AAV9-Mediated FIG4 Delivery Prolongs Life Span in Charcot-Marie-Tooth Disease Type 4J Mouse Model
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Anti-VAC14 (Aa 711-760) Polyclonal Antibody (CABT-BL5957) This Product Is for Research Use Only and Is Not Intended for Diagnostic Use
Anti-VAC14 (aa 711-760) polyclonal antibody (CABT-BL5957) This product is for research use only and is not intended for diagnostic use. PRODUCT INFORMATION Product Overview Rabbit polyclonal antibody to Human VAC14. Antigen Description The content of phosphatidylinositol 3, 5-bisphosphate (PtdInsP2) in endosomal membranes changes dynamically with fission and fusion events that generate or absorb intracellular transport vesicles. VAC14 is a component of a trimolecular complex that tightly regulates the level of PtdInsP2. Other components of this complex are the PtdInsP2-synthesizing enzyme PIKFYVE (MIM 609414) and the PtdInsP2 phosphatase FIG4 (MIM 609390). VAC14 functions as an activator of PIKFYVE (Sbrissa et al., 2007 Immunogen Synthetic peptide, corresponding to a region within C terminal amino acids 711-760 (QLLSHRLQCV PNPELLQTED SLKAAPKSQK ADSPSIDYAE LLQHFEKVQN) of Human VAC14. Isotype IgG Source/Host Rabbit Species Reactivity Human Purification Immunogen affinity purified Conjugate Unconjugated Sequence Similarities Belongs to the VAC14 family.Contains 6 HEAT repeats. Cellular Localization Endosome membrane. Microsome membrane. Mainly associated with membranes of the late endocytic pathway. Format Liquid Size 50 μg Buffer 97% PBS, 2% Sucrose Preservative None Storage Shipped at 4°C. Upon delivery aliquot and store at -20°C. Avoid repeated freeze/thaw cycles. 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 1 © Creative Diagnostics All Rights Reserved BACKGROUND Introduction The content of phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2) in endosomal membranes changes dynamically with fission and fusion events that generate or absorb intracellular transport vesicles. VAC14 is a component of a trimolecular complex that tightly regulates the level of PtdIns(3,5)P2. -
Analysis of Gene Expression Data for Gene Ontology
ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Robert Daniel Macholan May 2011 ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION Robert Daniel Macholan Thesis Approved: Accepted: _______________________________ _______________________________ Advisor Department Chair Dr. Zhong-Hui Duan Dr. Chien-Chung Chan _______________________________ _______________________________ Committee Member Dean of the College Dr. Chien-Chung Chan Dr. Chand K. Midha _______________________________ _______________________________ Committee Member Dean of the Graduate School Dr. Yingcai Xiao Dr. George R. Newkome _______________________________ Date ii ABSTRACT A tremendous increase in genomic data has encouraged biologists to turn to bioinformatics in order to assist in its interpretation and processing. One of the present challenges that need to be overcome in order to understand this data more completely is the development of a reliable method to accurately predict the function of a protein from its genomic information. This study focuses on developing an effective algorithm for protein function prediction. The algorithm is based on proteins that have similar expression patterns. The similarity of the expression data is determined using a novel measure, the slope matrix. The slope matrix introduces a normalized method for the comparison of expression levels throughout a proteome. The algorithm is tested using real microarray gene expression data. Their functions are characterized using gene ontology annotations. The results of the case study indicate the protein function prediction algorithm developed is comparable to the prediction algorithms that are based on the annotations of homologous proteins. -
Mouse Germ Line Mutations Due to Retrotransposon Insertions Liane Gagnier1, Victoria P
Gagnier et al. Mobile DNA (2019) 10:15 https://doi.org/10.1186/s13100-019-0157-4 REVIEW Open Access Mouse germ line mutations due to retrotransposon insertions Liane Gagnier1, Victoria P. Belancio2 and Dixie L. Mager1* Abstract Transposable element (TE) insertions are responsible for a significant fraction of spontaneous germ line mutations reported in inbred mouse strains. This major contribution of TEs to the mutational landscape in mouse contrasts with the situation in human, where their relative contribution as germ line insertional mutagens is much lower. In this focussed review, we provide comprehensive lists of TE-induced mouse mutations, discuss the different TE types involved in these insertional mutations and elaborate on particularly interesting cases. We also discuss differences and similarities between the mutational role of TEs in mice and humans. Keywords: Endogenous retroviruses, Long terminal repeats, Long interspersed elements, Short interspersed elements, Germ line mutation, Inbred mice, Insertional mutagenesis, Transcriptional interference Background promoter and polyadenylation motifs and often a splice The mouse and human genomes harbor similar types of donor site [10, 11]. Sequences of full-length ERVs can TEs that have been discussed in many reviews, to which encode gag, pol and sometimes env, although groups of we refer the reader for more in depth and general infor- LTR retrotransposons with little or no retroviral hom- mation [1–9]. In general, both human and mouse con- ology also exist [6–9]. While not the subject of this re- tain ancient families of DNA transposons, none view, ERV LTRs can often act as cellular enhancers or currently active, which comprise 1–3% of these genomes promoters, creating chimeric transcripts with genes, and as well as many families or groups of retrotransposons, have been implicated in other regulatory functions [11– which have caused all the TE insertional mutations in 13]. -
Molecular Mechanisms Involved Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis
Virginia Commonwealth University VCU Scholars Compass Theses and Dissertations Graduate School 2010 Molecular Mechanisms Involved Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis Ryan Fassnacht Virginia Commonwealth University Follow this and additional works at: https://scholarscompass.vcu.edu/etd Part of the Physiology Commons © The Author Downloaded from https://scholarscompass.vcu.edu/etd/2246 This Thesis is brought to you for free and open access by the Graduate School at VCU Scholars Compass. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of VCU Scholars Compass. For more information, please contact [email protected]. Ryan C. Fassnacht 2010 All Rights Reserved Molecular Mechanisms Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science at Virginia Commonwealth University. by Ryan Christopher Fassnacht, B.S. Hampden Sydney University, 2005 M.S. Virginia Commonwealth University, 2010 Director: Valeria Mas, Ph.D., Associate Professor of Surgery and Pathology Division of Transplant Department of Surgery Virginia Commonwealth University Richmond, Virginia July 9, 2010 Acknowledgement The Author wishes to thank his family and close friends for their support. He would also like to thank the members of the molecular transplant team for their help and advice. This project would not have been possible with out the help of Dr. Valeria Mas and her endearing -
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. -
Inhibition of Pikfyve Using YM201636 Suppresses the Growth of Liver Cancer Via the Induction of Autophagy
ONCOLOGY REPORTS 41: 1971-1979, 2019 Inhibition of PIKfyve using YM201636 suppresses the growth of liver cancer via the induction of autophagy JIU-ZHOU HOU1, ZHUO-QING XI1, JIE NIU1, WEI LI1, XIAO WANG1, CHAO LIANG1, HUA SUN1, DONG FANG1 and SONG-QIANG XIE2 1Institute for Innovative Drug Design and Evaluation; 2Institute of Chemical Biology, School of Pharmacy, Henan University, Kaifeng, Henan 475004, P.R. China Received May 9, 2018; Accepted December 6, 2018 DOI: 10.3892/or.2018.6928 Abstract. Liver cancer is among the most common types Introduction of cancer worldwide. The aim of the present study was to investigate whether the phosphatidylinositol-3-phos- Liver cancer is one of the most common types of cancer world- phate 5-kinase (PIKfyve) inhibitor, YM201636, exerts wide, ranking as the third leading cause of cancer-associated anti-proliferative effects on liver cancer. The methods used in mortality (1). Despite the great advances in the use of modern the present study included MTT assay, flow cytometry, western surgical techniques in combination with chemotherapy, the blot analysis and an allograft mouse model of liver cancer. The overall 5-year survival rate for patients with liver cancer results revealed that YM201636 inhibited the proliferation of remains poor (2). Therefore, novel strategies for the anticancer HepG2 and Huh-7 cells in a dose-dependent manner. HepG2 therapy of liver cancer are urgently required. and Huh-7 cells exhibited strong monodansylcadaverine Phosphatidylinositol-3-phosphate 5-kinase (PIKfyve) is a staining following treatment with YM201636. Accordingly, lipid kinase that phosphorylates phosphatidylinositol-3-phos- YM201636 treatment increased the expression of the phate (PI3P) to generate phosphatidylinositol 3,5-bisphosphate autophagosome-associated marker protein microtubule-asso- [PtdIns(3,5)P2] or phosphatidylinositol 5-phosphate ciated 1A/1B light chain 3-II in HepG2 and Huh-7 cells. -
Protein Identities in Evs Isolated from U87-MG GBM Cells As Determined by NG LC-MS/MS
Protein identities in EVs isolated from U87-MG GBM cells as determined by NG LC-MS/MS. No. Accession Description Σ Coverage Σ# Proteins Σ# Unique Peptides Σ# Peptides Σ# PSMs # AAs MW [kDa] calc. pI 1 A8MS94 Putative golgin subfamily A member 2-like protein 5 OS=Homo sapiens PE=5 SV=2 - [GG2L5_HUMAN] 100 1 1 7 88 110 12,03704523 5,681152344 2 P60660 Myosin light polypeptide 6 OS=Homo sapiens GN=MYL6 PE=1 SV=2 - [MYL6_HUMAN] 100 3 5 17 173 151 16,91913397 4,652832031 3 Q6ZYL4 General transcription factor IIH subunit 5 OS=Homo sapiens GN=GTF2H5 PE=1 SV=1 - [TF2H5_HUMAN] 98,59 1 1 4 13 71 8,048185945 4,652832031 4 P60709 Actin, cytoplasmic 1 OS=Homo sapiens GN=ACTB PE=1 SV=1 - [ACTB_HUMAN] 97,6 5 5 35 917 375 41,70973209 5,478027344 5 P13489 Ribonuclease inhibitor OS=Homo sapiens GN=RNH1 PE=1 SV=2 - [RINI_HUMAN] 96,75 1 12 37 173 461 49,94108966 4,817871094 6 P09382 Galectin-1 OS=Homo sapiens GN=LGALS1 PE=1 SV=2 - [LEG1_HUMAN] 96,3 1 7 14 283 135 14,70620005 5,503417969 7 P60174 Triosephosphate isomerase OS=Homo sapiens GN=TPI1 PE=1 SV=3 - [TPIS_HUMAN] 95,1 3 16 25 375 286 30,77169764 5,922363281 8 P04406 Glyceraldehyde-3-phosphate dehydrogenase OS=Homo sapiens GN=GAPDH PE=1 SV=3 - [G3P_HUMAN] 94,63 2 13 31 509 335 36,03039959 8,455566406 9 Q15185 Prostaglandin E synthase 3 OS=Homo sapiens GN=PTGES3 PE=1 SV=1 - [TEBP_HUMAN] 93,13 1 5 12 74 160 18,68541938 4,538574219 10 P09417 Dihydropteridine reductase OS=Homo sapiens GN=QDPR PE=1 SV=2 - [DHPR_HUMAN] 93,03 1 1 17 69 244 25,77302971 7,371582031 11 P01911 HLA class II histocompatibility antigen, -
TMEM106B in Humans and Vac7 and Tag1 in Yeast Are Predicted to Be Lipid Transfer Proteins
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.12.435176; this version posted March 12, 2021. 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. TMEM106B in humans and Vac7 and Tag1 in yeast are predicted to be lipid transfer proteins Tim P. Levine* UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, United Kingdom. ORCID 0000-0002-7231-0775 *Corresponding author and lead contact: [email protected] Data availability statement: The data that support this study are freely available in Harvard Dataverse at https://dataverse.harvard.edu/dataverse/LEA_2. Acknowledgements: work was funded by the Higher Education Funding Council for England and the NIHR Moorfields Biomedical Research Centre Conflict of interest disclosure: the author declares that there is no conflict of interest Keywords: Structural bioinformatics, Lipid transfer protein, LEA_2, TMEM106B, Vac7, YLR173W, Endosome, Lysosome Running Title: TMEM106B & Vac7: lipid transfer proteins 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.12.435176; this version posted March 12, 2021. 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 TMEM106B is an integral membrane protein of late endosomes and lysosomes involved in neuronal function, its over-expression being associated with familial frontotemporal lobar degeneration, and under-expression linked to hypomyelination. It has also been identified in multiple screens for host proteins required for productive SARS-CoV2 infection. Because standard approaches to understand TMEM106B at the sequence level find no homology to other proteins, it has remained a protein of unknown function. -
Cellular and Molecular Signatures in the Disease Tissue of Early
Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of -
Mutations in Pi(3,5)P2 Signaling and Neurodegeneration in Mouse and Human
MUTATIONS IN PI(3,5)P2 SIGNALING AND NEURODEGENERATION IN MOUSE AND HUMAN by Clement Y. Chow A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Human Genetics) in The University of Michigan 2008 Doctoral Committee: Professor Miriam H. Meisler, Chair Professor Sally A. Camper Professor David Ginsburg Associate Professor David C. Kohrman Assistant Professor Geoffrey G. Murphy Clement Y. Chow 2008 To my wife, Candace For all her love and support ii ACKNOWLEDGEMENTS I would first like to thank my mentor, Miriam Meisler. She is the consummate scientist. Miriam is inquisitive and interested in a wide range of topics. This trait has taught me to always ask the right questions and be skeptical of conclusions that are not supported by data. Miriam’s unending desire to make each oral presentation perfect drove me to improve my own skills. I came to this lab without any public presentation skills, but I am now greatly improved in my presentation abilities, a skill crucial for a successful scientific career. Miriam is a perfectionist when it comes to writing and always encouraged me to do the same. I will continue to strive to perfect my writing abilities. I came to the lab wanting to positionally clone a mouse mutant. I told Miriam that I would stay in the lab if she allowed me to do so. She was supportive and excited from the beginning, allowing me to pursue a project with an unknown future. This allowed me to learn, first hand, many aspects of genetics that such a project provides. -
Biological Sciences—Genetics Human Genetic Variation in VAC14 Regulates Salmonella Invasion and Typhoid Feve
Classification: Biological Sciences—Genetics Human genetic variation in VAC14 regulates Salmonella invasion and typhoid fever through modulation of cholesterol 5 Monica I. Alvarez1, Luke C. Glover1, Peter Luo1, Liuyang Wang1, Elizabeth Theusch2, Stefan H. Oehlers1,3,4, Eric M. Walton1, Trinh Thi Bich Tram5, Yu-Lin Kuang2, Jerome I. Rotter6, Colleen M. McClean7, Nguyen Tran Chinh8, Marisa W. Medina2, David M. Tobin1,7, Sarah J. Dunstan9, Dennis C. Ko1,10 Affiliations: 10 1Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA. 2Children’s Hospital Oakland Research Institute, Oakland, CA 94609, USA. 3Tuberculosis Research Program, Centenary Institute, Camperdown, NSW 2050, Australia 4Sydney Medical School, The University of Sydney, Newtown, Australia 15 5Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. 6Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA. 7Department of Immunology, School of Medicine, Duke University, Durham, NC 27710, USA. 20 8Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. 9Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia. 10Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA. *To whom correspondence should be addressed: [email protected]. 25 1 Abstract Risk, severity, and outcome of infection depend on the -
Single Cell Spatial Chromatin Analysis of Fixed Immunocytochemically Identified Neuronal Cells
bioRxiv preprint doi: https://doi.org/10.1101/780387; this version posted September 24, 2019. 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. Title: Single Cell Spatial Chromatin Analysis of Fixed Immunocytochemically Identified Neuronal Cells One Sentence Summary: A new method, CHEX-seq (CHromatin eXposed), identifies the open- chromatin landscape in single fixed cells thereby allowing spatial chromatin analysis of selected cells in complex cellular environments. Authors: Jaehee Lee1,#, Youtao Lu2,#, Jinchun Wang3,#, Jifen Li1, Stephen A. Fisher2, C. Erik Nordgren2, Jean G. Rosario2, Stewart A. Anderson4, Alexandra V. Ulyanova5, Steven Brem5, H. Isaac Chen5, John A. Wolf5, M. Sean Grady5, Mimi Healy3, Junhyong Kim2,& and James Eberwine1,&, % Affiliations: 1 Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA, 2 Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104 USA, 3 Agilent Technologies, Inc., 5301 Stevens Creek Blvd, Santa Clara, CA 95051, USA, 4 Department of Psychiatry, Children’s Hospital of Philadelphia, ARC 517, 3615 Civic Center Blvd, Philadelphia, PA 19104, USA, 5Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. # These authors contributed equally to this manuscript. & These authors contributed equally to this manuscript. % Correspondence should be addressed to: James Eberwine, PhD University of Pennsylvania 37 John Morgan Building Philadelphia, PA 19104 [email protected] bioRxiv preprint doi: https://doi.org/10.1101/780387; this version posted September 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.