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SUPPLEMENTARY DATA Supplementary Table 1. Polyphenolic composition of the red grape extract used during the study. Powder humidity (%) 4.2 Total Polyphenols as catechin equivalent (eq) (%) 108.2 Total Polyphenols as gallic acid equivalent (%) 64.4 (Folin–Ciocalteu method) Procyanidins as catechin equivalent (%) 17.9 (Vanillin method) Procyanidins profile by High Performance Liquid Chromatography (HPLC) (%): Catechin as catechin eq 2.07 Epicatechin as epicatechin eq 0.53 Procyanidin dimer B1 as dimer B1 eq 1.97 Procyanidin dimer B1 as dimer B2 eq 1.11 Anthocyanins (Ribereau Gayon method) (%) 4.3 Anthocyanins profile by (HPLC) (%): Delphinidin as delphinidin eq 0.08 Cyanidin as cyanidin eq 0.014 Petunidin as petunidin eq 0.1 Peonidin as peonidin eq 0.11 Malvidin as malvidin eq 0.1 Resveratrol by HPLC as trans resveratrol eq (ppm) 533 Pesticides (ppm) In compliance with (Liste Pharmacopée Européenne 5ème Ed) European regulations ©2012 American Diabetes Association. Published online at http://care.diabetesjournals.org/lookup/suppl/doi:10.2337/dc12-1652/-/DC1 SUPPLEMENTARY DATA Supplementary Table 2. RT-PCR primer sequences. CKMT2 forward : CTCATCGATGACCACTTTCTG CKMT2 reverse : ATTCCACATGAACTCCCAGC CPT1b forward :TACAACAGGTGGTTTGACA CPT1b reverse: CAGAGGTGCCCAATGATG UCP3 forward: ATGGACGCCTACAGAACCAT UCP3 reverse: CTGGGCCACCATCTTTATCA PGC1a forward: TCCTCTGACCCCAGAGTCAC PGC1a reverse: CTTGGTTGGCTTTATGAGGAGG NRF1 forward: GCTGCTGCTGTGGCAACAGG NRF1 reverse: TTGGGTTTGGAGGGTGAGAT NRF2 forward: CCAAGTCCTGCATTGGGTGG NRF2 reverse: GCAAAAACTGCCATAGTTGG PPARa forward: GCTATCATTACGGAGTCCACG PPARa reverse: AGCTGCGGTCGCACTTGTCA PPARb forward: ACTGCCGCTTCCAGAAGTGC PPARb reverse: GCCACCAGCTTCCTCTTCTC ©2012 American Diabetes Association. Published online at http://care.diabetesjournals.org/lookup/suppl/doi:10.2337/dc12-1652/-/DC1 SUPPLEMENTARY DATA Supplementary Table 3. Systemic and muscle antioxidant defenses: vitamin E, plasma SOD, GSH/GSSG (18PCB/20PP); muscle Gpx, Mn- SOD, SOD, catalase activities (9PCB/10PP). There were no significant differences among groups. Values are given as means ± SEM (18PCB/20PP). Post 8wk Post 6d Fructose after 8wk Baseline supplementation supplementation PCB PP PCB PP PCB PP Plasma vitamin E (µmol/L) 26.3 ± 1.4 25.3 ± 1.9 25.0 ± 1.8 24.3 ± 1.1 25.0 ± 1.8 25.5 ± 1.8 SOD activity (U/mg Hb) 1.60 ± 0.11 1.64 ± 0.06 1.61 ± 0.05 1.50 ± 0.09 1.67 ± 0.09 1.62 ± 0.07 GSH/GSSG 20.85 ± 2.78 18.59 ± 2.31 20.92 ± 3.41 16.73 ± 1.62 18.60 ± 2.62 18.59 ± 2.02 GPx (mU/g wet weight) 6518 ± 500 6390 ± 890 6598 ± 533 6220 ± 482 5916 ± 521 6904 ± 635 Mn-SOD (U/g wet weight) 58 ± 4 63 ± 7 66 ± 5 64 ± 6 73 ± 9 66 ± 6 SOD (U/g wet weight) 264 ± 14 272 ± 18 265 ± 15 269 ± 13 283 ± 14 298 ± 12 Catalase (U/g wet weight) 9553 ± 1626 8851 ± 1745 8570 ± 1352 8191 ± 1661 7246 ± 1439 8009 ± 1189 ©2012 American Diabetes Association. Published online at http://care.diabetesjournals.org/lookup/suppl/doi:10.2337/dc12-1652/-/DC1 SUPPLEMENTARY DATA Supplementary Table 4. Inflammatory cytokines and adipokines throughout study exploration visits; plasma inflammatory cytokines and adipokines of reruited subjects. There were no significant differences among groups.Values are given as means ± SEM (18PCB/20PP). Post 6d Fructose after 8wk Baseline Post 8wk supplementation supplementation PCB PP PCB PP PCB PP IL-1ɑ (pg/ml) 1.10 ± 0.25 1.08 ± 0.12 1.10 ± 0.22 0.93 ± 0.06 1.06 ± 0.18 1.01 ± 0.08 IL-1β (pg/ml) 1.40 ± 0.06 1.48 ± 0.07 1.44 ± 0.06 1.64 ± 0.17 1.45 ± 0.08 1.49 ± 0.06 IL-6 (pg/ml) 1.73 ± 0.26 1.84 ± 0.28 1.56 ± 0.18 1.57 ± 0.25 1.46 ± 0.14 1.64 ± 0.19 IL-4 (pg/ml) 2.05 ± 0.20 2.51 ± 0.20 2.35 ± 0.22 2.40 ± 0.20 2.41 ± 0.22 2.27 ± 0.33 TNF-ɑ (pg/ml) 2.51 ± 0.19 2.86 ± 0.21 2.50 ± 0.17 2.70 ± 0.22 2.84 ± 0.27 2.79 ± 0.19 Interferon-ɣ (pg/ml) 2.28 ± 0.19 2.68 ± 0.30 2.26 ± 0.23 2.32 ± 0.16 2.04 ± 0.05 2.29 ± 0.20 Adiponectin (µg/ml) 9.6 ± 1.1 7.3 ± 0.7 9.9 ± 1.1 7.8 ± 1.1 9.3 ± 1.0 7.5 ± 1.0 Leptin (ng/ml) 25.7 ± 4.8 22.6 ± 4.1 27.5 ± 4.8 24.9 ± 5.0 28.6 ± 5.5 25.3 ± 4.6 Ghrelin (pg/ml) 439 ± 66 307 ± 46 387 ± 52 349 ± 43 441 ± 49 354 ± 46 Resistin (ng/ml) 3.6 ± 0.4 3.9 ± 0.3 3.7 ± 0.5 3.6 ± 0.4 3.8 ± 0.6 3.5 ± 0.3 ©2012 American Diabetes Association. Published online at http://care.diabetesjournals.org/lookup/suppl/doi:10.2337/dc12-1652/-/DC1 SUPPLEMENTARY DATA Supplementary Table 5. List of the differentially regulated genes in reponse to Polyphenols/Placebo between the 2 groups. Symbol Gene Name Gene ID FC PCB FC PP ratio PCB/PP p-value ARHGEF26 Rho guanine nucleotide exchange factor (GEF) 26 26084 1.28 ± 0.07 0.93 ± 0.05 1.38 0.0007 SEL1L3 sel-1 suppressor of lin-12-like 3 (C. elegans) 23231 1.16 ± 0.03 0.92 ± 0.04 1.26 0.0007 NELL1 NEL-like 1 (chicken) 4745 0.63 ± 0.11 1.30 ± 0.14 0.48 0.002 ZNF44 zinc finger protein 44 51710 1.08 ± 0.06 0.77 ± 0.06 1.41 0.002 ENO1 enolase 1, (alpha) 2023 0.79 ± 0.07 1.33 ± 0.14 0.60 0.002 ABLIM3 actin binding LIM protein family, member 3 22885 1.16 ± 0.03 0.95 ± 0.04 1.22 0.002 FAM217A family with sequence similarity 217, member A 222826 0.66 ± 0.11 1.35 ± 0.15 0.49 0.002 DLEU2L deleted in lymphocytic leukemia 2-like 79469 0.80 ± 0.12 1.67 ± 0.21 0.48 0.002 BC067907 clone IMAGE 30330955 0.78 ± 0.07 1.08 ± 0.06 0.73 0.002 IGFN1 immunoglobulin-like and fibronectin type III domain containing 1 91156 1.29 ± 0.28 0.47 ± 0.09 2.75 0.003 SMG6 Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans) 23293 1.19 ± 0.07 0.93 ± 0.03 1.29 0.003 TUSC3 tumor suppressor candidate 3 7991 1.21 ± 0.07 0.90 ± 0.07 1.35 0.003 HNRNPA1L2 heterogeneous nuclear ribonucleoprotein A1-like 2 144983 1.07 ± 0.04 0.87 ± 0.03 1.23 0.003 LRRK2 leucine-rich repeat kinase 2 120892 0.88 ± 0.05 1.18 ± 0.07 0.74 0.003 AGAP2 ArfGAP with GTPase domain, ankyrin repeat and PH domain 2 116986 1.01 ± 0.04 1.27 ± 0.06 0.80 0.003 DAZAP2 DAZ associated protein 2 9802 1.10 ± 0.05 0.87 ± 0.04 1.26 0.003 ART3 ADP-ribosyltransferase 3 419 1.01 ± 0.07 1.56 ± 0.17 0.65 0.004 TMEM214 transmembrane protein 214 54867 1.08 ± 0.04 0.89 ± 0.03 1.22 0.004 SCIMP SLP adaptor and CSK interacting membrane protein 388325 0.64 ± 0.12 1.21 ± 0.20 0.53 0.004 HPYR1 Helicobacter pylori responsive 1 93668 0.78 ± 0.09 1.77 ± 0.37 0.44 0.004 HGS hepatocyte growth factor-regulated tyrosine kinase substrate 9146 1.10 ± 0.05 0.89 ± 0.03 1.24 0.004 GZF1 GDNF-inducible zinc finger protein 1 64412 1.08 ± 0.05 0.88 ± 0.03 1.23 0.005 SUB1 SUB1 homolog (S. cerevisiae) 10923 1.10 ± 0.04 0.92 ± 0.02 1.20 0.005 ©2012 American Diabetes Association. Published online at http://care.diabetesjournals.org/lookup/suppl/doi:10.2337/dc12-1652/-/DC1 SUPPLEMENTARY DATA Symbol Gene Name Gene ID FC PCB FC PP ratio PCB/PP p-value TGIF1 TGFB-induced factor homeobox 1 7050 0.88 ± 0.11 1.39 ± 0.14 0.64 0.005 TRB@ T cell receptor beta locus 6957 0.80 ± 0.06 1.20 ± 0.11 0.66 0.005 MTMR1 myotubularin related protein 1 8776 1.40 ± 0.16 0.84 ± 0.09 1.66 0.005 ECHDC1 enoyl CoA hydratase domain containing 1 55862 1.08 ± 0.04 0.88 ± 0.04 1.23 0.005 SLC16A6 solute carrier family 16, member 6 (monocarboxylic acid transporter 7) 9120 0.71 ± 0.10 1.19 ± 0.14 0.60 0.005 CHN2 chimerin (chimaerin) 2 1124 0.78 ± 0.09 1.40 ± 0.22 0.56 0.005 DRAM1 DNA-damage regulated autophagy modulator 1 55332 1.10 ± 0.04 0.90 ± 0.04 1.22 0.006 HSD11B1 hydroxysteroid (11-beta) dehydrogenase 1 3290 1.25 ± 0.13 0.86 ± 0.05 1.46 0.006 PGM3 phosphoglucomutase 3 5238 1.14 ± 0.04 0.94 ± 0.03 1.21 0.006 RNGTT RNA guanylyltransferase and 5'-phosphatase 8732 0.70 ± 0.07 1.03 ± 0.08 0.68 0.006 AATF apoptosis antagonizing transcription factor 26574 1.05 ± 0.03 0.89 ± 0.03 1.19 0.006 ABLIM3 actin binding LIM protein family, member 3 22885 1.17 ± 0.06 0.92 ± 0.05 1.27 0.006 AIM2 absent in melanoma 2 9447 0.57 ± 0.11 1.57 ± 0.36 0.36 0.007 LBX1 ladybird homeobox 1 10660 0.92 ± 0.04 1.17 ± 0.06 0.79 0.007 KPNB1 karyopherin (importin) beta 1 3837 1.16 ± 0.04 0.94 ± 0.04 1.23 0.007 LIMD1 LIM domains containing 1 8994 0.84 ± 0.07 1.51 ± 0.24 0.56 0.007 TTC37 tetratricopeptide repeat domain 37 9652 0.92 ± 0.04 1.14 ± 0.05 0.81 0.007 GRM7 glutamate receptor, metabotropic 7 2917 0.65 ± 0.06 1.42 ± 0.39 0.46 0.007 COL19A1 collagen, type XIX, alpha 1 1310 1.35 ± 0.50 7.49 ± 3.88 0.18 0.007 CRB1 crumbs homolog 1 (Drosophila) 23418 1.28 ± 0.15 0.72 ± 0.14 1.79 0.007 ERO1L ERO1-like (S.
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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.
  • Download The

    Download The

    PROBING THE INTERACTION OF ASPERGILLUS FUMIGATUS CONIDIA AND HUMAN AIRWAY EPITHELIAL CELLS BY TRANSCRIPTIONAL PROFILING IN BOTH SPECIES by POL GOMEZ B.Sc., The University of British Columbia, 2002 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in THE FACULTY OF GRADUATE STUDIES (Experimental Medicine) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) January 2010 © Pol Gomez, 2010 ABSTRACT The cells of the airway epithelium play critical roles in host defense to inhaled irritants, and in asthma pathogenesis. These cells are constantly exposed to environmental factors, including the conidia of the ubiquitous mould Aspergillus fumigatus, which are small enough to reach the alveoli. A. fumigatus is associated with a spectrum of diseases ranging from asthma and allergic bronchopulmonary aspergillosis to aspergilloma and invasive aspergillosis. Airway epithelial cells have been shown to internalize A. fumigatus conidia in vitro, but the implications of this process for pathogenesis remain unclear. We have developed a cell culture model for this interaction using the human bronchial epithelium cell line 16HBE and a transgenic A. fumigatus strain expressing green fluorescent protein (GFP). Immunofluorescent staining and nystatin protection assays indicated that cells internalized upwards of 50% of bound conidia. Using fluorescence-activated cell sorting (FACS), cells directly interacting with conidia and cells not associated with any conidia were sorted into separate samples, with an overall accuracy of 75%. Genome-wide transcriptional profiling using microarrays revealed significant responses of 16HBE cells and conidia to each other. Significant changes in gene expression were identified between cells and conidia incubated alone versus together, as well as between GFP positive and negative sorted cells.
  • Biochemical and Cellular Studies of Vertebrate Globins

    Biochemical and Cellular Studies of Vertebrate Globins

    Biochemical and Cellular Studies of Vertebrate Globins By Shun Wilford Tse Thesis submitted for the degree of Doctor of Philosophy School of Biological Sciences University of East Anglia September 2015 © This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that no quotations from the thesis, nor any information derived there-from may be published without the author's prior, written consent. Abstract Human cytoglobin is a small heme-containing protein in the globin superfamily with a wide range of tissue and organ distribution. Although several cellular functions have been proposed for cytoglobin, the exact physiological function is still not fully defined. Recently, cytoglobin has been implicated to have a regulatory role in cancer cells to control cell proliferation and migration depending on cellular oxygen level. In order to gain a better understanding of a structure-to-function relationship of cytoglobin as a heme-protein and to evaluate its possible physiological function(s) in cancer cells, a combination of techniques, including protein engineering and advanced spectroscopies, was deployed. In this study, recombinant human cytoglobin purified from E.coli was purified as a monomeric protein, but displayed a dimeric property in solution. An intra-molecular disulphide bond is formed within the protein which has a redox potential at ca -280 mV. Advanced spectroscopic studies confirmed a low-spin bis-histidyl heme in cytoglobin in both ferric and ferrous state regardless of the state of the disulphide bond. Furthermore, nitrite reductase activitiy in globins was investigated in detail using myoglobin as a model to explore the biochemical basis of the distal histidine residue in determining activity.