DOCSLIB.ORG

Supplementary Materials

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine 334.4 3.73 45.83 1.22 0.24 0.9 0.27 8.41 Moupinamid huanglian MOL008647 313.4 2.86 86.71 0.55 -0.5 0.3 0.33 3.71 e 11alpha,12alp ha-epoxy- 3beta-23- baishao MOL001910 dihydroxy-30- 470.7 3.91 64.77 0.09 -0.6 0.4 0.27 2.62 norolean-20- en-28,12beta- olide paeoniflorge baishao MOL001918 318.4 0.79 87.59 -0.09 -0.6 0.4 0.37 7.45 none (3S,5R,8R,9R,1 0S,14S)-3,17- dihydroxy- 4,4,8,10,14- pentamethyl- baishao MOL001919 2,3,5,6,7,9- 358.5 2.69 43.56 0 -0.4 0.5 0.35 4.34 hexahydro- 1H- cyclopenta[a]p henanthrene- 15,16-dione baishao MOL001921 Lactiflorin 462.5 -0.57 49.12 -1.13 -1.8 0.8 0.34 7.26 baishao MOL001924 paeoniflorin 480.5 -1.28 53.87 -1.47 -1.9 0.8 0.34 13.9 paeoniflorin_ baishao MOL001925 318.4 0.46 68.18 -0.34 -0.7 0.4 0.39 8.81 qt baishao MOL001928 albiflorin_qt 318.4 0.42 66.64 -0.49 -0.9 0.3 0.41 6.54 benzoyl baishao MOL001930 584.6 0.81 31.27 -0.69 -1.2 0.8 0.29 -1.9 paeoniflorin baishao MOL000211 Mairin 456.8 6.52 55.38 0.73 0.22 0.8 0.26 8.87 beta- baishao MOL000358 414.8 8.08 36.91 1.32 0.99 0.8 0.23 5.36 sitosterol baishao MOL000359 sitosterol 414.8 8.08 36.91 1.32 0.87 0.8 0.22 5.37 baishao MOL000422 kaempferol 286.3 1.77 41.88 0.26 -0.6 0.2 0 14.7 baishao MOL000492 (+)-catechin 290.3 1.92 54.83 -0.03 -0.7 0.2 0 0.61 asperglaucid zhimu MOL001677 444.6 4.02 58.02 0.28 -0.2 0.5 0.42 6.88 e zhimu MOL001944 Marmesin 246.3 2.03 50.28 0.52 0.07 0.2 0.3 -0.1 Mangiferolic zhimu MOL003773 442.8 6.47 36.16 0.66 -0.1 0.8 0.25 5.71 acid zhimu MOL000422 kaempferol 286.3 1.77 41.88 0.26 -0.6 0.2 0 14.7 Anhydroicari zhimu MOL004373 368.4 3.88 45.41 0.72 0.01 0.4 0 15 tin Anemarsapo zhimu MOL004489 432.7 3.92 60.06 0.43 -0.3 0.8 0.18 4.61 nin F_qt Chrysanthem zhimu MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin zhimu MOL004497 Hippeastrine 315.4 1.17 51.65 0.02 -0.5 0.6 0.32 8.09 Timosaponin zhimu MOL004514 416.7 4.77 35.26 0.42 -0.5 0.9 0.2 4.32 B III_qt zhimu MOL000449 Stigmasterol 412.8 7.64 43.83 1.44 1 0.8 0.22 5.57 zhimu MOL004528 Icariin I 676.7 0.77 41.58 -2.06 -3.1 0.6 0.25 18 Anemarsapo zhimu MOL004540 416.7 4.97 35.5 0.43 -0.5 0.9 0.2 3.98 nin C_qt Anemarsapo zhimu MOL004542 448.8 4.53 30.67 0.34 -0.2 0.9 0.17 5.14 nin E_qt (Z)-3-(4- hydroxy-3- methoxy- phenyl)-N-[2- MOL000483 zhimu (4- 313.4 2.86 118.4 0.51 -0.3 0.3 0 4.26 hydroxyphenyl )ethyl]acrylami de zhimu MOL000546 diosgenin 414.7 4.63 80.88 0.82 0.27 0.8 0.19 4.14 coumaroyltyr zhimu MOL000631 283.4 2.88 112.9 0.6 -0.2 0.2 0.41 5.63 amine beta- congrong MOL000358 414.8 8.08 36.91 1.32 0.99 0.8 0.23 5.36 sitosterol congrong MOL005320 arachidonate 304.5 6.41 45.57 1.27 0.58 0.2 0.26 7.56 congrong MOL005384 suchilactone 368.4 3.73 57.52 0.82 0.28 0.6 0.28 9.03 congrong MOL007563 Yangambin 446.5 2.6 57.53 0.67 0.01 0.8 0.14 3.61 congrong MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 [(7S,8R)-7- hydroxy- 5,6,7,8- tetrahydro- 3H-pyrrolizin- 1-yl]methyl congrong MOL008864 (2R)-2- 299.4 0.2 35.35 -0.27 -0.5 0.2 0.24 0.55 hydroxy-2-(1- hydroxyethyl)- 3- methylbutano ate congrong MOL008871 Marckine 475.7 5.3 37.05 0.86 -0.1 0.7 0.17 13.6 bajitian MOL001506 Supraene 410.8 11.33 33.55 2.08 1.73 0.4 0.27 2.72 bajitian MOL002879 Diop 390.6 7.44 43.59 0.79 0.26 0.4 0.28 3.6 Ethyl oleate bajitian MOL002883 310.6 7.44 32.4 1.4 1.1 0.2 0.19 4.85 (NF) beta- bajitian MOL000358 414.8 8.08 36.91 1.32 0.99 0.8 0.23 5.36 sitosterol bajitian MOL000359 sitosterol 414.8 8.08 36.91 1.32 0.87 0.8 0.22 5.37 Alizarin-2- bajitian MOL006147 254.3 2.53 32.81 0.62 -0.1 0.2 0 30.8 methylether 2-hydroxy- 1,5- dimethoxy-6- MOL009495 328.3 2.31 95.85 0.54 -0.2 0.4 0.24 30 bajitian (methoxymeth yl)-9,10- anthraquinone 1,5,7- trihydroxy-6- methoxy-2- MOL009496 330.3 1.79 80.42 0.27 -0.6 0.4 0.24 28.3 bajitian methoxymeth ylanthraceneq uinone 1,6- dihydroxy-5- methoxy-2- MOL009500 314.3 2.06 104.5 0.37 -0.3 0.3 0.28 29 bajitian (methoxymeth yl)-9,10- anthraquinone 1-hydroxy-3- methoxy- MOL009503 254.3 2.53 104.3 0.59 -0.2 0.2 0.39 30.8 bajitian 9,10- anthraquinone 1-hydroxy-6- hydroxymethy MOL009504 254.3 1.94 81.77 -0.04 -0.8 0.2 0.42 30.8 bajitian lanthracenequ inone 2-hydroxy- 1,8- dimethoxy-7- MOL009513 328.3 2.31 112.3 0.46 -0.3 0.4 0.25 29.4 bajitian methoxymeth ylanthraceneq uinone (2R,3S)-(+)- 3',5- Dihydroxy-4 MOL009519 332.3 1.99 77.24 0.13 -0.4 0.3 0.29 14.1 bajitian ,7- dimethoxydih ydroflavonol 3beta,20(R),5- bajitian MOL009524 alkenyl- 414.8 8.08 36.91 1.36 0.89 0.8 0.22 5.22 stigmastol 3beta-24S(R)- butyl-5- MOL009525 456.9 9.25 35.35 1.36 0.79 0.8 0.23 7.04 bajitian alkenyl- cholestol bajitian MOL009537 americanin A 328.3 2.3 46.71 -0.08 -1 0.4 0.41 2.6 Asperuloside bajitian MOL009541 582.6 -1.03 45.47 -1.39 -1.7 0.8 0.34 20.7 tetraacetate bajitian MOL009551 isoprincepin 494.5 2.52 49.12 -0.18 -1.5 0.8 0.32 3 2- hydroxyethyl 5-hydroxy-2- (2- MOL009558 332.3 1.41 62.32 -1.02 -1.7 0.3 0.37 17.6 bajitian hydroxybenzo yl)-4- (hydroxymeth yl)benzoate bajitian MOL009562 Ohioensin-A 372.4 3.57 38.13 0.6 -0.2 0.8 0.41 15.1 (2R)-2- [(3S,5R,10S,13 R,14R,16R,17R )-3,16- dihydroxy- 4,4,10,13,14- pentamethyl- 2,3,5,6,12,15,1 fuling MOL000273 6,17- 470.8 5.41 30.93 0.01 -0.8 0.8 0 6.81 octahydro- 1H- cyclopenta[a]p henanthren- 17-yl]-6- methylhept- 5-enoic acid trametenolic fuling MOL000275 456.8 7.03 38.71 0.52 -0.1 0.8 0 7.78 acid 7,9(11)- fuling MOL000276 dehydropach 526.8 6.1 35.11 0.03 -0.9 0.8 0 7.34 ymic acid fuling MOL000279 Cerevisterol 430.7 5.15 37.96 0.28 -0.4 0.8 0 5.31 (2R)-2- [(3S,5R,10S,13 R,14R,16R,17R )-3,16- dihydroxy- 4,4,10,13,14- pentamethyl- 2,3,5,6,12,15,1 fuling MOL000280 6,17- 484.8 5.72 31.07 0.05 -0.7 0.8 0 7.42 octahydro- 1H- cyclopenta[a]p henanthren- 17-yl]-5- isopropyl- hex-5-enoic acid ergosta- fuling MOL000282 7,22E-dien- 398.7 7.18 43.51 1.32 0.91 0.7 0 5.11 3beta-ol Ergosterol fuling MOL000283 430.7 7.17 40.36 0.84 0.34 0.8 0 3.43 peroxide (2R)-2- [(5R,10S,13R, 14R,16R,17R) -16- hydroxy-3- keto- 4,4,10,13,14- pentamethyl fuling MOL000285 482.8 5.68 38.26 0.12 -0.6 0.8 0 6.77 - 1,2,5,6,12,15, 16,17- octahydrocy clopenta[a]p henanthren- 17-yl]-5- isopropyl- 3beta- Hydroxy-24- fuling MOL000287 methylene- 470.8 7.33 38.7 0.61 -0 0.8 0 6.59 8-lanostene- pachymic21-oic acid fuling MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid fuling MOL000290 498.8 5.94 30.61 -0.14 -0.9 0.8 0 8.26 A Poricoic acid fuling MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B poricoic acid fuling MOL000292 482.8 7.11 38.15 0.32 -0.4 0.8 0 7.73 C fuling MOL000296 hederagenin 414.8 8.08 36.91 1.32 0.96 0.8 0 5.35 dehydroebur fuling MOL000300 453.8 6.35 44.17 0.38 -0.2 0.8 0.04 7.04 icoic acid 24- yinyanghuMOL001510 epicampeste 400.8 7.63 37.58 1.43 1.15 0.7 0.21 4.5 rol Linoleyl yinyanghuMOL001645 308.6 6.85 42.1 1.36 1.08 0.2 0.21 7.48 acetate poriferast-5- yinyanghuMOL001771 414.8 8.08 36.91 1.45 1.14 0.8 0 5.07 en-3beta-ol yinyanghuMOL001792 DFV 256.3 2.57 32.76 0.51 -0.3 0.2 0.42 17.9 yinyanghuMOL003044 Chryseriol 300.3 2.32 35.85 0.39 -0.5 0.3 0.32 16.3 8- yinyanghuMOL003542 Isopentenyl- 354.4 3.63 38.04 0.53 -0.5 0.4 0 15.4 kaempferol yinyanghuMOL000359 sitosterol 414.8 8.08 36.91 1.32 0.87 0.8 0.22 5.37 yinyanghuMOL000422 kaempferol 286.3 1.77 41.88 0.26 -0.6 0.2 0 14.7 yinyanghuMOL004367 olivil 376.4 1.68 62.23 -0.16 -0.8 0.4 0 2.27 Anhydroicari yinyanghuMOL004373 368.4 3.88 45.41 0.72 0.01 0.4 0 15 tin C- Homoerythri nan, 1,6- yinyanghuMOL004380 didehydro- 329.5 2.89 39.14 1.02 0.68 0.5 0 6.58 3,15,16- trimethoxy-, Yinyanghuo(3.beta.)- yinyanghuMOL004382 420.5 4.2 56.96 0.38 -0.5 0.8 0 14.4 YinyanghuoA yinyanghuMOL004384 336.4 3.39 45.67 0.75 -0.1 0.5 0 15.7 YinyanghuoC yinyanghuMOL004386 352.4 3.12 51.63 0.51 -0.5 0.6 0 15.5 E 6-hydroxy- 11,12- dimethoxy- 2,2- dimethyl- 1,8-dioxo- yinyanghuMOL004388 370.4 2.75 60.64 0.34 -0.1 0.7 0 1.22 2,3,4,8- tetrahydro- 1H- isochromeno [3,4- h]isoquinolin 8-(3- methylbut- yinyanghuMOL004391 2-enyl)-2- 290.4 4.99 48.54 1.53 0.99 0.3 0 18.7 phenyl- chromone Anhydroicari tin-3-O- yinyanghuMOL004394 676.7 0.77 41.58 -1.59 -2.9 0.6 0 16.2 alpha-L- rhamnoside 1,2-bis(4-
Recommended publications
  • Genetic Mutation Analysis of High and Low Igy Chickens by Capture Sequencing

    Genetic Mutation Analysis of High and Low Igy Chickens by Capture Sequencing

    animals Article Genetic Mutation Analysis of High and Low IgY Chickens by Capture Sequencing 1,2, 1,2, 1,3 1,2 1,2 1,2 Qiao Wang y , Fei Wang y, Lu Liu , Qinghe Li , Ranran Liu , Maiqing Zheng , Huanxian Cui 1,2, Jie Wen 1,2 and Guiping Zhao 1,2,4,* 1 Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; [email protected] (Q.W.); [email protected] (F.W.); [email protected] (L.L.); [email protected] (Q.L.); [email protected] (R.L.); [email protected] (M.Z.); [email protected] (H.C.); [email protected] (J.W.) 2 State Key Laboratory of Animal Nutrition, Beijing 100193, China 3 College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China 4 School of Life Science and Engineering, Foshan University, Foshan 528225, China * Correspondence: [email protected] These authors contributed equally to this work. y Received: 6 March 2019; Accepted: 20 May 2019; Published: 23 May 2019 Simple Summary: Immunoglobulin Y (IgY) is the major antibody produced by hens and it endows their offspring with effective humoral immunity against the pathogens. In previous research, we identified 13 genomic regions that were significantly associated with the serum IgY level or antibody responses to sheep red-blood-cells, but the specific mutations in these regions have not been reported. Therefore, we screened for variations in these regions in White Leghorn and Beijing-You chickens with high and low IgY. Our study identified 35,154 mutations and 829 Indels which were associated with IgY levels in both lines.
  • The Expression of the Human Apolipoprotein Genes and Their Regulation by Ppars

    The Expression of the Human Apolipoprotein Genes and Their Regulation by Ppars

    CORE Metadata, citation and similar papers at core.ac.uk Provided by UEF Electronic Publications The expression of the human apolipoprotein genes and their regulation by PPARs Juuso Uski M.Sc. Thesis Biochemistry Department of Biosciences University of Kuopio June 2008 Abstract The expression of the human apolipoprotein genes and their regulation by PPARs. UNIVERSITY OF KUOPIO, the Faculty of Natural and Environmental Sciences, Curriculum of Biochemistry USKI Juuso Oskari Thesis for Master of Science degree Supervisors Prof. Carsten Carlberg, Ph.D. Merja Heinäniemi, Ph.D. June 2008 Keywords: nuclear receptors; peroxisome proliferator-activated receptor; PPAR response element; apolipoprotein; lipid metabolism; high density lipoprotein; low density lipoprotein. Lipids are any fat-soluble, naturally-occurring molecules and one of their main biological functions is energy storage. Lipoproteins carry hydrophobic lipids in the water and salt-based blood environment for processing and energy supply in liver and other organs. In this study, the genomic area around the apolipoprotein genes was scanned in silico for PPAR response elements (PPREs) using the in vitro data-based computer program. Several new putative REs were found in surroundings of multiple lipoprotein genes. The responsiveness of those apolipoprotein genes to the PPAR ligands GW501516, rosiglitazone and GW7647 in the HepG2, HEK293 and THP-1 cell lines were tested with real-time PCR. The APOA1, APOA2, APOB, APOD, APOE, APOF, APOL1, APOL3, APOL5 and APOL6 genes were found to be regulated by PPARs in direct or secondary manners. Those results provide new insights in the understanding of lipid metabolism and so many lifestyle diseases like atherosclerosis, type 2 diabetes, heart disease and stroke.
  • Seq2pathway Vignette

    Seq2pathway Vignette

    seq2pathway Vignette Bin Wang, Xinan Holly Yang, Arjun Kinstlick May 19, 2021 Contents 1 Abstract 1 2 Package Installation 2 3 runseq2pathway 2 4 Two main functions 3 4.1 seq2gene . .3 4.1.1 seq2gene flowchart . .3 4.1.2 runseq2gene inputs/parameters . .5 4.1.3 runseq2gene outputs . .8 4.2 gene2pathway . 10 4.2.1 gene2pathway flowchart . 11 4.2.2 gene2pathway test inputs/parameters . 11 4.2.3 gene2pathway test outputs . 12 5 Examples 13 5.1 ChIP-seq data analysis . 13 5.1.1 Map ChIP-seq enriched peaks to genes using runseq2gene .................... 13 5.1.2 Discover enriched GO terms using gene2pathway_test with gene scores . 15 5.1.3 Discover enriched GO terms using Fisher's Exact test without gene scores . 17 5.1.4 Add description for genes . 20 5.2 RNA-seq data analysis . 20 6 R environment session 23 1 Abstract Seq2pathway is a novel computational tool to analyze functional gene-sets (including signaling pathways) using variable next-generation sequencing data[1]. Integral to this tool are the \seq2gene" and \gene2pathway" components in series that infer a quantitative pathway-level profile for each sample. The seq2gene function assigns phenotype-associated significance of genomic regions to gene-level scores, where the significance could be p-values of SNPs or point mutations, protein-binding affinity, or transcriptional expression level. The seq2gene function has the feasibility to assign non-exon regions to a range of neighboring genes besides the nearest one, thus facilitating the study of functional non-coding elements[2]. Then the gene2pathway summarizes gene-level measurements to pathway-level scores, comparing the quantity of significance for gene members within a pathway with those outside a pathway.
  • Pancreatic Beta Cells Express a Diverse Set Ofhomeobox Genes

    Pancreatic Beta Cells Express a Diverse Set Ofhomeobox Genes

    Proc. Nati. Acad. Sci. USA Vol. 91, pp. 12203-12207, December 1994 Biochemistry Pancreatic beta cells express a diverse set of homeobox genes (Lim motif/Lmx gene/Nkx gene/Alx gene/Vdx homeobox) ABRAHAM RUDNICK*t, THAI YEN LING*, HIROKI ODAGIRI*, WILLIAM J. RUTTER*t, AND MICHAEL S. GERMAN*t§ *Hormone Research Institute and Departments of tMedicine and tBiochemistry and Biophysics, University of California, San Francisco, CA 94143-0534 Contributed by William J. Rutter, August 22, 1994 ABSTRACT Homeobox genes, which are found in all RIPE3B element (16) and the P1 element (8) [also called CT1 eukaryotic organisms, encode transcriptional regulators in- (9)] lie on either side of the IEB1 element. The A/T elements volved in cell-type differentiation and development. Several and the E boxes function synergistically: none of the ele- homeobox genes encoding homeodomain proteins that bind and ments can function in isolation, but combination of an E box activate the insulin gene promoter have been described. In an and an A/T element results in dramatic activation of tran- attempt to identify additional beta-cell homeodomain proteins, scription (11, 16, 19). A number of complexes from beta-cell we designed primers based on the sequences of beta-cell nuclei bind to the A/T elements (6, 8-11, 16, 19). Some homeobox genes cdx3 and lmxl and the Drosophia homeodo- proteins in these complexes have been cloned, and they all main protein Antennapedia and used these primers to amplffy contain homeodomains. The A/T-binding proteins that have inserts by PCR from an insulinoma cDNA library.
  • Loss-Of-Function Mutation in the Dioxygenase-Encoding FTO Gene

    Loss-Of-Function Mutation in the Dioxygenase-Encoding FTO Gene

    Loss-of-Function Mutation in the Dioxygenase-Encoding FTO Gene Causes Severe Growth Retardation and Multiple Malformations Sarah Boissel, Orit Reish, Karine Proulx, Hiroko Kawagoe-Takaki, Barbara Sedgwick, Giles Yeo, David Meyre, Christelle Golzio, Florence Molinari, Noman Kadhom, et al. To cite this version: Sarah Boissel, Orit Reish, Karine Proulx, Hiroko Kawagoe-Takaki, Barbara Sedgwick, et al.. Loss-of- Function Mutation in the Dioxygenase-Encoding FTO Gene Causes Severe Growth Retardation and Multiple Malformations. American Journal of Human Genetics, Elsevier (Cell Press), 2009, 85 (1), pp.106-111. 10.1016/j.ajhg.2009.06.002. hal-02044723 HAL Id: hal-02044723 https://hal.archives-ouvertes.fr/hal-02044723 Submitted on 21 Feb 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. REPORT Loss-of-Function Mutation in the Dioxygenase-Encoding FTO Gene Causes Severe Growth Retardation and Multiple Malformations Sarah Boissel,1,7 Orit Reish,2,7 Karine Proulx,3,7 Hiroko Kawagoe-Takaki,4 Barbara Sedgwick,4 Giles S.H. Yeo,3 David Meyre,5 Christelle Golzio,1 Florence Molinari,1 Noman Kadhom,1 Heather C. Etchevers,1 Vladimir Saudek,3 I. Sadaf Farooqi,3 Philippe Froguel,5,6 Tomas Lindahl,4 Stephen O’Rahilly,3 Arnold Munnich,1 and Laurence Colleaux1,* FTO is a nuclear protein belonging to the AlkB-related non-haem iron- and 2-oxoglutarate-dependent dioxygenase family.
  • Defining Functional Interactions During Biogenesis of Epithelial Junctions

    Defining Functional Interactions During Biogenesis of Epithelial Junctions

    ARTICLE Received 11 Dec 2015 | Accepted 13 Oct 2016 | Published 6 Dec 2016 | Updated 5 Jan 2017 DOI: 10.1038/ncomms13542 OPEN Defining functional interactions during biogenesis of epithelial junctions J.C. Erasmus1,*, S. Bruche1,*,w, L. Pizarro1,2,*, N. Maimari1,3,*, T. Poggioli1,w, C. Tomlinson4,J.Lees5, I. Zalivina1,w, A. Wheeler1,w, A. Alberts6, A. Russo2 & V.M.M. Braga1 In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases. 1 National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. 2 Computing Department, Imperial College London, London SW7 2AZ, UK. 3 Bioengineering Department, Faculty of Engineering, Imperial College London, London SW7 2AZ, UK. 4 Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    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.
  • Neurodegenerative Triplet Repeat Expansion Disorders

    Neurodegenerative Triplet Repeat Expansion Disorders

    The Pharma Innovation Journal 2018; 7(11): 34-40 ISSN (E): 2277- 7695 ISSN (P): 2349-8242 NAAS Rating: 5.03 Neurodegenerative triplet repeat expansion disorders: TPI 2018; 7(11): 34-40 © 2018 TPI A review www.thepharmajournal.com Received: 15-09-2018 Accepted: 20-10-2018 Mitesh Patel, RK Patel, Tushar Chauhan, Jigar Suthar and Sanjay Dave Mitesh Patel Genetics Group of Gujarat Abstract Diagnostic Centre, Mehsana, Epigenetic alterations are the major causes of triplet repeat expansion. The repetitive DNA expands of its Gujarat, India normal length results in sever neurodegenerative conditions. The common types of triplet repeat expansion (TNE) disorders are: Huntington disease, Friedreich ataxia, myotonic dystrophy, SBMA and RK Patel SCA1 out of which Huntington disease, SBMA and SCA1 are categorized as a poly glutamine disorder Sandor Animal Biogenics Pvt. due to the repeat of CAG. In contrast, the friedreich ataxia is occurred due to expansion of the GAA Ltd., Hyderabad, Telangana, whereas myotonic dystrophy is due to the expansion of CTG. The triplet disease follows the mechanism India of anticipation in which the onset of the disease increases with age. Conclusively, no clear mechanism can explain the origin of the disease. The pre mutation can be expanded in full mutation in successive Tushar Chauhan Genetics Group of Gujarat generations and the number of repeats increased with each generation. TNE can observe in both somatic Diagnostic Centre, Mehsana, as well as germ line tissues. Gujarat, India Keywords: triplet repeat expansion disorder, trinucleotide repeats, Huntington disease, SBMA, SCA1, Jigar Suthar friedreich ataxia Genetics Group of Gujarat Diagnostic Centre, Mehsana, Introduction Gujarat, India Since the early 1990s, a new class of molecular disease has been characterized based upon the Sanjay Dave presence of unstable and abnormal expansions of DNA-triplets (Trinucleotides).
  • Polyclonal Antibody to ARFGAP3 (C-Term) - Aff - Purified

    Polyclonal Antibody to ARFGAP3 (C-Term) - Aff - Purified

    OriGene Technologies, Inc. OriGene Technologies GmbH 9620 Medical Center Drive, Ste 200 Schillerstr. 5 Rockville, MD 20850 32052 Herford UNITED STATES GERMANY Phone: +1-888-267-4436 Phone: +49-5221-34606-0 Fax: +1-301-340-8606 Fax: +49-5221-34606-11 [email protected] [email protected] AP15932PU-N Polyclonal Antibody to ARFGAP3 (C-term) - Aff - Purified Alternate names: ADP-ribosylation factor GTPase-activating protein 3, ARF GAP 3, ARFGAP1 Quantity: 0.1 mg Concentration: 0.5 mg/ml Background: The protein encoded by this gene is a GTPase-activating protein (GAP) which associates with the Golgi apparatus and which is thought to interact with ADP- ribosylation factor 1 (ARF1). The encoded protein likely promotes hydrolysis of ARF1-bound GTP, which is required for the dissociation of coat proteins from Golgi- derived membranes and vesicles. Dissociation of the coat proteins is a prerequisite for the fusion of these vesicles with target compartments. The activity of this protein is sensitive to phospholipids. This gene was originally known as ARFGAP1, but that is now the name of a related but different gene. Uniprot ID: Q9NP61 NCBI: NP_055385.3 GeneID: 26286 Host: Goat Immunogen: Peptide from C Terminus of the protein sequence according to NP_055385.3; NP_001135765.1 Genename: ARFGAP3 AA Sequence: C-NGVVTSIQDRYGS Format: State: Liquid Ig fraction Purification: Ammonium sulphate precipitation followed by antigen affinity chromatography using the immunizing peptide Buffer System: Tris saline, 0.02% sodium azide, pH7.3 with 0.5% bovine serum albumin Applications: Peptide ELISA: Limit dilution 1:8000. Western blot: 1-3 µg/ml.
  • The Role of High Density Lipoprotein Compositional and Functional Heterogeneity in Metabolic Disease

    The Role of High Density Lipoprotein Compositional and Functional Heterogeneity in Metabolic Disease

    The role of high density lipoprotein compositional and functional heterogeneity in metabolic disease By Scott M. Gordon B.S. State University of New York College at Brockport October, 2012 A Dissertation Presented to the Faculty of The University of Cincinnati College of Medicine in partial fulfillment of the requirements for the Degree of Doctor of Philosophy from the Pathobiology and Molecular Medicine graduate program W. Sean Davidson Ph.D. (Chair) David Askew Ph.D. Professor and Thesis Chair Professor Department of Pathology Department of Pathology University of Cincinnati University of Cincinnati Francis McCormack M.D. Gangani Silva Ph.D. Professor Assistant Professor Department of Pathology Department of Pathology University of Cincinnati University of Cincinnati Jason Lu Ph.D. Assistant Professor Division of Bioinformatics Cincinnati Children’s Hospital i Abstract High density lipoproteins (HDL) are complexes of phospholipid, cholesterol and protein that circulate in the blood. Epidemiological studies have demonstrated a strong inverse correlation between plasma levels of HDL associated cholesterol (HDL-C) and the incidence of cardiovascular disease (CVD). Clinically, HDL-C is often measured and used in combination with low density lipoprotein cholesterol (LDL-C) to assess overall cardiovascular health. HDL have been shown to possess a wide variety of functional attributes which likely contribute to this protection including anti-inflammatory and anti- oxidative properties and the ability to remove excess cholesterol from peripheral tissues and deliver it to the liver for excretion, a process known as reverse cholesterol transport. This functional diversity might be explained by the complexity of HDL composition. Recent studies have taken advantage of advances in mass spectrometry technologies to characterize the proteome of total HDL finding that over 50 different proteins can associate with these particles.
  • Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice

    Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice

    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Nutrition Publications and Other Works Nutrition 12-19-2010 Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P. Stewart Marshall University Hyoung Y. Kim University of Tennessee - Knoxville, [email protected] Arnold M. Saxton University of Tennessee - Knoxville, [email protected] Jung H. Kim Marshall University Follow this and additional works at: https://trace.tennessee.edu/utk_nutrpubs Part of the Animal Sciences Commons, and the Nutrition Commons Recommended Citation BMC Genomics 2010, 11:713 doi:10.1186/1471-2164-11-713 This Article is brought to you for free and open access by the Nutrition at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Nutrition Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Stewart et al. BMC Genomics 2010, 11:713 http://www.biomedcentral.com/1471-2164/11/713 RESEARCH ARTICLE Open Access Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P Stewart1, Hyoung Yon Kim2, Arnold M Saxton3, Jung Han Kim1* Abstract Background: Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/ JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia.
  • 1 Supporting Information for a Microrna Network Regulates

    1 Supporting Information for a Microrna Network Regulates

    Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia.