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Bioinformatics Approach for Pattern of Myelin-Specific Proteins And
CORE Metadata, citation and similar papers at core.ac.uk Provided by Qazvin University of Medical Sciences Repository Biotech Health Sci. 2016 November; 3(4):e38278. doi: 10.17795/bhs-38278. Published online 2016 August 16. Research Article Bioinformatics Approach for Pattern of Myelin-Specific Proteins and Related Human Disorders Samiie Pouragahi,1,2,3 Mohammad Hossein Sanati,4 Mehdi Sadeghi,2 and Marjan Nassiri-Asl3,* 1Department of Molecular Medicine, School of Medicine, Qazvin university of Medical Sciences, Qazvin, IR Iran 2Department of Bioinformatics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, IR Iran 3Department of Pharmacology, Cellular and Molecular Research Center, School of Medicine, Qazvin university of Medical Sciences, Qazvin, IR Iran 4Department of Molecular Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, IR Iran *Corresponding author: Marjan Nassiri-Asl, School of Medicine, Qazvin University of Medical Sciences, Qazvin, IR Iran. Tel: +98-2833336001, Fax: +98-2833324971, E-mail: [email protected] Received 2016 April 06; Revised 2016 May 30; Accepted 2016 June 22. Abstract Background: Recent neuroinformatic studies, on the structure-function interaction of proteins, causative agents basis of human disease have implied that dysfunction or defect of different protein classes could be associated with several related diseases. Objectives: The aim of this study was the use of bioinformatics approaches for understanding the structure, function and relation- ship of myelin protein 2 (PMP2), a myelin-basic protein in the basis of neuronal disorders. Methods: A collection of databases for exploiting classification information systematically, including, protein structure, protein family and classification of human disease, based on a new approach was used. -
A Mutation in DNA Polymerase Α Rescues WEE1KO Sensitivity to HU
International Journal of Molecular Sciences Article A Mutation in DNA Polymerase α Rescues WEE1KO Sensitivity to HU Thomas Eekhout 1,2 , José Antonio Pedroza-Garcia 1,2 , Pooneh Kalhorzadeh 1,2, Geert De Jaeger 1,2 and Lieven De Veylder 1,2,* 1 Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium; [email protected] (T.E.); [email protected] (J.A.P.-G.); [email protected] (P.K.); [email protected] (G.D.J.) 2 Center for Plant Systems Biology, VIB, 9052 Gent, Belgium * Correspondence: [email protected] Abstract: During DNA replication, the WEE1 kinase is responsible for safeguarding genomic integrity by phosphorylating and thus inhibiting cyclin-dependent kinases (CDKs), which are the driving force of the cell cycle. Consequentially, wee1 mutant plants fail to respond properly to problems arising during DNA replication and are hypersensitive to replication stress. Here, we report the identification of the pola-2 mutant, mutated in the catalytic subunit of DNA polymerase α, as a suppressor mutant of wee1. The mutated protein appears to be less stable, causing a loss of interaction with its subunits and resulting in a prolonged S-phase. Keywords: replication stress; DNA damage; cell cycle checkpoint Citation: Eekhout, T.; Pedroza- 1. Introduction Garcia, J.A.; Kalhorzadeh, P.; De Jaeger, G.; De Veylder, L. A Mutation DNA replication is a highly complex process that ensures the chromosomes are in DNA Polymerase α Rescues correctly replicated to be passed onto the daughter cells during mitosis. Replication starts WEE1KO Sensitivity to HU. Int. -
Supplementary Table 1. Down-Regulation of Oligodendrocyte Genes in Schizophrenia
Supplementary Table 1. Down-regulation of oligodendrocyte genes in schizophrenia Schizophrenia ID Accession Symbol product fold change P value oligodendrocyte transcription factors 36018_at AJ001183 SOX10 SRY (sex determining region Y)-box 10 -1.60 0.001 40624_at U48250 OLIG2 oligodendrocyte lineage transcription factor 2 -1.30 0.019 32187_at AB028973 MYT1 myelin transcription factor 1 1.12 0.571 33539_at W28567 MYEF2 myelin expression factor 2 -1.04 0.887 oligodendrocyte-expressed genes 38558_at M29273 MAG myelin associated glycoprotein -1.76 0.004 41158_at M54927 PLP1 proteolipid protein 1 -1.50 0.011 38499_s_at D28113 MOBP myelin-associated oligodendrocyte basic protein -1.59 0.017 35903_at M63623 OMG oligodendrocyte myelin glycoprotein -1.15 0.022 38653_at D11428 PMP22 peripheral myelin protein 22 -1.28 0.058 38051_at X76220 MAL mal, T-cell differentiation protein -1.11 0.065 612_s_at M19650 CNP 2',3'-cyclic nucleotide 3' phosphodiesterase -1.17 0.072 32538_at S95936 TF transferrin -1.48 0.098 32612_at X04412 GSN gelsolin (amyloidosis, Finnish type) -1.23 0.118 39598_at X04325 GJB1 gap junction protein, beta 1, 32kDa -1.10 0.416 37867_at Z48051 MOG myelin oligodendrocyte glycoprotein 1.39 0.600 35328_at AF055023 NF1 neurofibromin 1 -1.03 0.973 35817_at M13577 MBP myelin basic protein 1.02 1 other oligodendrocyte-related genes 41346_at AJ007583 LARGE like-glycosyltransferase -1.02 0.786 32719_at L41827 NRG1 neuregulin 1 1.07 0.792 1585_at M34309 ERBB3 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 -1.10 0.294 40387_at U80811 -
Oup Radres Rrz001 289..297 ++
Journal of Radiation Research, Vol. 60, No. 3, 2019, pp. 289–297 doi: 10.1093/jrr/rrz001 Advance Access Publication: 26 February 2019 Ionizing radiation affects the composition of the proteome of extracellular vesicles released by head-and-neck cancer cells in vitro Agata Abramowicz1, Anna Wojakowska1, Lukasz Marczak2, Malgorzata Lysek-Gladysinska3, Mateusz Smolarz1, Michael D. Story4, Joanna Polanska5, Piotr Widlak1 and Monika Pietrowska1,* 1Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska–Curie Institute–Oncology Center, Gliwice Branch, ul. Wybrzeze Armii Krajowej 15, 44-101 Gliwice, Poland 2Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznan, Poland 3The Jan Kochanowski University in Kielce, Institute of Biology, Department of Cell Biology and Electron Microscopy, ul. Swietokrzyska 15, 25-406 Kielce, Poland 4University of Texas Southwestern Medical Center, Department of Radiation Oncology, Division of Molecular Radiation Biology, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA 5Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, ul. Akademicka 16, 44-100 Gliwice, Poland *Corresponding author. Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska–Curie Institute–Oncology Center, Gliwice Branch, ul. Wybrzeze Armii Krajowej 15, 44-101 Gliwice, Poland. Tel: +0048-32-278-9627; Fax: +0048-32-278-9840; Email: [email protected] (Received 29 August 2018; revised 7 November 2018; editorial decision 8 January 2019) ABSTRACT Exosomes and other extracellular vesicles are key players in cell-to-cell communication, and it has been proposed that they are involved in different aspects of the response to ionizing radiation, including transmitting the radiation-induced bystander effect and mediating radioresistance. -
The Classification of Esterases: an Important Gene Family Involved in Insecticide Resistance - a Review
Mem Inst Oswaldo Cruz, Rio de Janeiro, Vol. 107(4): 437-449, June 2012 437 The classification of esterases: an important gene family involved in insecticide resistance - A Review Isabela Reis Montella1,2, Renata Schama1,2,3/+, Denise Valle1,2,3 1Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz-Fiocruz, Av. Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brasil 2Instituto de Biologia do Exército, Rio de Janeiro, RJ, Brasil 3Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, RJ, Brasil The use of chemical insecticides continues to play a major role in the control of disease vector populations, which is leading to the global dissemination of insecticide resistance. A greater capacity to detoxify insecticides, due to an increase in the expression or activity of three major enzyme families, also known as metabolic resistance, is one major resistance mechanisms. The esterase family of enzymes hydrolyse ester bonds, which are present in a wide range of insecticides; therefore, these enzymes may be involved in resistance to the main chemicals employed in control programs. Historically, insecticide resistance has driven research on insect esterases and schemes for their classification. Currently, several different nomenclatures are used to describe the esterases of distinct species and a universal standard classification does not exist. The esterase gene family appears to be rapidly evolving and each insect species has a unique complement of detoxification genes with only a few orthologues across species. The examples listed in this review cover different aspects of their biochemical nature. However, they do not appear to contribute to reliably distinguish among the different resistance mechanisms. -
Identification and Characterization of TPRKB Dependency in TP53 Deficient Cancers
Identification and Characterization of TPRKB Dependency in TP53 Deficient Cancers. by Kelly Kennaley A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Molecular and Cellular Pathology) in the University of Michigan 2019 Doctoral Committee: Associate Professor Zaneta Nikolovska-Coleska, Co-Chair Adjunct Associate Professor Scott A. Tomlins, Co-Chair Associate Professor Eric R. Fearon Associate Professor Alexey I. Nesvizhskii Kelly R. Kennaley [email protected] ORCID iD: 0000-0003-2439-9020 © Kelly R. Kennaley 2019 Acknowledgements I have immeasurable gratitude for the unwavering support and guidance I received throughout my dissertation. First and foremost, I would like to thank my thesis advisor and mentor Dr. Scott Tomlins for entrusting me with a challenging, interesting, and impactful project. He taught me how to drive a project forward through set-backs, ask the important questions, and always consider the impact of my work. I’m truly appreciative for his commitment to ensuring that I would get the most from my graduate education. I am also grateful to the many members of the Tomlins lab that made it the supportive, collaborative, and educational environment that it was. I would like to give special thanks to those I’ve worked closely with on this project, particularly Dr. Moloy Goswami for his mentorship, Lei Lucy Wang, Dr. Sumin Han, and undergraduate students Bhavneet Singh, Travis Weiss, and Myles Barlow. I am also grateful for the support of my thesis committee, Dr. Eric Fearon, Dr. Alexey Nesvizhskii, and my co-mentor Dr. Zaneta Nikolovska-Coleska, who have offered guidance and critical evaluation since project inception. -
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. -
Redundancy in Ribonucleotide Excision Repair: Competition, Compensation, and Cooperation
DNA Repair 29 (2015) 74–82 Contents lists available at ScienceDirect DNA Repair j ournal homepage: www.elsevier.com/locate/dnarepair Redundancy in ribonucleotide excision repair: Competition, compensation, and cooperation ∗ Alexandra Vaisman, Roger Woodgate Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA a r t i c l e i n f o a b s t r a c t Article history: The survival of all living organisms is determined by their ability to reproduce, which in turn depends Received 1 November 2014 on accurate duplication of chromosomal DNA. In order to ensure the integrity of genome duplication, Received in revised form 7 February 2015 DNA polymerases are equipped with stringent mechanisms by which they select and insert correctly Accepted 9 February 2015 paired nucleotides with a deoxyribose sugar ring. However, this process is never 100% accurate. To fix Available online 16 February 2015 occasional mistakes, cells have evolved highly sophisticated and often redundant mechanisms. A good example is mismatch repair (MMR), which corrects the majority of mispaired bases and which has been Keywords: extensively studied for many years. On the contrary, pathways leading to the replacement of nucleotides Ribonucleotide excision repair with an incorrect sugar that is embedded in chromosomal DNA have only recently attracted significant Nucleotide excision repair attention. This review describes progress made during the last few years in understanding such path- Mismatch repair Ribonuclease H ways in both prokaryotes and eukaryotes. Genetic studies in Escherichia coli and Saccharomyces cerevisiae Flap endonuclease demonstrated that MMR has the capacity to replace errant ribonucleotides, but only when the base is DNA polymerase I mispaired. -
Basic Protein Detect Circulating Antibodies in Ataxic Horses Siobhan P Ellison Tom J Kennedy Austin Li
Neuritogenic Peptides Derived from Equine Myelin P2 Basic Protein Detect Circulating Antibodies in Ataxic Horses Siobhan P Ellison Tom J Kennedy Austin Li Corresponding Author: Siobhan P. Ellison, DVM PhD 15471 NW 112th Ave Reddick, Fl 32686 Phone: 352-591-3221 Fax: 352-591-4318 e-mail: [email protected] KEY WORDS: Need Keywords nosis of EPM. No cross-reactivity between the antigens was observed. An evaluation of the agreement between the assays (McNe- ABSTRACT mar’s test) suggests as CRP values increase, the likelihood of a positive MPP ELISA also Polyneuritis equi is an immune-mediated increases. Clinical signs of EPM may be neurodegenerative condition in horses that is due to an immune-mediated polyneuropathy related to circulating demyelinating anti- that involves complex in vivo interactions bodies against equine myelin basic protein with the IL6 pathway because MPP antibod- 2 (MP ). The present study examined the 2 ies and elevated CRP concentrations were presence of circulating demyelinating anti- detected in some horses with S. neurona bodies against neuritogenic peptides of MP 2 sarcocystosis. in sera from horses suspected of equine pro- tozoal encephalomyelitis (EPM), a neurode- INTRODUCTION generative condition in horses that may be Polyneuritis equi is a neurodegenerative immune-mediated. The goals of this study condition in horses that is related to circulat- were to develop serum ELISA tests that may ing demyelinating antibodies against equine identify neuroinflammatory conditions in myelin basic protein 2 (MP2). The clinical horses with EPM and indirectly relate the signs of polyneuritis equi (PE) are simi- pathogenesis of inflammation to IL6 by se- lar to equine protozoal myeloencephalitis rum C-reactive protein (CRP) concentration. -
Supplementary Tables
Supplementary Tables Supplementary Table S1: Preselected miRNAs used in feature selection Univariate Cox proportional hazards regression analysis of the endpoint freedom from recurrence in the training set (DKTK-ROG sample) allowed the pre-selection of 524 miRNAs (P< 0.5), which were used in the feature selection. P-value was derived from log-rank test. miRNA p-value miRNA p-value miRNA p-value miRNA p-value hsa-let-7g-3p 0.0001520 hsa-miR-1304-3p 0.0490161 hsa-miR-7108-5p 0.1263245 hsa-miR-6865-5p 0.2073121 hsa-miR-6825-3p 0.0004257 hsa-miR-4298 0.0506194 hsa-miR-4453 0.1270967 hsa-miR-6893-5p 0.2120664 hsa-miR-668-3p 0.0005188 hsa-miR-484 0.0518625 hsa-miR-200a-5p 0.1276345 hsa-miR-25-3p 0.2123829 hsa-miR-3622b-3p 0.0005885 hsa-miR-6851-3p 0.0531446 hsa-miR-6090 0.1278692 hsa-miR-3189-5p 0.2136060 hsa-miR-6885-3p 0.0006452 hsa-miR-1276 0.0557418 hsa-miR-148b-3p 0.1279811 hsa-miR-6073 0.2139702 hsa-miR-6875-3p 0.0008188 hsa-miR-3173-3p 0.0559962 hsa-miR-4425 0.1288330 hsa-miR-765 0.2141536 hsa-miR-487b-5p 0.0011381 hsa-miR-650 0.0564616 hsa-miR-6798-3p 0.1293342 hsa-miR-338-5p 0.2153079 hsa-miR-210-5p 0.0012316 hsa-miR-6133 0.0571407 hsa-miR-4472 0.1300006 hsa-miR-6806-5p 0.2173515 hsa-miR-1470 0.0012822 hsa-miR-4701-5p 0.0571720 hsa-miR-4465 0.1304841 hsa-miR-98-5p 0.2184947 hsa-miR-6890-3p 0.0016539 hsa-miR-202-3p 0.0575741 hsa-miR-514b-5p 0.1308790 hsa-miR-500a-3p 0.2185577 hsa-miR-6511b-3p 0.0017165 hsa-miR-4733-5p 0.0616138 hsa-miR-378c 0.1317442 hsa-miR-4515 0.2187539 hsa-miR-7109-3p 0.0021381 hsa-miR-595 0.0629350 hsa-miR-3121-3p -
Potent Inhibition of Human Telomerase by U-73122
Journal of Biomedical Science (2006) 13:667–674 667 DOI 10.1007/s11373-006-9100-z Potent inhibition of human telomerase by U-73122 Yi-Jui Chen, Wei-Yun Sheng, Pei-Rong Huang & Tzu-Chien V. Wang* Department of Molecular and Cellular Biology, Chang Gung University, Kwei-San, Tao-Yuan, 333, Taiwan Received 28 April 2006; accepted 14 June 2006 Ó 2006 National Science Council, Taipei Key words: alkylating agents, cancer therapyzU-73122, N-ethylmaleimide, telomerase inhibitor Summary Telomerase activity is repressed in normal human somatic cells, but is activated in most cancers, suggesting that telomerase may be an important target for cancer therapy. In this study, we report that U-73122, an amphiphilic alkylating agent that is commonly used as an inhibitor for phospholipase C, is also a potent and selective inhibitor of human telomerase. The inhibition of telomerase by U-73122 was attributed primarily to the pyrrole-2,5-dione group, since its structural analog U-73343 did not inhibit telomerase. In confirmation, we observed that telomerase was inhibited by N-ethylmaleimide, but not N-ethylsuccinimide. The IC50 value of U-73122 for the in vitro inhibition of telomerase activity is 0.2 lM, which is comparable to or slightly more sensitive than that for phospholipase C. The inhibitory action of U-73122 on telomerase appears to be rather selective since the presence of externally added proteins did not protect the inhibition and the IC50 values for the other enzymes tested in this study were at least an order of magnitude higher than that for telomerase. Furthermore, we demonstrate that U-73122 can inhibit telomerase in hemato- poietic cancer cells. -
Atherosclerosis-Susceptible and Atherosclerosis-Resistant Pigeon Aortic Cells Express Different Genes in Vivo
University of New Hampshire University of New Hampshire Scholars' Repository New Hampshire Agricultural Experiment Station Publications New Hampshire Agricultural Experiment Station 7-1-2013 Atherosclerosis-susceptible and atherosclerosis-resistant pigeon aortic cells express different genes in vivo Janet L. Anderson University of New Hampshire, [email protected] C. M. Ashwell University of New Hampshire - Main Campus S. C. Smith University of New Hampshire - Main Campus R. Shine University of New Hampshire - Main Campus E. C. Smith University of New Hampshire - Main Campus See next page for additional authors Follow this and additional works at: https://scholars.unh.edu/nhaes Part of the Poultry or Avian Science Commons Recommended Citation J. L. Anderson, C. M. Ashwell, S. C. Smith, R. Shine, E. C. Smith and R. L. Taylor, Jr. Atherosclerosis- susceptible and atherosclerosis-resistant pigeon aortic cells express different genes in vivo Poultry Science (2013) 92 (10): 2668-2680 doi:10.3382/ps.2013-03306 This Article is brought to you for free and open access by the New Hampshire Agricultural Experiment Station at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in New Hampshire Agricultural Experiment Station Publications by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. Authors Janet L. Anderson, C. M. Ashwell, S. C. Smith, R. Shine, E. C. Smith, and Robert L. Taylor Jr. This article is available at University of New Hampshire Scholars' Repository: https://scholars.unh.edu/nhaes/207 Atherosclerosis-susceptible and atherosclerosis-resistant pigeon aortic cells express different genes in vivo J.