Biological Pathways, Candidate Genes, and Molecular Markers Associated with Quality-Of-Life Domains: an Update
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Phosphorylation of Synaptojanin Differentially Regulates Endocytosis of Functionally Distinct Synaptic Vesicle Pools
8882 • The Journal of Neuroscience, August 24, 2016 • 36(34):8882–8894 Cellular/Molecular Phosphorylation of Synaptojanin Differentially Regulates Endocytosis of Functionally Distinct Synaptic Vesicle Pools X Junhua Geng,1* Liping Wang,1,2* Joo Yeun Lee,1,4 XChun-Kan Chen,1 and Karen T. Chang1,3,4 1Zilkha Neurogenetic Institute, 2Department of Biochemistry and Molecular Biology, and 3Department of Cell and Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, and 4Neuroscience Graduate Program, University of Southern California, Los Angeles, California 90089 The rapid replenishment of synaptic vesicles through endocytosis is crucial for sustaining synaptic transmission during intense neuronal activity. Synaptojanin (Synj), a phosphoinositide phosphatase, is known to play an important role in vesicle recycling by promoting the uncoating of clathrin following synaptic vesicle uptake. Synj has been shown to be a substrate of the minibrain (Mnb) kinase, a fly homolog of the dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A); however, the functional impacts of Synj phosphorylation by Mnb are not well understood. Here we identify that Mnb phosphorylates Synj at S1029 in Drosophila. We find that phosphorylation of Synj at S1029 enhances Synj phosphatase activity, alters interaction between Synj and endophilin, and promotes efficient endocytosis of the active cycling vesicle pool (also referred to as exo-endo cycling pool) at the expense of reserve pool vesicle endocytosis. Dephosphorylated Synj, on the other hand, is deficient in the endocytosis of the active recycling pool vesicles but maintains reserve pool vesicle endocytosis to restore total vesicle pool size and sustain synaptic transmission. Together, our findings reveal a novel role for Synj in modulating reserve pool vesicle endocytosis and further indicate that dynamic phosphorylation and dephosphorylation of Synj differentially maintain endocytosis of distinct functional synaptic vesicle pools. -
Nuclear and Mitochondrial Genome Defects in Autisms
UC Irvine UC Irvine Previously Published Works Title Nuclear and mitochondrial genome defects in autisms. Permalink https://escholarship.org/uc/item/8vq3278q Journal Annals of the New York Academy of Sciences, 1151(1) ISSN 0077-8923 Authors Smith, Moyra Spence, M Anne Flodman, Pamela Publication Date 2009 DOI 10.1111/j.1749-6632.2008.03571.x License https://creativecommons.org/licenses/by/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California THE YEAR IN HUMAN AND MEDICAL GENETICS 2009 Nuclear and Mitochondrial Genome Defects in Autisms Moyra Smith, M. Anne Spence, and Pamela Flodman Department of Pediatrics, University of California, Irvine, California In this review we will evaluate evidence that altered gene dosage and structure im- pacts neurodevelopment and neural connectivity through deleterious effects on synap- tic structure and function, and evidence that the latter are key contributors to the risk for autism. We will review information on alterations of structure of mitochondrial DNA and abnormal mitochondrial function in autism and indications that interactions of the nuclear and mitochondrial genomes may play a role in autism pathogenesis. In a final section we will present data derived using Affymetrixtm SNP 6.0 microar- ray analysis of DNA of a number of subjects and parents recruited to our autism spectrum disorders project. We include data on two sets of monozygotic twins. Col- lectively these data provide additional evidence of nuclear and mitochondrial genome imbalance in autism and evidence of specific candidate genes in autism. We present data on dosage changes in genes that map on the X chromosomes and the Y chro- mosome. -
SYNJ2 Antibody (Monoclonal) (M02) Mouse Monoclonal Antibody Raised Against a Partial Recombinant SYNJ2
10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 SYNJ2 Antibody (monoclonal) (M02) Mouse monoclonal antibody raised against a partial recombinant SYNJ2. Catalog # AT4124a Specification SYNJ2 Antibody (monoclonal) (M02) - Product Information Application WB Primary Accession O15056 Other Accession NM_003898 Reactivity Human Host mouse Clonality Monoclonal Isotype IgG2a Kappa Calculated MW 165538 SYNJ2 Antibody (monoclonal) (M02) - Additional Information Antibody Reactive Against Recombinant Protein.Western Blot detection against Gene ID 8871 Immunogen (36.74 KDa) . Other Names Synaptojanin-2, Synaptic inositol 1, 5-trisphosphate 5-phosphatase 2, SYNJ2, KIAA0348 Target/Specificity SYNJ2 (NP_003889, 1396 a.a. ~ 1495 a.a) partial recombinant protein with GST tag. MW of the GST tag alone is 26 KDa. Dilution WB~~1:500~1000 Format Clear, colorless solution in phosphate buffered saline, pH 7.2 . Western Blot analysis of SYNJ2 expression in transfected 293T cell line by SYNJ2 Storage monoclonal antibody (M02), clone 2H8. Store at -20°C or lower. Aliquot to avoid repeated freezing and thawing. Lane 1: SYNJ2 transfected lysate(92.2 KDa). Lane 2: Non-transfected lysate. Precautions SYNJ2 Antibody (monoclonal) (M02) is for research use only and not for use in diagnostic or therapeutic procedures. SYNJ2 Antibody (monoclonal) (M02) - Protocols Page 1/3 10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 Provided below are standard protocols that you may find useful for product applications. • Western Blot • Blocking Peptides • Dot Blot • Immunohistochemistry • Immunofluorescence • Immunoprecipitation • Flow Cytomety • Cell Culture Western blot analysis of SYNJ2 over-expressed 293 cell line, cotransfected with SYNJ2 Validated Chimera RNAi ( (Cat # AT4124a ) SYNJ2 Antibody (monoclonal) (M02) - Background The gene is a member of the inositol-polyphosphate 5-phosphatase family. -
A Gene-Level Methylome-Wide Association Analysis Identifies Novel
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.13.201376; this version posted July 14, 2020. 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 A gene-level methylome-wide association analysis identifies novel 2 Alzheimer’s disease genes 1 1 2 3 4 3 Chong Wu , Jonathan Bradley , Yanming Li , Lang Wu , and Hong-Wen Deng 1 4 Department of Statistics, Florida State University; 2 5 Department of Biostatistics & Data Science, University of Kansas Medical Center; 3 6 Population Sciences in the Pacific Program, University of Hawaii Cancer center; 4 7 Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, 8 Tulane University School of Medicine 9 Corresponding to: Chong Wu, Assistant Professor, Department of Statistics, Florida State 10 University, email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.13.201376; this version posted July 14, 2020. 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. 11 Abstract 12 Motivation: Transcriptome-wide association studies (TWAS) have successfully facilitated the dis- 13 covery of novel genetic risk loci for many complex traits, including late-onset Alzheimer’s disease 14 (AD). However, most existing TWAS methods rely only on gene expression and ignore epige- 15 netic modification (i.e., DNA methylation) and functional regulatory information (i.e., enhancer- 16 promoter interactions), both of which contribute significantly to the genetic basis ofAD. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Leukaemia Section
Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL INIST-CNRS Leukaemia Section Short Communication t(7;14)(q35;q32.1) TRB/TCL1A inv(14)(q11q32.1) TRA-TRD/TCL1A t(14;14)(q11;q32.1) TRA-TRD/TCL1A Tatiana Gindina Raisa Gorbacheva Memorial Institute of Children's Oncology, Hematology and Transplantation at First Pavlov St. Petersburg State Medical University, Saint-Petersburg, Russia Published in Atlas Database: June 2018 Online updated version : http://AtlasGeneticsOncology.org/Anomalies/inv14ID2049.html Printable original version : http://documents.irevues.inist.fr/bitstream/handle/2042/70184/06-2018-inv14ID2049.pdf DOI: 10.4267/2042/70184 This article is an update of : Boyer J. t(7;14)(q35;q32.1) TRB@/TCL1A. Atlas Genet Cytogenet Oncol Haematol 2001;5(3) This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2019 Atlas of Genetics and Cytogenetics in Oncology and Haematology TRD; B lymphoblastic leukaemia/lymphoma; T Abstract lymphoblastic leukaemia/lymphoma; Adult T-cell Review on t(7;14)(q35;q32), inv(14)(q11q32) and leukemia/lymphoma; T-cell prolymphocytic t(14;14)(q11;q32), with data on clinics, and the leukemia; Angioimmunoblastic T-cell lymphoma; genes involved. Chronic lymphocytic leukemia; syndrome; Mycosis Keywords fungoides; Hepatosplenic T-cell lymphoma; Acute Chromosome 7; Chromosome 14; TCL1A; TRA; myeloid leukaemia; Ataxia telangiectasia. Left: inv(14)(q11q32)and i(8q), G- banding - Courtesy Jean Luc Lai; right: inv(14)(q11q32) and t(14)(14) with i(7q), G- banding - Courtesy Tatiana Gindina. Atlas Genet Cytogenet Oncol Haematol. 2019; 23(4) 90 t(7;14)(q35;q32.1) TRB/TCL1A Gindina T inv(14)(q11q32.1) TRA-TRD/TCL1A t(14;14)(q11;q32.1) TRA-TRD/TCL1A Cytogenetics Clinics and pathology Chromosomal abnormalities are detected in most T- Disease PLL after culture with mitogens like PHA. -
Urocortin 3 Overexpression Reduces ER Stress and Heat Shock Response in 3T3‑L1 Adipocytes Sina Kavalakatt1, Abdelkrim Khadir1, Dhanya Madhu1, Heikki A
www.nature.com/scientificreports OPEN Urocortin 3 overexpression reduces ER stress and heat shock response in 3T3‑L1 adipocytes Sina Kavalakatt1, Abdelkrim Khadir1, Dhanya Madhu1, Heikki A. Koistinen2,3,4, Fahd Al‑Mulla5, Jaakko Tuomilehto4,6, Jehad Abubaker1 & Ali Tiss 1* The neuropeptide urocortin 3 (UCN3) has a benefcial efect on metabolic disorders, such as obesity, diabetes, and cardiovascular disease. It has been reported that UCN3 regulates insulin secretion and is dysregulated with increasing severity of obesity and diabetes. However, its function in the adipose tissue is unclear. We investigated the overexpression of UCN3 in 3T3‑L1 preadipocytes and diferentiated adipocytes and its efects on heat shock response, ER stress, infammatory markers, and glucose uptake in the presence of stress‑inducing concentrations of palmitic acid (PA). UCN3 overexpression signifcantly downregulated heat shock proteins (HSP60, HSP72 and HSP90) and ER stress response markers (GRP78, PERK, ATF6, and IRE1α) and attenuated infammation (TNFα) and apoptosis (CHOP). Moreover, enhanced glucose uptake was observed in both preadipocytes and mature adipocytes, which is associated with upregulated phosphorylation of AKT and ERK but reduced p‑JNK. Moderate efects of UCN3 overexpression were also observed in the presence of 400 μM of PA, and macrophage conditioned medium dramatically decreased the UCN3 mRNA levels in diferentiated 3T3‑L1 cells. In conclusion, the benefcial efects of UCN3 in adipocytes are refected, at least partially, by the improvement in cellular -
Endocrine Cell Type Sorting and Mature Architecture in the Islets Of
www.nature.com/scientificreports OPEN Endocrine cell type sorting and mature architecture in the islets of Langerhans require expression of Received: 16 April 2018 Accepted: 4 July 2018 Roundabout receptors in β cells Published: xx xx xxxx Melissa T. Adams, Jennifer M. Gilbert, Jesus Hinojosa Paiz, Faith M. Bowman & Barak Blum Pancreatic islets of Langerhans display characteristic spatial architecture of their endocrine cell types. This architecture is critical for cell-cell communication and coordinated hormone secretion. Islet architecture is disrupted in type-2 diabetes. Moreover, the generation of architecturally correct islets in vitro remains a challenge in regenerative approaches to type-1 diabetes. Although the characteristic islet architecture is well documented, the mechanisms controlling its formation remain obscure. Here, we report that correct endocrine cell type sorting and the formation of mature islet architecture require the expression of Roundabout (Robo) receptors in β cells. Mice with whole-body deletion of Robo1 and conditional deletion of Robo2 either in all endocrine cells or selectively in β cells show complete loss of endocrine cell type sorting, highlighting the importance of β cells as the primary organizer of islet architecture. Conditional deletion of Robo in mature β cells subsequent to islet formation results in a similar phenotype. Finally, we provide evidence to suggest that the loss of islet architecture in Robo KO mice is not due to β cell transdiferentiation, cell death or loss of β cell diferentiation or maturation. Te islets of Langerhans display typical, species-specifc architecture, with distinct spatial organization of their various endocrine cell types1–5. In the mouse, the core of the islet is composed mostly of insulin-secreting β cells, while glucagon-secreting α cells, somatostatin-secreting δ cells and pancreatic polypeptide-secreting PP cells are located at the islet periphery3. -
Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
Genome-Wide Association Study in Collaborative Cross Mice Revealed a Skeletal
bioRxiv preprint doi: https://doi.org/10.1101/094698; this version posted December 16, 2016. 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 4.0 International license. Title Genome-wide association study in Collaborative Cross mice revealed a skeletal role for Rhbdf2 Authors Roei Levy1,2, Clemence Levet3, Keren Cohen1, Matthew Freeman3, Richard Mott4, Fuad Iraqi5, Yankel Gabet1 Affiliations 1 Department of Anatomy and Anthropology, 2 Department of Human Molecular Genetics and Biochemistry, and 5 Department of Clinical Microbiology and Immunology, Sackler Medical School, Tel Aviv University. 3 Dunn School of Pathology, South Parks Road, Oxford OX1 3RE. 4 UCL Genetics Institute, University College London, Gower St., London, WC1E 6BT, UK. Abstract A growing concern that overshadows the increased life expectancy developed countries have been witnessing during the last decades is an accompanying bone loss, which often manifests as osteoporosis. Despite ongoing efforts in utilizing genomic data to fully map the genes responsible for bone remodeling, a detailed picture remains to be desired. Here we took advantage of the phenotypic and genetic diversity innate in Collaborative Cross (CC) mice to identify genetic variants associated with microstructural bone characteristics. 1 bioRxiv preprint doi: https://doi.org/10.1101/094698; this version posted December 16, 2016. 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. -
Supplemental Information
Supplemental information Dissection of the genomic structure of the miR-183/96/182 gene. Previously, we showed that the miR-183/96/182 cluster is an intergenic miRNA cluster, located in a ~60-kb interval between the genes encoding nuclear respiratory factor-1 (Nrf1) and ubiquitin-conjugating enzyme E2H (Ube2h) on mouse chr6qA3.3 (1). To start to uncover the genomic structure of the miR- 183/96/182 gene, we first studied genomic features around miR-183/96/182 in the UCSC genome browser (http://genome.UCSC.edu/), and identified two CpG islands 3.4-6.5 kb 5’ of pre-miR-183, the most 5’ miRNA of the cluster (Fig. 1A; Fig. S1 and Seq. S1). A cDNA clone, AK044220, located at 3.2-4.6 kb 5’ to pre-miR-183, encompasses the second CpG island (Fig. 1A; Fig. S1). We hypothesized that this cDNA clone was derived from 5’ exon(s) of the primary transcript of the miR-183/96/182 gene, as CpG islands are often associated with promoters (2). Supporting this hypothesis, multiple expressed sequences detected by gene-trap clones, including clone D016D06 (3, 4), were co-localized with the cDNA clone AK044220 (Fig. 1A; Fig. S1). Clone D016D06, deposited by the German GeneTrap Consortium (GGTC) (http://tikus.gsf.de) (3, 4), was derived from insertion of a retroviral construct, rFlpROSAβgeo in 129S2 ES cells (Fig. 1A and C). The rFlpROSAβgeo construct carries a promoterless reporter gene, the β−geo cassette - an in-frame fusion of the β-galactosidase and neomycin resistance (Neor) gene (5), with a splicing acceptor (SA) immediately upstream, and a polyA signal downstream of the β−geo cassette (Fig. -
Piccolo, a Presynaptic Zinc Finger Protein Structurally Related to Bassoon
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Neuron, Vol. 25, 203±214, January, 2000, Copyright 2000 by Cell Press Piccolo, a Presynaptic Zinc Finger Protein Structurally Related to Bassoon Steven D. Fenster,*# Wook Joon Chung,*# presynaptic cytoskeletal matrix (PCM) (Landis et al., Rong Zhai,*# Claudia Cases-Langhoff,*# Britta Voss,² 1988; Hirokawa et al., 1989; Gotow et al., 1991) that is Abigail M. Garner,² Udo Kaempf,§ Stefan Kindler,³ thought to play a role in maintaining the neurotransmitter § Eckart D. Gundelfinger, and Craig C. Garner*k release site in register with the postsynaptic reception *Department of Neurobiology apparatus, regulating the mobilization of SVs and the University of Alabama at Birmingham refilling of release sites. Mechanistically, the PCM may Birmingham, Alabama 35294 define sites where SVs fuse and recycle through the ² Center for Molecular Neurobiology clustering of the exo- and endocytotic machinery. ³ Institute for Cellular Biochemistry SV cycling is a multistep process that involves vesicle and Clinical Neurobiology mobilization from a reserve pool, docking at active University of Hamburg zones, and calcium-dependent fusion (SuÈ dhof, 1995; D-20246 Hamburg Hanson et al., 1997). The latter two steps require the § Leibniz Institute for Neurobiology formation of a complex composed of the vesicle SNARE D-39118 Magdeburg VAMP2/Synaptobrevin and two target SNAREs, syn- Federal Republic of Germany taxin and SNAP-25 (SuÈ dhof, 1995; Hanson et al., 1997). In addition, a family of low molecular weight GTPases are likely to be involved in SV cycling with rab3 and rab5 Summary regulating exocytotic and endocytotic events, respec- tively (Ferro-Novick and Novick, 1993; Hess et al., 1993; Piccolo is a novel component of the presynaptic cy- SuÈ dhof, 1995).