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Supplemental Materials Genome-wide Mapping of SMAD Target genes Reveals the Role of BMP Signaling in Embryonic Stem Cell Fate Determination Teng Fei1#, Kai Xia2#, Zhongwei Li1^, Bing Zhou2^, Shanshan Zhu2^, Hua Chen1, Jianping Zhang1, Zhang Chen2, Huasheng Xiao3, Jing-Dong J. Han2*, Ye-Guang Chen1* Supplemental Methods Supplemental References Supplemental Figures S1–S17 Supplemental Tables S1-S9 1 Supplemental Methods Cell culture and antibodies Murine R1 ES cells were first plated on mitomycin-treated murine embryonic fibroblasts (MEFs) and grown under typical ES cell conditions (DMEM supplemented with 15% fetal calf serum, leukemia inhibitory factor (LIF), non-essential amino acids, GlutaMax-I (Invitrogen Gibco), beta-mercaptoethanol and penicillin/streptomycin. For ChIP assay, cells were cultured on gelatinized tissue culture plates for two passages to eliminate MEFs. KO-DMEM and Knockout serum replacement (Invitrogen Gibco) were used to substitute DMEM and fetal calf serum for feeder free culture. For ChIP experiments and immunoblotting, we used affinity-purified SMAD1/5 and SMAD4 antibodies that can recognize a specific band corresponding to endogenous SMAD proteins in R1 ES cells (Fig. S1A). Rabbit anti-SMAD1/5 antibody was generated with recombinant human SMAD1-linker (aa145-267)-His, and rabbit anti-SMAD4 antibody with recombinant human SMAD4-linker (aa144-316)-His. Anti-SMAD1/5 antibody can recognize both overexpressed SMAD1 and SMAD5 proteins but minimally SMAD8 (Fig. S1B). Phospho-SMAD1/5 antibody was purchased from Chemicon International (AB3848) and anti-nestin antibody from Chemicon International (MAB353). H3K27me3 antibody (ab6002) and histone H3 antibody (ab1791) were from Abcam. GFP (SC-8334), GST (SC-138), His (SC-803) antibody were from Santa Cruz Biotech. -
Protein Interaction Network of Alternatively Spliced Isoforms from Brain Links Genetic Risk Factors for Autism
ARTICLE Received 24 Aug 2013 | Accepted 14 Mar 2014 | Published 11 Apr 2014 DOI: 10.1038/ncomms4650 OPEN Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism Roser Corominas1,*, Xinping Yang2,3,*, Guan Ning Lin1,*, Shuli Kang1,*, Yun Shen2,3, Lila Ghamsari2,3,w, Martin Broly2,3, Maria Rodriguez2,3, Stanley Tam2,3, Shelly A. Trigg2,3,w, Changyu Fan2,3, Song Yi2,3, Murat Tasan4, Irma Lemmens5, Xingyan Kuang6, Nan Zhao6, Dheeraj Malhotra7, Jacob J. Michaelson7,w, Vladimir Vacic8, Michael A. Calderwood2,3, Frederick P. Roth2,3,4, Jan Tavernier5, Steve Horvath9, Kourosh Salehi-Ashtiani2,3,w, Dmitry Korkin6, Jonathan Sebat7, David E. Hill2,3, Tong Hao2,3, Marc Vidal2,3 & Lilia M. Iakoucheva1 Increased risk for autism spectrum disorders (ASD) is attributed to hundreds of genetic loci. The convergence of ASD variants have been investigated using various approaches, including protein interactions extracted from the published literature. However, these datasets are frequently incomplete, carry biases and are limited to interactions of a single splicing isoform, which may not be expressed in the disease-relevant tissue. Here we introduce a new interactome mapping approach by experimentally identifying interactions between brain-expressed alternatively spliced variants of ASD risk factors. The Autism Spliceform Interaction Network reveals that almost half of the detected interactions and about 30% of the newly identified interacting partners represent contribution from splicing variants, emphasizing the importance of isoform networks. Isoform interactions greatly contribute to establishing direct physical connections between proteins from the de novo autism CNVs. Our findings demonstrate the critical role of spliceform networks for translating genetic knowledge into a better understanding of human diseases. -
Muscarinic Acetylcholine Type 1 Receptor Activity Constrains Neurite Outgrowth by Inhibiting Microtubule Polymerization and Mito
fnins-12-00402 June 26, 2018 Time: 12:46 # 1 ORIGINAL RESEARCH published: 26 June 2018 doi: 10.3389/fnins.2018.00402 Muscarinic Acetylcholine Type 1 Receptor Activity Constrains Neurite Outgrowth by Inhibiting Microtubule Polymerization and Mitochondrial Trafficking in Adult Sensory Neurons Mohammad G. Sabbir1*, Nigel A. Calcutt2 and Paul Fernyhough1,3 1 Division of Neurodegenerative Disorders, St. Boniface Hospital Research Centre, Winnipeg, MB, Canada, 2 Department of Pathology, University of California, San Diego, San Diego, CA, United States, 3 Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB, Canada The muscarinic acetylcholine type 1 receptor (M1R) is a metabotropic G protein-coupled Edited by: receptor. Knockout of M1R or exposure to selective or specific receptor antagonists Roberto Di Maio, elevates neurite outgrowth in adult sensory neurons and is therapeutic in diverse University of Pittsburgh, United States models of peripheral neuropathy. We tested the hypothesis that endogenous M1R Reviewed by: activation constrained neurite outgrowth via a negative impact on the cytoskeleton Roland Brandt, University of Osnabrück, Germany and subsequent mitochondrial trafficking. We overexpressed M1R in primary cultures Rick Dobrowsky, of adult rat sensory neurons and cell lines and studied the physiological and The University of Kansas, United States molecular consequences related to regulation of cytoskeletal/mitochondrial dynamics *Correspondence: and neurite outgrowth. In adult primary neurons, overexpression of M1R caused Mohammad G. Sabbir disruption of the tubulin, but not actin, cytoskeleton and significantly reduced neurite [email protected] outgrowth. Over-expression of a M1R-DREADD mutant comparatively increased neurite Specialty section: outgrowth suggesting that acetylcholine released from cultured neurons interacts This article was submitted to with M1R to suppress neurite outgrowth. -
1 Supporting Information for a Microrna Network Regulates
Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia. -
Evidence for Conformational Change-Induced Hydrolysis of Β-Tubulin-GTP
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.08.288019; this version posted September 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Evidence for conformational change-induced hydrolysis of β-tubulin-GTP Mohammadjavad Paydar1 and Benjamin H. Kwok1† 1 Institute for Research in Immunology and Cancer (IRIC), Département de médecine, Université de Montréal, P.O. Box 6128, Station Centre-Ville, Montréal, QC H3C 3J7, Canada. † Corresponding author: B. H. Kwok: [email protected] Keywords: Kinesin, Kif2A, MCAK, motor protein, microtubules, tubulin, GTP hydrolysis Abbreviations NM: Neck+Motor MD: Motor domain MT: Microtubule Running title: Tubulin GTP hydrolysis 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.08.288019; this version posted September 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. ABSTRACT Microtubules, protein polymers of α/β-tubulin dimers, form the structural framework for many essential cellular processes including cell shape formation, intracellular transport, and segregation of chromosomes during cell division. It is known that tubulin-GTP hydrolysis is closely associated with microtubule polymerization dynamics. However, the precise roles of GTP hydrolysis in tubulin polymerization and microtubule depolymerization, and how it is initiated are still not clearly defined. We report here that tubulin-GTP hydrolysis can be triggered by conformational change induced by the depolymerizing kinesin-13 proteins or by the stabilizing chemical agent paclitaxel. We provide biochemical evidence that conformational change precedes tubulin-GTP hydrolysis, confirming this process is mechanically driven and structurally directional. -
1/05661 1 Al
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date _ . ... - 12 May 2011 (12.05.2011) W 2 11/05661 1 Al (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12Q 1/00 (2006.0 1) C12Q 1/48 (2006.0 1) kind of national protection available): AE, AG, AL, AM, C12Q 1/42 (2006.01) AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, (21) Number: International Application DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, PCT/US20 10/054171 HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, (22) International Filing Date: KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, 26 October 2010 (26.10.2010) ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, (25) Filing Language: English SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, (26) Publication Language: English TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: (84) Designated States (unless otherwise indicated, for every 61/255,068 26 October 2009 (26.10.2009) US kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, (71) Applicant (for all designated States except US): ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, MYREXIS, INC. -
Altered Proteins in the Hippocampus of Patients with Mesial Temporal Lobe Epilepsy
pharmaceuticals Article Altered Proteins in the Hippocampus of Patients with Mesial Temporal Lobe Epilepsy Daniele Suzete Persike 1,2, Jose Eduardo Marques-Carneiro 1,3 , Mariana Leão de Lima Stein 4, Elza Marcia Targas Yacubian 1, Ricardo Centeno 1, Mauro Canzian 5 and Maria José da Silva Fernandes 1,* 1 Departamento de Neurologia/Neurocirurgia, Escola Paulista de Medicina, Universidade Federal de São Paulo–UNIFESP, Rua Pedro de Toledo, 669, CEP, São Paulo 04039-032, Brazil; [email protected] (D.S.P.); [email protected] (J.E.M.-C.); [email protected] (E.M.T.Y.); [email protected] (R.C.) 2 Department of Medicinal Chemistry, College of Pharmacy, University of Dohuk-UoD, Kurdistan Region 1006AJ, Iraq 3 INSERM U1114, Neuropsychologie Cognitive et Physiopathologie de la Schizophrenie, 1 pl de l’Hopital, 67091 Strasbourg, France 4 Departamento de Micro-Imuno-Parasito, Disciplina de Biologia Celular, Escola Paulista de Medicina, UNIFESP, São Paulo 04039-032, Brasil; [email protected] 5 Instituto do Coração (INCOR), Departamento de Anatomia Patológica, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo 04039-032, Brasil; [email protected] * Correspondence: [email protected]; Tel.: +964-750-288-0486 or +55-115-576-4848 Received: 22 August 2018; Accepted: 26 September 2018; Published: 30 September 2018 Abstract: Mesial temporal lobe epilepsy (MTLE) is usually associated with drug-resistant seizures and cognitive deficits. Efforts have been made to improve the understanding of the pathophysiology of MTLE for new therapies. In this study, we used proteomics to determine the differential expression of proteins in the hippocampus of patients with MTLE compared to control samples. -
(DPYSL2) with Schizophrenia in Japanese Subjects
Journal of Human Genetics (2010) 55, 469–472 & 2010 The Japan Society of Human Genetics All rights reserved 1434-5161/10 $32.00 www.nature.com/jhg SHORT COMMUNICATION A two-stage case–control association study of the dihydropyrimidinase-like 2 gene (DPYSL2) with schizophrenia in Japanese subjects Takayoshi Koide1,7, Branko Aleksic1,7, Yoshihito Ito1,7, Hinako Usui1, Akira Yoshimi2, Toshiya Inada3, Michio Suzuki4, Ryota Hashimoto5,7,8, Masatoshi Takeda5,8, Nakao Iwata6,7 and Norio Ozaki1,7 We examined the association of schizophrenia (SCZ) and dihydropyrimidinase-like 2 (DPYSL2), also known as collapsin response mediator protein 2, which regulates axonal growth and branching. We genotyped 20 tag single nucleotide polymorphisms (SNPs) in 1464 patients and 1310 controls. There were two potential associations in a screening population of 384 patients and 384 controls (rs2585458: P¼0.046, rs4733048: P¼0.014). However, we could not replicate these associations in a confirmatory population of 1080 patients and 926 controls (rs2585458: P¼0.39, rs4733048: P¼0.70) or a joint analysis (rs2585458: P¼0.72, rs4733048: P¼0.10). We conclude that DPYSL2 does not have a major function in SCZ in Japanese subjects. Journal of Human Genetics (2010) 55, 469–472; doi:10.1038/jhg.2010.38; published online 23 April 2010 Keywords: case–control study; DPYSL2; imputation; Japanese subjects; neuronal polarity; schizophrenia INTRODUCTION DPYSL2 is located on chromosome 8p21.2. This region has been Schizophrenia (SCZ) is a severe debilitating neuropsychiatric disorder reported as positive in meta-analysis of genome-wide linkage studies that affects B1% of the general population. -
Changes in Dpysl2 Expression Are Associated with Prenatally Stressed Rat Offspring and Susceptibility to Schizophrenia in Humans
1574 INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 35: 1574-1586, 2015 Changes in Dpysl2 expression are associated with prenatally stressed rat offspring and susceptibility to schizophrenia in humans HWAYOUNG LEE1, JAESOON JOO1, SEONG-SU NAH2, JONG WOO KIM3, HYUNG-KI KIM1, JUN-TACK KWON1, HWA-YOUNG LEE4, YOUNG OCK KIM5 and HAK-JAE KIM1,6 1Department of Clinical Pharmacology, 2Division of Rheumatology, Department of Internal Medicine, College of Medicine, Soonchunhyang University, Cheonan; 3Department of Neuropsychiatry, School of Medicine, Kyunghee University, Seoul; 4Department of Psychiatry, College of Medicine, Soonchunhyang University, Cheonan; 5Development of Ginseng and Medical Plants Research Institute, Rural Administration, Eumseong; 6Soonchunhyang Medical Research Institute, College of Medicine, Soonchunhyang University, Cheonan, Republic of Korea Received August 22, 2014; Accepted March 26, 2015 DOI: 10.3892/ijmm.2015.2161 Abstract. Exposure to stress during critical periods of fetal development of schizophrenia. Taken together with previous brain development is an environmental risk factor for the studies investigating the association between the DPYSL2 development of schizophrenia in adult offspring. In the gene and schizophrenia, the present findings may contribute present study, a repeated-variable stress paradigm was applied additional evidence regarding developmental theories of the to pregnant rats during the last week of gestation, which is pathophysiology of schizophrenia. analogous to the second trimester of brain development -
The Mechanisms of Microtubule Catastrophe and Rescue: Implications from Analysis of a Dimer-Scale Computational Model
M BoC | ARTICLE The mechanisms of microtubule catastrophe and rescue: implications from analysis of a dimer-scale computational model Gennady Margolina,b,*,†, Ivan V. Gregorettib,c,*,†, Trevor M. Cickovskid,‡, Chunlei Lia,b, Wei Shia,b,§, Mark S. Albera,b,e, and Holly V. Goodsonb,c aDepartment of Applied and Computational Mathematics and Statistics, bInterdisciplinary Center for the Study of Biocomplexity, cDepartment of Chemistry and Biochemistry, and dDepartment of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556; eDepartment of Medicine, Indiana University School of Medicine, Indianapolis, IN 40202 ABSTRACT Microtubule (MT) dynamic instability is fundamental to many cell functions, but Monitoring Editor its mechanism remains poorly understood, in part because it is difficult to gain information Alexander Mogilner about the dimer-scale events at the MT tip. To address this issue, we used a dimer-scale com- University of California, Davis putational model of MT assembly that is consistent with tubulin structure and biochemistry, Received: Aug 12, 2011 displays dynamic instability, and covers experimentally relevant spans of time. It allows us to Revised: Nov 30, 2011 correlate macroscopic behaviors (dynamic instability parameters) with microscopic structures Accepted: Dec 13, 2011 (tip conformations) and examine protofilament structure as the tip spontaneously progresses through both catastrophe and rescue. The model’s behavior suggests that several commonly held assumptions about MT dynamics should be reconsidered. Moreover, it predicts that short, interprotofilament “cracks” (laterally unbonded regions between protofilaments) exist even at the tips of growing MTs and that rapid fluctuations in the depths of these cracks influ- ence both catastrophe and rescue. -
EFFECTS of BLOOD FEEDING on the TRANSCRIPTOME of the MALPIGHIAN TUBULES in the ASIAN TIGER MOSQUITO AEDES ALBOPICTUS Thesis
EFFECTS OF BLOOD FEEDING ON THE TRANSCRIPTOME OF THE MALPIGHIAN TUBULES IN THE ASIAN TIGER MOSQUITO AEDES ALBOPICTUS Thesis Presented in Partial Fulfillment of the Requirements for the Degree Master in Science in the Graduate School of The Ohio State University By Carlos J. Esquivel Palma, B.S. Graduate Program in Entomology The Ohio State University 2015 Master’s Examination Committee: Dr. Peter M. Piermarini, Advisor Dr. David L. Denlinger Dr. Andrew P. Michel Copyright by Carlos J. Esquivel Palma 2015 Abstract Mosquitoes are one of the major threats to human health worldwide. They are vectors of protozoans, arboviruses, and filarial nematodes that cause diseases in humans and animals. The Asian tiger mosquito Aedes albopictus is a vector of medically important arboviruses such as dengue fever, chikungunya fever, yellow fever, eastern equine encephalitis, La Crosse encephalitis, and West Nile fever. Control of these diseases often involves control of the mosquito vectors with chemical insecticides. However, the use of a limited number of chemicals with similar modes of actions has led to resistance in several mosquito species. The development of new insecticides with novel modes of action is considered a promising strategy to overcome resistance. The Piermarini lab has recently shown that the renal (Malpighian) tubules of mosquitoes are promising physiological targets to disrupt for killing mosquitoes via a novel mode of action. The Malpighian tubules play a critical role in the acute processing of blood meals, by mediating the rapid excretion of water and ions derived from the ingested blood. However, the physiological roles of Malpighian tubules during the chronic processing of blood meals after the initial diuresis is complete (~1-2 h after feeding) are not known. -
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BASIC RESEARCH www.jasn.org Phosphoproteomic Analysis Reveals Regulatory Mechanisms at the Kidney Filtration Barrier †‡ †| Markus M. Rinschen,* Xiongwu Wu,§ Tim König, Trairak Pisitkun,¶ Henning Hagmann,* † † † Caroline Pahmeyer,* Tobias Lamkemeyer, Priyanka Kohli,* Nicole Schnell, †‡ †† ‡‡ Bernhard Schermer,* Stuart Dryer,** Bernard R. Brooks,§ Pedro Beltrao, †‡ Marcus Krueger,§§ Paul T. Brinkkoetter,* and Thomas Benzing* *Department of Internal Medicine II, Center for Molecular Medicine, †Cologne Excellence Cluster on Cellular Stress | Responses in Aging-Associated Diseases, ‡Systems Biology of Ageing Cologne, Institute for Genetics, University of Cologne, Cologne, Germany; §Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland; ¶Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; **Department of Biology and Biochemistry, University of Houston, Houston, Texas; ††Division of Nephrology, Baylor College of Medicine, Houston, Texas; ‡‡European Molecular Biology Laboratory–European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom; and §§Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany ABSTRACT Diseases of the kidney filtration barrier are a leading cause of ESRD. Most disorders affect the podocytes, polarized cells with a limited capacity for self-renewal that require tightly controlled signaling to maintain their integrity, viability, and function. Here, we provide an atlas of in vivo phosphorylated, glomerulus- expressed