Original Article DSTYK Kinase Domain Ablation Impaired the Mice Capabilities of Learning and Memory in Water Maze Test
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Plenary and Platform Abstracts
American Society of Human Genetics 68th Annual Meeting PLENARY AND PLATFORM ABSTRACTS Abstract #'s Tuesday, October 16, 5:30-6:50 pm: 4. Featured Plenary Abstract Session I Hall C #1-#4 Wednesday, October 17, 9:00-10:00 am, Concurrent Platform Session A: 6. Variant Insights from Large Population Datasets Ballroom 20A #5-#8 7. GWAS in Combined Cancer Phenotypes Ballroom 20BC #9-#12 8. Genome-wide Epigenomics and Non-coding Variants Ballroom 20D #13-#16 9. Clonal Mosaicism in Cancer, Alzheimer's Disease, and Healthy Room 6A #17-#20 Tissue 10. Genetics of Behavioral Traits and Diseases Room 6B #21-#24 11. New Frontiers in Computational Genomics Room 6C #25-#28 12. Bone and Muscle: Identifying Causal Genes Room 6D #29-#32 13. Precision Medicine Initiatives: Outcomes and Lessons Learned Room 6E #33-#36 14. Environmental Exposures in Human Traits Room 6F #37-#40 Wednesday, October 17, 4:15-5:45 pm, Concurrent Platform Session B: 24. Variant Interpretation Practices and Resources Ballroom 20A #41-#46 25. Integrated Variant Analysis in Cancer Genomics Ballroom 20BC #47-#52 26. Gene Discovery and Functional Models of Neurological Disorders Ballroom 20D #53-#58 27. Whole Exome and Whole Genome Associations Room 6A #59-#64 28. Sequencing-based Diagnostics for Newborns and Infants Room 6B #65-#70 29. Omics Studies in Alzheimer's Disease Room 6C #71-#76 30. Cardiac, Valvular, and Vascular Disorders Room 6D #77-#82 31. Natural Selection and Human Phenotypes Room 6E #83-#88 32. Genetics of Cardiometabolic Traits Room 6F #89-#94 Wednesday, October 17, 6:00-7:00 pm, Concurrent Platform Session C: 33. -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
Identifying Factors That Conctribute to Phenotypic Heterogeneity in Melanoma Progression
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2012 Identifying factors that conctribute to Phenotypic heterogeneity in melanoma progression Widmer, Daniel Simon Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-73667 Dissertation Originally published at: Widmer, Daniel Simon. Identifying factors that conctribute to Phenotypic heterogeneity in melanoma progression. 2012, University of Zurich, Faculty of Medicine. Eidgenössische Technische Hochschule Zürich Swiss Federal Institute of Technology Zurich Identifying factors that conctribute to Phenotypic heterogeneity in melanoma progression Daniel Simon Widmer 2012 Diss ETH No. 20537 DISS. ETH NO. 20537 IDENTIFYING FACTORS THAT CONTRIBUTE TO PHENOTYPIC HETEROGENEITY IN MELANOMA PROGRESSION A dissertation submitted to ETH ZURICH for the degree of Doctor of Sciences presented by Daniel Simon Widmer Master of Science UZH University of Zurich born on February 26th 1982 citizen of Gränichen AG accepted on the recommendation of Professor Sabine Werner, examinor Professor Reinhard Dummer, co-examinor Professor Michael Detmar, co-examinor 2012 Contents 1. ZUSAMMENFASSUNG...................................................................................................... 7 2. SUMMARY ................................................................................................................... 11 3. INTRODUCTION ........................................................................................................... -
Gene Expression Profiling in Hepatocellular Carcinoma: Upregulation of Genes in Amplified Chromosome Regions
Modern Pathology (2008) 21, 505–516 & 2008 USCAP, Inc All rights reserved 0893-3952/08 $30.00 www.modernpathology.org Gene expression profiling in hepatocellular carcinoma: upregulation of genes in amplified chromosome regions Britta Skawran1, Doris Steinemann1, Anja Weigmann1, Peer Flemming2, Thomas Becker3, Jakobus Flik4, Hans Kreipe2, Brigitte Schlegelberger1 and Ludwig Wilkens1,2 1Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany; 2Institute of Pathology, Hannover Medical School, Hannover, Germany; 3Department of Visceral and Transplantation Surgery, Hannover Medical School, Hannover, Germany and 4Institute of Virology, Hannover Medical School, Hannover, Germany Cytogenetics of hepatocellular carcinoma and adenoma have revealed gains of chromosome 1q as a significant differentiating factor. However, no studies are available comparing these amplification events with gene expression. Therefore, gene expression profiling was performed on tumours cytogenetically well characterized by array-based comparative genomic hybridisation. For this approach analysis was carried out on 24 hepatocellular carcinoma and 8 hepatocellular adenoma cytogenetically characterised by array-based comparative genomic hybridisation. Expression profiles of mRNA were determined using a genome-wide microarray containing 43 000 spots. Hierarchical clustering analysis branched all hepatocellular adenoma from hepatocellular carcinoma. Significance analysis of microarray demonstrated 722 dysregulated genes in hepatocellular carcinoma. Gene set enrichment analysis detected groups of upregulated genes located in chromosome bands 1q22–42 seen also as the most frequently gained regions by comparative genomic hybridisation. Comparison of significance analysis of microarray and gene set enrichment analysis narrowed down the number of dysregulated genes to 18, with 7 genes localised on 1q22 (SCAMP3, IQGAP3, PYGO2, GPATC4, ASH1L, APOA1BP, and CCT3). In hepatocellular adenoma 26 genes in bands 11p15, 11q12, and 12p13 were upregulated. -
The Transcription Factor ST18 Regulates Proapoptotic and Proinflammatory Gene Expression in fibroblasts
The FASEB Journal • Research Communication The transcription factor ST18 regulates proapoptotic and proinflammatory gene expression in fibroblasts Julia Yang,* Michelle F. Siqueira,* Yugal Behl,* Mani Alikhani,† and Dana T. Graves*,1 *Department of Periodontology and Oral Biology, Boston University School of Dental Medicine, Boston, Massachusetts, USA; and †Department of Orthodontics, New York University College of Dentistry, New York, New York, USA ABSTRACT Suppression of tumorigenicity 18 (ST18) control genes that regulate inflammatory responses and the homologues neural zinc-finger protein-3 and protect the host from microbial infection, initiate (NZF3) and myelin transcription factor 3 (Myt3) are processes such as wound healing, and participate in a transcription factors with unknown function. Previous number of pathological processes (1–3). Inappropri- studies have established that they repress transcription ate activity of transcription factors has been shown to of a synthetic reporter construct consisting of the promote a number of pathologies, including athero- consensus sequence AAAGTTT linked to the thymidine sclerosis, cancer, arthritis, and diabetes (4–7). In kinase promoter. In addition, ST18 exhibits signifi- some cases, inhibiting a transcription factor such as cantly reduced expression in breast cancer and breast NF-B leads to reduced formation of atherosclerotic cancer cell lines. We report here for the first time lesions (6). evidence that ST18 mediates tumor necrosis factor Like inflammation, apoptosis is also influenced by (TNF) -␣ induced mRNA levels of proapoptotic and transcription factors that regulate the expression of proinflammatory genes in fibroblasts by mRNA profil- pro- or antiapoptotic genes. For example, CREB influ- ing and silencing with ST18 small interfering RNA ences apoptosis by enhancing expression of antiapop- (siRNA). -
PROGRAMMED FUNCTION of the TAMMAR MAMMARY GLAND; the Role of Milk Proteins in Gut Development
PROGRAMMED FUNCTION OF THE TAMMAR MAMMARY GLAND; The role of milk proteins in gut development by Sanjana Kuruppath Master of Science (MSc) Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy Deakin University February, 2014 Acknowledgements Thank You Almighty! I thank my family, friends and colleagues for their support without which completion of this thesis would not have been possible. First and most of all, I would like to express my sincere and deepest gratitude to my PhD supervisor Professor Kevin R Nicholas, for his constant guidance and support. I would not have been in a position to write this if he had not selected me as a student, given an opportunity to come to Australia and pursue my career in the field of scientific research. I assure, I had the best supervisor for my PhD. Under him, I had the freedom to manage and execute my project with his continuous support and timely guidance because of which I gradually grew as a confident researcher. I was always surprised to see him welcoming his students with a smiling and encouraging face, anytime they knock at his door! I greatly appreciate his commitment and passion towards research and the magical ability to continuously and convincingly promote his students to grow independently. I also thank him, from the bottom of my heart, for all the support and courage he gave me in my personal life too. I thank my co-supervisors, Dr Christophe Lefevre and Dr Julie A Sharp. I thank Christophe for his advice and assistance, mainly in the field of bioinformatics. -
Discovering Meaning from Biological Sequences: Focus on Predicting
Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2013 Discovering meaning from biological sequences: focus on predicting misannotated proteins, binding patterns, and G4-quadruplex secondary Carson Michael Andorf Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Bioinformatics Commons, and the Computer Sciences Commons Recommended Citation Andorf, Carson Michael, "Discovering meaning from biological sequences: focus on predicting misannotated proteins, binding patterns, and G4-quadruplex secondary" (2013). Graduate Theses and Dissertations. 13533. https://lib.dr.iastate.edu/etd/13533 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Discovering meaning from biological sequences: focus on predicting misannotated proteins, binding patterns, and G4-quadruplex secondary structures by Carson Michael Andorf A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Computer Science Program of Study Committee: Vasant Honavar, Co-major Professor Drena Dobbs, Co-major Professor David Fernandez-Baca Robert Jernigan Taner Sen Guang Song Iowa State University -
1 Supplemental Table 1. Comparison Among Q-RT-PCR, ISH-TMA And
Supplemental Table 1. Comparison among Q-RT-PCR, ISH-TMA and IHC for the detection of ErbB-2 in breast cancers. IHC ISH-TMA Q-RT-PCR Q-RT-PCR range Q-RT-PCR score 0 0 0* 0 0 0 0* 0 0 0 1 0 0 0 1 0 0 0 1 0 0 1 2 0 1 1 2 0 0 0 3 0 0 0 3 0 0 0 3 0 0 0 3 0 0 0 3 x<10 0 1 1 3 0 0 0 4 0 0 0 5 0 0 0 5 0 0 0 5 0 1 1 5 0 0 0 6 0 0 0 8 0 0 0 8 0 1 1 8 0 0 1 8 0 1 1 11 1 1 1 11 1 1 1 11 1 1 0 12 1 1 1 13 10<x<20 1 0 1 13 1 1 1 16 1 1 1 17 1 2 1 17 1 2 2 22 2 2 2 43 2 20<x<100 3 2 74 2 3 2 86 2 3 3 213 3 3 3 259 x>100 3 3 3 362 3 Legend to Supplemental Table 1. This experiment was set up to demonstrate that there is good semi-quantitative correlation between the levels of expression detected by ISH-TMA, IHC and Q-RT-PCR. We compared the three methods on levels of ErbB-2 expression in breast cancer, since ErbB-2 is overexpressed in breast cancers, over a wide range of levels. -
The Role of MITF in Regulating Human Pigmentation
The role of MITF in regulating human pigmentation Christian Praetorius Thesis for the degree of Philosophiae Doctor August 2014 UNIVERSITY OF ICELAND SCHOOL OF HEALTH SCIENCES FACULTY OF MEDICINE Hlutverk MITF við stjórnun húðlitar í mönnum Christian Praetorius Ritgerð til doktorsgráðu Umsjónarkennari Eiríkur Steingrímsson Doktorsnefnd Ólafur S. Andrésson Zophonías O. Jónsson Magnús Karl Magnússon Hendrik G. Stunnenberg August 2014 UNIVERSITY OF ICELAND SCHOOL OF HEALTH SCIENCES FACULTY OF MEDICINE The role of MITF in regulating human pigmentation Christian Praetorius Thesis for the degree of Philosophiae Doctor Supervisor Eiríkur Steingrímsson Doctoral Comittee Ólafur S. Andrésson Zophonías O. Jónsson Magnús Karl Magnússon Hendrik G. Stunnenberg August 2014 UNIVERSITY OF ICELAND SCHOOL OF HEALTH SCIENCES FACULTY OF MEDICINE Thesis for a doctoral degree at the University of Iceland. All right reserved. No part of this publication may be reproduced in any form without the prior permission of the copyright holder. © Christian Praetorius 2014 Document typeset with LATEX. ISBN: 978-9935-9200-2-7 Printing by Háskolaprent Reykjavík, Iceland 2014 Ágrip Þroskun litfruma og myndun sortuæxla er háð umritunarþættinum microphthal- mia associated transcription factor (MITF) en hann tilheyrir basic-helix-loop-helix leucine zipper (bHLH-LZ) fjölskyldunni. MITF stjórnar tjáningu fjölda gena í litfrumum og sortuæxlum, þar með talið gena sem eru mikilvæg fyrir framleiðslu litarefnisins melanin, og gena sem stjórna frumuhringnum, frumufari og lifun. Þessi þekktu markgen skýra þó ekki að fullu hlutverk MITF í litfrumum og sortuæxlum. Við notuðum tvískipta tjáningarrannsókn til að finna markgen MITF í sor- tuæxlum. Í fyrsta lagi leituðum við að genum sem fylgja tjáningarmynstri MITF gensins sortuæxlissýnum. -
AJHG the American Journal of Human Genetics
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Apollo AJHG The American Journal of Human Genetics Large intragenic deletion in DSTYK underlies autosomal recessive complicated spastic paraparesis (SPG23) --Manuscript Draft-- Manuscript Number: AJHG-D-16-00656R3 Full Title: Large intragenic deletion in DSTYK underlies autosomal recessive complicated spastic paraparesis (SPG23) Article Type: Report Corresponding Author: John A. McGrath, MD, PhD King's College London London, UNITED KINGDOM First Author: John A. McGrath, MD, PhD Order of Authors: John A. McGrath, MD, PhD John Y. W. Lee, BSc Chao-Kai Hsu, MD Magdalene Michael, PhD Arti Nanda, MD Lu Liu, PhD James R. McMillan, PhD Celine Pourreyron, PhD Takuya Takeichi, MD PhD Jakub Tolar, MD PhD Evan Reid, MD PhD Thomas Hayday, MSc Sergiu C. Blumen, MD Saif Abu-Mouch, MD PhD Rachel Straussberg, MD PhD Lina Basel-Vanagaite, MD PhD Yael Barhum, MD PhD Yasmin Zouabi, MD PhD Hejab Al-Ajmi, MD Hsin-Yu Huang Ting-Chien Lin Masashi Akiyama, MD PhD Julia Y Lee, MD W. H. Irwin McLean, DSc PhD Michael A. Simpson, PhD Maddy Parsons, PhD Abstract: SPG23 is an autosomal recessive neurodegenerative subtype of lower limb spastic paraparesis with additional diffuse skin and hair dyspigmentation at birth followed by further patchy pigment loss during childhood. Previously, genomewide linkage in an Arab-Israeli pedigree mapped the gene to an approximately 25-cM locus on Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation chromosome 1q24-q32. Using whole-exome sequencing in a further Palestinian- Jordanian SPG23 pedigree we identified a complex homozygous 4-kb deletion/20-bp insertion in DSTYK (dual serine-threonine and tyrosine protein kinase) in all four affected family members. -
Supplementary File 2B Revised
Supplementary file 2B. Differentially expressed genes in aldosteronomas compared to incidentalomas, ranked according to statistical significance. Acc UGCluster Name Symbol log Fold P - Value Adj. P-Value B Change AI002403 Hs.70312 Cytochrome c oxidase subunit VIIa polypeptide 2 (liver) COX7A2 1,64 1,7E-08 8,1E-05 9,80 N93695 Hs.54609 Glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme GCAT 1,26 2,1E-08 8,1E-05 9,63 N23599 Hs.43396 Transcribed locus 1,92 3,0E-08 8,1E-05 9,28 AA699317 Hs.474949 Ring-box 1 RBX1 1,65 3,7E-08 8,1E-05 9,11 AA491249 Hs.356440 Coiled-coil domain containing 72 CCDC72 1,26 3,9E-08 8,1E-05 9,05 T95745 Data not found 2,54 5,6E-08 8,5E-05 8,71 AA428627 Hs.694739 Nuclear pore complex interacting protein NPIP -1,42 6,0E-08 8,5E-05 8,65 R67915 Hs.268742 Proteasome maturation protein POMP 1,13 6,6E-08 8,5E-05 8,56 T70353 Hs.655728 Aminocarboxymuconate semialdehyde decarboxylase ACMSD -1,63 9,6E-08 8,5E-05 8,21 N74161 Hs.29189 ATPase, class VI, type 11A ATP11A -2,25 1,1E-07 8,5E-05 8,04 AA449463 Hs.632865 KIAA0220-like protein LOC23117 -1,85 1,2E-07 8,5E-05 8,03 W32281 Hs.534453 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13 NDUFA13 1,49 1,3E-07 8,5E-05 7,93 AA485358 Hs.9234 Transmembrane protein 147 TMEM147 1,59 1,3E-07 8,5E-05 7,91 AA670434 Hs.567438 Brain protein I3 BRI3 1,04 1,3E-07 8,5E-05 7,90 N68467 Hs.502823 Peroxiredoxin 5 PRDX5 1,80 1,4E-07 8,5E-05 7,88 H94471 Hs.592605 Occludin OCLN -1,28 1,4E-07 8,5E-05 7,88 AA282936 Hs.240 M-phase phosphoprotein 1 MPHOSPH1 -1,29 1,4E-07 8,5E-05 7,87 R43449 Hs.106529 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assem NDUFAF1 1,44 1,7E-07 9,7E-05 7,68 AA159669 Hs.708260 Transcribed locus, strongly similar to NP_112200.2 transmembrane protein 4 -1,99 1,8E-07 9,8E-05 7,61 H52503 Hs.673820 Transcribed locus -2,45 2,0E-07 9,8E-05 7,53 AA425295 Hs.662502 Transcribed locus 1,74 2,0E-07 9,8E-05 7,52 R77144 Hs.488835 Transmembrane protein 120A TMEM120A 1,83 2,1E-07 9,8E-05 7,48 AA670351 Hs.485262 Mitochondrial carrier homolog 1 (C. -
Supplementary Table 1. a Full List of Cancer Genes
Supplementary Table 1. A full list of cancer genes. Tumour Tumour Other Gene Gene full Entrez Chr Somat Germli Cancer Tissue Molecular Mut Translocati Other Chr Types Types Germline Syn Symbol name Gene ID Band ic ne Synd Type Genetics Types on Partner Synd (Somatic) (Germline) Mut Abl-interactor 10p11. ABI1; E3B1; ABI-1; ABI1 10006 10 yes AML L Dom T MLL 1 2 SSH3BP1; 10006 V-abl Abelson ABL1; p150; ABL; c- murine BCR; CML; ALL; ABL; JTK7; bcr/abl; v- ABL1 leukemia viral 25 9 9q34.1 yes L Dom T; Mis ETV6; T-ALL abl; P00519; 25; oncogene NUP214 ENSG00000097007 homolog 1 C-abl ABL2; ARG; RP11- oncogene 2; 1q24- 177A2_3; ABLL; ABL2 non-receptor 27 1 yes AML L Dom T ETV6 q25 ENSG00000143322; tyrosine P42684; 27 kinase Acyl-coa 2181; ASPM; synthetase PRO2194; ACS3; ACSL3 long-chain 2181 2 2q36 yes Prostate E Dom T ETV1 FACL3; O95573; family ENSG00000123983; member 3 ACSL3 CASC5; AF15Q14; AF15q14 Q8NG31; D40; AF15Q14 57082 15 15q14 yes AML L Dom T MLL protein ENSG00000137812; 57082 ALL1-fused MLLT11; Q13015; gene from AF1Q; AF1Q 10962 1 1q21 yes ALL L Dom T MLL chromosome ENSG00000213190; 1q 10962 SH3 protein Q9NZQ3; AF3P21; interacting WISH; ORF1; with Nck; 90 AF3p21 51517 3 3p21 yes ALL L Dom T MLL WASLBP; SPIN90; kda (ALL1 ENSG00000213672; fused gene NCKIPSD; 51517 from 3p21) 27125; Q9UHB7; ALL1 fused MCEF; AF5Q31; AF5q31 gene from 27125 5 5q31 yes ALL L Dom T MLL ENSG00000072364; 5q31 AFF4 KIAA0803; AKAP350; CG-NAP; MU-RMS- A kinase 40_16A; PRKA9; (PRKA) 7q21- Papillary AKAP9 10142 7 yes E Dom T BRAF YOTIAO; HYPERION; anchor protein q22 thyroid AKAP450; Q99996; (yotiao) 9 ENSG00000127914; 10142; AKAP9 P31749; AKT1_NEW; 207; V-akt murine Breast; ENSG00000142208; thymoma viral 14q32.