Supplementary Materials: from Viral Infections to Autistic Neurodevelopmental Disorders Via Cross-Reactivity
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Gene Symbol Gene Description ACVR1B Activin a Receptor, Type IB
Table S1. Kinase clones included in human kinase cDNA library for yeast two-hybrid screening Gene Symbol Gene Description ACVR1B activin A receptor, type IB ADCK2 aarF domain containing kinase 2 ADCK4 aarF domain containing kinase 4 AGK multiple substrate lipid kinase;MULK AK1 adenylate kinase 1 AK3 adenylate kinase 3 like 1 AK3L1 adenylate kinase 3 ALDH18A1 aldehyde dehydrogenase 18 family, member A1;ALDH18A1 ALK anaplastic lymphoma kinase (Ki-1) ALPK1 alpha-kinase 1 ALPK2 alpha-kinase 2 AMHR2 anti-Mullerian hormone receptor, type II ARAF v-raf murine sarcoma 3611 viral oncogene homolog 1 ARSG arylsulfatase G;ARSG AURKB aurora kinase B AURKC aurora kinase C BCKDK branched chain alpha-ketoacid dehydrogenase kinase BMPR1A bone morphogenetic protein receptor, type IA BMPR2 bone morphogenetic protein receptor, type II (serine/threonine kinase) BRAF v-raf murine sarcoma viral oncogene homolog B1 BRD3 bromodomain containing 3 BRD4 bromodomain containing 4 BTK Bruton agammaglobulinemia tyrosine kinase BUB1 BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) BUB1B BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) C9orf98 chromosome 9 open reading frame 98;C9orf98 CABC1 chaperone, ABC1 activity of bc1 complex like (S. pombe) CALM1 calmodulin 1 (phosphorylase kinase, delta) CALM2 calmodulin 2 (phosphorylase kinase, delta) CALM3 calmodulin 3 (phosphorylase kinase, delta) CAMK1 calcium/calmodulin-dependent protein kinase I CAMK2A calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha CAMK2B calcium/calmodulin-dependent -
'Stress–Response' Kinase Pathways in Alzheimer's Disease Progression
Available online at www.sciencedirect.com ScienceDirect Involvement of ‘stress–response’ kinase pathways in Alzheimer’s disease progression 1 Georges Mairet-Coello and Franck Polleux Alzheimer’s disease (AD) is the most prevalent cause of oligomers of Ab are causal to synaptic toxicity [2], trigger dementia, affecting more than 25 million people worldwide. synaptic dysfunction, synapse loss and impaired long- Current models of the pathophysiological mechanisms of AD term potentiation (LTP) [3]. The exact nature of the suggest that the accumulation of soluble oligomeric forms of Ab species (dimers, trimers, Ab*56, protofibrils) respon- amyloid-b (Ab) peptides causes early loss of excitatory sible for this early synaptotoxicity is still under investi- synapses and impairs synaptic plasticity. The signaling gation [4]. Most experimental designs use a mixture of pathways mediating Ab oligomer-induced impairment of various forms of synthetic Ab oligomers, or natural Ab synaptic plasticity and loss of excitatory synapses are only oligomers isolated from the brain of AD subjects, to beginning to be unraveled. Here, we review recent evidence induce rapid loss of excitatory synapses in hippocampal supporting the critical contribution of conserved ‘stress– and cortical neurons in vitro [5–10]. Transgenic mouse response’ kinase pathways in AD progression. models of AD engineered to overexpress human mutant forms of Amyloid Precursor Protein (hAPP), with or with- Addresses out overexpression of mutant presenilins (PS), produce The Scripps Research Institute, Dorris Neuroscience Center, Department of Molecular and Cellular Neuroscience, La Jolla, CA 92037- high levels of Ab1–40 and Ab1–42 peptides and oligo- 1000, USA mers, recapitulate the reduction of excitatory synapses, exhibit neuronal network dysfunction and cognitive def- Corresponding author: Polleux, Franck ([email protected]) 1 icits in spatial learning [6,11]. -
The Human Y Chromosome's Azoospermia Factor B (Azfb) Region
18 ORIGINAL ARTICLE J Med Genet: first published as 10.1136/jmg.40.1.18 on 1 January 2003. Downloaded from The human Y chromosome’s azoospermia factor b (AZFb) region: sequence, structure, and deletion analysis in infertile men A Ferlin, E Moro, A Rossi, B Dallapiccola, C Foresta ............................................................................................................................. J Med Genet 2003;40:18–24 See end of article for authors’ affiliations Microdeletions of the Y chromosome long arm are the most common mutations in infertile males, where ....................... they involve one or more “azoospermia factors” (AZFa, b, and c). Understanding of the AZF structure and gene content and mapping of the deletion breakpoints in infertile men are still incomplete. We Correspondence to: Professor C Foresta, have assembled a complete 4.3 Mb map of AZFb and surrounding regions by means of 38 BAC University of Padova, clones. The proximal part of AZFb consists of large repeated sequences organised in palindromes, but Department of Medical and most of it is single copy sequence. A number of known and novel genes and gene families map in this Surgical Sciences, Clinica interval, and most of them are testis specific or have testis specific transcripts. STS mapping allowed us Medica 3, Via Ospedale to identify four severely infertile subjects with a deletion in AZFb with similar breakpoints, therefore 105, 35128 Padova, Italy; [email protected] suggesting a common deletion mechanism. This deletion includes at least five single copy genes and two duplicated genes, but does not remove the historical AZFb candidate gene RBMY1. These data Revised version received suggest that other genes in AZFb may have important roles in spermatogenesis. -
Discovery of Candidate Genes for Stallion Fertility from the Horse Y Chromosome
DISCOVERY OF CANDIDATE GENES FOR STALLION FERTILITY FROM THE HORSE Y CHROMOSOME A Dissertation by NANDINA PARIA Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY August 2009 Major Subject: Biomedical Sciences DISCOVERY OF CANDIDATE GENES FOR STALLION FERTILITY FROM THE HORSE Y CHROMOSOME A Dissertation by NANDINA PARIA Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, Terje Raudsepp Committee Members, Bhanu P. Chowdhary William J. Murphy Paul B. Samollow Dickson D. Varner Head of Department, Evelyn Tiffany-Castiglioni August 2009 Major Subject: Biomedical Sciences iii ABSTRACT Discovery of Candidate Genes for Stallion Fertility from the Horse Y Chromosome. (August 2009) Nandina Paria, B.S., University of Calcutta; M.S., University of Calcutta Chair of Advisory Committee: Dr. Terje Raudsepp The genetic component of mammalian male fertility is complex and involves thousands of genes. The majority of these genes are distributed on autosomes and the X chromosome, while a small number are located on the Y chromosome. Human and mouse studies demonstrate that the most critical Y-linked male fertility genes are present in multiple copies, show testis-specific expression and are different between species. In the equine industry, where stallions are selected according to pedigrees and athletic abilities but not for reproductive performance, reduced fertility of many breeding stallions is a recognized problem. Therefore, the aim of the present research was to acquire comprehensive information about the organization of the horse Y chromosome (ECAY), identify Y-linked genes and investigate potential candidate genes regulating stallion fertility. -
Profiling Data
Compound Name DiscoveRx Gene Symbol Entrez Gene Percent Compound Symbol Control Concentration (nM) JNK-IN-8 AAK1 AAK1 69 1000 JNK-IN-8 ABL1(E255K)-phosphorylated ABL1 100 1000 JNK-IN-8 ABL1(F317I)-nonphosphorylated ABL1 87 1000 JNK-IN-8 ABL1(F317I)-phosphorylated ABL1 100 1000 JNK-IN-8 ABL1(F317L)-nonphosphorylated ABL1 65 1000 JNK-IN-8 ABL1(F317L)-phosphorylated ABL1 61 1000 JNK-IN-8 ABL1(H396P)-nonphosphorylated ABL1 42 1000 JNK-IN-8 ABL1(H396P)-phosphorylated ABL1 60 1000 JNK-IN-8 ABL1(M351T)-phosphorylated ABL1 81 1000 JNK-IN-8 ABL1(Q252H)-nonphosphorylated ABL1 100 1000 JNK-IN-8 ABL1(Q252H)-phosphorylated ABL1 56 1000 JNK-IN-8 ABL1(T315I)-nonphosphorylated ABL1 100 1000 JNK-IN-8 ABL1(T315I)-phosphorylated ABL1 92 1000 JNK-IN-8 ABL1(Y253F)-phosphorylated ABL1 71 1000 JNK-IN-8 ABL1-nonphosphorylated ABL1 97 1000 JNK-IN-8 ABL1-phosphorylated ABL1 100 1000 JNK-IN-8 ABL2 ABL2 97 1000 JNK-IN-8 ACVR1 ACVR1 100 1000 JNK-IN-8 ACVR1B ACVR1B 88 1000 JNK-IN-8 ACVR2A ACVR2A 100 1000 JNK-IN-8 ACVR2B ACVR2B 100 1000 JNK-IN-8 ACVRL1 ACVRL1 96 1000 JNK-IN-8 ADCK3 CABC1 100 1000 JNK-IN-8 ADCK4 ADCK4 93 1000 JNK-IN-8 AKT1 AKT1 100 1000 JNK-IN-8 AKT2 AKT2 100 1000 JNK-IN-8 AKT3 AKT3 100 1000 JNK-IN-8 ALK ALK 85 1000 JNK-IN-8 AMPK-alpha1 PRKAA1 100 1000 JNK-IN-8 AMPK-alpha2 PRKAA2 84 1000 JNK-IN-8 ANKK1 ANKK1 75 1000 JNK-IN-8 ARK5 NUAK1 100 1000 JNK-IN-8 ASK1 MAP3K5 100 1000 JNK-IN-8 ASK2 MAP3K6 93 1000 JNK-IN-8 AURKA AURKA 100 1000 JNK-IN-8 AURKA AURKA 84 1000 JNK-IN-8 AURKB AURKB 83 1000 JNK-IN-8 AURKB AURKB 96 1000 JNK-IN-8 AURKC AURKC 95 1000 JNK-IN-8 -
The Role of Y Chromosome Deletions in Male Infertility
European Journal of Endocrinology (2000) 142 418–430 ISSN 0804-4643 INVITED REVIEW The role of Y chromosome deletions in male infertility Kun Ma, Con Mallidis and Shalender Bhasin Division of Endocrinology, Metabolism and Molecular Medicine, Department of Internal Medicine, Charles R Drew University of Medicine and Science, 1731 East 120th Street, Los Angeles, California 90050, USA (Correspondence should be addressed to K Ma; Email: [email protected]) Abstract Male infertility affects approximately 2–7% of couples around the world. Over one in ten men who seek help at infertility clinics are diagnosed as severely oligospermic or azoospermic. Recent extensive molecular studies have revealed that deletions in the azoospermia factor region of the long arm of the Y chromosome are associated with severe spermatogenic impairment (absent or severely reduced germ cell development). Genetic research into male infertility, in the last 7 years, has resulted in the isolation of a great number of genes or gene families on the Y chromosome, some of which are believed to influence spermatogenesis. European Journal of Endocrinology 142 418–430 Introduction of Infertility, with the objective of creating a standard protocol for the investigation of infertile couples. Normal Defective spermatogenesis is the result of a multitude of semen was classified as containing a sperm concentra- causes, such as diseases, malnutrition, endocrinological 6 tion of at least 20 × 10 /ml, of which more than 40% disorders, genetic defects or environmental hazards (1). are progressively motile, more than 60% are alive, and Genetic defects, such as mutations and chromosomal over 50% show normal morphology. In addition, the abnormalities, have been estimated to account for at 6 semen should contain no more than 1 × 10 /ml of white least 30% of male infertility (2). -
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. -
UPSTREAM COMPONENTS of MTORC1 by Li Li a Dissertation
UPSTREAM COMPONENTS OF MTORC1 by Li Li A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Biological Chemistry) in The University of Michigan 2011 Doctoral Committee: Professor Kunliang Guan, Chair Professor Randal J. Kaufman Associate Professor Anne B. Vojtek Associate Professor Martin G. Myers Assistant Professor Diane C. Fingar © Li Li 2011 This work is dedicated to my parents. Without their support and guidance, I would not be where I am today. I also dedicate this work to my husband, for pushing me to the best I can. Last, and most importantly, I would like to dedicate this work to my fifteen months son for being well behaved during the last few months. You are the treasure of my life. ii ACKNOWLEDGEMENTS I would like to express my deep gratitude to my mentor Dr. Kun-Liang Guan for his direction, encouragement, and support during my graduate study. I am very thankful to him for his patience with me, enduring my naïve questions. That Dr. Guan is so approachable and enthusiastic about science set me an example on how to be a great PI and a great scientist. Next, I sincerely acknowledge the members of my thesis committee, Drs Randal J. Kaufman, Anne B. Vojtek, Diane C. Fingar and Martin G. Myers for their insightful suggestions and constructive criticism on my work. I would like to thank the current and former members of the Guan lab. All of them made the lab a great place to work. Especially, I would like to thank Bin Zhao, my husband, also a Guan lab member, for teaching me every lab techniques. -
Binding Specificities of Human RNA Binding Proteins Towards Structured
bioRxiv preprint doi: https://doi.org/10.1101/317909; this version posted March 1, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Binding specificities of human RNA binding proteins towards structured and linear 2 RNA sequences 3 4 Arttu Jolma1,#, Jilin Zhang1,#, Estefania Mondragón4,#, Teemu Kivioja2, Yimeng Yin1, 5 Fangjie Zhu1, Quaid Morris5,6,7,8, Timothy R. Hughes5,6, Louis James Maher III4 and Jussi 6 Taipale1,2,3,* 7 8 9 AUTHOR AFFILIATIONS 10 11 1Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden 12 2Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland 13 3Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom 14 4Department of Biochemistry and Molecular Biology and Mayo Clinic Graduate School of 15 Biomedical Sciences, Mayo Clinic College of Medicine and Science, Rochester, USA 16 5Department of Molecular Genetics, University of Toronto, Toronto, Canada 17 6Donnelly Centre, University of Toronto, Toronto, Canada 18 7Edward S Rogers Sr Department of Electrical and Computer Engineering, University of 19 Toronto, Toronto, Canada 20 8Department of Computer Science, University of Toronto, Toronto, Canada 21 #Authors contributed equally 22 *Correspondence: [email protected] 23 24 25 SUMMARY 26 27 Sequence specific RNA-binding proteins (RBPs) control many important 28 processes affecting gene expression. They regulate RNA metabolism at multiple 29 levels, by affecting splicing of nascent transcripts, RNA folding, base modification, 30 transport, localization, translation and stability. Despite their central role in most 31 aspects of RNA metabolism and function, most RBP binding specificities remain 32 unknown or incompletely defined. -
Tau Protein Modifications and Interactions: Their Role in Function and Dysfunction
Int. J. Mol. Sci. 2014, 15, 4671-4713; doi:10.3390/ijms15034671 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Review Tau Protein Modifications and Interactions: Their Role in Function and Dysfunction Anna Mietelska-Porowska, Urszula Wasik, Marcelina Goras, Anna Filipek and Grazyna Niewiadomska * Nencki Institute of Experimental Biology, Polish Academy of Science, 3 Pasteur Street, Warsaw 02-093, Poland; E-Mails: [email protected] (A.M.-P.); [email protected] (U.W.); [email protected] (M.G.); [email protected] (A.F.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +48-22-589-2409, Fax: +48-22-822-5342. Received: 29 November 2013; in revised form: 11 February 2014 / Accepted: 4 March 2014 / Published: 18 March 2014 Abstract: Tau protein is abundant in the central nervous system and involved in microtubule assembly and stabilization. It is predominantly associated with axonal microtubules and present at lower level in dendrites where it is engaged in signaling functions. Post-translational modifications of tau and its interaction with several proteins play an important regulatory role in the physiology of tau. As a consequence of abnormal modifications and expression, tau is redistributed from neuronal processes to the soma and forms toxic oligomers or aggregated deposits. The accumulation of tau protein is increasingly recognized as the neuropathological hallmark of a number of dementia disorders known as tauopathies. Dysfunction of tau protein may contribute to collapse of cytoskeleton, thereby causing improper anterograde and retrograde movement of motor proteins and their cargos on microtubules. -
DAZ (Z6Q): Sc-100705
SANTA CRUZ BIOTECHNOLOGY, INC. DAZ (Z6Q): sc-100705 BACKGROUND RECOMMENDED SUPPORT REAGENTS Spermatogenesis is the process by which male spermatogonia develop into To ensure optimal results, the following support reagents are recommended: mature spermatozoa. DAZ (deleted in azoospermia) are RNA-binding proteins 1) Western Blotting: use m-IgGk BP-HRP: sc-516102 or m-IgGk BP-HRP (Cruz that play an essential role in spermatogenesis. DAZ proteins influence the Marker): sc-516102-CM (dilution range: 1:1000-1:10000), Cruz Marker™ first stages of spermatogenesis and the maintenance of germ cell populations. Molecular Weight Standards: sc-2035, UltraCruz® Blocking Reagent: DAZ proteins (DAZ1, DAZ2, DAZ3, DAZ4 and DAZ5) are encoded by separate sc-516214 and Western Blotting Luminol Reagent: sc-2048. 2) Immunopre- genes on chromosome Y, each of which contain an AZFc domain in their cod- cipitation: use Protein A/G PLUS-Agarose: sc-2003 (0.5 ml agarose/2.0 ml). ing region. DAZ proteins are localized to the nucleus of spermatogonia, but 3) Immunofluorescence: use m-IgGk BP-FITC: sc-516140 or m-IgGk BP-PE: relocate to the cytoplasm during meiosis. DAZ proteins contain an RRM (RNA sc-516141 (dilution range: 1:50-1:200) with UltraCruz® Mounting Medium: recognition motif) domain that may regulate mRNA translation by binding sc-24941 or UltraCruz® Hard-set Mounting Medium: sc-359850. 4) Immuno- to the 3' UTR. Deletions in the genes encoding DAZ proteins may cause histochemistry: use m-IgGk BP-HRP: sc-516102 with DAB, 50X: sc-24982 azoospermia or oligospermia which can lead to male infertility. -
Partial Azfc Deletions and Duplications: Clinical Correlates in the Italian Population
FLORE Repository istituzionale dell'Università degli Studi di Firenze Partial AZFc deletions and duplications: clinical correlates in the Italian population. Questa è la Versione finale referata (Post print/Accepted manuscript) della seguente pubblicazione: Original Citation: Partial AZFc deletions and duplications: clinical correlates in the Italian population / Giachini C; Laface I; Guarducci E; Balercia G; Forti G; Krausz C.. - In: HUMAN GENETICS. - ISSN 0340-6717. - STAMPA. - 124(2008), pp. 399-410. Availability: This version is available at: 2158/333113 since: 2019-11-07T18:24:55Z Terms of use: Open Access La pubblicazione è resa disponibile sotto le norme e i termini della licenza di deposito, secondo quanto stabilito dalla Policy per l'accesso aperto dell'Università degli Studi di Firenze (https://www.sba.unifi.it/upload/policy-oa-2016-1.pdf) Publisher copyright claim: (Article begins on next page) 28 September 2021 Hum Genet (2008) 124:399–410 DOI 10.1007/s00439-008-0561-1 ORIGINAL INVESTIGATION Partial AZFc deletions and duplications: clinical correlates in the Italian population Claudia Giachini · Ilaria Laface · Elena Guarducci · Giancarlo Balercia · Gianni Forti · Csilla Krausz Received: 7 August 2008 / Accepted: 9 September 2008 / Published online: 21 September 2008 © Springer-Verlag 2008 Abstract The role of partial AZFc deletions of the Y potential methodological and selection biases were care- chromosome in spermatogenic impairment is currently fully avoided to detect the clinical signiWcance of partial debated. Recently, it was also reported that duplications of AZFc deletions and duplications. Our study provides strong the same region are associated with oligozoospermia in evidence that gr/gr deletion is a risk factor for impaired Han-Chinese men.