Diagnostic Yield of Array Comparative Genomic Hybridization in Adults with Autism Spectrum Disorders
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Whole-Genome Landscape of Pancreatic Neuroendocrine Tumours
Scarpa, A. et al. (2017) Whole-genome landscape of pancreatic neuroendocrine tumours. Nature, 543(7643), pp. 65-71. (doi:10.1038/nature21063) This is the author’s final accepted version. There may be differences between this version and the published version. You are advised to consult the publisher’s version if you wish to cite from it. http://eprints.gla.ac.uk/137698/ Deposited on: 12 December 2018 Enlighten – Research publications by members of the University of Glasgow http://eprints.gla.ac.uk Whole-genome landscape of pancreatic neuroendocrine tumours Aldo Scarpa1,2*§, David K. Chang3,4, 7,29,36* , Katia Nones5,6*, Vincenzo Corbo1,2*, Ann-Marie Patch5,6, Peter Bailey3,6, Rita T. Lawlor1,2, Amber L. Johns7, David K. Miller6, Andrea Mafficini1, Borislav Rusev1, Maria Scardoni2, Davide Antonello8, Stefano Barbi2, Katarzyna O. Sikora1, Sara Cingarlini9, Caterina Vicentini1, Skye McKay7, Michael C. J. Quinn5,6, Timothy J. C. Bruxner6, Angelika N. Christ6, Ivon Harliwong6, Senel Idrisoglu6, Suzanne McLean6, Craig Nourse3, 6, Ehsan Nourbakhsh6, Peter J. Wilson6, Matthew J. Anderson6, J. Lynn Fink6, Felicity Newell5,6, Nick Waddell6, Oliver Holmes5,6, Stephen H. Kazakoff5,6, Conrad Leonard5,6, Scott Wood5,6, Qinying Xu5,6, Shivashankar Hiriyur Nagaraj6, Eliana Amato1,2, Irene Dalai1,2, Samantha Bersani2, Ivana Cataldo1,2, Angelo P. Dei Tos10, Paola Capelli2, Maria Vittoria Davì11, Luca Landoni8, Anna Malpaga8, Marco Miotto8, Vicki L.J. Whitehall5,12,13, Barbara A. Leggett5,12,14, Janelle L. Harris5, Jonathan Harris15, Marc D. Jones3, Jeremy Humphris7, Lorraine A. Chantrill7, Venessa Chin7, Adnan M. Nagrial7, Marina Pajic7, Christopher J. Scarlett7,16, Andreia Pinho7, Ilse Rooman7†, Christopher Toon7, Jianmin Wu7,17, Mark Pinese7, Mark Cowley7, Andrew Barbour18, Amanda Mawson7†, Emily S. -
Pediatric and Perinatal Pathology (1842-1868)
VOLUME 33 | SUPPLEMENT 2 | MARCH 2020 MODERN PATHOLOGY ABSTRACTS PEDIATRIC AND PERINATAL PATHOLOGY (1842-1868) LOS ANGELES CONVENTION CENTER FEBRUARY 29-MARCH 5, 2020 LOS ANGELES, CALIFORNIA 2020 ABSTRACTS | PLATFORM & POSTER PRESENTATIONS EDUCATION COMMITTEE Jason L. Hornick, Chair William C. Faquin Rhonda K. Yantiss, Chair, Abstract Review Board Yuri Fedoriw and Assignment Committee Karen Fritchie Laura W. Lamps, Chair, CME Subcommittee Lakshmi Priya Kunju Anna Marie Mulligan Steven D. Billings, Interactive Microscopy Subcommittee Rish K. Pai Raja R. Seethala, Short Course Coordinator David Papke, Pathologist-in-Training Ilan Weinreb, Subcommittee for Unique Live Course Offerings Vinita Parkash David B. Kaminsky (Ex-Officio) Carlos Parra-Herran Anil V. Parwani Zubair Baloch Rajiv M. Patel Daniel Brat Deepa T. Patil Ashley M. Cimino-Mathews Lynette M. Sholl James R. Cook Nicholas A. Zoumberos, Pathologist-in-Training Sarah Dry ABSTRACT REVIEW BOARD Benjamin Adam Billie Fyfe-Kirschner Michael Lee Natasha Rekhtman Narasimhan Agaram Giovanna Giannico Cheng-Han Lee Jordan Reynolds Rouba Ali-Fehmi Anthony Gill Madelyn Lew Michael Rivera Ghassan Allo Paula Ginter Zaibo Li Andres Roma Isabel Alvarado-Cabrero Tamara Giorgadze Faqian Li Avi Rosenberg Catalina Amador Purva Gopal Ying Li Esther Rossi Roberto Barrios Anuradha Gopalan Haiyan Liu Peter Sadow Rohit Bhargava Abha Goyal Xiuli Liu Steven Salvatore Jennifer Boland Rondell Graham Yen-Chun Liu Souzan Sanati Alain Borczuk Alejandro Gru Lesley Lomo Anjali Saqi Elena Brachtel Nilesh Gupta Tamara -
Ck1δ Over-Expressing Mice Display ADHD-Like Behaviors, Frontostriatal Neuronal Abnormalities and Altered Expressions of ADHD-Candidate Genes
Molecular Psychiatry (2020) 25:3322–3336 https://doi.org/10.1038/s41380-018-0233-z ARTICLE CK1δ over-expressing mice display ADHD-like behaviors, frontostriatal neuronal abnormalities and altered expressions of ADHD-candidate genes 1 1 1 2 1 1 1 Mingming Zhou ● Jodi Gresack ● Jia Cheng ● Kunihiro Uryu ● Lars Brichta ● Paul Greengard ● Marc Flajolet Received: 8 November 2017 / Revised: 4 July 2018 / Accepted: 18 July 2018 / Published online: 19 October 2018 © Springer Nature Limited 2018 Abstract The cognitive mechanisms underlying attention-deficit hyperactivity disorder (ADHD), a highly heritable disorder with an array of candidate genes and unclear genetic architecture, remain poorly understood. We previously demonstrated that mice overexpressing CK1δ (CK1δ OE) in the forebrain show hyperactivity and ADHD-like pharmacological responses to D- amphetamine. Here, we demonstrate that CK1δ OE mice exhibit impaired visual attention and a lack of D-amphetamine- induced place preference, indicating a disruption of the dopamine-dependent reward pathway. We also demonstrate the presence of abnormalities in the frontostriatal circuitry, differences in synaptic ultra-structures by electron microscopy, as 1234567890();,: 1234567890();,: well as electrophysiological perturbations of both glutamatergic and GABAergic transmission, as observed by altered frequency and amplitude of mEPSCs and mIPSCs. Furthermore, gene expression profiling by next-generation sequencing alone, or in combination with bacTRAP technology to study specifically Drd1a versus Drd2 medium spiny neurons, revealed that developmental CK1δ OE alters transcriptional homeostasis in the striatum, including specific alterations in Drd1a versus Drd2 neurons. These results led us to perform a fine molecular characterization of targeted gene networks and pathway analysis. Importantly, a large fraction of 92 genes identified by GWAS studies as associated with ADHD in humans are significantly altered in our mouse model. -
Reference Gene Validation Via RT–Qpcr for Human Ipsc-Derived Neural Stem Cells and Neural Progenitors
Molecular Neurobiology https://doi.org/10.1007/s12035-019-1538-x Reference Gene Validation via RT–qPCR for Human iPSC-Derived Neural Stem Cells and Neural Progenitors Justyna Augustyniak1 & Jacek Lenart2 & Gabriela Lipka1 & Piotr P. Stepien3 & Leonora Buzanska1 Received: 26 November 2018 /Accepted: 22 February 2019 # The Author(s) 2019 Abstract Correct selection of the reference gene(s) is the most important step in gene expression analysis. The aims of this study were to identify and evaluate the panel of possible reference genes in neural stem cells (NSC), early neural progenitors (eNP) and neural progenitors (NP) obtained from human-induced pluripotent stem cells (hiPSC). The stability of expression of genes commonly used as the reference in cells during neural differentiation is variable and does not meet the criteria for reference genes. In the present work, we evaluated the stability of expression of 16 candidate reference genes using the four most popular algorithms: the ΔCt method, BestKeeper, geNorm and NormFinder. All data were analysed using the online tool RefFinder to obtain a comprehensive ranking. Our results indicate that NormFinder is the best tool for reference gene selection in early stages of hiPSC neural differentiation. None of the 16 tested genes is suitable as reference gene for all three stages of development. We recommend using different genes (panel of genes) to normalise RT–qPCR data for each of the neural differentiation stages. Keywords human induced Pluripotent Stem Cell (hiPSC) . Neural Stem Cells . Neural -
CNV Analysis in 169 Patients with Bladder Exstrophy-Epispadias
von Lowtzow et al. BMC Medical Genetics (2016) 17:35 DOI 10.1186/s12881-016-0299-x RESEARCH ARTICLE Open Access CNV analysis in 169 patients with bladder exstrophy-epispadias complex Catharina von Lowtzow1, Andrea Hofmann1,2, Rong Zhang1,2, Florian Marsch1, Anne-Karoline Ebert3, Wolfgang Rösch4, Raimund Stein5, Thomas M. Boemers6, Karin Hirsch7, Carlo Marcelis8, Wouter F. J. Feitz9, Alfredo Brusco10, Nicola Migone10, Massimo Di Grazia11, Susanne Moebus12, Markus M. Nöthen1,2, Heiko Reutter1,13, Michael Ludwig14*† and Markus Draaken1,2† Abstract Background: The bladder exstrophy-epispadias complex (BEEC) represents the severe end of the congenital uro-rectal malformation spectrum. Initial studies have implicated rare copy number variations (CNVs), including recurrent duplications of chromosomal region 22q11.21, in BEEC etiology. Methods: To detect further CNVs, array analysis was performed in 169 BEEC patients. Prior to inclusion, 22q11.21 duplications were excluded using multiplex ligation-dependent probe amplification. Results: Following the application of stringent filter criteria, seven rare CNVs were identified: n = 4, not present in 1307 in-house controls; n = 3, frequency of <0.002 in controls. These CNVs ranged from 1 to 6.08 Mb in size. To identify smaller CNVs, relaxed filter criteria used in the detection of previously reported BEEC associated chromosomal regions were applied. This resulted in the identification of six additional rare CNVs: n = 4, not present in 1307 in-house controls; n = 2, frequency <0.0008 in controls. These CNVs ranged from 0.03–0.08 Mb in size. For 10 of these 13 CNVs, confirmation and segregation analyses were performed (5 of maternal origin; 5 of paternal origin). -
PDF Datasheet
Product Datasheet BEND2 Overexpression Lysate NBL1-09637 Unit Size: 0.1 mg Store at -80C. Avoid freeze-thaw cycles. Protocols, Publications, Related Products, Reviews, Research Tools and Images at: www.novusbio.com/NBL1-09637 Updated 3/17/2020 v.20.1 Earn rewards for product reviews and publications. Submit a publication at www.novusbio.com/publications Submit a review at www.novusbio.com/reviews/destination/NBL1-09637 Page 1 of 2 v.20.1 Updated 3/17/2020 NBL1-09637 BEND2 Overexpression Lysate Product Information Unit Size 0.1 mg Concentration The exact concentration of the protein of interest cannot be determined for overexpression lysates. Please contact technical support for more information. Storage Store at -80C. Avoid freeze-thaw cycles. Buffer RIPA buffer Target Molecular Weight 87.7 kDa Product Description Description Transient overexpression lysate of BEN domain containing 2 (BEND2) The lysate was created in HEK293T cells, using Plasmid ID RC206228 and based on accession number NM_153346. The protein contains a C-MYC/DDK Tag. Gene ID 139105 Gene Symbol BEND2 Species Human Notes HEK293T cells in 10-cm dishes were transiently transfected with a non-lipid polymer transfection reagent specially designed and manufactured for large volume DNA transfection. Transfected cells were cultured for 48hrs before collection. The cells were lysed in modified RIPA buffer (25mM Tris-HCl pH7.6, 150mM NaCl, 1% NP-40, 1mM EDTA, 1xProteinase inhibitor cocktail mix, 1mM PMSF and 1mM Na3VO4, and then centrifuged to clarify the lysate. Protein concentration was measured by BCA protein assay kit.This product is manufactured by and sold under license from OriGene Technologies and its use is limited solely for research purposes. -
Misexpression of Cancer/Testis (Ct) Genes in Tumor Cells and the Potential Role of Dream Complex and the Retinoblastoma Protein Rb in Soma-To-Germline Transformation
Michigan Technological University Digital Commons @ Michigan Tech Dissertations, Master's Theses and Master's Reports 2019 MISEXPRESSION OF CANCER/TESTIS (CT) GENES IN TUMOR CELLS AND THE POTENTIAL ROLE OF DREAM COMPLEX AND THE RETINOBLASTOMA PROTEIN RB IN SOMA-TO-GERMLINE TRANSFORMATION SABHA M. ALHEWAT Michigan Technological University, [email protected] Copyright 2019 SABHA M. ALHEWAT Recommended Citation ALHEWAT, SABHA M., "MISEXPRESSION OF CANCER/TESTIS (CT) GENES IN TUMOR CELLS AND THE POTENTIAL ROLE OF DREAM COMPLEX AND THE RETINOBLASTOMA PROTEIN RB IN SOMA-TO- GERMLINE TRANSFORMATION", Open Access Master's Thesis, Michigan Technological University, 2019. https://doi.org/10.37099/mtu.dc.etdr/933 Follow this and additional works at: https://digitalcommons.mtu.edu/etdr Part of the Cancer Biology Commons, and the Cell Biology Commons MISEXPRESSION OF CANCER/TESTIS (CT) GENES IN TUMOR CELLS AND THE POTENTIAL ROLE OF DREAM COMPLEX AND THE RETINOBLASTOMA PROTEIN RB IN SOMA-TO-GERMLINE TRANSFORMATION By Sabha Salem Alhewati A THESIS Submitted in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE In Biological Sciences MICHIGAN TECHNOLOGICAL UNIVERSITY 2019 © 2019 Sabha Alhewati This thesis has been approved in partial fulfillment of the requirements for the Degree of MASTER OF SCIENCE in Biological Sciences. Department of Biological Sciences Thesis Advisor: Paul Goetsch. Committee Member: Ebenezer Tumban. Committee Member: Zhiying Shan. Department Chair: Chandrashekhar Joshi. Table of Contents List of figures .......................................................................................................................v -
Datasheet Blank Template
SAN TA C RUZ BI OTEC HNOL OG Y, INC . REEP5 (E-13): sc-133405 BACKGROUND RECOMMENDED SECONDARY REAGENTS REEP5 (receptor expression-enhancing protein 5), also known as C5orf18, To ensure optimal results, the following support (secondary) reagents are DP1, TB2 or D5S346, is a 189 amino acid multi-pass membrane protein. recommended: 1) Western Blotting: use goat anti-rabbit IgG-HRP: sc-2004 Thought to promote the functional cell surface expression of olfactory recep - (dilution range: 1:2000-1:100,000) or Cruz Marker™ compatible goat anti- tors, REEP5 belongs to the DP1 family and is encoded by a gene that maps rabbit IgG-HRP: sc-2030 (dilution range: 1:2000-1:5000), Cruz Marker™ to chromosome 5. With 181 million base pairs encoding around 1,000 genes, Molecular Weight Standards: sc-2035, TBS Blotto A Blocking Reagent: chromosome 5 is about 6% of human genomic DNA. Chromosome 5 is sc-2333 and Western Blotting Luminol Reagent: sc-2048. 2) Immunoprecip- asso ciated with Cockayne syndrome through the ERCC8 gene and familial itation: use Protein A/G PLUS-Agarose: sc-2003 (0.5 ml agarose/2.0 ml). adenomatous polyposis through the adenomatous polyposis coli (APC) tumor 3) Immunofluorescence: use goat anti-rabbit IgG-FITC: sc-2012 (dilution suppressor gene. Treacher Collins syndrome is also chromosome 5 associat ed range: 1:100-1:400) or goat anti-rabbit IgG-TR: sc-2780 (dilution range: and is caused by insertions or deletions within the TCOF1 gene. Deletion of 1:100-1:400) with UltraCruz™ Mounting Medium: sc-24941. the p arm of chromosome 5 leads to Cri-du-chat syndrome. -
Pancreatic Cancer Metabolism
Published OnlineFirst March 3, 2017; DOI: 10.1158/2159-8290.CD-RW2017-044 RESEARCH WATCH Pancreatic Cancer Major finding: PanNET mutations affect Concept: Comprehensive molecular anal- Impact: The comprehensive identifica- DNA damage repair, chromatin remodeling, ysis of 102 clinically sporadic PanNETs tion of PanNET genetic alterations may telomere maintenance, and mTOR signaling. uncovers essential PanNET pathways. aid risk stratification and treatment. WHOLE-GENOME SEQUENCING DEFINES THE MUTATIONAL LANDSCAPE OF PanNETS Pancreatic neuroendocrine tumors (PanNET) are exhibited increased telomere length. There were classifi ed into three groups: low grade (G1), inter- an average of 29 structural rearrangements per mediate grade (G2), and high grade (G3). G3 Pan- tumor, with rearrangements leading to inactiva- NETs have a universally poor prognosis, whereas tion of tumor suppressors such as MTAP, ARID2, G1 and G2 tumors have an unpredictable clinical SMARCA4, MLL3, CDKN2A, and SETD2, or creating course. A better understanding of the molecular oncogenic gene fusions. In total, 66 somatic in- underpinnings of the disease may enable better frame gene fusions were identifi ed, including three risk stratifi cation and the identifi cation of patients EWSR1 fusion events leading to EWSR1–BEND2 or who might benefi t from early aggressive therapy. Scarpa and EWSR1–FLI1. Although EWSR1–FLI1 is a characteristic Ewing colleagues performed comprehensive molecular analyses of sarcoma fusion gene, the morphologic and pathologic features 102 clinically sporadic PanNETs. Whole-genome sequencing were consistent with PanNETs. RNA sequencing of 30 Pan- of 98 PanNETs defi ned fi ve distinct mutational signatures: NET tumors found that common genetic alterations affected MUTYH, APOBEC, BRCA-defi ciency, age, and COSMIC signa- DNA damage and repair, chromatin remodeling, telomere ture 5. -
On the Role of Chromosomal Rearrangements in Evolution
On the role of chromosomal rearrangements in evolution: Reconstruction of genome reshuffling in rodents and analysis of Robertsonian fusions in a house mouse chromosomal polymorphism zone by Laia Capilla Pérez A thesis submitted for the degree of Doctor of Philosophy in Animal Biology Supervisors: Dra. Aurora Ruiz-Herrera Moreno and Dr. Jacint Ventura Queija Institut de Biotecnologia i Biomedicina (IBB) Departament de Biologia Cel·lular, Fisiologia i Immunologia Departament de Biologia Animal, Biologia Vegetal i Ecologia Universitat Autònoma de Barcelona Supervisor Supervisor PhD candidate Aurora Ruiz-Herrera Moreno Jacint Ventura Queija Laia Capilla Pérez Bellaterra, 2015 A la mare Al pare Al mano “Visto a la luz de la evolución, la biología es, quizás, la ciencia más satisfactoria e inspiradora. Sin esa luz, se convierte en un montón de hechos varios, algunos de ellos interesantes o curiosos, pero sin formar ninguna visión conjunta.” Theodosius Dobzhansky “La evolución es tan creativa. Por eso tenemos jirafas.” Kurt Vonnegut This thesis was supported by grants from: • Ministerio de Economía y Competitividad (CGL2010-15243 and CGL2010- 20170). • Generalitat de Catalunya, GRQ 1057. • Ministerio de Economía y Competitividad. Beca de Formación de Personal Investigador (FPI) (BES-2011-047722). • Ministerio de Economía y Competitividad. Beca para la realización de estancias breves (EEBB-2011-07350). Covers designed by cintamontserrat.blogspot.com INDEX Abstract 15-17 Acronyms 19-20 1. GENERAL INTRODUCTION 21-60 1.1 Chromosomal rearrangements -
Marine Mammal Protection Act and Endangered Species Act Lmplementation Program 1 999
National Marine Fisheries Service U.S DEPARTMENT OF COMMERCE AFSC PROCESSED REPORT 2OOO.1 1 Marine Mammal Protection Act and Endangered Species Act lmplementation Program 1 999 December 2000 This report does not constitute a publication and is for information only. All data herein are to be considered provisional. ERRATA NOTICE This document is being made available in .PDF format for the convenience of users; however, the accuracy and correctness of the document can only be certified as was presented in the original hard copy format. Inaccuracies in the OCR scanning process may influence text searches of the .PDF file. Light or faded ink in the original document may also affect the quality of the scanned document. Marine Mammal Protection Act and Endangered Species Act Implementation Program 1999 Edited by: Anita L. Lopez Douglas P. DeMaster Annual Reports ofresearch carried out on the population biologt of marine mammals by the National Marine Mammal Laboratory to meet the 1994 amendments to the Marine Mammal Protection Act and the Endangered Species Act Submitted to: Office of Protected Resources National Marine Fisheries Service 1335 East-West Highway Silver Spring, MD 20910 National Oceanic and Atmospheric Administration National Marine Fisheries Service Alaska Fisheries Science Center National Marine Mammal Laboratory 7600 Sand Point Way Northeast Seattle, WA 98115-0070 December 2000 Preface Beginning in 1991, the National Marine Mammal Laboratory NMML) has been partially funded by the National Marine Fisheries Service's (NÀ/ßS) Office of Protected Resources to determine the abundance of selected species in U.S. waters of the eastern North Pacific Ocean. -
Single-Cell RNA Sequencing of Human, Macaque, and Mouse Testes Uncovers Conserved and Divergent Features of Mammalian Spermatogenesis
bioRxiv preprint doi: https://doi.org/10.1101/2020.03.17.994509; this version posted March 18, 2020. 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. Single-cell RNA sequencing of human, macaque, and mouse testes uncovers conserved and divergent features of mammalian spermatogenesis Adrienne Niederriter Shami1,7, Xianing Zheng1,7, Sarah K. Munyoki2,7, Qianyi Ma1, Gabriel L. Manske3, Christopher D. Green1, Meena Sukhwani2, , Kyle E. Orwig2*, Jun Z. Li1,4*, Saher Sue Hammoud1,3,5,6,8* 1Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA 2 Department of Obstetrics, Gynecology and Reproductive Sciences, Integrative Systems Biology Graduate Program, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA. 3 Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA 4 Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA 5 Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA 6Department of Urology, University of Michigan, Ann Arbor, MI, USA 7 These authors contributed equally 8 Lead Contact * Correspondence: [email protected] (K.E.O.), [email protected] (J.Z.L.), [email protected] (S.S.H.) bioRxiv preprint doi: https://doi.org/10.1101/2020.03.17.994509; this version posted March 18, 2020. 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. Summary Spermatogenesis is a highly regulated process that produces sperm to transmit genetic information to the next generation.