The P5-Atpase ATP13A1 Modulates MR1-Mediated Antigen Presentation
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
FK506-Binding Protein 12.6/1B, a Negative Regulator of [Ca2+], Rescues Memory and Restores Genomic Regulation in the Hippocampus of Aging Rats
This Accepted Manuscript has not been copyedited and formatted. The final version may differ from this version. A link to any extended data will be provided when the final version is posted online. Research Articles: Neurobiology of Disease FK506-Binding Protein 12.6/1b, a negative regulator of [Ca2+], rescues memory and restores genomic regulation in the hippocampus of aging rats John C. Gant1, Eric M. Blalock1, Kuey-Chu Chen1, Inga Kadish2, Olivier Thibault1, Nada M. Porter1 and Philip W. Landfield1 1Department of Pharmacology & Nutritional Sciences, University of Kentucky, Lexington, KY 40536 2Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294 DOI: 10.1523/JNEUROSCI.2234-17.2017 Received: 7 August 2017 Revised: 10 October 2017 Accepted: 24 November 2017 Published: 18 December 2017 Author contributions: J.C.G. and P.W.L. designed research; J.C.G., E.M.B., K.-c.C., and I.K. performed research; J.C.G., E.M.B., K.-c.C., I.K., and P.W.L. analyzed data; J.C.G., E.M.B., O.T., N.M.P., and P.W.L. wrote the paper. Conflict of Interest: The authors declare no competing financial interests. NIH grants AG004542, AG033649, AG052050, AG037868 and McAlpine Foundation for Neuroscience Research Corresponding author: Philip W. Landfield, [email protected], Department of Pharmacology & Nutritional Sciences, University of Kentucky, 800 Rose Street, UKMC MS 307, Lexington, KY 40536 Cite as: J. Neurosci ; 10.1523/JNEUROSCI.2234-17.2017 Alerts: Sign up at www.jneurosci.org/cgi/alerts to receive customized email alerts when the fully formatted version of this article is published. -
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. -
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. -
The Small G Protein Arl8 Contributes to Lysosomal Function and Long-Range Axonal Transport in Drosophila
This is a repository copy of The small G protein Arl8 contributes to lysosomal function and long-range axonal transport in Drosophila. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/134948/ Version: Accepted Version Article: Rosa-Ferreira, Cláudia, Sweeney, Sean orcid.org/0000-0003-2673-9578 and Munro, Sean (Accepted: 2018) The small G protein Arl8 contributes to lysosomal function and long- range axonal transport in Drosophila. Biology Open. (In Press) https://doi.org/10.1242/bio.035964 Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ The small G protein Arl8 contributes to lysosomal function and long-range axonal transport in Drosophila Cláudia Rosa-Ferreira1 , Sean T. Sweeney2 and Sean Munro1* 1: MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK 2: Department of Biology University of York York YO10 5DD UK *: Corresponding author. Email: [email protected] © 2018. -
Genome-Wide Screen Identifies Genes Whose Inactivation Confer Resistance to Cisplatin in Saccharomyces Cerevisiae
Research Article Genome-Wide Screen Identifies Genes Whose Inactivation Confer Resistance to Cisplatin in Saccharomyces cerevisiae Ruea-Yea Huang, Martha Eddy, Marija Vujcic, and David Kowalski Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York Abstract therapy (1). This may be due to the genomic instability of tumors, To identify novel genes that mediate cellular resistance to which gives rise to mutations or defects in multiple molecular cisplatin, we have screened the collection of Saccharomyces pathways. Both gain-of-function and loss-of-function mutations cerevisiae deletion strains. We have found reproducibly 22 can confer resistance to platinum compounds. The best known genes/open reading frames (ORF), which when deleted, confer examples are the loss of DNA mismatch repair (MMR) genes, resistance to cisplatin at a concentration that is lethal to wild- hMLH1, hMSH2, or hPMS2 (1, 4). MMR proteins function in type cells. Complementation of individual deletion strains recognition of damaged DNA adducts. Previous studies indicate with the corresponding wild-type gene abolished cisplatin that mutation or methylation-mediated silencing of these genes resistance, confirming that specific gene deletions caused the results in failure to recognize the adduct and propagate a signal to resistance. Twenty of the genes/ORFs identified have not been the apoptotic machinery, thereby producing low-level resistance to previously linked to cisplatin resistance and belong to several cisplatin (5). In addition, cisplatin treatment can enrich for malignant populations of cells that have lost DNA mismatch distinct functional groups. Major functional groups encode proteins involved in nucleotide metabolism, mRNA catabo- repair both in vitro and in vivo (4). -
Molecular Mechanism for the Subversion of the Retromer Coat By
Molecular mechanism for the subversion of the PNAS PLUS retromer coat by the Legionella effector RidL Miguel Romano-Morenoa, Adriana L. Rojasa, Chad D. Williamsonb, David C. Gershlickb, María Lucasa, Michail N. Isupovc, Juan S. Bonifacinob, Matthias P. Machnerd,1, and Aitor Hierroa,e,1 aStructural Biology Unit, Centro de Investigación Cooperativa en Biociencias, 48160 Derio, Spain; bCell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892; cThe Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter EX4 4SB, United Kingdom; dDivision of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892; and eIKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain Edited by Ralph R. Isberg, Howard Hughes Medical Institute and Tufts University School of Medicine, Boston, MA, and approved November 13, 2017 (received for review August 30, 2017) Microbial pathogens employ sophisticated virulence strategies to VAMP7 together with several Rab GTPases that function along cause infections in humans. The intracellular pathogen Legionella distinct trafficking pathways (18), and the Tre-2/Bub2/Cdc16 pneumophila encodes RidL to hijack the host scaffold protein domain family member 5 (TBC1D5), a GTPase-activating pro- VPS29, a component of retromer and retriever complexes critical for tein (GAP) that causes Rab7 inactivation and redistribution to endosomal cargo recycling. Here, we determined the crystal structure the cytosol (14). of L. pneumophila RidL in complex with the human VPS29–VPS35 Recent biochemical and structural characterization of single retromer subcomplex. A hairpin loop protruding from RidL inserts subunits and subcomplexes from retromer have provided insights into a conserved pocket on VPS29 that is also used by cellular ligands, into its modular architecture and mechanisms of action. -
A Yeast Phenomic Model for the Influence of Warburg Metabolism on Genetic Buffering of Doxorubicin Sean M
Santos and Hartman Cancer & Metabolism (2019) 7:9 https://doi.org/10.1186/s40170-019-0201-3 RESEARCH Open Access A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Sean M. Santos and John L. Hartman IV* Abstract Background: The influence of the Warburg phenomenon on chemotherapy response is unknown. Saccharomyces cerevisiae mimics the Warburg effect, repressing respiration in the presence of adequate glucose. Yeast phenomic experiments were conducted to assess potential influences of Warburg metabolism on gene-drug interaction underlying the cellular response to doxorubicin. Homologous genes from yeast phenomic and cancer pharmacogenomics data were analyzed to infer evolutionary conservation of gene-drug interaction and predict therapeutic relevance. Methods: Cell proliferation phenotypes (CPPs) of the yeast gene knockout/knockdown library were measured by quantitative high-throughput cell array phenotyping (Q-HTCP), treating with escalating doxorubicin concentrations under conditions of respiratory or glycolytic metabolism. Doxorubicin-gene interaction was quantified by departure of CPPs observed for the doxorubicin-treated mutant strain from that expected based on an interaction model. Recursive expectation-maximization clustering (REMc) and Gene Ontology (GO)-based analyses of interactions identified functional biological modules that differentially buffer or promote doxorubicin cytotoxicity with respect to Warburg metabolism. Yeast phenomic and cancer pharmacogenomics data were integrated to predict differential gene expression causally influencing doxorubicin anti-tumor efficacy. Results: Yeast compromised for genes functioning in chromatin organization, and several other cellular processes are more resistant to doxorubicin under glycolytic conditions. Thus, the Warburg transition appears to alleviate requirements for cellular functions that buffer doxorubicin cytotoxicity in a respiratory context. -
Anti-ARL8B Antibody (ARG43276)
Product datasheet [email protected] ARG43276 Package: 50 μg anti-ARL8B antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes ARL8B Tested Reactivity Hu, Ms Tested Application IHC-P, WB Host Rabbit Clonality Polyclonal Isotype IgG Target Name ARL8B Antigen Species Human Immunogen Recombinant protein corresponding to aa. 20-186 of Human ARL8B. Conjugation Un-conjugated Alternate Names Novel small G protein indispensable for equal chromosome segregation 1; ARL10C; ADP-ribosylation factor-like protein 8B; Gie1; ADP-ribosylation factor-like protein 10C Application Instructions Application table Application Dilution IHC-P 1:100 WB 4 µg/ml Application Note * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Positive Control Mouse brain, NIH/3T3 and Jurkat Calculated Mw 22 kDa Observed Size ~ 22 kDa Properties Form Liquid Purification Caprylic acid ammonium sulfate precipitation purified. Buffer 0.01 M PBS (pH 7.4), 0.03% Proclin 300 and 50% Glycerol. Preservative 0.03% Proclin 300 Stabilizer 50% Glycerol Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. www.arigobio.com 1/2 Note For laboratory research only, not for drug, diagnostic or other use. Bioinformation Gene Symbol ARL8B Gene Full Name ADP-ribosylation factor-like 8B Function Plays a role in lysosome motility (PubMed:16537643, PubMed:25898167). -
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. -
Transcriptional Profiling of Long Non-Coding Rnas and Novel
Brunner et al. Genome Biology 2012, 13:R75 http://genomebiology.com/2012/13/8/R75 RESEARCH Open Access Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers Alayne L Brunner1, Andrew H Beck1,2, Badreddin Edris1,3, Robert T Sweeney1, Shirley X Zhu1, Rui Li1, Kelli Montgomery1, Sushama Varma1, Thea Gilks1, Xiangqian Guo1, Joseph W Foley3, Daniela M Witten4, Craig P Giacomini1,5, Ryan A Flynn6, Jonathan R Pollack1, Robert Tibshirani7,8, Howard Y Chang6, Matt van de Rijn1 and Robert B West1* Abstract Background: Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs, as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-type-specific biomarkers. However, despite the potential importance of long non-coding RNAs to the cancer field, no comprehensive survey of long non-coding RNA expression across various cancers has been reported. Results: We performed a sequencing-based transcriptional survey of both known long non-coding RNAs and novel intergenic transcripts across a panel of 64 archival tumor samples comprising 17 diagnostic subtypes of adenocarcinomas, squamous cell carcinomas and sarcomas. We identified hundreds of transcripts from among the known 1,065 long non-coding RNAs surveyed that showed variability in transcript levels between the tumor types and are therefore potential biomarker candidates. We discovered 1,071 novel intergenic transcribed regions and demonstrate that these show similar patterns of variability between tumor types.