Haploinsufficiency of Autism Causative Gene Tbr1 Impairs Olfactory
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Legends for Supplemental Figures and Tables Figure S1. Expression of Tlx during retinogenesis. (A) Staged embryos were stained for β- galactosidase knocked into the Tlx locus to indicate Tlx expression. Tlx was expressed in the neural blast layer in the early phase of neural retina development (blue signal). (B) Expression of Tlx in neural retina was quantified using Q-PCR at multiple developmental stages. Figure S2. Expression of p27kip1 and cyclin D1 (Ccnd1) at various developmental stages in wild-type or Tlx-/- retinas. (A) Q-PCR analysis of p27kip1 mRNA expression. (B) Western blotting analysis of p27kip1 protein expression. (C) Q-PCR analysis of cyclin D1 mRNA expression. Figure S3. Q-PCR analysis of mRNA expression of Sf1 (A), Lrh1 (B), and Atn1 (C) in wild-type mouse retinas. RNAs from testis and liver were used as controls. Table S1. List of genes dysregulated both at E15.5 and P0 Tlx-/- retinas. Gene E15.5 P0 Cluste Gene Title Fold Fold r Name p-value p-value Change Change nuclear receptor subfamily 0, group B, Nr0b1 1.65 0.0024 2.99 0.0035 member 1 1 Pou4f3 1.91 0.0162 2.39 0.0031 POU domain, class 4, transcription factor 3 1 Tcfap2d 2.18 0.0000 2.37 0.0001 transcription factor AP-2, delta 1 Zic5 1.66 0.0002 2.02 0.0218 zinc finger protein of the cerebellum 5 1 Zfpm1 1.85 0.0030 1.88 0.0025 zinc finger protein, multitype 1 1 Pten 1.60 0.0155 1.82 0.0131 phospatase and tensin homolog 2 Itgb5 -1.85 0.0063 -1.85 0.0007 integrin beta 5 2 Gpr49 6.86 0.0001 15.16 0.0001 G protein-coupled receptor 49 3 Cmkor1 2.60 0.0007 2.72 0.0013 -
KLF2 Induced
UvA-DARE (Digital Academic Repository) The transcription factor KLF2 in vascular biology Boon, R.A. Publication date 2008 Link to publication Citation for published version (APA): Boon, R. A. (2008). The transcription factor KLF2 in vascular biology. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:23 Sep 2021 Supplementary data: Genes induced by KLF2 Dekker et al. LocusLink Accession Gene Sequence Description Fold p-value ID number symbol change (FDR) 6654 AK022099 SOS1 cDNA FLJ12037 fis, clone HEMBB1001921. 100.00 5.9E-09 56999 AF086069 ADAMTS9 full length insert cDNA clone YZ35C05. 100.00 1.2E-09 6672 AF085934 SP100 full length insert cDNA clone YR57D07. 100.00 6.7E-13 9031 AF132602 BAZ1B Williams Syndrome critical region WS25 mRNA, partial sequence. -
T-Brain Regulates Archenteron Induction Signal 5207 Range of Amplification
Development 129, 5205-5216 (2002) 5205 Printed in Great Britain © The Company of Biologists Limited 2002 DEV5034 T-brain homologue (HpTb) is involved in the archenteron induction signals of micromere descendant cells in the sea urchin embryo Takuya Fuchikami1, Keiko Mitsunaga-Nakatsubo1, Shonan Amemiya2, Toshiya Hosomi1, Takashi Watanabe1, Daisuke Kurokawa1,*, Miho Kataoka1, Yoshito Harada3, Nori Satoh3, Shinichiro Kusunoki4, Kazuko Takata1, Taishin Shimotori1, Takashi Yamamoto1, Naoaki Sakamoto1, Hiraku Shimada1 and Koji Akasaka1,† 1Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan 2Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan 3Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan 4LSL, Nerima-ku, Tokyo 178-0061, Japan *Present address: Evolutionary Regeneration Biology Group, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan †Author for correspondence (e-mail: [email protected]) Accepted 30 July 2002 SUMMARY Signals from micromere descendants play a crucial role in cells, the initial specification of primary mesenchyme cells, sea urchin development. In this study, we demonstrate that or the specification of endoderm. HpTb expression is these micromere descendants express HpTb, a T-brain controlled by nuclear localization of β-catenin, suggesting homolog of Hemicentrotus pulcherrimus. HpTb is expressed that -
Accompanies CD8 T Cell Effector Function Global DNA Methylation
Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function Christopher D. Scharer, Benjamin G. Barwick, Benjamin A. Youngblood, Rafi Ahmed and Jeremy M. Boss This information is current as of October 1, 2021. J Immunol 2013; 191:3419-3429; Prepublished online 16 August 2013; doi: 10.4049/jimmunol.1301395 http://www.jimmunol.org/content/191/6/3419 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2013/08/20/jimmunol.130139 Material 5.DC1 References This article cites 81 articles, 25 of which you can access for free at: http://www.jimmunol.org/content/191/6/3419.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists by guest on October 1, 2021 • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function Christopher D. Scharer,* Benjamin G. Barwick,* Benjamin A. Youngblood,*,† Rafi Ahmed,*,† and Jeremy M. -
What, If Anything, Is Rodent Prefrontal Cortex?
Review Cognition and Behavior What, If Anything, Is Rodent Prefrontal Cortex? Mark Laubach,1 Linda M. Amarante,1 Kyra Swanson,1 and Samantha R. White1 https://doi.org/10.1523/ENEURO.0315-18.2018 1Department of Biology and Center for Behavioral Neuroscience, American University, Washington, DC 20016 Visual Abstract Prefrontal cortex (PFC) means different things to different people. In recent years, there has been a major increase in publications on the PFC, especially using mice. However, inconsistencies in the nomenclature and anatomical boundaries of PFC areas has made it difficult for researchers to compare data and interpret findings across species. We conducted a meta-analysis of publications on the PFC of humans and rodents and found dramatic differences in the focus of research on these species. In addition, we compared anatomical terms and criteria across several common rodent brain atlases and found inconsistencies among, and even within, leading atlases. To assess the impact of these issues on the research community, we conducted a survey of established PFC researchers on their use of anatomical terms and found little consensus. We report on the results of the survey and propose an alternative scheme for interpreting data Significance Statement Studies on prefrontal parts of the rodent cerebral cortex have appeared at an increasing rate in recent years. However, there has been no consensus on the terms used to describe the rodent prefrontal cortex (PFC) or how it relates to the PFC of monkeys and humans. To address these issues, we conducted a meta-analysis of publications on the PFC across species, a review of rodent brain atlases, a survey of PFC researchers on anatomic terms, and an analysis of how species differences in the corpus callosum might help relate PFC areas across species. -
UNIVERSITY of CALIFORNIA RIVERSIDE Investigations Into The
UNIVERSITY OF CALIFORNIA RIVERSIDE Investigations into the Role of TAF1-mediated Phosphorylation in Gene Regulation A Dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Cell, Molecular and Developmental Biology by Brian James Gadd December 2012 Dissertation Committee: Dr. Xuan Liu, Chairperson Dr. Frank Sauer Dr. Frances M. Sladek Copyright by Brian James Gadd 2012 The Dissertation of Brian James Gadd is approved Committee Chairperson University of California, Riverside Acknowledgments I am thankful to Dr. Liu for her patience and support over the last eight years. I am deeply indebted to my committee members, Dr. Frank Sauer and Dr. Frances Sladek for the insightful comments on my research and this dissertation. Thanks goes out to CMDB, especially Dr. Bachant, Dr. Springer and Kathy Redd for their support. Thanks to all the members of the Liu lab both past and present. A very special thanks to the members of the Sauer lab, including Silvia, Stephane, David, Matt, Stephen, Ninuo, Toby, Josh, Alice, Alex and Flora. You have made all the years here fly by and made them so enjoyable. From the Sladek lab I want to thank Eugene, John, Linh and Karthi. Special thanks go out to all the friends I’ve made over the years here. Chris, Amber, Stephane and David, thank you so much for feeding me, encouraging me and keeping me sane. Thanks to the brothers for all your encouragement and prayers. To any I haven’t mentioned by name, I promise I haven’t forgotten all you’ve done for me during my graduate years. -
Transcriptional Regulatory Networks in Neocortical Development
Review From trans to cis: transcriptional regulatory networks in neocortical development 1 1 1,2 Mikihito Shibata , Forrest O. Gulden , and Nenad Sestan 1 Department of Neurobiology and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA 2 Department of Psychiatry and Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT 06510, USA Transcriptional mechanisms mediated by the binding of tions among TFs and CREs form the central core of tran- transcription factors (TFs) to cis-acting regulatory ele- scriptional regulatory networks (TRNs) (Box 1) [1]. ments (CREs) in DNA play crucial roles in directing gene Interactions between TFs and CREs are complex, dynam- expression. While TFs have been extensively studied, ic,andmodulatedbyvariousepigeneticprocesses[12].While less effort has gone towards the identification and func- individual CREs may be regulated by the competitive or tional characterization of CREs and associated epigenet- cooperative binding of many TFs, multiple CREs may also ic modulation. However, owing to methodological and confer transcriptional control over the expression of any analytical advances, more comprehensive studies of single gene [12]. Furthermore, TFs and CREs regulate regulatory elements and mechanisms are now possible. transcription together with their cognate transcriptional We summarize recent progress in integrative analyses of cofactors, chromatin regulators, epigenetic modifications, these regulatory components in the development of the RNA-binding proteins, and non-coding RNAs [2,13]. This cerebral neocortex, the part of the brain involved in combinatorial and multi-level transcriptional regulation cognition and complex behavior. These studies are greatly increases the complexity of gene expression regula- uncovering not only the underlying transcriptional reg- tion, facilitating the unique spatio-temporal patterns nec- ulatory networks, but also how these networks are essary for tissue development and function [3]. -
The Virtual Mouse Brain: a Computational Neuroinformatics Platform to Study Whole Mouse Brain Dynamics
bioRxiv preprint doi: https://doi.org/10.1101/123406; this version posted April 3, 2017. 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 4.0 International license. The Virtual Mouse Brain: a computational neuroinformatics platform to study whole mouse brain dynamics Francesca Melozzi, Marmaduke M. Woodman, Viktor K. Jirsa∗, Christophe Bernard∗ Aix Marseille Univ, Inserm, INS, Institut de Neurosciences des Systèmes, Marseille, France ∗equally contributing last authors Correspondence author: [email protected] Abstract Connectome-based modeling of large-scale brain network dynamics enables causal in silico interrogation of the brain’s structure-function relationship, necessitating the close integration of diverse neuroinformatics fields. Here we extend the open-source simulation software The Virtual Brain to whole mouse brain network modeling based on individual diffusion Magnetic Resonance Imaging (dMRI)-based or tracer-based detailed mouse connectomes. We provide practical examples on how to use The Virtual Mouse Brain to simulate brain activity, such as seizure propagation and the switching behavior of the resting state dynamics in health and disease. The Virtual Mouse Brain enables theoretically driven experimental planning and ways to test predictions in the numerous strains of mice available to study brain function in normal and pathological conditions. Introduction -
Consideration of Layer-Specific Marker Expression
Cerebral Cortex March 2011;21:588--596 doi:10.1093/cercor/bhq125 Advance Access publication July 12, 2010 Neocortical Layer Formation of Human Developing Brains and Lissencephalies: Consideration of Layer-Specific Marker Expression Takashi Saito1,2, Sae Hanai1,2, Sachio Takashima3, Eiji Nakagawa2, Shin Okazaki4, Takeshi Inoue5, Rie Miyata6, Kyoko Hoshino7, Takumi Akashi8, Masayuki Sasaki2, Yu-ichi Goto1, Masaharu Hayashi6 and Masayuki Itoh1 1Department of Mental Retardation and Birth Defect Research, National Center of Neurology and Psychiatry, Kodaira, 187-8502, Japan, 2Department of Child Neurology, The Hospital of National Center of Neurology and Psychiatry, Kodaira, 187-8551, Japan, 3Yanagawa Institute of Handicapped Children, International University of Health and Welfare, Fukuoka, 832-0058, Japan, 4Department of Pediatrics, Osaka City General Hospital, Osaka, 534-0021, Japan, 5Department of Pathology and Laboratory Medicine, Osaka City General Hospital, Osaka, 534-0021, Japan, 6Department of Clinical Neuropathology, Tokyo Metropolitan Institute of Neuroscience, Fuchu, 183-8526, Japan, 7Department of Pediatrics, Saitama Medical Center, Kawagoe, 350-8550, Japan and 8Department of Pathology and Laboratory Medicine, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan Takashi Saito and Masayuki Itoh have contributed equally to this work. Downloaded from Address correspondence to M Itoh, Department of Mental Retardation and Birth Defect Research, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo 187-8502, Japan. Email: [email protected]. To investigate layer-specific molecule expression in human de- each layer has a specific function with a synaptic connection. veloping neocortices, we performed immunohistochemistry of the In each step, specific genes have important roles, and the http://cercor.oxfordjournals.org/ layer-specific markers (TBR1, FOXP1, SATB2, OTX1, CUTL1, and molecular mechanism is well known in rodent brains (Arlotta CTIP2), using frontal neocortices of the dorsolateral precentral gyri et al. -
Rh]DIAZEPAM BINDING in MAMMALIAN CENTRAL NERVOUS SYSTEM: a PHARMACOLOGICAL CHARACTERIZATION
0270-6474/81/0102-0218$02.00/O The Journal of Neuroscience Copyright 0 Society for Neuroscience Vol. 1, No. 2, pp. 218-225 Printed in U.S.A. February 1981 rH]DIAZEPAM BINDING IN MAMMALIAN CENTRAL NERVOUS SYSTEM: A PHARMACOLOGICAL CHARACTERIZATION DOROTHY W. GALLAGER,*, ’ PIERRE MALLORGA,* WOLFGANG OERTEL,# RICHARD HENNEBERRY,$ AND JOHN TALLMAN* * Biological Psychiatry Branch, National Institute of Mental Health, $Laboratory of Clinical Science, National Institute of Mental Health, and SLaboratory of Molecular Biology, National Institute of General Medical Sciences, Bethesda, Maryland 20205 Abstract Two types of benzodiazepine binding sites for [3H]diazepam in mammalian central nervous tissue were identified using selective in vitro tissue culture and in situ kainic acid lesion techniques. These two binding sites were pharmacologically distinguished by differential displacement of the [3H]diazepam radioligand using the centrally active benzodiazepine, clonazepam, and the centrally inactive benzodiazepine, R05-4864. Clonazepam-displaceable binding sites were found to be located principally on neuronal membranes, while R05-4864-displaceable binding sites were found to be located on non-neuronal elements. These pharmacological distinctions can be used to characterize the predominant cell types which bind benzodiazepines in nervous tissue. It is suggested that one quantitative measure of different cell populations is the ratio of clonazepam- to R05-4864-displaceable [3H]diazepam binding within a single neuronal tissue sample. Binding sites for benzodiazepines in brain which have sites on the kidney cells, although possessing a high high affinity and show saturability and stereospecificity affinity for [3H]diazepam, showed an entirely different have been described (Squires and Braestrup, 1977; Moh- pharmacological spectrum from the brain site. -
Pallial Origin of Basal Forebrain Cholinergic Neurons in the Nucleus
ERRATUM 4565 Development 138, 4565 (2011) doi:10.1242/dev.074088 © 2011. Published by The Company of Biologists Ltd Pallial origin of basal forebrain cholinergic neurons in the nucleus basalis of Meynert and horizontal limb of the diagonal band nucleus Ana Pombero, Carlos Bueno, Laura Saglietti, Monica Rodenas, Jordi Guimera, Alexandro Bulfone and Salvador Martinez There was an error in the ePress version of Development 138, 4315-4326 published on 24 August 2011. In Fig. 7P, the P-values are not given in the legend. For region 2, P=0.02; for region 3, P=0.003. The final online issue and print copy are correct. We apologise to authors and readers for this error. DEVELOPMENT RESEARCH ARTICLE 4315 Development 138, 4315-4326 (2011) doi:10.1242/dev.069534 © 2011. Published by The Company of Biologists Ltd Pallial origin of basal forebrain cholinergic neurons in the nucleus basalis of Meynert and horizontal limb of the diagonal band nucleus Ana Pombero1, Carlos Bueno1, Laura Saglietti2, Monica Rodenas1, Jordi Guimera3, Alexandro Bulfone4 and Salvador Martinez1,* SUMMARY The majority of the cortical cholinergic innervation implicated in attention and memory originates in the nucleus basalis of Meynert and in the horizontal limb of the diagonal band nucleus of the basal prosencephalon. Functional alterations in this system give rise to neuropsychiatric disorders as well as to the cognitive alterations described in Parkinson and Alzheimer’s diseases. Despite the functional importance of these basal forebrain cholinergic neurons very little is known about their origin and development. Previous studies suggest that they originate in the medial ganglionic eminence of the telencephalic subpallium; however, our results identified Tbr1-expressing, reelin-positive neurons migrating from the ventral pallium to the subpallium that differentiate into cholinergic neurons in the basal forebrain nuclei projecting to the cortex. -
Integrative Bulk and Single-Cell Profiling of Premanufacture T-Cell Populations Reveals Factors Mediating Long-Term Persistence of CAR T-Cell Therapy
Published OnlineFirst April 5, 2021; DOI: 10.1158/2159-8290.CD-20-1677 RESEARCH ARTICLE Integrative Bulk and Single-Cell Profiling of Premanufacture T-cell Populations Reveals Factors Mediating Long-Term Persistence of CAR T-cell Therapy Gregory M. Chen1, Changya Chen2,3, Rajat K. Das2, Peng Gao2, Chia-Hui Chen2, Shovik Bandyopadhyay4, Yang-Yang Ding2,5, Yasin Uzun2,3, Wenbao Yu2, Qin Zhu1, Regina M. Myers2, Stephan A. Grupp2,5, David M. Barrett2,5, and Kai Tan2,3,5 Downloaded from cancerdiscovery.aacrjournals.org on October 1, 2021. © 2021 American Association for Cancer Research. Published OnlineFirst April 5, 2021; DOI: 10.1158/2159-8290.CD-20-1677 ABSTRACT The adoptive transfer of chimeric antigen receptor (CAR) T cells represents a breakthrough in clinical oncology, yet both between- and within-patient differences in autologously derived T cells are a major contributor to therapy failure. To interrogate the molecular determinants of clinical CAR T-cell persistence, we extensively characterized the premanufacture T cells of 71 patients with B-cell malignancies on trial to receive anti-CD19 CAR T-cell therapy. We performed RNA-sequencing analysis on sorted T-cell subsets from all 71 patients, followed by paired Cellular Indexing of Transcriptomes and Epitopes (CITE) sequencing and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) on T cells from six of these patients. We found that chronic IFN signaling regulated by IRF7 was associated with poor CAR T-cell persistence across T-cell subsets, and that the TCF7 regulon not only associates with the favorable naïve T-cell state, but is maintained in effector T cells among patients with long-term CAR T-cell persistence.