Neuronal Deletion of Gtf2i, Associated with Williams Syndrome, Causes Behavioral and Myelin Alterations Rescuable by a Remyelinating Drug
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Computational Genome-Wide Identification of Heat Shock Protein Genes in the Bovine Genome [Version 1; Peer Review: 2 Approved, 1 Approved with Reservations]
F1000Research 2018, 7:1504 Last updated: 08 AUG 2021 RESEARCH ARTICLE Computational genome-wide identification of heat shock protein genes in the bovine genome [version 1; peer review: 2 approved, 1 approved with reservations] Oyeyemi O. Ajayi1,2, Sunday O. Peters3, Marcos De Donato2,4, Sunday O. Sowande5, Fidalis D.N. Mujibi6, Olanrewaju B. Morenikeji2,7, Bolaji N. Thomas 8, Matthew A. Adeleke 9, Ikhide G. Imumorin2,10,11 1Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria 2International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA 3Department of Animal Science, Berry College, Mount Berry, GA, 30149, USA 4Departamento Regional de Bioingenierias, Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico 5Department of Animal Production and Health, Federal University of Agriculture, Abeokuta, Nigeria 6Usomi Limited, Nairobi, Kenya 7Department of Animal Production and Health, Federal University of Technology, Akure, Nigeria 8Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA 9School of Life Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa 10School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30032, USA 11African Institute of Bioscience Research and Training, Ibadan, Nigeria v1 First published: 20 Sep 2018, 7:1504 Open Peer Review https://doi.org/10.12688/f1000research.16058.1 Latest published: 20 Sep 2018, 7:1504 https://doi.org/10.12688/f1000research.16058.1 Reviewer Status Invited Reviewers Abstract Background: Heat shock proteins (HSPs) are molecular chaperones 1 2 3 known to bind and sequester client proteins under stress. Methods: To identify and better understand some of these proteins, version 1 we carried out a computational genome-wide survey of the bovine 20 Sep 2018 report report report genome. -
Better Models for Brain Disease NEWS FEATURE Traditional Animal Models Have Had Limited Success Mimicking Mental Illnesses
NEWS FEATURE Better models for brain disease NEWS FEATURE Traditional animal models have had limited success mimicking mental illnesses. Emerging technologies offer the potential for a major model upgrade. Helen H. Shen, Science Writer Starting with just a tiny chunk of skin, neuroscientist Flora Vaccarino tries to unlock mysteries hidden inside the brains of people with autism. By introducing certain genes to the skin cells, the Yale University School of Medicine researcher reprograms them to an embryo-like state, turning them into induced plu- ripotent stem cells (iPSCs); and with two more months of nurturing and tinkering, Vaccarino can guide the cells to develop into small balls of neural tissue akin to miniature human brains. Less than two millimeters across, these “cerebral organoids” don’t look or work exactly like full brains. But they contain many of the same cell types and un- dergo some of the same key developmental pro- cesses as fetal brains. Also key, the cells perfectly match the genetic makeup of the adults and children with autism who donated the original skin samples, allowing Vaccarino’s team to track the very beginnings of their disorder. Human brain tissue usually can’t be collected and studied until after death, and by then, it can be too late to glean important insights. “You don’t get to see the same person’s cells progressing through a series of steps and time points, like we do with these organo- ids,” Vaccarino explains. “The organoids are a very powerful system. You can actually change things and see what the outcome is going to be.” Neurons such as these, derived from the induced pluripotent stem cells of a Parkinson’s Predicting outcomes and, crucially, developing disease patient, are on the forefront of efforts to improve models for brain disease. -
Gill-Chronicles.Pdf
“This is a story about how a compelling theme atracts world-class scientists.” JACK GILL D THE LINDA AND JACK GILL CENTER FOR BIOMOLECUlAR SCIIEN:CE COLLEGE OF ARTS+ SCIEttCES ADDICTION NEURODEGENERATION CENTER for ALS NEURODEVELOPMENT BIOMOLECULAR SCIENCE CHRONICLES, ALZHEIMER’S OBESITY DIRECTOR AND GILL CHAIR GILL CHAIR ANXIETY PAIN Hui-Chen Lu Richard DiMarchi The Linda and Jack Gill Center for Biomolecular Science Indiana University Bloomington AUTISM PARKINSON’S Multidisciplinary Science Building II 702 North Walnut Grove Avenue Bloomington, IN 47405 GILL CHAIR GILL CHAIR CONTACT: Andrea Hohmann Ken Mackie IMMUNE FUNCTION PTSD Phone: 812-856-1930 Fax: 812-856-1359 gillcenter.indiana.edu WRITING INFLAMMATION SCHIZOPHRENIA Elisabeth Andrews GRAPHIC DESIGN GILL CHAIR GILL SCHOLAR Kaye Lee Johnston Dan Tracey Cary Lai PHOTOGRAPHY ITCH SOMATOSENSATION Anna Power Teeter Maximillian Tortoriello Ann Schertz Courtesy Photos MEMORY STRESS COVER IMAGE PROGRAM ADMINISTRATIVE Stephanie Mauthner & MANAGER ASSISTANT Katherine Fisher (Tracey Lab) Trisha Turner Jana England METABOLISM TRAUMATIC BRAIN INJURY 1 A MESSAGE FROM THE EXECUTIVE DEAN OF THE IU COLLEGE OF ARTS AND SCIENCES The Gill Center is a compelling example of what is possible when talented scientists are granted agency to work in community. “To raise new As a synergistic team of neuroscientists, they are questions, new able to combine their knowledge, creativity, and skill to venture far beyond the boundaries of what is possibilities, to known, and return with new insights into the nervous system that could only be found through collective regard old problems effort. Their life-enhancing discoveries belong to all of us, and their wonder, persistence, and desire to create from a new angle, a better world reflect the better angels of our nature. -
Signature Redacted Thesis Supervisor Certified By
Single-Cell Transcriptomics of the Mouse Thalamic Reticular Nucleus by Taibo Li S.B., Massachusetts Institute of Technology (2015) Submitted to the Department of Electrical Engineering and Computer Science in partial fulfillment of the requirements for the degree of Master of Engineering in Electrical Engineering and Computer Science at the MASSACHUSETTS INSTITUTE OF TECHNOLOGY June 2017 @ Massachusetts Institute of Technology 2017. All rights reserved. A uthor ... ..................... Department of Electrical Engineering and Computer Science May 25, 2017 Certified by. 3ignature redacted Guoping Feng Poitras Professor of Neuroscience, MIT Signature redacted Thesis Supervisor Certified by... Kasper Lage Assistant Professor, Harvard Medical School Thesis Supervisor Accepted by . Signature redacted Christopher Terman Chairman, Masters of Engineering Thesis Committee MASSACHUSETTS INSTITUTE 0) OF TECHNOLOGY w AUG 14 2017 LIBRARIES 2 Single-Cell Transcriptomics of the Mouse Thalamic Reticular Nucleus by Taibo Li Submitted to the Department of Electrical Engineering and Computer Science on May 25, 2017, in partial fulfillment of the requirements for the degree of Master of Engineering in Electrical Engineering and Computer Science Abstract The thalamic reticular nucleus (TRN) is strategically located at the interface between the cortex and the thalamus, and plays a key role in regulating thalamo-cortical in- teractions. Current understanding of TRN neurobiology has been limited due to the lack of a comprehensive survey of TRN heterogeneity. In this thesis, I developed an integrative computational framework to analyze the single-nucleus RNA sequencing data of mouse TRN in a data-driven manner. By combining transcriptomic, genetic, and functional proteomic data, I discovered novel insights into the molecular mecha- nisms through which TRN regulates sensory gating, and suggested targeted follow-up experiments to validate these findings. -
Supplemental Figures
Supplemental Figures Supplemental figure legends Figure S1 | Testing the pre-clustering heuristic. (A) (Left) Default, unsupervised heuristic sets a cut of 7% of the total dendrogram depth, which results in 52 pre-clusters. (Right) The numerical model calculated using the 52 pre-clusters. Xc1 and Xc2 represent the expression (in a binned UMIs grid) of a given gene X in two cells c1 and c2 belonging to the same pre-cluster. The cumulative distribution plot estimates the frequency, hence likelihood, of an expression change. (B) (Left) Forcing a cut of only 4% creates 1152 pre-clusters, more than 20-fold increase compared to the default 7% depth. Also, given the reduction of the average cluster size and the consequent reduction of possible intra-cluster pair-wise comparison, the number of data points used to fit the model decreases of more than 5-fold compared to default 7% cut (from 3.79E+9 to 6.56E+8). (Right) Despite this, the difference between the numerical model of 4% cut and 7% cut is marginal. (C) (Left) Forcing a cut of 20% creates only 9 pre-clusters, which is less than the number of final clusters (in this case, 11) and therefore represents a miscalculated configuration. Still the difference between the numerical model of 20% cut and 7% cut is marginal (right). (D) Also switching from Pearson to Spearman correlation is associated with neglectable differences in the numerical model. (E) (Top) Number of pre-clusters associated with the different cutting depths, correlations metrics (Pearson, Spearman) or linkage metrics (complete or Weighted average distance, WPGMA, instead of default Ward’s). -
Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in -
The HSP70 Chaperone Machinery: J Proteins As Drivers of Functional Specificity
REVIEWS The HSP70 chaperone machinery: J proteins as drivers of functional specificity Harm H. Kampinga* and Elizabeth A. Craig‡ Abstract | Heat shock 70 kDa proteins (HSP70s) are ubiquitous molecular chaperones that function in a myriad of biological processes, modulating polypeptide folding, degradation and translocation across membranes, and protein–protein interactions. This multitude of roles is not easily reconciled with the universality of the activity of HSP70s in ATP-dependent client protein-binding and release cycles. Much of the functional diversity of the HSP70s is driven by a diverse class of cofactors: J proteins. Often, multiple J proteins function with a single HSP70. Some target HSP70 activity to clients at precise locations in cells and others bind client proteins directly, thereby delivering specific clients to HSP70 and directly determining their fate. In their native cellular environment, polypeptides are participates in such diverse cellular functions. Their constantly at risk of attaining conformations that pre- functional diversity is remarkable considering that vent them from functioning properly and/or cause them within and across species, HSP70s have high sequence to aggregate into large, potentially cytotoxic complexes. identity. They share a single biochemical activity: an Molecular chaperones guide the conformation of proteins ATP-dependent client-binding and release cycle com- throughout their lifetime, preventing their aggregation bined with client protein recognition, which is typi- by protecting interactive surfaces against non-productive cally rather promiscuous. This apparent conundrum interactions. Through such inter actions, molecular chap- is resolved by the fact that HSP70s do not work alone, erones aid in the folding of nascent proteins as they are but rather as ‘HSP70 machines’, collaborating with synthesized by ribosomes, drive protein transport across and being regulated by several cofactors. -
Chromosomal Microarray Analysis in Turkish Patients with Unexplained Developmental Delay and Intellectual Developmental Disorders
177 Arch Neuropsychitry 2020;57:177−191 RESEARCH ARTICLE https://doi.org/10.29399/npa.24890 Chromosomal Microarray Analysis in Turkish Patients with Unexplained Developmental Delay and Intellectual Developmental Disorders Hakan GÜRKAN1 , Emine İkbal ATLI1 , Engin ATLI1 , Leyla BOZATLI2 , Mengühan ARAZ ALTAY2 , Sinem YALÇINTEPE1 , Yasemin ÖZEN1 , Damla EKER1 , Çisem AKURUT1 , Selma DEMİR1 , Işık GÖRKER2 1Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey 2Faculty of Medicine, Department of Child and Adolescent Psychiatry, Trakya University, Edirne, Turkey ABSTRACT Introduction: Aneuploids, copy number variations (CNVs), and single in 39 (39/123=31.7%) patients. Twelve CNV variant of unknown nucleotide variants in specific genes are the main genetic causes of significance (VUS) (9.75%) patients and 7 CNV benign (5.69%) patients developmental delay (DD) and intellectual disability disorder (IDD). were reported. In 6 patients, one or more pathogenic CNVs were These genetic changes can be detected using chromosome analysis, determined. Therefore, the diagnostic efficiency of CMA was found to chromosomal microarray (CMA), and next-generation DNA sequencing be 31.7% (39/123). techniques. Therefore; In this study, we aimed to investigate the Conclusion: Today, genetic analysis is still not part of the routine in the importance of CMA in determining the genomic etiology of unexplained evaluation of IDD patients who present to psychiatry clinics. A genetic DD and IDD in 123 patients. diagnosis from CMA can eliminate genetic question marks and thus Method: For 123 patients, chromosome analysis, DNA fragment analysis alter the clinical management of patients. Approximately one-third and microarray were performed. Conventional G-band karyotype of the positive CMA findings are clinically intervenable. -
Dichotomous Parvalbumin Interneuron Populations in Dorsolateral and Dorsomedial Striatum
Dichotomous parvalbumin interneuron populations in dorsolateral and dorsomedial striatum The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Monteiro, Patricia et al. "Dichotomous parvalbumin interneuron populations in dorsolateral and dorsomedial striatum." Journal of Physiology (August 2018): 3695-3707 © 2018 The Authors and The Physiological Society As Published http://dx.doi.org/10.1113/jp275936 Publisher Wiley Version Author's final manuscript Citable link https://hdl.handle.net/1721.1/126428 Terms of Use Creative Commons Attribution-Noncommercial-Share Alike Detailed Terms http://creativecommons.org/licenses/by-nc-sa/4.0/ DOI: 10.1113/JP275936 Dichotomous parvalbumin interneuron populations in dorsolateral and dorsomedial striatum Patricia Monteiro 1,2,3,4, Boaz Barak1, Yang Zhou1, Rebecca McRae1, Diana Rodrigues4, Ian R. Wickersham1 and Guoping Feng1,2 1McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences; Massachusetts Institute of Technology; Cambridge, MA, 02139; USA 2Stanley Center for Psychiatric Research; Broad Institute of MIT and Harvard; Cambridge, MA, 02139; USA 3PhD Programme in Experimental Biology and Biomedicine (PDBEB), Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra, 3004; Portugal 4Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho and ICVS/3B‟s - PT Government Associate Laboratory, Braga/Guimarães, 4710–057; Portugal Conflict of Interest: the -
Functional Consequences of Mutations in Postsynaptic Scaffolding Proteins and Relevance to Psychiatric Disorders
NE35CH03-Ting ARI 12 May 2012 21:39 Functional Consequences of Mutations in Postsynaptic Scaffolding Proteins and Relevance to Psychiatric Disorders Jonathan T. Ting,1,2,∗ Joao˜ Pec¸a,1,∗ and Guoping Feng1,3 1McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; email: [email protected], [email protected], [email protected] 2Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, 27710 3Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, 02142 Annu. Rev. Neurosci. 2012. 35:49–71 Keywords First published online as a Review in Advance on PSD95, AKAP, SAPAP, Shank, Homer, psychiatric disorders April 20, 2012 The Annual Review of Neuroscience is online at Abstract neuro.annualreviews.org Annu. Rev. Neurosci. 2012.35:49-71. Downloaded from www.annualreviews.org Functional studies on postsynaptic scaffolding proteins at excitatory This article’s doi: synapses have revealed a plethora of important roles for synaptic struc- 10.1146/annurev-neuro-062111-150442 ture and function. In addition, a convergence of recent in vivo func- Access provided by Massachusetts Institute of Technology (MIT) on 06/29/17. For personal use only. Copyright c 2012 by Annual Reviews. tional evidence together with human genetics data strongly suggest that All rights reserved mutations in a variety of these postsynaptic scaffolding proteins may 0147-006X/12/0721-0049$20.00 contribute to the etiology of diverse human psychiatric disorders such ∗These authors contributed equally as schizophrenia, autism spectrum disorders, and obsessive-compulsive spectrum disorders. Here we review the most recent evidence for several key postsynaptic scaffolding protein families and explore how mouse ge- netics and human genetics have intersected to advance our knowledge concerning the contributions of these important players to complex brain function and dysfunction. -
Impaired Complex I Repair Causes Recessive Leber's Hereditary Optic
The Journal of Clinical Investigation RESEARCH ARTICLE Impaired complex I repair causes recessive Leber’s hereditary optic neuropathy Sarah L. Stenton,1,2 Natalia L. Sheremet,3 Claudia B. Catarino,4 Natalia A. Andreeva,3 Zahra Assouline,5 Piero Barboni,6 Ortal Barel,7,8,9 Riccardo Berutti,1,2 Igor Bychkov,10 Leonardo Caporali,11 Mariantonietta Capristo,11 Michele Carbonelli,11 Maria L. Cascavilla,6 Peter Charbel Issa,12,13 Peter Freisinger,14 Sylvie Gerber,15 Daniele Ghezzi,16,17 Elisabeth Graf,1,2 Juliana Heidler,18 Maja Hempel,19 Elise Heon,20 Yulya S. Itkis,10 Elisheva Javasky,7,8,9 Josseline Kaplan,15 Robert Kopajtich,1,2 Cornelia Kornblum,21 Reka Kovacs-Nagy,1,22 Tatiana D. Krylova,10 Wolfram S. Kunz,23 Chiara La Morgia,11,24 Costanza Lamperti,16 Christina Ludwig,25 Pedro F. Malacarne,26 Alessandra Maresca,11 Johannes A. Mayr,27 Jana Meisterknecht,18 Tatiana A. Nevinitsyna,3 Flavia Palombo,11 Ben Pode-Shakked,8,28,29 Maria S. Shmelkova,3 Tim M. Strom,1 Francesca Tagliavini,11 Michal Tzadok,8,30 Amelie T. van der Ven,19 Catherine Vignal-Clermont,31 Matias Wagner,1,2 Ekaterina Y. Zakharova,10 Nino V. Zhorzholadze,3 Jean-Michel Rozet,15 Valerio Carelli,11,24 Polina G. Tsygankova,10 Thomas Klopstock,4,32,33 Ilka Wittig,18,34 and Holger Prokisch1,2 1Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany. 2Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany. 3Federal State Budgetary Institution of Science “Research Institute of Eye Diseases,” Moscow, Russia. 4Department of Neurology, Friedrich-Baur-Institute, University Hospital of the Ludwig-Maximilians-Universität München, Munich, Germany. -
Supplementary Information
Supplementary information: Supplementary figure legends 1-6 Supplementary figures 1-6 1 Supplementary figure legends Figure S1 Differential expression analysis in neuronal progenitors derived from WB (WB2, a) and Dup7 (Dup7.1/2, b,c) syndrome patients compared to a healthy control. (a,b,c) Differential expression analysis of genes within the disease related region using five DE tools and displaying the top 2500 genes. For the genes located in the deleted (a) or amplified (b,c) region the p-values of are shown in Z-score scale (red: down-regulated; blue: up-regulated). Genes correctly assigned as down- or up-regulated are highlighted by grey. (d) Average number of detected down- (red) and up-regulated (blue) genes in the two WB and Dup7 patients, respectively, compared to healthy donor and using the top 2000 (left) or top 1500 (right) genes for each tool. Figure S2 Benchmarking bigSCale using simulated datasets. (a) Characteristics of the simulated datasets sim_10x (red) and sim_NPC (green) in terms of library sizes (left), distribution of zeros per gene (middle) and distribution of zero per cell (right). (b-e) Partial AUCs of ROC curves computed across tools in the simulated datasets sim_10x (b,c) and sim_NPC (d,e). The bigSCale method shows highest sensitivity at high specificity (>90%, grey area) at both group size conditions (1:2, b,d and 1:10, c,e). Figure S3 BigSCale analysis of 3,005 mouse cortical and hippocampal cells [11]. (a) Comparison of bigSCale and BackSPIN in the detection of markers for oligodendrocytes in the turquois cluster (high expression, yellow; low expression, blue).