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Supplementary Figure (Legends in the main text): S1 Supplementary S2‐ qPCR data and IMAGE clones A Gene Symbol Genbank % PCR Ct range (average) Ct range (average) Ct range (average) GCRMA Efficiency Sampe 1 Sample 2 Sample 3 Intensity Ribosomal protein L35a BM191771 100% 13-20.5 (17.5) 14.3-19 (16.7) 18.7-24.7 (22.3) 2236 Ribosomal S13 BJ084503 100% 15.7‐22.5 (18.6) 17.4‐21.2 (19.2) 21.3‐27 (26.4) 2052 Ferritin S64727 100% 18.9-23.8 (21.8) 21.1-25.6 (23.4) 28.5-34.7 (31.3) 901 Solute carrier member 25 CB563860 83% 12.5-21.2 (17.9) 14.4-20 (17.6) 20.8-25.8 (23.7) 765.3 Ubiquitin C CB206065 100% 24.6-29.2 (26.5) 25.8-30.6 (27.9) 26.4-39.7 (29.9) 372.9 67 Kd laminin receptor 1 CB755985 110% 22.5-26.7 (24.8) 20.8-25.3 (22.8) 27.8-31.7 (30) 294.6 Cyclophilin A BG348966 105% 22.2-26.4 (24.5) 20.6-25.9 (23.2) 27.1-32.7 (30) 167.7 Xenopus laevis ribosomal protein S2e CD329022 100% 20.8-25 (22.9) 19.7-23.9 (21.9) 30.6-35.6 (34.1) 113.8 tumor protein translationally controlled-1 CD301671 100% 15.4‐20.5 (17.8) 19.6‐23.5 (21.4) 26.1-29.7 (29.6) 85.5 Translaon iniaon factor eIF‐5A CB563706 98% 28.3-32.5 (30.4) 31.3-38 (34) 34.9-39 (37) 71.9 Thymosin beta 4 peptide D10692 97% 23.7-30.3 (27.6) 24.3-30.8 (27.4) 33.9-38.2 (37.2) 70.3 Alpha-tubulin CB561888 97% 24.7-28.9 (26.7) 24.3-28.2 (27.4) 33.9-38.2 (37.2) 40.4 Xenopus laevis H3 histone, family 3A BU909613 100% 18.5-24.1 (21.2) 21.6-26.5 (23.9) 25.6-31.6 (28.9) 38.1 Xenopus laevis FSTL1 protein BG345976 97% 33.3-35.5 (34.1) 33.5-39 (35) - 30.6 BMP1 L12249 110% 33.9-36.2 (34.7) 34-37.4 (35.1) 36.6‐38.9 (37.3) 29.6 Tissue inhibitor of metalloproteinase 3 AF549963 97% 32.3-37.4 (34.7) 31.9-34.1 (32.9) 32-36 (33.4) 25 TaF1b BG552197 105% 31.8-36.2 (33.2) 31-32.8 (31.6) (37.5) 20.7 Furin M80472 110% (36.3) (37.6) - 15.7 Xenopus laevis protein kinase-delta2 (PKC-delta2) BG811331 100% (36.8) (36.8) (35.7) 13.5 Xnot protein Z19577 80% 33.1-35.8 (34.9) 31.5-38 (33.8) (36.3) 12.1 Casein kinase 1 epsilon AF183394 93% 34-37.8 (35.9) 36.4-38 (37.2) - 12.1 Septin 1 BJ081653 105% 32.8-35.3 (34.4) 33.9-35.8 (34.8) 32.2-34.8 (33.9) 10 14,3, 3 zeta BC041235 100% 30.6-35.8 (32.4) 30-35.4 (31.6) 30.3-35.4 (32.7) 10 Xenopus laevis immunoglobulin light chain type III mRNA CB198194 100% (37.5) (37.3) - 9.3 T cell receptor beta/TCR VDJ BV1SI BJ1 U60425 83% (32.7) - - 9.2 Xenopus laevis splicing factor 3a, subunit 2, 66kDa BC041254 100% 27.7-33.9 (31.2) 28.3-33.4 (31.3) 34.3‐38.9 (37.8) 9.1 Xenopus laevis centromere protein N BU913968 100% (34.2) (35.1) - 8.5 wnt-1 related (wnt-7a), L07533 93% 33.7-35.7 (34.4) 34.8-39.6 (36.1) - 7.9 Xenopus laevis NIF protein BI448570 110% 33.6-35.6 (34.9) 34.3-39 (34.7) - 7 Xenopus laevis, Similar to vacuolar protein sorting protein 4a BC042314 100% 31.6-32.1 (31.9) 32.5-33.6 (33.1) (34.2) 6.8 lmo4 protein AJ511277 115% 30.2-34.2 (31.2) 29.9-35.5 (32.3) 33.2-35.1 (34) 6.3 Fucolectin/X-Epilectin BJ044577 110% (33.7) (34.4) - 6.2 profilin BC046719 93% 32.7-38.8 (32.8) 32.6-36.4 (33.6) - 6 Reticulon-1 CD325641 110% (35.4) (35) (36.8) 5.7 Xenopus laevis p53-induced protein BE506430 100% 33.5-38.2 (35.8) 34.6-39.5 (35.5) (36.9) 5.5 BRAF-Serin/threonine-kinase B-type Raf kinase (diagnostic of tumors) BJ097766 80% (38) (37.1) (37.8) 5.1 Beta-tubulin BI940525 100% 28.8-32.8 (30.1) 28.3-31.6 (30.1) 30.1-35.6 (32.3) 5 GAPDH BC043972 93% - - - ‐ Genes for which primers did not work Genebank %PCR GCRMA Intensity Histocompatibility 13 BJ075766 ‐ 11.165282 Ephrin A3 BE678880 ‐ 12.398508 B IMAGE clones used for riboprobe synthesis Accession # IMAGE clones Xenopus laevis, Similar to vacuolar protein sorting protein 4a BC042314 4684120 Xenopus laevis mRNA for eph receptor tyrosine kinase (ephB4b) BQ734396 4682617 Ephrin A3 BC054997 6881147 Xenopus laevis H3 histone, family 3A BU909613 6635295 Xenopus laevis glyceraldehyde-3-phosphate dehydrogenase (GAPDH) BC043972 5571163 Cyclophilin A BC041536 5543670 Ribosomal S13 BC056028 4959636 Solute carrier member 25 BC043821 5543210 eIF5A BC045007 5542286 Ferritin BC060381 4030710 Thymosin beta 4 peptide BC169631 9041265 Ubiquitin C BC054976 6881420 67 Kd laminin receptor 1 BC046271 5572059 Alpha-tubulin BC097546 5572530 Xenopus laevis splicing factor 3a BC041254 4724871 Supplementary Figure S3 Supplementary List S4A Growth cone mRNAs idenfied in X.laevis stage 32 ('old'). Systemac Raw Common Genbank Gene Symbol Descripon Blast search Xl.1079.1.S1_at 2318.879 ferrin; n‐2 S64727 ferrin ferrin protein Xl.26216.1.S1_a_at 2235.968 rpl35a BM191771 rpl35a‐prov Ribosomal protein L35a Xl.17412.1.S1_at 2052.347 rps13 BJ084503 rps13‐prov Ribosomal protein S13 Xl.1787.2.S1_a_at 1920.799 MGC52591 BJ076931 MGC52591 ; MGC82136Similar to ribosomal protein S20 Xl.5846.6.S1_at 1218.066 ubc CB199365 mp67‐A‐prov Ubiquin C Xl.8257.1.S1_at 1079.965 MGC82973 CB590943 MGC82973 MGC82973 protein mRNA for ribosomal protein L37 Xl.7875.1.S1_a_at 765.2939 slc25a5 CB563860 slc25a5‐prov Solute carrier family 25, member 5 Xl.26216.2.S1_x_at 736.9016 rpl35a BG037819 rpl35a‐prov Ribosomal protein L35a Xl.7813.1.S1_at 602.2251 MGC85404 AW460845 MGC85404 MGC85404 protein similar to 60S RIBOSOMAL PROTEIN L38 Xl.25553.2.S1_x_at 511.0385 rps27 CD100226 rps27‐prov Ribosomal protein S27 Xl.8902.2.S1_a_at 500.3896 iff‐2 BJ090982 iff‐2‐prov Translaon iniaon factor eIF‐5A Xl.2346.1.S1_s_at 472.8415 MGC114875 BG037725 Hypothecal protein MGC114875 ribosomal protein S29 Xl.25553.1.S1_at 460.0627 rps27 CB200084 rps27‐prov Ribosomal protein S27 Xl.23700.1.S1_at 430.656 MGC82151 BJ043919 MGC82151 MGC82151 protein ribosomal protein S25 (rps25) Xl.21377.1.S1_a_at 390.3853 MGC81176 CB563956 MGC81176 Hypothecal protein MGC81176 ribosomal protein S4 Xl.6271.1.S1_at 386.4876 rpl15; MGC53462; MGC81851BC046569 rpl15‐prov ribosomal protein L15 Xl.5846.10.S1_at 372.8823 ubc CB206065 Ubiquin C Xl.6198.1.S1_at 371.7322 MGC130892 AW782650 Hypothecal protein MGC130892 ribosomal protein S15a Xl.8337.1.S1_at 361.3837 MGC82841 CB591965 MGC82841 MGC82841 protein ribosomal protein S17 Xl.26096.2.S1_at 356.7911 rpl27 CB563838 rpl27‐prov Ribosomal protein L27 Xl.20022.1.S1_at 352.896 rps14; MGC53662; MGC130808BC041512 rps14‐prov ribosomal protein S14 Xl.26095.1.S1_at 346.8538 MGC85374 CB200836 MGC85374 MGC85374 protein Unknown Xl.2617.1.S1_at 294.5482 lamr1 CB755985 lamr1‐prov Laminin receptor 1 (ribosomal protein SA, 67 kDA) Xl.6.1.S1_s_at 277.8798 ribosomal protein S1a; Rps3; MGC53327BC042230 ribosomal protein S1aribosomal protein S1a protein Xl.17432.1.S1_at 265.6118 eef1a‐s; EF‐1‐ALPHA‐SBC043843 eef1a‐s eukaryoc translaon elongaon factor 1 alpha Xl.5846.6.S1_x_at 264.6016 ubc CB199365 mp67‐A‐prov Ubiquin C Xl.3560.1.S1_at 238.3601 rpl30 CB197021 rpl30‐prov Ribosomal protein L30 Xl.1556.1.S1_a_at 235.1515 MGC64285 AW782555 MGC64285 Hypothecal protein MGC64285 similar to ribosomal protein L21 Xl.6.1.S1_at 225.5389 ribosomal protein S1a; Rps3; MGC53327BC042230 ribosomal protein S1aribosomal protein S1a protein Xl.1728.1.S1_at 223.813 arbp; MGC53408 BC042268 arbp‐prov acidic ribosomal protein P0 Xl.19115.1.S1_at 216.7019 MGC116477 AW643120 Hypothecal protein MGC116477 Unknown Xl.855.1.S1_at 207.0858 rpS8A M21485 rpS8A ; rpS8B ribosomal protein S8 Xl.848.1.S1_s_at 204.7582 MGC53393 BC042258 MGC52733 ; MGC53393similar to ribosomal protein L5 Xl.23778.1.S1_at 197.8129 MGC78859 BJ083903 MGC78859 Hypothecal protein MGC78859 similar to ribosomal protein L31 Xl.5166.1.S1_at 194.4164 rpl10a; MGC53614 BC041308 rpl10a‐prov ribosomal protein L10a Xl.2.1.S1_at 193.9232 MGC64315 X06222 MGC64315 major mRNA for ribosomal protein L14a Xl.24754.1.S1_a_at 192.2005 rps19 BF613270 rps19‐prov Ribosomal protein S19 Xl.149.1.S1_at 184.0751 rpls3‐b BC041299 LOC443740 Ribosomal protein S3B Xl.3463.2.S1_a_at 180.3435 LOC446289 CD360580 gnb2l1‐prov Hypothecal protein LOC446289 Guanine nucleode binding protein Xl.21861.1.S1_at 179.053 rps‐6; MGC64259 L19996 rps‐6‐prov ribosomal Protein, Small subunit (28.1 kD) (rps‐6) Xl.4111.1.S1_at 174.3131 hsc70; MGC52655 BC041201 hsc70‐prov Heat shock cognate protein 70 Xl.3425.1.S1_at 170.7611 rps9; MGC52774 BC041242 rps9‐prov ribosomal protein S9 Xl.3265.1.S1_at 167.7417 CypA BG348966 CypA Cyclophilin A Xl.25553.1.S1_x_at 165.266 rps27 CB200084 rps27‐prov Ribosomal protein S27 Xl.26204.1.S1_a_at 153.3365 rps11 CB563414 rps11‐prov Ribosomal protein S11 Xl.2346.1.S1_at 148.3353 MGC114875 BG037725 Hypothecal protein MGC114875 ribosomal protein S5 (rps5) Xl.8381.1.S1_at 148.0577 MGC86356 AW148275 MGC86356 MGC86356 protein 40S RIBOSOMAL PROTEIN S26 Xl.4552.1.S1_at 143.1863 MGC82306 BJ055450 MGC82306 Hypothecal protein MGC82306 ribosomal protein S18 Xl.1257.1.S1_at 133.5591 Nme1 CB942270 Nme1 NM23/nucleoside diphosphate kinase Xl.26461.1.S1_at 130.711 rpl22 X64207 rpl22 ribosomal protein L22 Xl.2125.1.S1_at 129.9928 MGC82877 BI442833 MGC82877 MGC82877 protein diazepam binding inhibitor (dbi) Xl.2227.1.S1_at 122.9055 rpl8 CD329008 rpl8‐prov Ribosomal protein L8 Xl.854.1.S1_at 117.4697 MGC52733 BC041227 MGC52733 similar to ribosomal protein L5 Xl.25283.1.S1_s_at 116.6993 MGC85348 BU904283 MGC85348 MGC85348 protein Danio rerio ribosomal protein L23a (rpl23a) Xl.3573.1.A1_at 116.3949 rpl10; MGC53488 BC044716 rpl10‐prov ribosomal protein L10 Xl.6036.1.S1_at 113.7826 rps2e CD329022 sop‐prov Ribosomal protein S2e Xl.8052.1.S1_at 110.255 MGC83421 BQ736109 rps8‐prov ; MGC83421MGC83421 protein ribosomal protein S8 (rps8) Xl.24113.1.S1_at 109.4218 MGC85310 BJ055307 MGC85310 MGC85310 protein ribosomal protein L11 Xl.5269.1.S1_at 107.4279 MGC64558 BC044685 MGC64558 hypothecal protein MGC64558 ferrin Xl.23400.1.S1_s_at 105.278
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    Supplemental Table B ARGs in alphabetical order Symbol Title 3 months 6 months 9 months 12 months 23 months ANOVA Direction Category 38597 septin 2 1557 ± 44 1555 ± 44 1579 ± 56 1655 ± 26 1691 ± 31 0.05219 up Intermediate 0610031j06rik kidney predominant protein NCU-G1 491 ± 6 504 ± 14 503 ± 11 527 ± 13 534 ± 12 0.04747 up Early Adult 1G5 vesicle-associated calmodulin-binding protein 662 ± 23 675 ± 17 629 ± 16 617 ± 20 583 ± 26 0.03129 down Intermediate A2m alpha-2-macroglobulin 262 ± 7 272 ± 8 244 ± 6 290 ± 7 353 ± 16 0.00000 up Midlife Aadat aminoadipate aminotransferase (synonym Kat2) 180 ± 5 201 ± 12 223 ± 7 244 ± 14 275 ± 7 0.00000 up Early Adult Abca2 ATP-binding cassette, sub-family A (ABC1), member 2 958 ± 28 1052 ± 58 1086 ± 36 1071 ± 44 1141 ± 41 0.05371 up Early Adult Abcb1a ATP-binding cassette, sub-family B (MDR/TAP), member 1A 136 ± 8 147 ± 6 147 ± 13 155 ± 9 185 ± 13 0.01272 up Midlife Acadl acetyl-Coenzyme A dehydrogenase, long-chain 423 ± 7 456 ± 11 478 ± 14 486 ± 13 512 ± 11 0.00003 up Early Adult Acadvl acyl-Coenzyme A dehydrogenase, very long chain 426 ± 14 414 ± 10 404 ± 13 411 ± 15 461 ± 10 0.01017 up Late Accn1 amiloride-sensitive cation channel 1, neuronal (degenerin) 242 ± 10 250 ± 9 237 ± 11 247 ± 14 212 ± 8 0.04972 down Late Actb actin, beta 12965 ± 310 13382 ± 170 13145 ± 273 13739 ± 303 14187 ± 269 0.01195 up Midlife Acvrinp1 activin receptor interacting protein 1 304 ± 18 285 ± 21 274 ± 13 297 ± 21 341 ± 14 0.03610 up Late Adk adenosine kinase 1828 ± 43 1920 ± 38 1922 ± 22 2048 ± 30 1949 ± 44 0.00797 up Early
  • 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.
  • 4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation

    4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation

    Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4).
  • The Porcine Major Histocompatibility Complex and Related Paralogous Regions: a Review Patrick Chardon, Christine Renard, Claire Gaillard, Marcel Vaiman

    The Porcine Major Histocompatibility Complex and Related Paralogous Regions: a Review Patrick Chardon, Christine Renard, Claire Gaillard, Marcel Vaiman

    The porcine Major Histocompatibility Complex and related paralogous regions: a review Patrick Chardon, Christine Renard, Claire Gaillard, Marcel Vaiman To cite this version: Patrick Chardon, Christine Renard, Claire Gaillard, Marcel Vaiman. The porcine Major Histocom- patibility Complex and related paralogous regions: a review. Genetics Selection Evolution, BioMed Central, 2000, 32 (2), pp.109-128. 10.1051/gse:2000101. hal-00894302 HAL Id: hal-00894302 https://hal.archives-ouvertes.fr/hal-00894302 Submitted on 1 Jan 2000 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. Genet. Sel. Evol. 32 (2000) 109–128 109 c INRA, EDP Sciences Review The porcine Major Histocompatibility Complex and related paralogous regions: a review Patrick CHARDON, Christine RENARD, Claire ROGEL GAILLARD, Marcel VAIMAN Laboratoire de radiobiologie et d’etude du genome, Departement de genetique animale, Institut national de la recherche agronomique, Commissariat al’energie atomique, 78352, Jouy-en-Josas Cedex, France (Received 18 November 1999; accepted 17 January 2000) Abstract – The physical alignment of the entire region of the pig major histocompat- ibility complex (MHC) has been almost completed. In swine, the MHC is called the SLA (swine leukocyte antigen) and most of its class I region has been sequenced.
  • Yeast Genome Gazetteer P35-65

    Yeast Genome Gazetteer P35-65

    gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal