Supporting Appendix 2: Confounding Genes Linked to Parkin (Park2)
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32-2748: PSMB1 Recombinant Protein Description Product Info
9853 Pacific Heights Blvd. Suite D. San Diego, CA 92121, USA Tel: 858-263-4982 Email: [email protected] 32-2748: PSMB1 Recombinant Protein Alternative HC5,PSC5,PMSB1,FLJ25321,KIAA1838,PSMB1,Proteasome subunit beta type-1,Proteasome component Name : C5,Macropain subunit C5,Multicatalytic endopeptidase complex subunit C5,Proteasome gamma chain. Description Source : Escherichia Coli. PSMB1 Human Recombinant fused to 37 amino acid His Tag at N-terminal produced in E.Coli is a single, non-glycosylated, polypeptide chain containing 250 amino acids (30-241) and having a molecular mass of 27.7 kDa. The PSMB1 is purified by proprietary chromatographic techniques. PSMB1 is part of the proteasome B-type family, also identified as the T1B family, that is a 20S core beta subunit. PSMB1 is tightly linked to the TBP (TATA-binding protein) gene in human and in mouse, and is transcribed in the opposite orientation in both species.The main function of PSMB1 is its degradation activity of unnecessary or damaged proteins by proteolysis. PSMB1 is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with arg, phe, tyr, leu, and glu adjacent to the leaving group at neutral or slightly basic ph. the proteasome has an atp-dependent proteolytic activity. Product Info Amount : 10 µg Purification : Greater than 95.0% as determined by SDS-PAGE. Content : The PSMB1 solution contains 20mM Tris-HCl pH-8, 1mM DTT and 10% glycerol. PSMB1 Recombinant Human although stable at 4°C for 30 days, should be stored desiccated Storage condition : below -20°C for periods greater than 30 days. -
King's Research Portal
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by King's Research Portal King’s Research Portal DOI: 10.1016/j.biotechadv.2017.05.004 Document Version Publisher's PDF, also known as Version of record Link to publication record in King's Research Portal Citation for published version (APA): Neville, J. J., Orlando, J., Mann, K., McCloskey, B., & Antoniou, M. N. (2017). Ubiquitous Chromatin-opening Elements (UCOEs): Applications in biomanufacturing and gene therapy. BIOTECHNOLOGY ADVANCES, 557- 564. DOI: 10.1016/j.biotechadv.2017.05.004 Citing this paper Please note that where the full-text provided on King's Research Portal is the Author Accepted Manuscript or Post-Print version this may differ from the final Published version. If citing, it is advised that you check and use the publisher's definitive version for pagination, volume/issue, and date of publication details. And where the final published version is provided on the Research Portal, if citing you are again advised to check the publisher's website for any subsequent corrections. General rights Copyright and moral rights for the publications made accessible in the Research Portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognize and abide by the legal requirements associated with these rights. •Users may download and print one copy of any publication from the Research Portal for the purpose of private study or research. •You may not further distribute the material or use it for any profit-making activity or commercial gain •You may freely distribute the URL identifying the publication in the Research Portal Take down policy If you believe that this document breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. -
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. -
Recombinant Human PSMB1 Protein Catalog Number: ATGP0275
Recombinant human PSMB1 protein Catalog Number: ATGP0275 PRODUCT INPORMATION Expression system E.coli Domain 30-241aa UniProt No. P20618 NCBI Accession No. NP_002784.1 Alternative Names Proteasome subunit beta type-1, Proteasome subunit, beta type-1, PSC5, Proteasome subunit, beta type-1 FLJ25321, HC5, KIAA1838, Macropain subunit C5, Multicatalytic endopeptidase complex subunit C5, Proteasome (prosome macropain) subunit beta type 1, Proteasome beta 1 subunit, Proteasome component C5, Proteasome gamma chain, Proteasome subunit HC5, Proteasome subunit beta type 1, PSMB 1, PSMB1. PRODUCT SPECIFICATION Molecular Weight 27.7 kDa (250aa) confirmed by MALDI-TOF Concentration 1mg/ml (determined by Bradford assay) Formulation Liquid in. 20mM Tris-HCl buffer (pH 8.0) containing 1mM DTT, 10% glycerol Purity > 95% by SDS-PAGE Tag His-Tag Application SDS-PAGE Storage Condition Can be stored at +2C to +8C for 1 week. For long term storage, aliquot and store at -20C to -80C. Avoid repeated freezing and thawing cycles. BACKGROUND Description PSMB1 (Proteasome subunit, beta type-1) encodes a member of the proteasome B-type family, also known as the T1B family, that is a 20S core beta subunit. This is tightly linked to the TBP (TATA-binding protein) gene in human and in mouse, and is transcribed in the opposite orientation in both species. The main function of PSMB1 1 Recombinant human PSMB1 protein Catalog Number: ATGP0275 is to degrade unnecessary or damaged proteins by proteolysis. Recombinant human PSMB1 protein, fused to His- tag at N-terminus, was expressed in E. coli and purified by using conventional chromatography. Amino acid Sequence <MRGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDRWGSHM>FS PYVFNGGTIL AIAGEDFAIV ASDTRLSEGF SIHTRDSPKC YKLTDKTVIG CSGFHGDCLT LTKIIEARLK MYKHSNNKAM TTGAIAAMLS TILYSRRFFP YYVYNIIGGL DEEGKGAVYS FDPVGSYQRD SFKAGGSASA MLQPLLDNQV GFKNMQNVEH VPLSLDRAMR LVKDVFISAA ERDVYTGDAL RICIVTKEGI REETVSLRKD General References Coux O., et al. -
PSMB1 Polyclonal Antibody Gene Symbol: PSMB1
PSMB1 polyclonal antibody Gene Symbol: PSMB1 Gene Alias: FLJ25321, HC5, KIAA1838, PMSB1, PSC5 Catalog Number: PAB22318 Gene Summary: The proteasome is a multicatalytic Regulatory Status: For research use only (RUO) proteinase complex with a highly ordered ring-shaped Product Description: Rabbit polyclonal antibody raised 20S core structure. The core structure is composed of 4 against recombinant PSMB1. rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta Immunogen: Recombinant protein corresponding to subunits. Proteasomes are distributed throughout amino acids of human PSMB1. eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a Sequence: non-lysosomal pathway. An essential function of a YQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVP modified proteasome, the immunoproteasome, is the LSLDRAMRLVKDVFISAAERDVYTGDALRICIVTKEGIR processing of class I MHC peptides. This gene encodes EETVSLRKD a member of the proteasome B-type family, also known as the T1B family, that is a 20S core beta subunit. This Host: Rabbit gene is tightly linked to the TBP (TATA-binding protein) gene in human and in mouse, and is transcribed in the Reactivity: Human,Mouse,Rat opposite orientation in both species. [provided by RefSeq] Applications: IHC-P, WB (See our web site product page for detailed applications information) Protocols: See our web site at http://www.abnova.com/support/protocols.asp or product page for detailed protocols Form: Liquid Purification: Antigen affinity purification Isotype: IgG Recommend Usage: Immunohistochemistry (1:200-1:500) Western Blot (1:250-1:500) The optimal working dilution should be determined by the end user. -
Role of Phytochemicals in Colon Cancer Prevention: a Nutrigenomics Approach
Role of phytochemicals in colon cancer prevention: a nutrigenomics approach Marjan J van Erk Promotor: Prof. Dr. P.J. van Bladeren Hoogleraar in de Toxicokinetiek en Biotransformatie Wageningen Universiteit Co-promotoren: Dr. Ir. J.M.M.J.G. Aarts Universitair Docent, Sectie Toxicologie Wageningen Universiteit Dr. Ir. B. van Ommen Senior Research Fellow Nutritional Systems Biology TNO Voeding, Zeist Promotiecommissie: Prof. Dr. P. Dolara University of Florence, Italy Prof. Dr. J.A.M. Leunissen Wageningen Universiteit Prof. Dr. J.C. Mathers University of Newcastle, United Kingdom Prof. Dr. M. Müller Wageningen Universiteit Dit onderzoek is uitgevoerd binnen de onderzoekschool VLAG Role of phytochemicals in colon cancer prevention: a nutrigenomics approach Marjan Jolanda van Erk Proefschrift ter verkrijging van graad van doctor op gezag van de rector magnificus van Wageningen Universiteit, Prof.Dr.Ir. L. Speelman, in het openbaar te verdedigen op vrijdag 1 oktober 2004 des namiddags te vier uur in de Aula Title Role of phytochemicals in colon cancer prevention: a nutrigenomics approach Author Marjan Jolanda van Erk Thesis Wageningen University, Wageningen, the Netherlands (2004) with abstract, with references, with summary in Dutch ISBN 90-8504-085-X ABSTRACT Role of phytochemicals in colon cancer prevention: a nutrigenomics approach Specific food compounds, especially from fruits and vegetables, may protect against development of colon cancer. In this thesis effects and mechanisms of various phytochemicals in relation to colon cancer prevention were studied through application of large-scale gene expression profiling. Expression measurement of thousands of genes can yield a more complete and in-depth insight into the mode of action of the compounds. -
Anti-Inflammatory Role of Curcumin in LPS Treated A549 Cells at Global Proteome Level and on Mycobacterial Infection
Anti-inflammatory Role of Curcumin in LPS Treated A549 cells at Global Proteome level and on Mycobacterial infection. Suchita Singh1,+, Rakesh Arya2,3,+, Rhishikesh R Bargaje1, Mrinal Kumar Das2,4, Subia Akram2, Hossain Md. Faruquee2,5, Rajendra Kumar Behera3, Ranjan Kumar Nanda2,*, Anurag Agrawal1 1Center of Excellence for Translational Research in Asthma and Lung Disease, CSIR- Institute of Genomics and Integrative Biology, New Delhi, 110025, India. 2Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India. 3School of Life Sciences, Sambalpur University, Jyoti Vihar, Sambalpur, Orissa, 768019, India. 4Department of Respiratory Sciences, #211, Maurice Shock Building, University of Leicester, LE1 9HN 5Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia- 7003, Bangladesh. +Contributed equally for this work. S-1 70 G1 S 60 G2/M 50 40 30 % of cells 20 10 0 CURI LPSI LPSCUR Figure S1: Effect of curcumin and/or LPS treatment on A549 cell viability A549 cells were treated with curcumin (10 µM) and/or LPS or 1 µg/ml for the indicated times and after fixation were stained with propidium iodide and Annexin V-FITC. The DNA contents were determined by flow cytometry to calculate percentage of cells present in each phase of the cell cycle (G1, S and G2/M) using Flowing analysis software. S-2 Figure S2: Total proteins identified in all the three experiments and their distribution betwee curcumin and/or LPS treated conditions. The proteins showing differential expressions (log2 fold change≥2) in these experiments were presented in the venn diagram and certain number of proteins are common in all three experiments. -
The Pathogenetic Role of Β-Cell Mitochondria in Type 2 Diabetes
236 3 Journal of M Fex et al. Mitochondria in β-cells 236:3 R145–R159 Endocrinology REVIEW The pathogenetic role of β-cell mitochondria in type 2 diabetes Malin Fex1, Lisa M Nicholas1, Neelanjan Vishnu1, Anya Medina1, Vladimir V Sharoyko1, David G Nicholls1, Peter Spégel1,2 and Hindrik Mulder1 1Department of Clinical Sciences in Malmö, Unit of Molecular Metabolism, Lund University Diabetes Centre, Clinical Research Center, Malmö University Hospital, Lund University, Malmö, Sweden 2Department of Chemistry, Center for Analysis and Synthesis, Lund University, Sweden Correspondence should be addressed to H Mulder: [email protected] Abstract Mitochondrial metabolism is a major determinant of insulin secretion from pancreatic Key Words β-cells. Type 2 diabetes evolves when β-cells fail to release appropriate amounts f TCA cycle of insulin in response to glucose. This results in hyperglycemia and metabolic f coupling signal dysregulation. Evidence has recently been mounting that mitochondrial dysfunction f oxidative phosphorylation plays an important role in these processes. Monogenic dysfunction of mitochondria is a f mitochondrial transcription rare condition but causes a type 2 diabetes-like syndrome owing to β-cell failure. Here, f genetic variation we describe novel advances in research on mitochondrial dysfunction in the β-cell in type 2 diabetes, with a focus on human studies. Relevant studies in animal and cell models of the disease are described. Transcriptional and translational regulation in mitochondria are particularly emphasized. The role of metabolic enzymes and pathways and their impact on β-cell function in type 2 diabetes pathophysiology are discussed. The role of genetic variation in mitochondrial function leading to type 2 diabetes is highlighted. -
Modulation of Mitochondrial DNA Copy Number in a Model of Glioblastoma
Sun and St John Epigenetics & Chromatin (2018) 11:53 https://doi.org/10.1186/s13072-018-0223-z Epigenetics & Chromatin RESEARCH Open Access Modulation of mitochondrial DNA copy number in a model of glioblastoma induces changes to DNA methylation and gene expression of the nuclear genome in tumours Xin Sun1,2 and Justin C. St John1,2* Abstract Background: There are multiple copies of mitochondrial DNA (mtDNA) present in each cell type, and they are strictly regulated in a cell-specifc manner by a group of nuclear-encoded mtDNA-specifc replication factors. This strict regu- lation of mtDNA copy number is mediated by cell-specifc DNA methylation of these replication factors. Glioblastoma multiforme, HSR-GBM1, cells are hyper-methylated and maintain low mtDNA copy number to support their tumori- genic status. We have previously shown that when HSR-GBM1 cells with 50% of their original mtDNA content were inoculated into mice, tumours grew more aggressively than non-depleted cells. However, when the cells possessed only 3% and 0.2% of their original mtDNA content, tumour formation was less frequent and the initiation of tumori- genesis was signifcantly delayed. Importantly, the process of tumorigenesis was dependent on mtDNA copy number being restored to pre-depletion levels. Results: By performing whole genome MeDIP-Seq and RNA-Seq on tumours generated from cells possessing 100%, 50%, 0.3% and 0.2% of their original mtDNA content, we determined that restoration of mtDNA copy number caused signifcant changes to both the nuclear methylome and its transcriptome for each tumour type. The afected genes were specifcally associated with gene networks and pathways involving behaviour, nervous system development, cell diferentiation and regulation of transcription and cellular processes. -
Comparative Transcriptomics Identifies Potential Stemness-Related Markers for Mesenchymal Stromal/Stem Cells
bioRxiv preprint doi: https://doi.org/10.1101/2021.05.25.445659; this version posted May 26, 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. Comparative Transcriptomics Identifies Potential Stemness-Related Markers for Mesenchymal Stromal/Stem Cells Authors Myret Ghabriel 1, Ahmed El Hosseiny 1, 2, Ahmed Moustafa*1, 2 and Asma Amleh*1, 2 Affiliations 1Biotechnology Program, American University in Cairo, New Cairo 11835, Egypt 2Department of Biology, American University in Cairo, New Cairo 11835, Egypt *Corresponding authors: Ahmed Moustafa [email protected] Asma Amleh [email protected]. Abstract Mesenchymal stromal/stem cells (MSCs) are multipotent cells residing in multiple tissues with the capacity for self-renewal and differentiation into various cell types. These properties make them promising candidates for regenerative therapies. MSC identification is critical in yielding pure populations for successful therapeutic applications; however, the criteria for MSC identification proposed by the International Society for Cellular Therapy (ISCT) is inconsistent across different tissue sources. In this study, we aimed to identify potential markers to be used together with the ISCT’s criteria to provide a more accurate means of MSC identification. Thus, we carried out a comparative analysis of the expression of human and mouse MSCs derived from multiple tissues to identify the common differentially expressed genes. We show that six members of the proteasome degradation system are similarly expressed across MSCs derived from bone marrow, adipose tissue, amnion, and umbilical cord. -
Supplementary Table 2
Supplementary Table 2. Differentially Expressed Genes following Sham treatment relative to Untreated Controls Fold Change Accession Name Symbol 3 h 12 h NM_013121 CD28 antigen Cd28 12.82 BG665360 FMS-like tyrosine kinase 1 Flt1 9.63 NM_012701 Adrenergic receptor, beta 1 Adrb1 8.24 0.46 U20796 Nuclear receptor subfamily 1, group D, member 2 Nr1d2 7.22 NM_017116 Calpain 2 Capn2 6.41 BE097282 Guanine nucleotide binding protein, alpha 12 Gna12 6.21 NM_053328 Basic helix-loop-helix domain containing, class B2 Bhlhb2 5.79 NM_053831 Guanylate cyclase 2f Gucy2f 5.71 AW251703 Tumor necrosis factor receptor superfamily, member 12a Tnfrsf12a 5.57 NM_021691 Twist homolog 2 (Drosophila) Twist2 5.42 NM_133550 Fc receptor, IgE, low affinity II, alpha polypeptide Fcer2a 4.93 NM_031120 Signal sequence receptor, gamma Ssr3 4.84 NM_053544 Secreted frizzled-related protein 4 Sfrp4 4.73 NM_053910 Pleckstrin homology, Sec7 and coiled/coil domains 1 Pscd1 4.69 BE113233 Suppressor of cytokine signaling 2 Socs2 4.68 NM_053949 Potassium voltage-gated channel, subfamily H (eag- Kcnh2 4.60 related), member 2 NM_017305 Glutamate cysteine ligase, modifier subunit Gclm 4.59 NM_017309 Protein phospatase 3, regulatory subunit B, alpha Ppp3r1 4.54 isoform,type 1 NM_012765 5-hydroxytryptamine (serotonin) receptor 2C Htr2c 4.46 NM_017218 V-erb-b2 erythroblastic leukemia viral oncogene homolog Erbb3 4.42 3 (avian) AW918369 Zinc finger protein 191 Zfp191 4.38 NM_031034 Guanine nucleotide binding protein, alpha 12 Gna12 4.38 NM_017020 Interleukin 6 receptor Il6r 4.37 AJ002942 -
Overexpression of the Mitochondrial Methyltransferase TFB1M in The
HMG Advance Access published October 12, 2015 1 Overexpression of the mitochondrial methyltransferase TFB1M in the mouse does not impact mitoribosomal methylation status or hearing Seungmin Lee1, Simon Rose2, Metodi D. Metodiev3, Lore Becker4,5, Alexandra Vernaleken4,5,6, Thomas Klopstock5,6, Valerie Gailus-Durner4, Helmut Fuchs4, Downloaded from Martin Hrabě de Angelis4,6,7,8, Stephen Douthwaite2, Nils-Göran Larsson1,9,* 1Department of Laboratory Medicine, Karolinska Institutet, Retzius väg 8, 171 77 http://hmg.oxfordjournals.org/ Stockholm, Sweden 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark 3INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, at GSF Forschungszentrum on October 16, 2015 75015 Paris, France 4German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Munich/Neuherberg, Germany 5Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University, Munich, Germany 6German Center for Vertigo and Balance Disorders, Munich, Germany 7Chair of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising-Weihenstephan, Germany 8German Center for Diabetes Research (DZD), Ingostaedter Landstr. 1, 85764 Neuherberg, Germany 9Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, 50931 Cologne, Germany © The Author 2015. Published by Oxford