Four-Dimensional Live Imaging of Apical Biosynthetic Trafficking Reveals a Post-Golgi Sorting Role of Apical Endosomal Intermediates
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Anti-Rab11 Antibody (ARG41900)
Product datasheet [email protected] ARG41900 Package: 100 μg anti-Rab11 antibody Store at: -20°C Summary Product Description Goat Polyclonal antibody recognizes Rab11 Tested Reactivity Hu, Ms, Rat, Dog, Mk Tested Application IHC-Fr, IHC-P, WB Host Goat Clonality Polyclonal Isotype IgG Target Name Rab11 Antigen Species Mouse Immunogen Purified recombinant peptides within aa. 110 to the C-terminus of Mouse Rab11a, Rab11b and Rab11c (Rab25). Conjugation Un-conjugated Alternate Names RAB11A: Rab-11; Ras-related protein Rab-11A; YL8 RAB11B: GTP-binding protein YPT3; H-YPT3; Ras-related protein Rab-11B RAB25: RAB11C; CATX-8; Ras-related protein Rab-25 Application Instructions Application table Application Dilution IHC-Fr 1:100 - 1:400 IHC-P 1:100 - 1:400 WB 1:250 - 1:2000 Application Note IHC-P: Antigen Retrieval: Heat mediation was recommended. * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Positive Control Hepa cell lysate Calculated Mw 24 kDa Observed Size ~ 26 kDa Properties Form Liquid Purification Affinity purification with immunogen. Buffer PBS, 0.05% Sodium azide and 20% Glycerol. Preservative 0.05% Sodium azide www.arigobio.com 1/3 Stabilizer 20% Glycerol Concentration 3 mg/ml 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. Note For laboratory research only, not for drug, diagnostic or other use. -
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. -
Functional Role of the C-Terminal Amphipathic Helix 8 of Olfactory Receptors and Other G Protein-Coupled Receptors
International Journal of Molecular Sciences Review Functional Role of the C-Terminal Amphipathic Helix 8 of Olfactory Receptors and Other G Protein-Coupled Receptors Takaaki Sato 1,*, Takashi Kawasaki 1, Shouhei Mine 1 and Hiroyoshi Matsumura 2 1 Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorioka, Ikeda, Osaka 563-8577, Japan; [email protected] (T.K.); [email protected] (S.M.) 2 College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-72-751-8342 Academic Editor: Kathleen Van Craenenbroeck Received: 28 September 2016; Accepted: 14 November 2016; Published: 18 November 2016 Abstract: G protein-coupled receptors (GPCRs) transduce various extracellular signals, such as neurotransmitters, hormones, light, and odorous chemicals, into intracellular signals via G protein activation during neurological, cardiovascular, sensory and reproductive signaling. Common and unique features of interactions between GPCRs and specific G proteins are important for structure-based design of drugs in order to treat GPCR-related diseases. Atomic resolution structures of GPCR complexes with G proteins have revealed shared and extensive interactions between the conserved DRY motif and other residues in transmembrane domains 3 (TM3), 5 and 6, and the target G protein C-terminal region. However, the initial interactions formed between GPCRs and their specific G proteins remain unclear. Alanine scanning mutagenesis of the murine olfactory receptor S6 (mOR-S6) indicated that the N-terminal acidic residue of helix 8 of mOR-S6 is responsible for initial transient and specific interactions with chimeric Gα15_olf, resulting in a response that is 2.2-fold more rapid and 1.7-fold more robust than the interaction with Gα15. -
Open Questions: What About the 'Other' Rho Gtpases?
Ridley BMC Biology (2016) 14:64 DOI 10.1186/s12915-016-0289-7 COMMENT Open Access Open questions: what about the ‘other’ Rho GTPases? Anne J. Ridley Abstract know if they interact with and/or regulate the activity of other family members. Indeed, by studying only RhoA, Rho GTPases have many and diverse roles in cell Rac1 and Cdc42, we are likely to be missing the real physiology, and some family members are very well functions of many GEFs and GAPs because their targets studied, including RhoA, Rac1 and Cdc42. But many in cells are among the other Rho GTPases. are relatively neglected, and fundamental questions Interestingly, four family members—Rnd1, Rnd2, Rnd3 about their mechanisms and functions remain open. and RhoH—are ‘atypical’, in that they are known to be constitutively GTP-bound and do not hydrolyse GTP: much less is known about how these family members Rho GTPases are household names for anyone who are regulated. RhoU and RhoV have high intrinsic GDP/ works on eukaryotic cell migration and their functions GTP exchange rates, so are unlikely to need GEFs for in cell migration, cell division and cell polarity are de- activation but could still be turned off by GAPs [1, 4]. scribed in most textbooks on cell biology. Yet most of For two other members, RhoBTB1 and RhoBTB2, the what we know about Rho GTPases comes from studying Rho domains are quite divergent in sequence from other a small subset of the many different family members, family members and they are unlikely to be regulated by namely RhoA, Rac1 and Cdc42. -
Mitosomes in Entamoeba Histolytica Contain a Sulfate Activation Pathway
Mitosomes in Entamoeba histolytica contain a sulfate activation pathway Fumika Mi-ichi, Mohammad Abu Yousuf, Kumiko Nakada-Tsukui, and Tomoyoshi Nozaki1 Department of Parasitology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan Edited by Andrew Roger, Dalhousie University, Halifax, NS, Canada, and accepted by the Editorial Board October 19, 2009 (received for review June 25, 2009) Hydrogenosomes and mitosomes are mitochondrion-related or- and M. balamuthi lack the ISC system, and instead possess the ganelles in anaerobic/microaerophilic eukaryotes with highly re- nitrogen fixation (NIF) system, which is most likely derived from an duced and divergent functions. The full diversity of their content ancestral nitrogen fixing -proteobacterium by lateral gene transfer and function, however, has not been fully determined. To under- (22, 24). Only 5 proteins have been demonstrated in E. histolytica stand the central role of mitosomes in Entamoeba histolytica,a mitosomes: Cpn60 (8–10, 12), Cpn10 (13), mitochondrial Hsp70 parasitic protozoon that causes amoebic dysentery and liver ab- (11, 15), pyridine nucleotide transhydrogenase (PNT) (2, 8), and scesses, we examined the proteomic profile of purified mitosomes. mitochondria carrier family (MCF, ADP/ATP transporter) (14), Using 2 discontinuous Percoll gradient centrifugation and MS and the central role of mitosomes in E. histolytica remains unknown. analysis, we identified 95 putative mitosomal proteins. Immuno- Analysis of the genome of E. histolytica has not revealed any fluorescence assay showed that 3 proteins involved in sulfate additional information regarding the function of mitosomes and activation, ATP sulfurylase, APS kinase, and inorganic pyrophos- thus, a proteomic analysis of mitosomes seems to be the best phatase, as well as sodium/sulfate symporter, involved in sulfate approach to understand its structure and function (1, 2). -
(12) United States Patent (10) Patent No.: US 9,695.227 B2 Steyaert Et Al
USOO9695227B2 (12) United States Patent (10) Patent No.: US 9,695.227 B2 Steyaert et al. (45) Date of Patent: Jul. 4, 2017 (54) BINDING DOMAINS DIRECTED AGAINST (58) Field of Classification Search GPCRG PROTEIN COMPLEXES AND USES None DERVED THEREOF See application file for complete search history. (56) References Cited (75) Inventors: Jan Steyaert, Beersel (BE); Els Pardon, Lubbeek (BE); Toon U.S. PATENT DOCUMENTS Laeremans, Dworp (BE); Brian 5,721,121 A 2/1998 Etcheverry et al. Kobilka, Palo Alto, CA (US): Soren 2007/OO77597 A1 4/2007 Gilchrist et al. Rasmussen, Frederiksberg (DK); 2007/0231830 A1 10/2007 Gilchrist et al. Sebastian Granier, Menlo Park, CA (US); Roger K. Sunahara, Ann Arbor, FOREIGN PATENT DOCUMENTS MI (US) WO 94.04678 A1 3, 1994 WO 993.7681 A2 7, 1999 (73) Assignees: Vrije Universiteit Brussel, Brussels WO OO43507 A2 T 2000 (BE); VIB VZW, Ghent (BE); The WO O190190 A2 11/2001 Board of Trustees of the Leland WO O2O85945 A2 10, 2002 Stanford Junior Universitv, Palo Alto, WO O3O25O2O A1 3, 2003 CA (US); The Regents of the WO O3035694 A2 5, 2003 WO 2004035614 A1 4/2004 University of Michigan, Ann Arbor, WO 2004.049.794 A2 6, 2004 MI (US) WO 2006086883 A1 8, 2006 WO 2009051633 4/2009 (*) Notice: Subject to any disclaimer, the term of this WO 2009,147.196 A1 12/2009 patent is extended or adjusted under 35 WO 2010043650 A2 4/2010 WO 201OO6674.0 A1 6, 2010 U.S.C. 154(b) by 594 days. WO 2012007593 A1 1, 2012 (21) Appl. -
Drosophila and Human Transcriptomic Data Mining Provides Evidence for Therapeutic
Drosophila and human transcriptomic data mining provides evidence for therapeutic mechanism of pentylenetetrazole in Down syndrome Author Abhay Sharma Institute of Genomics and Integrative Biology Council of Scientific and Industrial Research Delhi University Campus, Mall Road Delhi 110007, India Tel: +91-11-27666156, Fax: +91-11-27662407 Email: [email protected] Nature Precedings : hdl:10101/npre.2010.4330.1 Posted 5 Apr 2010 Running head: Pentylenetetrazole mechanism in Down syndrome 1 Abstract Pentylenetetrazole (PTZ) has recently been found to ameliorate cognitive impairment in rodent models of Down syndrome (DS). The mechanism underlying PTZ’s therapeutic effect is however not clear. Microarray profiling has previously reported differential expression of genes in DS. No mammalian transcriptomic data on PTZ treatment however exists. Nevertheless, a Drosophila model inspired by rodent models of PTZ induced kindling plasticity has recently been described. Microarray profiling has shown PTZ’s downregulatory effect on gene expression in fly heads. In a comparative transcriptomics approach, I have analyzed the available microarray data in order to identify potential mechanism of PTZ action in DS. I find that transcriptomic correlates of chronic PTZ in Drosophila and DS counteract each other. A significant enrichment is observed between PTZ downregulated and DS upregulated genes, and a significant depletion between PTZ downregulated and DS dowwnregulated genes. Further, the common genes in PTZ Nature Precedings : hdl:10101/npre.2010.4330.1 Posted 5 Apr 2010 downregulated and DS upregulated sets show enrichment for MAP kinase pathway. My analysis suggests that downregulation of MAP kinase pathway may mediate therapeutic effect of PTZ in DS. Existing evidence implicating MAP kinase pathway in DS supports this observation. -
A Novel Rab11-Rab3a Cascade Required for Lysosome Exocytosis
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.06.434066; this version posted March 6, 2021. 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. A novel Rab11-Rab3a cascade required for lysosome exocytosis Cristina Escrevente1,*, Liliana Bento-Lopes1*, José S Ramalho1, Duarte C Barral1,† 1 iNOVA4Health, CDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal. * These authors contributed equally to this work. † Correspondence should be sent to: Duarte C Barral, CEDOC, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria 130, 1169-056, Lisboa, Portugal, Tel: +351 218 803 102, Fax: +351 218 803 006, [email protected]. (ORCID 0000-0001-8867-2407). Abbreviations used in this paper: FIP, Rab11-family of interacting protein; GEF, guanine nucleotide exchange factor; LE, late endosomes; LRO, lysosome-related organelle; NMIIA, non-muscle myosin heavy chain IIA; Slp-4a, synaptotagmin-like protein 4a. 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.06.434066; this version posted March 6, 2021. 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. Abstract Lysosomes are dynamic organelles, capable of undergoing exocytosis. This process is crucial for several cellular functions, namely plasma membrane repair. -
Bioinformatics Analysis of Autophagy-Related Lncrnas in Esophageal Carcinoma
Bioinformatics analysis of autophagy-related lncRNAs in esophageal carcinoma Dan Wu Shanxi Medical University Yi Ding Xinjiang Medical University junbai fan ( [email protected] ) Shanxi Medical University https://orcid.org/0000-0003-3132-1715 Research article Keywords: Autophagy, Bioinformatics analysis, Esophageal carcinoma Posted Date: November 17th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-60567/v2 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at Combinatorial Chemistry & High Throughput Screening on June 24th, 2021. See the published version at https://doi.org/10.2174/1386207324666210624143452. Page 1/19 Abstract Background: Esophageal carcinoma (ESCA) is a malignant tumor with high invasiveness and mortality. Autophagy has multiple roles in the development of cancer; however, there are limited data on autophagy genes associated with long non-coding RNAs (lncRNAs) in ESCA. The purpose of this study was to screen potential diagnostic and prognostic molecules, and to identify gene co-expression networks associated with autophagy in ESCA. Methods: We downloaded transcriptome expression proles from The Cancer Genome Atlas and autophagy-related gene data from the Human Autophagy Database, and analyzed the co-expression of mRNAs and lncRNAs. In addition, the diagnostic and prognostic value of autophagy-related lncRNAs was analyzed by multivariate Cox regression. Furthermore, Kyoto Encyclopedia of Genes and Genomes analysis was carried out for high-risk patients, and enriched pathways were analyzed by gene set enrichment analysis. Results: The results showed that genes of high-risk patients were enriched in protein export and spliceosome. -
Supplementary Table 1: Significantly
Supplementary Table 1: Significantly upregulated genes in the “malignant” cluster of PNETs (p<0.05) Fold change Gene (WDEC/WDET) FEV protein 11.61 adenylate cyclase 2 (brain) 4.47 nuclear receptor subfamily 4, group A, member 2 4.45 growth arrest and DNA-damage-inducible, beta 3.28 plexin B1 3.10 neuronal PAS domain protein 2 2.92 caldesmon 1 2.81 drebrin 1 2.43 hypothetical protein BC013764 2.41 TGFB-induced factor (TALE family homeobox) 2.26 Homo sapiens cDNA FLJ12843 fis, clone NT2RP2003293, mRNA sequence 2.17 nuclear prelamin A recognition factor 2.15 chromobox homolog 4 (Pc class homolog, Drosophila) 2.14 RuvB (E coli homolog)-like 1 [Homo sapiens], mRNA sequence 2.03 latent transforming growth factor beta binding protein 4 2.02 putative glialblastoma cell differentiation-related 1.92 hypothetical protein FLJ10298 1.92 protein tyrosine phosphatase type IVA, member 1 1.90 ADP-ribosylation factor-like 4 1.88 NIMA (never in mitosis gene a)-related kinase 7 1.87 RAB11B, member RAS oncogene family 1.87 myelin transcription factor 1 1.86 centaurin, beta 2 1.83 Homo sapiens cDNA FLJ38575 fis, clone HCHON2007046, mRNA sequence 1.83 SH3 domain binding glutamic acid-rich protein like 3 1.81 immunoglobulin heavy constant gamma 3 (G3m marker) 1.77 chromobox homolog 3 (HP1 gamma homolog, Drosophila) 1.74 basic transcription element binding protein 1 1.73 H1 histone family, member X 1.73 protein phosphatase 2A, regulatory subunit B' (PR 53) 1.73 Homo sapiens cDNA FLJ30096 fis, clone BNGH41000045, mRNA sequence 1.73 KIAA0397 gene product 1.71 OK/SW-CL.4 [Homo sapiens], mRNA sequence 1.69 high-mobility group 20B 1.69 phosphoserine phosphatase 1.68 Homo sapiens mRNA; cDNA DKFZp434B142 (from clone DKFZp434B142), mRNA sequence 1.67 nuclear mitotic apparatus protein 1 1.67 hypothetical protein 628 1.66 PRKC, apoptosis, WT1, regulator 1.64 E3 ubiquitin ligase SMURF1 1.64 chromodomain protein, Y chromosome-like 1.63 hypothetical protein FLJ21839 1.62 hypothetical protein MGC2550 1.62 Suppl. -
ARL13B, PDE6D, and CEP164 Form a Functional Network for INPP5E Ciliary Targeting
ARL13B, PDE6D, and CEP164 form a functional network for INPP5E ciliary targeting Melissa C. Humberta,b, Katie Weihbrechta,b, Charles C. Searbyb,c, Yalan Lid, Robert M. Poped, Val C. Sheffieldb,c, and Seongjin Seoa,1 aDepartment of Ophthalmology and Visual Sciences, bDepartment of Pediatrics, cHoward Hughes Medical Institute, and dProteomics Facility, University of Iowa, Iowa City, IA 52242 Edited by Kathryn V. Anderson, Sloan-Kettering Institute, New York, NY, and approved October 19, 2012 (received for review June 28, 2012) Mutations affecting ciliary components cause a series of related polydactyly, skeletal defects, cleft palate, and cerebral develop- genetic disorders in humans, including nephronophthisis (NPHP), mental defects (11). Inactivation of Inpp5e in adult mice results in Joubert syndrome (JBTS), Meckel-Gruber syndrome (MKS), and Bar- obesity and photoreceptor degeneration. Interestingly, many pro- det-Biedl syndrome (BBS), which are collectively termed “ciliopa- teins that localize to cilia, including INPP5E, RPGR, PDE6 α and thies.” Recent protein–protein interaction studies combined with β subunits, GRK1 (Rhodopsin kinase), and GNGT1 (Transducin γ genetic analyses revealed that ciliopathy-related proteins form sev- chain), are prenylated (either farnesylated or geranylgeranylated), eral functional networks/modules that build and maintain the pri- and mutations in these genes or genes involved in their prenylation mary cilium. However, the precise function of many ciliopathy- (e.g., AIPL1 and RCE1) lead to photoreceptor -
Itga4 Cldn16 Cldn9 Cldn15 Cldn22 Ocln Esam
Supplementary material J Med Genet Table S1. List of 263 genes included in the AGS-LEUK panel. Axonal Guidance Signaling genes as AGS and Leukocyte transvasation genes as LEUK. List of genes (AGS) List of genes (LEUK) ABLIM1 CLDN11 ACTR3 MMP14 ADAM11 MMP15 ADAM23 CTNNA1 ADAMTS1 ENSG00000130396 ADAMTS4 CLDN6 ADAMTS9 MMP24 ARHGEF15 ARHGAP12 ARHGEF6 DLC1 ARPC1B TIMP2 BDNF RAPGEF3 BMP1 F11R BMP4 CLDN23 BMP6 CLDN8 BMP7 JAM3 CXCL12 CLDN3 CXCR4 ARHGAP8 DPYSL5 ICAM1 EFNA1 MMP16 EFNA5 JAM2 ENPEP CLDN7 EPHA1 TIMP3 EPHA3 VCAM1 EPHA5 CLDN5 EPHA7 MSN EPHB1 NOX3 EPHB2 ACTC1 EPHB4 VAV2 FGFR2 CLDN10 FZD1 RAP1GAP FZD10 VAV3 FZD5 MAPK10 FZD6 CTNNA2 GAB1 CDH5 GLI1 PECAM1 GLI3 CTNND1 GNA14 ITGA4 GNAI1 CLDN16 GNAO1 CLDN9 GNAS CLDN15 GNB4 CLDN22 GNG11 OCLN GNG2 ESAM Gallego-Martinez A, et al. J Med Genet 2019; 0:1–7. doi: 10.1136/jmedgenet-2019-106159 Supplementary material J Med Genet GNG7 ACTB IGF1 CYBA IRS1 CTNNB1 IRS2 MMP9 ITGA3 MAPK14 ITGB1 MAPK11 LIMK1 MAPK12 LIMK2 MAPK13 LINGO1 PRKCB LRRC4C PXN MME BCAR1 MMP11 THY1 MMP2 ARHGAP5 MRAS MYL2 MYL9 MYLPF NFATC4 RAP1A NGFR RAP1B NOTUM VASP NRP1 ACTN4 NTN3 ACTN1 NTRK2 VCL NTRK3 RAPGEF4 PAK3 ITK PAK4 VAV1 PAPPA2 PDGFA PDGFC PIK3CB PIK3R1 PLCE1 PLCH1 PLCH2 PLXNA2 PLXNB1 PLXND1 PPP3CA PRKACB PRKAR2A PRKAR2B PRKCA PRKCZ PRKD3 ROBO2 SDC2 SDCBP Gallego-Martinez A, et al. J Med Genet 2019; 0:1–7. doi: 10.1136/jmedgenet-2019-106159 Supplementary material J Med Genet SEMA3B SEMA3C SEMA3E SEMA3F SEMA4F SEMA4G SEMA5A SEMA6B SEMA6D SEMA7A SHC1 SLIT2 SLIT3 STK36 TUBA4A TUBB2B TUBB4A TUBB4B TUBB6 UNC5C UNC5D ENSG00000165197 WIPF1 WNT3 WNT5A WNT7A WNT7B NTNG1 NTNG2 LRRC4 NTN4 TRPC1 TRPC3 TRPC6 PPP3CB PPP3CC PPP3R1 NFATC2 NFATC3 PTK2 FYN RAC1 CDC42 ABLIM2 NCK1 PAK1 PAK2 Gallego-Martinez A, et al.