Adipocyte Xbp1s Promotes Adiponectin Multimerization and Systemic
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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. -
Snps) Distant from Xenobiotic Response Elements Can Modulate Aryl Hydrocarbon Receptor Function: SNP-Dependent CYP1A1 Induction S
Supplemental material to this article can be found at: http://dmd.aspetjournals.org/content/suppl/2018/07/06/dmd.118.082164.DC1 1521-009X/46/9/1372–1381$35.00 https://doi.org/10.1124/dmd.118.082164 DRUG METABOLISM AND DISPOSITION Drug Metab Dispos 46:1372–1381, September 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Single Nucleotide Polymorphisms (SNPs) Distant from Xenobiotic Response Elements Can Modulate Aryl Hydrocarbon Receptor Function: SNP-Dependent CYP1A1 Induction s Duan Liu, Sisi Qin, Balmiki Ray,1 Krishna R. Kalari, Liewei Wang, and Richard M. Weinshilboum Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.L., S.Q., B.R., L.W., R.M.W.) and Division of Biomedical Statistics and Informatics, Department of Health Sciences Research (K.R.K.), Mayo Clinic, Rochester, Minnesota Received April 22, 2018; accepted June 28, 2018 ABSTRACT Downloaded from CYP1A1 expression can be upregulated by the ligand-activated aryl fashion. LCLs with the AA genotype displayed significantly higher hydrocarbon receptor (AHR). Based on prior observations with AHR-XRE binding and CYP1A1 mRNA expression after 3MC estrogen receptors and estrogen response elements, we tested treatment than did those with the GG genotype. Electrophoretic the hypothesis that single-nucleotide polymorphisms (SNPs) map- mobility shift assay (EMSA) showed that oligonucleotides with the ping hundreds of base pairs (bp) from xenobiotic response elements AA genotype displayed higher LCL nuclear extract binding after (XREs) might influence AHR binding and subsequent gene expres- 3MC treatment than did those with the GG genotype, and mass dmd.aspetjournals.org sion. -
Protein Interactions in the Cancer Proteome† Cite This: Mol
Molecular BioSystems View Article Online PAPER View Journal | View Issue Small-molecule binding sites to explore protein– protein interactions in the cancer proteome† Cite this: Mol. BioSyst., 2016, 12,3067 David Xu,ab Shadia I. Jalal,c George W. Sledge Jr.d and Samy O. Meroueh*aef The Cancer Genome Atlas (TCGA) offers an unprecedented opportunity to identify small-molecule binding sites on proteins with overexpressed mRNA levels that correlate with poor survival. Here, we analyze RNA-seq and clinical data for 10 tumor types to identify genes that are both overexpressed and correlate with patient survival. Protein products of these genes were scanned for binding sites that possess shape and physicochemical properties that can accommodate small-molecule probes or therapeutic agents (druggable). These binding sites were classified as enzyme active sites (ENZ), protein–protein interaction sites (PPI), or other sites whose function is unknown (OTH). Interestingly, the overwhelming majority of binding sites were classified as OTH. We find that ENZ, PPI, and OTH binding sites often occurred on the same structure suggesting that many of these OTH cavities can be used for allosteric modulation of Creative Commons Attribution 3.0 Unported Licence. enzyme activity or protein–protein interactions with small molecules. We discovered several ENZ (PYCR1, QPRT,andHSPA6)andPPI(CASC5, ZBTB32,andCSAD) binding sites on proteins that have been seldom explored in cancer. We also found proteins that have been extensively studied in cancer that have not been previously explored with small molecules that harbor ENZ (PKMYT1, STEAP3,andNNMT) and PPI (HNF4A, MEF2B,andCBX2) binding sites. All binding sites were classified by the signaling pathways to Received 29th March 2016, which the protein that harbors them belongs using KEGG. -
The Physiological Functions of Mammalian Endoplasmic Oxidoreductin 1: on Disulfides and More
ANTIOXIDANTS & REDOX SIGNALING Volume 16, Number 10, 2012 FORUM REVIEW ARTICLE ª Mary Ann Liebert, Inc. DOI: 10.1089/ars.2011.4475 The Physiological Functions of Mammalian Endoplasmic Oxidoreductin 1: On Disulfides and More Thomas Ramming and Christian Appenzeller-Herzog Abstract Significance: The oxidative process of disulfide-bond formation is essential for the folding of most secretory and membrane proteins in the endoplasmic reticulum (ER). It is driven by electron relay pathways that transfer two electrons derived from the fusion of two adjacent cysteinyl side chains onto various types of chemical oxidants. The conserved, ER-resident endoplasmic oxidoreductin 1 (Ero1) sulfhydryl oxidases that reduce molecular oxygen to generate an active-site disulfide represent one of these pathways. In mammals, two family members exist, Ero1a and Ero1b. Recent Advances: The two mammalian Ero1 enzymes differ in transcriptional and post- translational regulation, tissue distribution, and catalytic turnover. A specific protein–protein interaction be- tween either isoform and protein disulfide isomerase (PDI) facilitates the propagation of disulfides from Ero1 via PDI to nascent polypeptides, and inbuilt oxidative shutdown mechanisms in Ero1a and Ero1b prevent excessive oxidation of PDI. Critical Issues: Besides disulfide-bond generation, Ero1a also regulates calcium release from the ER and the secretion of disulfide-linked oligomers through its reversible association with the chaperone ERp44. This review explores the functional repertoire and possible redundancy of mammalian Ero1 enzymes. Future Directions: Systematic analyses of different knockout mouse models will be the most promising strategy to shed new light on unique and tissue-specific roles of Ero1a and Ero1b. Moreover, in-depth characterization of the known physical interactions of Ero1 with peroxidases and PDI family members will help broaden our functional and mechanistic understanding of Ero1 enzymes. -
GSTK1 Rabbit Pab
Leader in Biomolecular Solutions for Life Science GSTK1 Rabbit pAb Catalog No.: A5226 1 Publications Basic Information Background Catalog No. This gene encodes a member of the kappa class of the glutathione transferase A5226 superfamily of enzymes that function in cellular detoxification. The encoded protein is localized to the peroxisome and catalyzes the conjugation of glutathione to a wide Observed MW range of hydrophobic substates facilitating the removal of these compounds from cells. 25KDa Alternative splicing results in multiple transcript variants. Calculated MW 20kDa/24kDa/25kDa/31kDa Category Primary antibody Applications WB, IHC, IF Cross-Reactivity Human, Mouse, Rat Recommended Dilutions Immunogen Information WB 1:500 - 1:2000 Gene ID Swiss Prot 373156 Q9Y2Q3 IHC 1:50 - 1:100 Immunogen 1:50 - 1:100 IF Recombinant fusion protein containing a sequence corresponding to amino acids 1-226 of human GSTK1 (NP_057001.1). Synonyms GSTK1;GST;GST 13-13;GST13;GST13-13;GSTK1-1;hGSTK1 Contact Product Information www.abclonal.com Source Isotype Purification Rabbit IgG Affinity purification Storage Store at -20℃. Avoid freeze / thaw cycles. Buffer: PBS with 0.02% sodium azide,50% glycerol,pH7.3. Validation Data Western blot analysis of extracts of various cell lines, using GSTK1 antibody (A5226) at 1:1000 dilution. Secondary antibody: HRP Goat Anti-Rabbit IgG (H+L) (AS014) at 1:10000 dilution. Lysates/proteins: 25ug per lane. Blocking buffer: 3% nonfat dry milk in TBST. Detection: ECL Basic Kit (RM00020). Exposure time: 60s. Immunohistochemistry of paraffin- Immunohistochemistry of paraffin- Immunohistochemistry of paraffin- embedded human lung cancer using embedded human liver cancer using embedded human thyroid cancer using GSTK1 Rabbit pAb (A5226) at dilution of GSTK1 Rabbit pAb (A5226) at dilution of GSTK1 Rabbit pAb (A5226) at dilution of 1:25 (40x lens). -
Identification of Novel Mouse Delta1 Target Genes: Combination of Transcriptomics and Proteomics
Institut für Experimentelle Genetik GSF – Forschungszentrum für Umwelt und Gesundheit Identification of novel mouse Delta1 target genes: Combination of transcriptomics and proteomics Christine Hutterer Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Univ.-Prof. Dr. A. Gierl Prüfer der Dissertation: 1. apl. Prof. Dr. J. Adamski 2. Univ.-Prof. Dr. W. Wurst Die Dissertation wurde am 31.01.2005 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 13.05.2005 angenommen. DANKSAGUNG Besonderer Dank gebührt Prof. Dr. Martin Hrabé de Angelis, Leiter des Instituts für experimentelle Genetik. Unter anderem durch seine Leidenschaft für die Wissenschaft wollte ich am IEG arbeiten. Ich möchte mich jedoch nicht nur für die wissenschaftlichen Ratschläge und Diskussionen bedanken, sondern auch für viele interessante nicht-wissenschaftliche Gespräche. Ebenfalls besonders bedanke ich mich bei meinem Doktorvater Dr. Jurek Adamski, dessen fachliche Meinung und positive Einstellung mich sehr motivierte. Großen Dank möchte ich der gesamten „Beckers-Arbeitsgruppe“ aussprechen. Allen voran Dr. Johannes Beckers, Leiter der Genregulation und Expression Profiling Arbeitsgruppe, für die Überlassung des Themas und die Betreuung meiner Doktorarbeit, die mir viel Entscheidungsfreiraum ließ, sowie für zahlreiche gute Ideen und lehrreiche Gespräche. Bei Tomek Mijalski möchte ich mich für seine stetige Hilfsbereitschaft und die entstandene Freundschaft besonders bedanken. Weiterhin bedanke ich mich ganz herzlich bei Dr. Sonja Becker für wertvolle Labortricks und Kniffe, die Durchsicht des Manuskripts und ihre herzliche Art. Vielen Dank an dieser Stelle auch an Kathrin Seidel für die gute technische Unterstützung im Labor und mit der Mausarbeit. -
Characterization of Visceral and Subcutaneous Adipose Tissue
J. Perinat. Med. 2016; 44(7): 813–835 Shali Mazaki-Tovi*, Adi L. Tarca, Edi Vaisbuch, Juan Pedro Kusanovic, Nandor Gabor Than, Tinnakorn Chaiworapongsa, Zhong Dong, Sonia S. Hassan and Roberto Romero* Characterization of visceral and subcutaneous adipose tissue transcriptome in pregnant women with and without spontaneous labor at term: implication of alternative splicing in the metabolic adaptations of adipose tissue to parturition DOI 10.1515/jpm-2015-0259 groups (unpaired analyses) and adipose tissue regions Received July 27, 2015. Accepted October 26, 2015. Previously (paired analyses). Selected genes were tested by quantita- published online March 19, 2016. tive reverse transcription-polymerase chain reaction. Abstract Results: Four hundred and eighty-two genes were differ- entially expressed between visceral and subcutaneous Objective: The aim of this study was to determine gene fat of pregnant women with spontaneous labor at term expression and splicing changes associated with par- (q-value < 0.1; fold change > 1.5). Biological processes turition and regions (visceral vs. subcutaneous) of the enriched in this comparison included tissue and vascu- adipose tissue of pregnant women. lature development as well as inflammatory and meta- Study design: The transcriptome of visceral and abdomi- bolic pathways. Differential splicing was found for 42 nal subcutaneous adipose tissue from pregnant women at genes [q-value < 0.1; differences in Finding Isoforms using term with (n = 15) and without (n = 25) spontaneous labor Robust Multichip Analysis scores > 2] between adipose was profiled with the Affymetrix GeneChip Human Exon tissue regions of women not in labor. Differential exon 1.0 ST array. Overall gene expression changes and the dif- usage associated with parturition was found for three ferential exon usage rate were compared between patient genes (LIMS1, HSPA5, and GSTK1) in subcutaneous tissues. -
Whole Egg Consumption Increases Gene Expression Within the Glutathione Pathway in the Liver of Zucker Diabetic Fatty Rats
Food Science and Human Nutrition Publications Food Science and Human Nutrition 11-3-2020 Whole egg consumption increases gene expression within the glutathione pathway in the liver of Zucker Diabetic Fatty rats Joe L. Webb Iowa State University Amanda E. Bries Iowa State University, [email protected] Brooke Vogel Iowa State University Claudia Carrillo Iowa State University, [email protected] Lily Harvison Iowa State University, [email protected] See next page for additional authors Follow this and additional works at: https://lib.dr.iastate.edu/fshn_hs_pubs Part of the Dietetics and Clinical Nutrition Commons, Endocrinology, Diabetes, and Metabolism Commons, Exercise Science Commons, Food Chemistry Commons, Human and Clinical Nutrition Commons, and the Molecular, Genetic, and Biochemical Nutrition Commons The complete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ fshn_hs_pubs/38. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Food Science and Human Nutrition at Iowa State University Digital Repository. It has been accepted for inclusion in Food Science and Human Nutrition Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Whole egg consumption increases gene expression within the glutathione pathway in the liver of Zucker Diabetic Fatty rats Abstract Nutrigenomic evidence supports the idea that Type 2 Diabetes Mellitus (T2DM) arises due to the interactions between the transcriptome, individual genetic profiles, lifestyle, and diet. Since eggs are a nutrient dense food containing bioactive ingredients that modify gene expression, our goal was to examine the role of whole egg consumption on the transcriptome during T2DM. -
9 Glutathione S-Transferases
Enzyme Systems that Metabolise Drugs and Other Xenobiotics. Edited by Costas Ioannides Copyright # 2001 John Wiley & Sons Ltd ISBNs: 0-471-894-66-4 %Hardback); 0-470-84630-5 %Electronic) 9 Glutathione S-transferases Philip J. Sherratt and John D. Hayes University of Dundee, UK Introduction Glutathione S-transferase GST; EC 2.5.1.18) isoenzymes are ubiquitously distributed in nature, being found in organisms as diverse as microbes, insects, plants, ®sh, birds andmammals Hayes andPulford1995). The transferases possess various activities andparticipate in several differenttypes of reaction. Most of these enzymes can catalyse the conjugation of reduced glutathione GSH) with compounds that contain an electrophilic centre through the formation of a thioether bondbetween the sulphur atom of GSH and the substrate Chasseaud 1979; Mannervik 1985). In addition to conjugation reactions, a number of GST isoenzymes exhibit other GSH-dependent catalytic activities including the reduction of organic hydroperoxides Ketterer et al. 1990) andisomerisation of various unsaturatedcompoundsBenson et al. 1977; Jakoby andHabig 1980). These enzymes also have several non-catalytic functions that relate to the sequestering of carcinogens, intracellular transport of a wide spectrum of hydrophobic ligands, and modulation of signal transduction pathways Listowsky 1993; Adler et al. 1999; Cho et al. 2001). Glutathione S-transferases represent a complex grouping of proteins. Two entirely distinct superfamilies of enzyme have evolved that possess transferase activity Hayes andStrange 2000). The ®rst enzymes to be characterisedwere the cytosolic, or soluble, GSTs BoylandandChasseaud1969; Mannervik 1985). To dateat least 16 members of this superfamily have been identi®ed in humans Board et al. 1997, 2000; Hayes and Strange 2000). -
Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in -
Resolution of Conflict Between Parental Genomes in a Hybrid Species
bioRxiv preprint doi: https://doi.org/10.1101/102970; this version posted January 25, 2017. 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. 1 Title: Resolution of conflict between parental genomes in a hybrid species 2 3 4 5 6 7 8 9 10 11 Fabrice Eroukhmanoff1†, Richard I. Bailey1,2†, Tore O. Elgvin1, Jo S. Hermansen1, Anna R. 12 Runemark1, Cassandra N. Trier1, Glenn-Peter Sætre1 13 1Department of Biosciences, Centre for Evolutionary and Ecological Synthesis, University of 14 Oslo, Norway. 2Division of Animal Evolutionary Biology, Department of Zoology, Faculty of 15 Science, Charles University in Prague, Viničná 7, 128 44 Praha, Czech Republic. 16 17 Corresponding author: [email protected] 18 19 †These authors contributed equally to the manuscript 20 21 22 23 24 25 26 1 bioRxiv preprint doi: https://doi.org/10.1101/102970; this version posted January 25, 2017. 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. 27 Abstract: 28 The development of reproductive barriers against parent species is crucial during hybrid 29 speciation, and post-zygotic isolation can be important in this process. Genetic 30 incompatibilities that normally isolate the parent species can become sorted in hybrids to form 31 reproductive barriers towards either parent. However, the extent to which this sorting process 32 is systematically biased and therefore predictable in which loci are involved and which alleles 33 are favored is largely unknown. -
Recombinant Human ERO1-Like Protein A/ERO1L (C-6His)
9853 Pacific Heights Blvd. Suite D. San Diego, CA 92121, USA Tel: 858-263-4982 Email: [email protected] 32-7771: Recombinant Human ERO1-Like Protein a/ERO1L (C-6His) Gene : ERO1A Gene ID : 30001 Uniprot ID : Q96HE7 Description Source: Human Cells. MW :53kD. Recombinant Human ERO1L is produced by our Mammalian expression system and the target gene encoding Glu24-His468 is expressed with a 6His tag at the C-terminus. ERO1-Like Protein a (ERO1L) is an enzyme that belongs to the EROs family. ERO1L is expressed at high level in esophagus and upper digestive tract. ERO1L is an essential oxidoreductase that oxidizes proteins in the endoplasmic reticulum to produce disulfide bonds. ERO1L acts by oxidizing directly P4HB/PDI isomerase through a direct disulfide exchange. It associates with ERP44, demonstrating that it does not oxidize all PDI related proteins and can discriminate between PDI and related proteins. Its reoxidation probably involves electron transfer to molecular oxygen via FAD. ERO1L may be responsible for a significant proportion of reactive oxygen species (ROS) in the cell. ERO1L responses to temperature stimulus, protein thiol-disulfide exchange, protein folding with or without chaperone cofactor and transport. Product Info Amount : 10 µg / 50 µg Content : Lyophilized from a 0.2 µm filtered solution of 20mM PB,150mM NaCl,pH7.4. Lyophilized protein should be stored at -20°C, though stable at room temperature for 3 weeks. Storage condition : Reconstituted protein solution can be stored at 4-7°C for 2-7 days. Aliquots of reconstituted samples are stable at -20°C for 3 months.