- vations suggest that Smu1 and RED relieve physical constraints arising from a short 5′SS-BS distance, thereby enabling spliceosomes to overcome structural challenges associated with the splicing of short introns. 1 Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. 2 Centre de Regulació Genòmica, The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain. 3 Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys, 08010 Barcelona, Spain. 4Present address: Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland. -
Uncoupling Intraflagellar Transport and Primary Cilia Formation Demonstrates Deep Integration of IFT in Hedgehog Signaling
bioRxiv preprint doi: https://doi.org/10.1101/226324; this version posted November 28, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Uncoupling Intraflagellar Transport and Primary Cilia Formation Demonstrates Deep Integration of IFT in Hedgehog Signaling Thibaut Eguether1, 2, Fabrice P Cordelieres3, Gregory J Pazour1, 4 1Program in Molecular Medicine University of Massachusetts Medical School Biotech II, Suite 213 373 Plantation Street Worcester, MA 01605, USA [email protected] 2Current address Université Pierre et Marie Curie U1157 INSERM / UMR 7203 ENS CNRS UPMC Faculté de Médecine Pierre et Marie Curie Etage 6 porte 606 27 rue de Chaligny 75012 Paris, France [email protected] 3Université de Bordeaux UMS 3420 CNRS-Université de Bordeaux-US4 INSERM, Bordeaux Imaging Center Pôle d’imagerie photonique Bordeaux F-33000, France [email protected] 4Corresponding Author Running Title: Uncoupling IFT and ciliogenesis Key words: Primary cilia, Intraflagellar Transport, IFT, Hedgehog Signaling Abbreviations: MEFs, mouse embryonic fibroblasts; SAG, smoothen agonist; IFT intraflagellar transport; FKBP, FK506 Binding Protein 12; FRB, FKBP12-rapamycin binding bioRxiv preprint doi: https://doi.org/10.1101/226324; this version posted November 28, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract The vertebrate hedgehog pathway is organized in primary cilia and hedgehog components relocate into or out of cilia during signaling. Defects in intraflagellar transport (IFT) typically disrupt ciliary assembly and attenuate hedgehog signaling. -
Noelia Díaz Blanco
Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr. -
Variation in Protein Coding Genes Identifies Information
bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Animal complexity and information flow 1 1 2 3 4 5 Variation in protein coding genes identifies information flow as a contributor to 6 animal complexity 7 8 Jack Dean, Daniela Lopes Cardoso and Colin Sharpe* 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Institute of Biological and Biomedical Sciences 25 School of Biological Science 26 University of Portsmouth, 27 Portsmouth, UK 28 PO16 7YH 29 30 * Author for correspondence 31 [email protected] 32 33 Orcid numbers: 34 DLC: 0000-0003-2683-1745 35 CS: 0000-0002-5022-0840 36 37 38 39 40 41 42 43 44 45 46 47 48 49 Abstract bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Animal complexity and information flow 2 1 Across the metazoans there is a trend towards greater organismal complexity. How 2 complexity is generated, however, is uncertain. Since C.elegans and humans have 3 approximately the same number of genes, the explanation will depend on how genes are 4 used, rather than their absolute number. -
The Pathogenetic Role of Β-Cell Mitochondria in Type 2 Diabetes
236 3 Journal of M Fex et al. Mitochondria in β-cells 236:3 R145–R159 Endocrinology REVIEW The pathogenetic role of β-cell mitochondria in type 2 diabetes Malin Fex1, Lisa M Nicholas1, Neelanjan Vishnu1, Anya Medina1, Vladimir V Sharoyko1, David G Nicholls1, Peter Spégel1,2 and Hindrik Mulder1 1Department of Clinical Sciences in Malmö, Unit of Molecular Metabolism, Lund University Diabetes Centre, Clinical Research Center, Malmö University Hospital, Lund University, Malmö, Sweden 2Department of Chemistry, Center for Analysis and Synthesis, Lund University, Sweden Correspondence should be addressed to H Mulder: [email protected] Abstract Mitochondrial metabolism is a major determinant of insulin secretion from pancreatic Key Words β-cells. Type 2 diabetes evolves when β-cells fail to release appropriate amounts f TCA cycle of insulin in response to glucose. This results in hyperglycemia and metabolic f coupling signal dysregulation. Evidence has recently been mounting that mitochondrial dysfunction f oxidative phosphorylation plays an important role in these processes. Monogenic dysfunction of mitochondria is a f mitochondrial transcription rare condition but causes a type 2 diabetes-like syndrome owing to β-cell failure. Here, f genetic variation we describe novel advances in research on mitochondrial dysfunction in the β-cell in type 2 diabetes, with a focus on human studies. Relevant studies in animal and cell models of the disease are described. Transcriptional and translational regulation in mitochondria are particularly emphasized. The role of metabolic enzymes and pathways and their impact on β-cell function in type 2 diabetes pathophysiology are discussed. The role of genetic variation in mitochondrial function leading to type 2 diabetes is highlighted. -
SARS-Cov-2 Restructures the Host Chromatin Architecture 2
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.20.453146; this version posted July 21, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 SARS-CoV-2 Restructures the Host Chromatin Architecture 2 3 Authors: Ruoyu Wang 1,2,†, Joo-Hyung Lee 1,†, Feng Xiong 1, Jieun Kim 3,4, Lana Al Hasani 1,2, Xiaoyi 4 Yuan 3,4, Pooja Shivshankar 1,3,4, Joanna Krakowiak 1, Chuangye Qi 1, Yanyu Wang 3,4, Holger K. 5 Eltzschig 2,3,4, Wenbo Li 1,2,* 6 7 Affiliations: 8 1 Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas 9 Health Science Center, Houston, 77030, TX, USA 10 2 Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and 11 UTHealth, Houston, 77030, TX, USA 12 3 Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center, 13 Houston, 77030, TX, USA 14 4 Center for Perioperative Medicine, McGovern Medical School, University of Texas Health Science 15 Center, Houston, 77030, TX, USA 16 17 † These authors contributed equally 18 * Correspondence: Wenbo Li, Ph.D. ([email protected]). MSB 6.161, Fannin Street, Houston, 19 Texas, 77030, USA; Tel: 713-500-6103. 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.20.453146; this version posted July 21, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
High Diagnostic Yield in Skeletal Ciliopathies Using Massively Parallel Genome Sequencing, Structural Variant Screening and RNA Analyses
Journal of Human Genetics (2021) 66:995–1008 https://doi.org/10.1038/s10038-021-00925-x ARTICLE High diagnostic yield in skeletal ciliopathies using massively parallel genome sequencing, structural variant screening and RNA analyses 1 1 2,3 4 1 Anna Hammarsjö ● Maria Pettersson ● David Chitayat ● Atsuhiko Handa ● Britt-Marie Anderlid ● 5 6 7 8 9 Marco Bartocci ● Donald Basel ● Dominyka Batkovskyte ● Ana Beleza-Meireles ● Peter Conner ● 10 11 12,13 7,14 15 Jesper Eisfeldt ● Katta M. Girisha ● Brian Hon-Yin Chung ● Eva Horemuzova ● Hironobu Hyodo ● 16 1 17 18,19 20 Liene Korņejeva ● Kristina Lagerstedt-Robinson ● Angela E. Lin ● Måns Magnusson ● Shahida Moosa ● 11 10 21 15 18,22 Shalini S. Nayak ● Daniel Nilsson ● Hirofumi Ohashi ● Naoko Ohashi-Fukuda ● Henrik Stranneheim ● 1 23 24 19,22 1 7,25 Fulya Taylan ● Rasa Traberg ● Ulrika Voss ● Valtteri Wirta ● Ann Nordgren ● Gen Nishimura ● 1 1 Anna Lindstrand ● Giedre Grigelioniene Received: 4 December 2020 / Revised: 31 March 2021 / Accepted: 31 March 2021 / Published online: 20 April 2021 © The Author(s) 2021. This article is published with open access Abstract Skeletal ciliopathies are a heterogenous group of disorders with overlapping clinical and radiographic features including 1234567890();,: 1234567890();,: bone dysplasia and internal abnormalities. To date, pathogenic variants in at least 30 genes, coding for different structural cilia proteins, are reported to cause skeletal ciliopathies. Here, we summarize genetic and phenotypic features of 34 affected individuals from 29 families with skeletal ciliopathies. Molecular diagnostic testing was performed using massively parallel sequencing (MPS) in combination with copy number variant (CNV) analyses and in silico filtering for variants in known skeletal ciliopathy genes. -
NDUFB6 (NM 182739) Human Tagged ORF Clone Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC219791 NDUFB6 (NM_182739) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: NDUFB6 (NM_182739) Human Tagged ORF Clone Tag: Myc-DDK Symbol: NDUFB6 Synonyms: B17; CI Vector: pCMV6-Entry (PS100001) E. coli Selection: Kanamycin (25 ug/mL) Cell Selection: Neomycin ORF Nucleotide >RC219791 representing NM_182739 Sequence: Red=Cloning site Blue=ORF Green=Tags(s) TTTTGTAATACGACTCACTATAGGGCGGCCGGGAATTCGTCGACTGGATCCGGTACCGAGGAGATCTGCC GCCGCGATCGCC ATGACGGGGTACACTCCGGATGAGAAACTGCGGCTGCAGCAGCTGCGAGAGCTGAGAAGGCGATGGCTGA AGGACCAGGAGCTGAGCCCTCGGGAGCCGGTGCTGCCCCCACAGAAGATGGGGCCTATGGAGAAATTCTG GAATAAATTTTTGGAGAATAAATCCCCTTGGAGGAAAATGGTCCATGGGGTATACAAAAAGAGTATCTTT GTTTTCACTCATGTACTTGTACCTGTCTGGATTATTCATTATTACATGAAGTATCATGTTTCTGGTGATA CAATTCTGGAGACTGGAGAAGTAATTCCACCAATGAAAGAATTTCCTGATCAACATCAT ACGCGTACGCGGCCGCTCGAGCAGAAACTCATCTCAGAAGAGGATCTGGCAGCAAATGATATCCTGGATT ACAAGGATGACGACGATAAGGTTTAA Protein Sequence: >RC219791 representing NM_182739 Red=Cloning site Green=Tags(s) MTGYTPDEKLRLQQLRELRRRWLKDQELSPREPVLPPQKMGPMEKFWNKFLENKSPWRKMVHGVYKKSIF VFTHVLVPVWIIHYYMKYHVSGDTILETGEVIPPMKEFPDQHH TRTRPLEQKLISEEDLAANDILDYKDDDDKV Restriction Sites: SgfI-MluI This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, -
THE FUNCTIONAL SIGNIFICANCE of MITOCHONDRIAL SUPERCOMPLEXES in C. ELEGANS by WICHIT SUTHAMMARAK Submitted in Partial Fulfillment
THE FUNCTIONAL SIGNIFICANCE OF MITOCHONDRIAL SUPERCOMPLEXES in C. ELEGANS by WICHIT SUTHAMMARAK Submitted in partial fulfillment of the requirements For the degree of Doctor of Philosophy Dissertation Advisor: Drs. Margaret M. Sedensky & Philip G. Morgan Department of Genetics CASE WESTERN RESERVE UNIVERSITY January, 2011 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of _____________________________________________________ candidate for the ______________________degree *. (signed)_______________________________________________ (chair of the committee) ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ (date) _______________________ *We also certify that written approval has been obtained for any proprietary material contained therein. Dedicated to my family, my teachers and all of my beloved ones for their love and support ii ACKNOWLEDGEMENTS My advanced academic journey began 5 years ago on the opposite side of the world. I traveled to the United States from Thailand in search of a better understanding of science so that one day I can return to my homeland and apply the knowledge and experience I have gained to improve the lives of those affected by sickness and disease yet unanswered by science. Ultimately, I hoped to make the academic transition into the scholarly community by proving myself through scientific research and understanding so that I can make a meaningful contribution to both the scientific and medical communities. The following dissertation would not have been possible without the help, support, and guidance of a lot of people both near and far. I wish to thank all who have aided me in one way or another on this long yet rewarding journey. My sincerest thanks and appreciation goes to my advisors Philip Morgan and Margaret Sedensky. -
Dottorato Di Ricerca Toscano Di Neuroscienze Profilo
DOTTORATO DI RICERCA TOSCANO DI NEUROSCIENZE CICLO XXVIII COORDINATORE Prof. Renato Corradetti PROFILO GENETICO ED EPIGENETICO IN PAZIENTI CON DEMENZA FRONTOTEMPORALE Settore Scientifico Disciplinare MED/26 Dottorando Tutor Dott.ssa Piaceri Irene Prof. Sorbi Sandro Coordinatore Prof. Renato Corradetti Anni 2012/2015 Indice INDICE INTRODUZIONE .............................................................................................1 1. DEMENZA FRONTOTEMPORALE ..................................................................2 1.1 Diagnosi Clinica ....................................................................................4 1.1.1 Variante comportamentale (bvFTD) ............................................5 1.1.2 Afasia primaria progressiva (PPA) ..............................................6 1.1.2.1 Afasia progressiva non fluente (PNFA) ...............................7 1.1.2.2 Demenza Semantica (SD) ......................................................8 1.1.3 Degenerazione corticobasale (CBD) e Paralisi sopranucleare progressiva (PSP) ....................................................................................9 1.2 FTD/SLA spectrum ............................................................................. 10 1.3 Aspetti Neuropatologici e Istopatologici ............................................... 11 2. LA GENETICA DELLA DEMENZA FRONTOTEMPORALE ............................... 14 2.1 MAPT ................................................................................................. 16 2.2 GRN................................................................................................... -
SZDB: a Database for Schizophrenia Genetic Research
Schizophrenia Bulletin vol. 43 no. 2 pp. 459–471, 2017 doi:10.1093/schbul/sbw102 Advance Access publication July 22, 2016 SZDB: A Database for Schizophrenia Genetic Research Yong Wu1,2, Yong-Gang Yao1–4, and Xiong-Jian Luo*,1,2,4 1Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China; 2Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China; 3CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China 4YGY and XJL are co-corresponding authors who jointly directed this work. *To whom correspondence should be addressed; Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; tel: +86-871-68125413, fax: +86-871-68125413, e-mail: [email protected] Schizophrenia (SZ) is a debilitating brain disorder with a Introduction complex genetic architecture. Genetic studies, especially Schizophrenia (SZ) is a severe mental disorder charac- recent genome-wide association studies (GWAS), have terized by abnormal perceptions, incoherent or illogi- identified multiple variants (loci) conferring risk to SZ. cal thoughts, and disorganized speech and behavior. It However, how to efficiently extract meaningful biological affects approximately 0.5%–1% of the world populations1 information from bulk genetic findings of SZ remains a and is one of the leading causes of disability worldwide.2–4 major challenge. There is a pressing