Neurogenomics Coursework (PDF)
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The Drosophila Blood-Brain Barrier: Development and Function of a Glial Endothelium
REVIEW ARTICLE published: 14 November 2014 doi: 10.3389/fnins.2014.00365 The Drosophila blood-brain barrier: development and function of a glial endothelium Stefanie Limmer , Astrid Weiler , Anne Volkenhoff , Felix Babatz and Christian Klämbt* Institut für Neuro- und Verhaltensbiologie, Universität Münster, Münster, Germany Edited by: The efficacy of neuronal function requires a well-balanced extracellular ion homeostasis Norman Ruthven Saunders, and a steady supply with nutrients and metabolites. Therefore, all organisms equipped University of Melbourne, Australia with a complex nervous system developed a so-called blood-brain barrier, protecting it Reviewed by: from an uncontrolled entry of solutes, metabolites or pathogens. In higher vertebrates, Alfredo Ghezzi, The University of Texas at Austin, USA this diffusion barrier is established by polarized endothelial cells that form extensive Brigitte Dauwalder, University of tight junctions, whereas in lower vertebrates and invertebrates the blood-brain barrier is Houston, USA exclusively formed by glial cells. Here, we review the development and function of the glial Marko Brankatschk, Max Planck blood-brain barrier of Drosophila melanogaster. In the Drosophila nervous system, at least Institute of Molecular Cell Biology and Genetics, Germany seven morphologically distinct glial cell classes can be distinguished. Two of these glial *Correspondence: classes form the blood-brain barrier. Perineurial glial cells participate in nutrient uptake and Christian Klämbt, Institut für Neuro- establish a first diffusion barrier. The subperineurial glial (SPG) cells form septate junctions, und Verhaltensbiologie, Universität which block paracellular diffusion and thus seal the nervous system from the hemolymph. Münster, Badestr. 9, We summarize the molecular basis of septate junction formation and address the different 48140 Münster, Germany e-mail: [email protected] transport systems expressed by the blood-brain barrier forming glial cells. -
Mixed Ancestry Analysis of Whole-Genome Sequencing Reveals
medRxiv preprint doi: https://doi.org/10.1101/2021.08.09.21261801; this version posted August 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Mixed ancestry analysis of whole-genome sequencing reveals common, rare, and structural variants associated with posterior urethral valves Melanie MY Chan,1 Omid Sadeghi-Alavijeh,1 Horia C Stanescu,1 Catalin D Voinescu,1 Glenda M Beaman,2,3 Marcin Zaniew,4 Stefanie Weber,5 Alina C Hilger,6,7 William G Newman,2,3 Adrian S Woolf,8,9 John O Connolly,1,10 Dan Wood,10 Alexander Stuckey,11 Athanasios Kousathanas,11 Genomics England Research Consortium,11 Robert Kleta,1,12 Detlef Bockenhauer,1,12 Adam P Levine,1,13 and Daniel P Gale1* 1Department of Renal Medicine, University College London, London, NW3 2PF, UK. 2Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK. 3Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, M13 9PL, UK. 4Department of Pediatrics, University of Zielona Góra, 56-417 Zielona Góra, Poland. 5Department of Pediatric Nephrology, University of Marburg, 35037 Marburg, Germany. 6Children’s Hospital, University of Bonn, 53113 Bonn, Germany. 7Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany. 1 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. -
Understanding Neurodevelopmental Disorders: the Promise of Regulatory Variation in the 30Utrome
Biological Psychiatry Review Understanding Neurodevelopmental Disorders: The Promise of Regulatory Variation in the 30UTRome Kai A. Wanke, Paolo Devanna, and Sonja C. Vernes ABSTRACT Neurodevelopmental disorders have a strong genetic component, but despite widespread efforts, the specific genetic factors underlying these disorders remain undefined for a large proportion of affected individuals. Given the accessibility of exome sequencing, this problem has thus far been addressed from a protein-centric standpoint; however, protein-coding regions only make up w1% to 2% of the human genome. With the advent of whole genome sequencing we are in the midst of a paradigm shift as it is now possible to interrogate the entire sequence of the human genome (coding and noncoding) to fill in the missing heritability of complex disorders. These new technologies bring new challenges, as the number of noncoding variants identified per individual can be overwhelming, making it prudent to focus on noncoding regions of known function, for which the effects of variation can be predicted and directly tested to assess pathogenicity. The 30UTRome is a region of the noncoding genome that perfectly fulfills these criteria and is of high interest when searching for pathogenic variation related to complex neurodevelopmental disorders. Herein, we review the regulatory roles of the 30UTRome as binding sites for microRNAs or RNA binding proteins, or during alternative polyadenylation. We detail existing evidence that these regions contribute to neuro- developmental disorders and outline strategies for identification and validation of novel putatively pathogenic vari- ation in these regions. This evidence suggests that studying the 30UTRome will lead to the identification of new risk factors, new candidate disease genes, and a better understanding of the molecular mechanisms contributing to neurodevelopmental disorders. -
Structural Variation in the 3D Genome
REVIEWS TRANSLATIONAL GENETICS Structural variation in the 3D genome Malte Spielmann 1, Darío G. Lupiáñez2 and Stefan Mundlos 3,4* Abstract | Structural and quantitative chromosomal rearrangements, collectively referred to as structural variation (SV), contribute to a large extent to the genetic diversity of the human genome and thus are of high relevance for cancer genetics, rare diseases and evolutionary genetics. Recent studies have shown that SVs can not only affect gene dosage but also modulate basic mechanisms of gene regulation. SVs can alter the copy number of regulatory elements or modify the 3D genome by disrupting higher- order chromatin organization such as topologically associating domains. As a result of these position effects, SVs can influence the expression of genes distant from the SV breakpoints, thereby causing disease. The impact of SVs on the 3D genome and on gene expression regulation has to be considered when interpreting the pathogenic potential of these variant types. Structural variation The application of molecular karyotyping and, more the position and/or function of cis- regulatory elements, (SV). Genetic variation that recently, next- generation sequencing (NGS) has such as promoters and enhancers. Owing to advances in includes all structural and revealed the enormous structural complexity of the 3D genome mapping technologies, it is now becoming quantitative chromosomal human genome1–3. Structural and quantitative chromo- increasingly evident that position effects are the result of rearrangements, that is, deletions and duplications, as somal rearrangements, collectively referred to as much more complex alterations than just changes in the well as copy- number-neutral structural variation (SV), include deletions, duplications, linear genome. -
Comparison of Structural and Short Variants Detectedby Linked-Read
cancers Article Comparison of Structural and Short Variants Detected by Linked-Read and Whole-Exome Sequencing in Multiple Myeloma Ashwini Kumar 1,2 , Sadiksha Adhikari 1,2, Matti Kankainen 2,3,4,5 and Caroline A. Heckman 1,2,* 1 Institute for Molecular Medicine Finland-FIMM, HiLIFE-Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Tukholmankatu 8, 00290 Helsinki, Finland; ashwini.kumar@helsinki.fi (A.K.); sadiksha.adhikari@helsinki.fi (S.A.) 2 iCAN Digital Precision Cancer Medicine, University of Helsinki, 00014 Helsinki, Finland; matti.kankainen@helsinki.fi 3 Medical and Clinical Genetics, University of Helsinki, Helsinki University Hospital, 00029 Helsinki, Finland 4 Translational Immunology Research Program and Department of Clinical Chemistry, University of Helsinki, 00290 Helsinki, Finland 5 Hematology Research Unit Helsinki, Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland * Correspondence: caroline.heckman@helsinki.fi; Tel.: +358-29-412-5769 Simple Summary: The wide variety of next-generation sequencing technologies requires thorough evaluation and understanding of their advantages and shortcomings of these different approaches prior to their implementation in a precision medicine setting. Here, we compared the performance of two DNA sequencing methods, whole-exome and linked-read exome sequencing, to detect large Citation: Kumar, A.; Adhikari, S.; structural variants (SVs) and short variants in eight multiple myeloma (MM) patient cases. For three Kankainen, M.; Heckman, C.A. patient cases, matched tumor-normal samples were sequenced with both methods to compare somatic Comparison of Structural and Short SVs and short variants. The methods’ clinical relevance was also evaluated, and their sensitivity Variants Detected by Linked-Read and specificity to detect MM-specific cytogenetic alterations and other short variants were measured. -
How Important Are Structural Variants for Speciation?
G C A T T A C G G C A T genes Review How Important Are Structural Variants for Speciation? Linyi Zhang 1,*, Radka Reifová 2, Zuzana Halenková 2 and Zachariah Gompert 1 1 Department of Biology, Utah State University, Logan, UT 84322, USA; [email protected] 2 Department of Zoology, Faculty of Science, Charles University, 12800 Prague, Czech Republic; [email protected] (R.R.); [email protected] (Z.H.) * Correspondence: [email protected] Abstract: Understanding the genetic basis of reproductive isolation is a central issue in the study of speciation. Structural variants (SVs); that is, structural changes in DNA, including inversions, translocations, insertions, deletions, and duplications, are common in a broad range of organisms and have been hypothesized to play a central role in speciation. Recent advances in molecular and statistical methods have identified structural variants, especially inversions, underlying ecologically important traits; thus, suggesting these mutations contribute to adaptation. However, the contribu- tion of structural variants to reproductive isolation between species—and the underlying mechanism by which structural variants most often contribute to speciation—remain unclear. Here, we review (i) different mechanisms by which structural variants can generate or maintain reproductive isolation; (ii) patterns expected with these different mechanisms; and (iii) relevant empirical examples of each. We also summarize the available sequencing and bioinformatic methods to detect structural variants. Lastly, we suggest empirical approaches and new research directions to help obtain a more complete assessment of the role of structural variants in speciation. Citation: Zhang, L.; Reifová, R.; Keywords: reproductive isolation; hybridization; suppressed recombination Halenková, Z.; Gompert, Z. -
A Bridge Between Genes and Brain Activities Juko Ando
【Grant-in-Aid for Scientific Research(S)】 Humanities and Social Sciences (Social sciences) Title of Project:A Twin Study on Sociability and Mental Health: A Bridge between Genes and Brain Activities Juko Ando (Keio University, Faculty of Letters, Professor ) Research Area:behavioral genetics, psychology, brain science, genomics Keyword:twin, genetics, environment, 【Purpose and Background of the Research】 at home and in campus (3) brain structure/function studies by NIRS and At the coming of the dawn of a behavioral MRI neurogenomics era, it has been becoming (4) molecular genetic studies by whole genome rapidly possible to clarify the mechanism in wide SNP scan which how genes and behavior are connected. 【Expected Research Achievements and This can be realized with the integration work Scientific Significance】 of traditional behavioral genetics, recent Genetic and environmental influences on advances of brain sciences, and molecular adaptive social behavior, mental health, and genetics. learning abilities will be clarified. We focus The purpose of this study is to clarify how specifically on “gene-environment interaction” in which genetic effects are manifested sociability, mental health, and related differently in different environmental psychological traits are being developed situations, and “gene- environment correlation” through interactive processes of genes and in which genes are selected by and/or select environment via neurological structures and specific environmental situations. Brain structure and functioning as well as responsible -
Rgma) Induces Neuropathological and Behavioral Changes That Closely Resemble Parkinson's Disease
This Accepted Manuscript has not been copyedited and formatted. The final version may differ from this version. Research Articles: Neurobiology of Disease Repulsive guidance molecule a (RGMa) induces neuropathological and behavioral changes that closely resemble Parkinson's disease J.a. Korecka1, E. B. Moloney1, R. Eggers1, B. Hobo1, S. Scheffer1, N. Ras-Verloop1, R.j. Pasterkamp2, D.f. Swaab3, A.b. Smit4, R.e. Van Kesteren4, K. Bossers1 and J. Verhaagen1,4 1Department of Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, An Institute of the Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands 2Department of Translational Neuroscience, Brain Center Rudolf Magnus, Utrecht University, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands 3Department of Neuropsychiatric Disorders, Netherlands Institute for Neuroscience, An Institute of the Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands 4Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1085-1087, 1081 HV, The Netherlands DOI: 10.1523/JNEUROSCI.0084-17.2017 Received: 8 January 2017 Revised: 12 July 2017 Accepted: 11 August 2017 Published: 21 August 2017 Author contributions: JK- experimental design, experimental execution, acquiring data, analyzing data, writing the manuscript; EM- experimental execution, acquiring data, analyzing data, writing the manuscript; RE- experimental execution, experimental design; BH-experimental execution; SS- experimental execution, acquiring data, analyzing data; NRV- experimental execution, acquiring data, analyzing data; RP- experimental design, providing reagents; DS- experimental design,; AS- experimental design, ; RK- experimental design,; KB- experimental design, experimental execution, help with analyzing the data, writing the manuscript; JV- experimental design, writing the manuscript Conflict of Interest: The authors declare no competing financial interests. -
Depression-Associated Gene Negr1-Fgfr2 Pathway Is Altered by Antidepressant Treatment
cells Article Depression-Associated Gene Negr1-Fgfr2 Pathway Is Altered by Antidepressant Treatment Lucia Carboni 1,* , Francesca Pischedda 2, Giovanni Piccoli 2, Mario Lauria 3,4 , Laura Musazzi 5 , Maurizio Popoli 6, Aleksander A. Mathé 7 and Enrico Domenici 2,4 1 Department of Pharmacy and Biotechnology, Alma Mater Studiorum Università di Bologna, 40126 Bologna, Italy 2 Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; [email protected] (F.P.); [email protected] (G.P.); [email protected] (E.D.) 3 Department of Mathematics, University of Trento, 38123 Trento, Italy; [email protected] 4 Fondazione The Microsoft Research—University of Trento Centre for Computational and Systems Biology (COSBI), 38068 Rovereto (Trento), Italy 5 School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; [email protected] 6 Laboratory of Neuropsychopharmacology and Functional Neurogenomics, Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, 20133 Milano, Italy; [email protected] 7 Karolinska Institutet, Department of Clinical Neuroscience, SE-11221 Stockholm, Sweden; [email protected] * Correspondence: [email protected]; Tel.: +39-051-209-1793 Received: 30 June 2020; Accepted: 28 July 2020; Published: 31 July 2020 Abstract: The Negr1 gene has been significantly associated with major depression in genetic studies. Negr1 encodes for a cell adhesion molecule cleaved by the protease Adam10, thus activating Fgfr2 and promoting neuronal spine plasticity. We investigated whether antidepressants modulate the expression of genes belonging to Negr1-Fgfr2 pathway in Flinders sensitive line (FSL) rats, in a corticosterone-treated mouse model of depression, and in mouse primary neurons. -
Structural Variation: the Genome’S Hidden Architecture Monya Baker
TECHNOLOGY FEATURE Uncovering variants 134 Calling for more algorithms 135 Box 1: Getting a bigger picture 136 Structural variation: the genome’s hidden architecture Monya Baker Next-generation sequencing is uncovering more variants than ever before, but it also faces limitations. The Austrian monk Gregor Mendel may tend to take dip- number of nucleotides, structural varia- have founded the science of genetics, but his loidy as the default. tion accounts for more differences between ideas now limit genomic studies, according to Even microarrays human genomes than the more extensively Jim Lupski, a molecular geneticist at Baylor designed to assess studied single-nucleotide differences. A 2010 College of Medicine in Texas. “Mendelian copy number gen- study estimated that such “non-SNP varia- thinking is to genetics as Newtonian think- erally assume that tion” totaled about 50 megabases per human ing is to physics. We saw a whole new world most individuals genome4. when Einstein came along.” carry exactly two Conditions including autism, schizophre- According to Mendelian principles, indi- copies of any partic- nia and Crohn’s disease have all been associ- viduals inherit exactly two copies of each ular region, which ated with structural variation. And uncov- gene—one from each parent. Genes on sex Next-generation can throw off some ering structural variation will be essential chromosomes have long been recognized as sequencing is revealing calculations. for understanding heterogeneity within exceptions, but genetic deletions and duplica- new variation, but With the excep- tumors, says Jan Korbel, who studies struc- tions also break the rules, and in ways that are it won’t be able to tions of very large tural variation at the European Molecular find everything, much harder to track. -
LSD1 Modulates Stress-Evoked Transcription of Immediate Early Genes and Emotional Behavior
LSD1 modulates stress-evoked transcription of immediate early genes and emotional behavior Francesco Rusconia,1, Barbara Grilloa,2, Luisa Ponzonib,2, Silvia Bassanic, Emanuela Toffoloa, Leda Paganinia, Alessandra Malleid, Daniela Braidab, Maria Passafaroc, Maurizio Popolid, Mariaelvina Salab,c, and Elena Battagliolia,c,1 aLaboratory of Neuroepigenetics, Dipartimento di Biotecnologie Mediche e Medicina Traslazionale and Centro di Eccellenza per le Malattie Neurodegenerative (CEND), Università degli Studi di Milano, 20133 Milan, Italy; bDipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20129 Milan, Italy; cNational Research Council Institute of Neuroscience, 20129 Milan, Italy; and dLaboratory of Neuropsychopharmacology and Functional Neurogenomics, Dipartimento di Scienze Farmacologiche e Biomolecolari and CEND, Università degli Studi di Milano, 20133 Milan, Italy Edited by Huda Akil, University of Michigan, Ann Arbor, MI, and approved February 19, 2016 (received for review June 18, 2015) Behavioral changes in response to stressful stimuli can be con- of target genes (12–14) suggests that modulation of exon E8a trolled via adaptive epigenetic changes in neuronal gene expres- splicing may represent a mechanism for fine-tuning the transcrip- sion. Here we indicate a role for the transcriptional corepressor tion of selected targets. The generation of a mouse model lacking Lysine-Specific Demethylase 1 (LSD1) and its dominant-negative microexon E8a (neuroLSD1KO mice) allowed us to characterize -
The Neuropharmacogenomical Perspectives of Bipolar Disorders
TINJAUAN PUSTAKA The Neuropharmacogenomical Perspectives of Bipolar Disorders Dito Anurogo 1S2 Biomedical Sciences, Faculty of Medicine, Universitas Gadjah Mada (FK UGM), Yogyakarta, Indonesia 2Indonesian Literacy Fellowship (ILF), UKM Jurnal Paradigma, FAM, IYHPS, HIMMPAS, ILC, HMP 3Health consultant in detik.com ABSTRACT Bipolar disorder (BD), also known as manic-depressive illness, is a brain disorder causing unusual shifts in mood, energy, activity levels, and the ability to carry out daily tasks, caused by multifactorial and enigmatic etiologies. The main objective of this overview is to review recent findings and critically evaluate BD based on neurogenomics and pharmacogenomics perspectives, through searching appropriate online database sources and relevant bibliographies. Recent studies and references explain genome-wide significant loci for bipolar disorder (polygenetics), potential biomarkers (apoptosis and neurotrophic factors, immuno-inflammatory factors, neurotrophins, BDNF, IGF-1, VEGF, etc.), dysregulation of immuno-inflammatory mechanisms, the role of neuroplasticity in the pathophysiology and treatment of BD, genetic effect of lithium response in BD. Stem cells, omics technologies, and optogenetics is considered to be effective strategies to overcome BD. Keywords: Biomarkers, bipolar disorder (BD), neurogenomics, neuropharmacogenomics, neuroplasticity, optogenetics, pharmacogenomics. ABSTRAK Bipolar disorder (BD), dikenal pula sebagai manic-depressive illness, adalah gangguan otak dengan etiologi enigmatik dan multifaktorial