The Genetic Bases of Speech Sound Disorders: Evidence from Spoken and Written Language
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Primate Specific Retrotransposons, Svas, in the Evolution of Networks That Alter Brain Function
Title: Primate specific retrotransposons, SVAs, in the evolution of networks that alter brain function. Olga Vasieva1*, Sultan Cetiner1, Abigail Savage2, Gerald G. Schumann3, Vivien J Bubb2, John P Quinn2*, 1 Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, U.K 2 Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK 3 Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, D-63225 Germany *. Corresponding author Olga Vasieva: Institute of Integrative Biology, Department of Comparative genomics, University of Liverpool, Liverpool, L69 7ZB, [email protected] ; Tel: (+44) 151 795 4456; FAX:(+44) 151 795 4406 John Quinn: Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK, [email protected]; Tel: (+44) 151 794 5498. Key words: SVA, trans-mobilisation, behaviour, brain, evolution, psychiatric disorders 1 Abstract The hominid-specific non-LTR retrotransposon termed SINE–VNTR–Alu (SVA) is the youngest of the transposable elements in the human genome. The propagation of the most ancient SVA type A took place about 13.5 Myrs ago, and the youngest SVA types appeared in the human genome after the chimpanzee divergence. Functional enrichment analysis of genes associated with SVA insertions demonstrated their strong link to multiple ontological categories attributed to brain function and the disorders. SVA types that expanded their presence in the human genome at different stages of hominoid life history were also associated with progressively evolving behavioural features that indicated a potential impact of SVA propagation on a cognitive ability of a modern human. -
A Narrative Review of the Intervention Techniques for Childhood Apraxia of Speech Katherine Mahoney
Undergraduate Review Volume 11 Article 15 2015 A Narrative Review of the Intervention Techniques for Childhood Apraxia of Speech Katherine Mahoney Follow this and additional works at: http://vc.bridgew.edu/undergrad_rev Recommended Citation Mahoney, Katherine (2015). A Narrative Review of the Intervention Techniques for Childhood Apraxia of Speech. Undergraduate Review, 11, 81-90. Available at: http://vc.bridgew.edu/undergrad_rev/vol11/iss1/15 This item is available as part of Virtual Commons, the open-access institutional repository of Bridgewater State University, Bridgewater, Massachusetts. Copyright © 2015 Katherine Mahoney in which the brain has difficulty motor planning for speech A Narrative Review of the (McCarty, 2013). The prognosis of CAS is emblematic of the time in which CAS is diagnosed and the intensity of the inter- Intervention Techniques vention (Velleman, 2003, p. 8). for Childhood Apraxia of CAS is a complex speech disorder affected by many factors. Speech Although CAS is a speech disorder that affects the motor planning skills for speech and the coordination of vocal tract muscle movements, the disorder does occur concurrently KATHERINE MAHONEY with phonological difficulties (Velleman, 2003, p. 2). There are many different symptoms that can occur with the disor- hildhood Apraxia of Speech (CAS) is a speech disorder der; however, there are no specific phonological characteristics that affects development of the motor planning skills that must be present in the diagnosis (Bauman-Waengler, 2012, needed for the production of speech. According to p.368). The technical report for CAS produced by the Ameri- C can Speech-Language-Hearing Association lists the following prevalence data, CAS affects approximately two children per 1,000 (Bauman-Waengler, 2012, p.366). -
FOXP2: a Gene for Language and Speech Hakim Arif
FOXP2: A gene for language and speech Hakim Arif The Dhaka University Journal of Linguistics: Vol. 2 No.3 February, 2009 activities of human beings either partially or at a severe range. Page: 173-184, Published on December 2009 by the Registrar, Dhaka In view of the said development in the field, this paper aims at University ISSN-2075-3098 providing with a brief description of the nature and characteristics of such a human gene called POXP2. FOXP2: A gene for language and speech Nowadays genomics, a new science dealing with the nature of mapping the genome or protein structure of human body, is a 1 Hakim Arif fascinating area of research in biosciences. Scientists in this 1. Associate Professor, Department of Linguistics, University discipline are frequently getting reflections of the genetic of Dhaka mapping of different physio-neuro-cognitive behaviours as well as manners of human beings hence unfolding the Abstract underlying pattern of their polymorphic DNA markers, Establishing the nature of relationship between Linguistics and bio-sciences, especially Genetic Studies is nether an including amino acid sequence of human proteins and its gene imagination today, nor an ambitious project at all, as structure (Botstein & Cherry, 1997). Interestingly, the number psychologists, linguists and genetic scientists started to put of such sequences of human gene mapping is exponentially there keen interest in this endeavour at the beginning of the twentieth-first century. The study of FOXP2-a potential increasing almost every year (Branden & Toose, 1999: 3). human gene responsible for the degeneration of half of the 2. Language and human gene members of famous KE family’s speech and language performances, starts an epoch-making initiative in this Language, one of the basic neuro-cognitive activities of human regard. -
Molecular Genetics of Dyslexia: an Overview
DYSLEXIA Published online in Wiley Online Library (wileyonlinelibrary.com). DOI: 10.1002/dys.1464 ■ Molecular Genetics of Dyslexia: An Overview Amaia Carrion-Castillo1*, Barbara Franke2 and Simon E. Fisher1,2 1Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands 2Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Netherlands Dyslexia is a highly heritable learning disorder with a complex underlying genetic architecture. Over the past decade, researchers have pinpointed a number of candidate genes that may con- tribute to dyslexia susceptibility. Here, we provide an overview of the state of the art, describing how studies have moved from mapping potential risk loci, through identification of associated gene variants, to characterization of gene function in cellular and animal model systems. Work thus far has highlighted some intriguing mechanistic pathways, such as neuronal migration, axon guidance, and ciliary biology, but it is clear that we still have much to learn about the molecular networks that are involved. We end the review by highlighting the past, present, and future contributions of the Dutch Dyslexia Programme to studies of genetic factors. In particular, we emphasize the importance of relating genetic information to intermediate neurobiological measures, as well as the value of incorporating longitudinal and developmental data into molecular designs. Copyright © 2013 John Wiley & Sons, Ltd. Keywords: molecular genetics; dyslexia; review INTRODUCTION Over the past decade or so, advances in molecular technologies have enabled researchers to begin pinpointing potential genetic risk factors implicated in human neurodevelopmental disorders (Graham & Fisher, 2013). A significant amount of work has focused on developmental dyslexia (specific reading disability). -
Inter-Chromosomal Variation in the Pattern of Human Population Genetic Structure Tesfaye M
PRIMARY RESEARCH Inter-chromosomal variation in the pattern of human population genetic structure Tesfaye M. Baye* Cincinnati Children’s Hospital Medical Center, Division of Asthma Research, Department of Pediatrics, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH 45229, USA *Correspondence to: Tel: þ1 513 803 2766; Fax: þ1 513 636 1657; E-mail: [email protected] Date received (in revised form): 1st March 2011 Abstract Emerging technologies now make it possible to genotype hundreds of thousands of genetic variations in individuals, across the genome. The study of loci at finer scales will facilitate the understanding of genetic variation at genomic and geographic levels. We examined global and chromosomal variations across HapMap populations using 3.7 million single nucleotide polymorphisms to search for the most stratified genomic regions of human populations and linked these regions to ontological annotation and functional network analysis. To achieve this, we used five complementary statistical and genetic network procedures: principal component (PC), cluster, discriminant, fix- ation index (FST) and network/pathway analyses. At the global level, the first two PC scores were sufficient to account for major population structure; however, chromosomal level analysis detected subtle forms of population structure within continental populations, and as many as 31 PCs were required to classify individuals into homo- geneous groups. Using recommended population ancestry differentiation measures, a total of 126 regions of the genome were catalogued. Gene ontology and networks analyses revealed that these regions included the genes encoding oculocutaneous albinism II (OCA2), hect domain and RLD 2 (HERC2), ectodysplasin A receptor (EDAR) and solute carrier family 45, member 2 (SLC45A2). -
Downloaded from Here
bioRxiv preprint doi: https://doi.org/10.1101/017566; this version posted November 19, 2015. 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 1 Testing for ancient selection using cross-population allele 2 frequency differentiation 1;∗ 3 Fernando Racimo 4 1 Department of Integrative Biology, University of California, Berkeley, CA, USA 5 ∗ E-mail: [email protected] 6 1 Abstract 7 A powerful way to detect selection in a population is by modeling local allele frequency changes in a 8 particular region of the genome under scenarios of selection and neutrality, and finding which model is 9 most compatible with the data. Chen et al. [2010] developed a composite likelihood method called XP- 10 CLR that uses an outgroup population to detect departures from neutrality which could be compatible 11 with hard or soft sweeps, at linked sites near a beneficial allele. However, this method is most sensitive 12 to recent selection and may miss selective events that happened a long time ago. To overcome this, 13 we developed an extension of XP-CLR that jointly models the behavior of a selected allele in a three- 14 population tree. Our method - called 3P-CLR - outperforms XP-CLR when testing for selection that 15 occurred before two populations split from each other, and can distinguish between those events and 16 events that occurred specifically in each of the populations after the split. -
Decoding the Genetics of Speech and Language
Available online at www.sciencedirect.com Decoding the genetics of speech and language 1 1,2 Sarah A Graham and Simon E Fisher Researchers are beginning to uncover the neurogenetic reading. Such disorders are heritable, presenting gate- pathways that underlie our unparalleled capacity for spoken ways into the underlying genetic landscape (Table 1) language. Initial clues come from identification of genetic risk [1 ,2 ]. Their diagnosis, treatment, and study is compli- factors implicated in developmental language disorders. The cated by heterogeneity and co-morbidity [3]. Neverthe- underlying genetic architecture is complex, involving a range of less, significant progress has been made in identifying and molecular mechanisms. For example, rare protein-coding studying risk genes, providing novel perspectives on the mutations of the FOXP2 transcription factor cause severe biological bases of human spoken language [4 ]. problems with sequencing of speech sounds, while common genetic risk variants of small effect size in genes like CNTNAP2, FOXP2 – first clues ATP2C2 and CMIP are associated with typical forms of The first gene implicated in speech and language was the language impairment. In this article, we describe how transcription factor FOXP2 [5]. It was discovered through investigations of these and other candidate genes, in humans, studies of a large pedigree, the KE family, in which fifteen animals and cellular models, are unravelling the connections people had severe problems co-ordinating speech (devel- between genes and cognition. This depends on opmental verbal dyspraxia, DVD, or childhood apraxia of interdisciplinary research at multiple levels, from determining speech, CAS) accompanied by wide-ranging linguistic molecular interactions and functional roles in neural cell- deficits [6]. -
Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ...................................................... -
The Pdx1 Bound Swi/Snf Chromatin Remodeling Complex Regulates Pancreatic Progenitor Cell Proliferation and Mature Islet Β Cell
Page 1 of 125 Diabetes The Pdx1 bound Swi/Snf chromatin remodeling complex regulates pancreatic progenitor cell proliferation and mature islet β cell function Jason M. Spaeth1,2, Jin-Hua Liu1, Daniel Peters3, Min Guo1, Anna B. Osipovich1, Fardin Mohammadi3, Nilotpal Roy4, Anil Bhushan4, Mark A. Magnuson1, Matthias Hebrok4, Christopher V. E. Wright3, Roland Stein1,5 1 Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 2 Present address: Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 3 Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 4 Diabetes Center, Department of Medicine, UCSF, San Francisco, California 5 Corresponding author: [email protected]; (615)322-7026 1 Diabetes Publish Ahead of Print, published online June 14, 2019 Diabetes Page 2 of 125 Abstract Transcription factors positively and/or negatively impact gene expression by recruiting coregulatory factors, which interact through protein-protein binding. Here we demonstrate that mouse pancreas size and islet β cell function are controlled by the ATP-dependent Swi/Snf chromatin remodeling coregulatory complex that physically associates with Pdx1, a diabetes- linked transcription factor essential to pancreatic morphogenesis and adult islet-cell function and maintenance. Early embryonic deletion of just the Swi/Snf Brg1 ATPase subunit reduced multipotent pancreatic progenitor cell proliferation and resulted in pancreas hypoplasia. In contrast, removal of both Swi/Snf ATPase subunits, Brg1 and Brm, was necessary to compromise adult islet β cell activity, which included whole animal glucose intolerance, hyperglycemia and impaired insulin secretion. Notably, lineage-tracing analysis revealed Swi/Snf-deficient β cells lost the ability to produce the mRNAs for insulin and other key metabolic genes without effecting the expression of many essential islet-enriched transcription factors. -
Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands That Promote Axonal Growth
Research Article: New Research Development Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth Jeremy S. Toma,1 Konstantina Karamboulas,1,ª Matthew J. Carr,1,2,ª Adelaida Kolaj,1,3 Scott A. Yuzwa,1 Neemat Mahmud,1,3 Mekayla A. Storer,1 David R. Kaplan,1,2,4 and Freda D. Miller1,2,3,4 https://doi.org/10.1523/ENEURO.0066-20.2020 1Program in Neurosciences and Mental Health, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada, 2Institute of Medical Sciences University of Toronto, Toronto, Ontario M5G 1A8, Canada, 3Department of Physiology, University of Toronto, Toronto, Ontario M5G 1A8, Canada, and 4Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada Abstract Peripheral nerves provide a supportive growth environment for developing and regenerating axons and are es- sential for maintenance and repair of many non-neural tissues. This capacity has largely been ascribed to paracrine factors secreted by nerve-resident Schwann cells. Here, we used single-cell transcriptional profiling to identify ligands made by different injured rodent nerve cell types and have combined this with cell-surface mass spectrometry to computationally model potential paracrine interactions with peripheral neurons. These analyses show that peripheral nerves make many ligands predicted to act on peripheral and CNS neurons, in- cluding known and previously uncharacterized ligands. While Schwann cells are an important ligand source within injured nerves, more than half of the predicted ligands are made by nerve-resident mesenchymal cells, including the endoneurial cells most closely associated with peripheral axons. At least three of these mesen- chymal ligands, ANGPT1, CCL11, and VEGFC, promote growth when locally applied on sympathetic axons. -
A Theoretical Molecular Network for Dyslexia
Molecular Psychiatry (2011) 16, 365–382 & 2011 Macmillan Publishers Limited All rights reserved 1359-4184/11 www.nature.com/mp FEATURE REVIEW A theoretical molecular network for dyslexia: integrating available genetic findings G Poelmans1, JK Buitelaar1, DL Pauls2 and B Franke3,4 1Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands; 2Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; 3Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands and 4Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands Developmental dyslexia is a common specific childhood learning disorder with a strong heritable component. Previous studies using different genetic approaches have identified several genetic loci and candidate genes for dyslexia. In this article, we have integrated the current knowledge on 14 dyslexia candidate genes suggested by cytogenetic findings, linkage and association studies. We found that 10 of the 14 dyslexia candidate genes (ROBO1, KIAA0319, KIAA0319L, S100B, DOCK4, FMR1, DIP2A, GTF2I, DYX1C1 and DCDC2) fit into a theoretical molecular network involved in neuronal migration and neurite outgrowth. Based on this, we also propose three novel dyslexia candidate genes (SLIT2, HMGB1 and VAPA) from known linkage regions, and we discuss the possible involvement of genes emerging from the two reported genome-wide association studies for reading impairment-related phenotypes in the identified network. Molecular Psychiatry (2011) 16, 365–382; doi:10.1038/mp.2010.105; published online 19 October 2010 Keywords: dyslexia; genetics; neurodevelopment; molecular network; bioinformatics Introduction parietotemporal and ventral occipitotemporal systems. -
Biolinguistics: Forays Into Human Cognitive Biology
doi 10.4436/JASS.91009 JASs Invited Reviews Journal of Anthropological Sciences Vol. 91 (2013), pp. 63-89 Biolinguistics: forays into human cognitive biology Cedric Boeckx ICREA (Catalan Institute for Advanced Studies), University of Barcelona, Department of General Linguistics, Gran via de les Cortes Catalanes 585, 08007 Barcelona, Spain e-mail: [email protected] Summary - The present article surveys the field of biolinguistics. It revisits the roots of the field’s core research agenda, then turns to the various factors that led to its recent re-emergence, and finally offers suggestions for future inquiry. The essay also serves to highlight certain conceptual issues that should be addressed if the field is to bear its interdisciplinary fruits. Keywords - Anthropology, Development, Evolution, Genetics, Linguistics, Neuroscience. Introduction The significant change caused by Chomsky’s review was to reorient scientific studies of lan- Biolinguistics refers to a branch of the cogni- guage towards more internalist issues, revolving tive sciences that focuses on uncovering the bio- around the cognitive capacity that human beings logical underpinnings of the human capacity to bring to the task of language acquisition, interpre- acquire at least one natural language. As such, tation, and production—what Chomsky (1965) and despite its name, it departs sharply from the dubbed “linguistic competence”. Chomsky went many subdisciplines of linguistics, which focus on to formulate a set of central, field-defining on how human languages are put to use in various questions, all of which led logically to the realm socio-cultural contexts. That such uses require a of biology, converging with the range of evidence (possibly complex and multi-faceted) biological revealed by Lenneberg (critical period, creoli- foundation cannot be seriously put into doubt, zation, language impairments, etc.) This was and biolinguistics takes that fundamental aspect in fact to be expected, as both Lenneberg and of human biology as its subject matter.