Effect of Fucoxanthinol on Pancreatic
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ANALYTICAL SCIENCES NOVEMBER 2020, VOL. 36 1 2020 © The Japan Society for Analytical Chemistry Supporting Information Fig. S1 Detailed MS/MS data of myoglobin. 17 2 ANALYTICAL SCIENCES NOVEMBER 2020, VOL. 36 Table S1 : The protein names (antigens) identified by pH 2.0 solution in the eluted-fraction. These proteins were identified one or more out of six analyses. Accession Description P08908 5-hydroxytryptamine receptor 1A OS=Homo sapiens GN=HTR1A PE=1 SV=3 - [5HT1A_HUMAN] Q9NRR6 72 kDa inositol polyphosphate 5-phosphatase OS=Homo sapiens GN=INPP5E PE=1 SV=2 - [INP5E_HUMAN] P82987 ADAMTS-like protein 3 OS=Homo sapiens GN=ADAMTSL3 PE=2 SV=4 - [ATL3_HUMAN] Q9Y6K8 Adenylate kinase isoenzyme 5 OS=Homo sapiens GN=AK5 PE=1 SV=2 - [KAD5_HUMAN] P02763 Alpha-1-acid glycoprotein 1 OS=Homo sapiens GN=ORM1 PE=1 SV=1 - [A1AG1_HUMAN] P19652 Alpha-1-acid glycoprotein 2 OS=Homo sapiens GN=ORM2 PE=1 SV=2 - [A1AG2_HUMAN] P01011 Alpha-1-antichymotrypsin OS=Homo sapiens GN=SERPINA3 PE=1 SV=2 - [AACT_HUMAN] P01009 Alpha-1-antitrypsin OS=Homo sapiens GN=SERPINA1 PE=1 SV=3 - [A1AT_HUMAN] P04217 Alpha-1B-glycoprotein OS=Homo sapiens GN=A1BG PE=1 SV=4 - [A1BG_HUMAN] P08697 Alpha-2-antiplasmin OS=Homo sapiens GN=SERPINF2 PE=1 SV=3 - [A2AP_HUMAN] P02765 Alpha-2-HS-glycoprotein OS=Homo sapiens GN=AHSG PE=1 SV=1 - [FETUA_HUMAN] P01023 Alpha-2-macroglobulin OS=Homo sapiens GN=A2M PE=1 SV=3 - [A2MG_HUMAN] P01019 Angiotensinogen OS=Homo sapiens GN=AGT PE=1 SV=1 - [ANGT_HUMAN] Q9NQ90 Anoctamin-2 OS=Homo sapiens GN=ANO2 PE=1 SV=2 - [ANO2_HUMAN] P01008 Antithrombin-III -
Universidade Estadual De Campinas Instituto De Biologia
UNIVERSIDADE ESTADUAL DE CAMPINAS INSTITUTO DE BIOLOGIA VERÔNICA APARECIDA MONTEIRO SAIA CEREDA O PROTEOMA DO CORPO CALOSO DA ESQUIZOFRENIA THE PROTEOME OF THE CORPUS CALLOSUM IN SCHIZOPHRENIA CAMPINAS 2016 1 VERÔNICA APARECIDA MONTEIRO SAIA CEREDA O PROTEOMA DO CORPO CALOSO DA ESQUIZOFRENIA THE PROTEOME OF THE CORPUS CALLOSUM IN SCHIZOPHRENIA Dissertação apresentada ao Instituto de Biologia da Universidade Estadual de Campinas como parte dos requisitos exigidos para a obtenção do Título de Mestra em Biologia Funcional e Molecular na área de concentração de Bioquímica. Dissertation presented to the Institute of Biology of the University of Campinas in partial fulfillment of the requirements for the degree of Master in Functional and Molecular Biology, in the area of Biochemistry. ESTE ARQUIVO DIGITAL CORRESPONDE À VERSÃO FINAL DA DISSERTAÇÃO DEFENDIDA PELA ALUNA VERÔNICA APARECIDA MONTEIRO SAIA CEREDA E ORIENTADA PELO DANIEL MARTINS-DE-SOUZA. Orientador: Daniel Martins-de-Souza CAMPINAS 2016 2 Agência(s) de fomento e nº(s) de processo(s): CNPq, 151787/2F2014-0 Ficha catalográfica Universidade Estadual de Campinas Biblioteca do Instituto de Biologia Mara Janaina de Oliveira - CRB 8/6972 Saia-Cereda, Verônica Aparecida Monteiro, 1988- Sa21p O proteoma do corpo caloso da esquizofrenia / Verônica Aparecida Monteiro Saia Cereda. – Campinas, SP : [s.n.], 2016. Orientador: Daniel Martins de Souza. Dissertação (mestrado) – Universidade Estadual de Campinas, Instituto de Biologia. 1. Esquizofrenia. 2. Espectrometria de massas. 3. Corpo caloso. -
Propranolol-Mediated Attenuation of MMP-9 Excretion in Infants with Hemangiomas
Supplementary Online Content Thaivalappil S, Bauman N, Saieg A, Movius E, Brown KJ, Preciado D. Propranolol-mediated attenuation of MMP-9 excretion in infants with hemangiomas. JAMA Otolaryngol Head Neck Surg. doi:10.1001/jamaoto.2013.4773 eTable. List of All of the Proteins Identified by Proteomics This supplementary material has been provided by the authors to give readers additional information about their work. © 2013 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 10/01/2021 eTable. List of All of the Proteins Identified by Proteomics Protein Name Prop 12 mo/4 Pred 12 mo/4 Δ Prop to Pred mo mo Myeloperoxidase OS=Homo sapiens GN=MPO 26.00 143.00 ‐117.00 Lactotransferrin OS=Homo sapiens GN=LTF 114.00 205.50 ‐91.50 Matrix metalloproteinase‐9 OS=Homo sapiens GN=MMP9 5.00 36.00 ‐31.00 Neutrophil elastase OS=Homo sapiens GN=ELANE 24.00 48.00 ‐24.00 Bleomycin hydrolase OS=Homo sapiens GN=BLMH 3.00 25.00 ‐22.00 CAP7_HUMAN Azurocidin OS=Homo sapiens GN=AZU1 PE=1 SV=3 4.00 26.00 ‐22.00 S10A8_HUMAN Protein S100‐A8 OS=Homo sapiens GN=S100A8 PE=1 14.67 30.50 ‐15.83 SV=1 IL1F9_HUMAN Interleukin‐1 family member 9 OS=Homo sapiens 1.00 15.00 ‐14.00 GN=IL1F9 PE=1 SV=1 MUC5B_HUMAN Mucin‐5B OS=Homo sapiens GN=MUC5B PE=1 SV=3 2.00 14.00 ‐12.00 MUC4_HUMAN Mucin‐4 OS=Homo sapiens GN=MUC4 PE=1 SV=3 1.00 12.00 ‐11.00 HRG_HUMAN Histidine‐rich glycoprotein OS=Homo sapiens GN=HRG 1.00 12.00 ‐11.00 PE=1 SV=1 TKT_HUMAN Transketolase OS=Homo sapiens GN=TKT PE=1 SV=3 17.00 28.00 ‐11.00 CATG_HUMAN Cathepsin G OS=Homo -
Synergistic Genetic Interactions Between Pkhd1 and Pkd1 Result in an ARPKD-Like Phenotype in Murine Models
BASIC RESEARCH www.jasn.org Synergistic Genetic Interactions between Pkhd1 and Pkd1 Result in an ARPKD-Like Phenotype in Murine Models Rory J. Olson,1 Katharina Hopp ,2 Harrison Wells,3 Jessica M. Smith,3 Jessica Furtado,1,4 Megan M. Constans,3 Diana L. Escobar,3 Aron M. Geurts,5 Vicente E. Torres,3 and Peter C. Harris 1,3 Due to the number of contributing authors, the affiliations are listed at the end of this article. ABSTRACT Background Autosomal recessive polycystic kidney disease (ARPKD) and autosomal dominant polycystic kidney disease (ADPKD) are genetically distinct, with ADPKD usually caused by the genes PKD1 or PKD2 (encoding polycystin-1 and polycystin-2, respectively) and ARPKD caused by PKHD1 (encoding fibrocys- tin/polyductin [FPC]). Primary cilia have been considered central to PKD pathogenesis due to protein localization and common cystic phenotypes in syndromic ciliopathies, but their relevance is questioned in the simple PKDs. ARPKD’s mild phenotype in murine models versus in humans has hampered investi- gating its pathogenesis. Methods To study the interaction between Pkhd1 and Pkd1, including dosage effects on the phenotype, we generated digenic mouse and rat models and characterized and compared digenic, monogenic, and wild-type phenotypes. Results The genetic interaction was synergistic in both species, with digenic animals exhibiting pheno- types of rapidly progressive PKD and early lethality resembling classic ARPKD. Genetic interaction be- tween Pkhd1 and Pkd1 depended on dosage in the digenic murine models, with no significant enhancement of the monogenic phenotype until a threshold of reduced expression at the second locus was breached. -
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. -
Comparative Transcriptome Analysis of Embryo Invasion in the Mink Uterus
Placenta 75 (2019) 16–22 Contents lists available at ScienceDirect Placenta journal homepage: www.elsevier.com/locate/placenta Comparative transcriptome analysis of embryo invasion in the mink uterus T ∗ Xinyan Caoa,b, , Chao Xua,b, Yufei Zhanga,b, Haijun Weia,b, Yong Liuc, Junguo Caoa,b, Weigang Zhaoa,b, Kun Baoa,b, Qiong Wua,b a Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China b State Key Laboratory for Molecular Biology of Special Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China c Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, College of Biological and Food Engineering, Fuyang Teachers College, Fuyang, China ABSTRACT Introduction: In mink, as many as 65% of embryos die during gestation. The causes and the mechanisms of embryonic mortality remain unclear. The purpose of our study was to examine global gene expression changes during embryo invasion in mink, and thereby to identify potential signaling pathways involved in implantation failure and early pregnancy loss. Methods: Illumina's next-generation sequencing technology (RNA-Seq) was used to analyze the differentially expressed genes (DEGs) in implantation (IMs) and inter- implantation sites (inter-IMs) of uterine tissue. Results: We identified a total of 606 DEGs, including 420 up- and 186 down-regulated genes in IMs compared to inter-IMs. Gene annotation analysis indicated multiple biological pathways to be significantly enriched for DEGs, including immune response, ECM complex, cytokine activity, chemokine activity andprotein binding. The KEGG pathway including cytokine-cytokine receptor interaction, Jak-STAT, TNF and the chemokine signaling pathway were the most enriched. -
Supplemental Table 1. Complete Gene Lists and GO Terms from Figure 3C
Supplemental Table 1. Complete gene lists and GO terms from Figure 3C. Path 1 Genes: RP11-34P13.15, RP4-758J18.10, VWA1, CHD5, AZIN2, FOXO6, RP11-403I13.8, ARHGAP30, RGS4, LRRN2, RASSF5, SERTAD4, GJC2, RHOU, REEP1, FOXI3, SH3RF3, COL4A4, ZDHHC23, FGFR3, PPP2R2C, CTD-2031P19.4, RNF182, GRM4, PRR15, DGKI, CHMP4C, CALB1, SPAG1, KLF4, ENG, RET, GDF10, ADAMTS14, SPOCK2, MBL1P, ADAM8, LRP4-AS1, CARNS1, DGAT2, CRYAB, AP000783.1, OPCML, PLEKHG6, GDF3, EMP1, RASSF9, FAM101A, STON2, GREM1, ACTC1, CORO2B, FURIN, WFIKKN1, BAIAP3, TMC5, HS3ST4, ZFHX3, NLRP1, RASD1, CACNG4, EMILIN2, L3MBTL4, KLHL14, HMSD, RP11-849I19.1, SALL3, GADD45B, KANK3, CTC- 526N19.1, ZNF888, MMP9, BMP7, PIK3IP1, MCHR1, SYTL5, CAMK2N1, PINK1, ID3, PTPRU, MANEAL, MCOLN3, LRRC8C, NTNG1, KCNC4, RP11, 430C7.5, C1orf95, ID2-AS1, ID2, GDF7, KCNG3, RGPD8, PSD4, CCDC74B, BMPR2, KAT2B, LINC00693, ZNF654, FILIP1L, SH3TC1, CPEB2, NPFFR2, TRPC3, RP11-752L20.3, FAM198B, TLL1, CDH9, PDZD2, CHSY3, GALNT10, FOXQ1, ATXN1, ID4, COL11A2, CNR1, GTF2IP4, FZD1, PAX5, RP11-35N6.1, UNC5B, NKX1-2, FAM196A, EBF3, PRRG4, LRP4, SYT7, PLBD1, GRASP, ALX1, HIP1R, LPAR6, SLITRK6, C16orf89, RP11-491F9.1, MMP2, B3GNT9, NXPH3, TNRC6C-AS1, LDLRAD4, NOL4, SMAD7, HCN2, PDE4A, KANK2, SAMD1, EXOC3L2, IL11, EMILIN3, KCNB1, DOK5, EEF1A2, A4GALT, ADGRG2, ELF4, ABCD1 Term Count % PValue Genes regulation of pathway-restricted GDF3, SMAD7, GDF7, BMPR2, GDF10, GREM1, BMP7, LDLRAD4, SMAD protein phosphorylation 9 6.34 1.31E-08 ENG pathway-restricted SMAD protein GDF3, SMAD7, GDF7, BMPR2, GDF10, GREM1, BMP7, LDLRAD4, phosphorylation -
A Functional Study of ADAMTS7 Gene Variants
A functional study of ADAMTS7 gene variants Xiangyuan Pu A thesis submitted to the University of London for the degree of Doctor of Philosophy Centre for Clinical Pharmacology William Harvey Research Institute Barts and the London School of Medicine and Dentistry Queen Mary, University of London March, 2014 I dedicate this thesis to my parents and my fiancée. Without their endless love, support and encouragement, none of my achievements would be possible. 2 Abstract Background: Recent studies have revealed an association between genetic variants at the ADAMTS7 (a disintegrin-like and metalloprotease with thrombospondin type 1 motif, 7) locus and susceptibility to coronary artery disease (CAD). ADAMTS-7 has been reported to facilitate vascular smooth muscle cell (VSMC) migration and promote neointima formation. We sought to study the functional mechanisms underlying this relationship and to further investigate the role of ADAMTS-7 in atherosclerosis. Methods and Results: In vitro assays showed that the CAD-associated non-synonymous single nucleotide polymorphism rs3825807, which results in a serine to proline (Ser-to- Pro) substitution at residue 214 in the ADAMTS-7 pro-domain, affected ADAMTS-7 pro- domain cleavage. Immunohistochemical analyses showed that ADAMTS-7 localised to vascular smooth muscle cells (VSMCs) and endothelial cells (ECs) in human coronary and carotid atherosclerotic plaques. Cell migration assays demonstrated that VSMCs and ECs from individuals who were homozygous for the adenine (A) allele (encoding the Ser214 isoform) had increased migratory ability compared with cells from individuals who were homozygous for the G allele (encoding the Pro214 isoform). Western blot analyses revealed that media conditioned by VSMCs of the A/A genotype contained more cleaved ADAMTS-7 pro-domain and more of the cleaved form of thrombospondin-5 (TSP-5, an ADAMTS-7 substrate that had been shown to be produced by VSMCs and inhibit VSMC migration). -
SUPPLEMENTARY MATERIAL Human Engineered Skeletal Muscle
SUPPLEMENTARY MATERIAL Human engineered skeletal muscle of hypaxial origin from pluripotent stem cells with advanced function and regenerative capacity Mina Shahriyari1,2, Md Rezaul Islam3, M. Sadman Sakib3, Anastasia Rika1,2, Dennis Krüger3, Lalit Kaurani3, Harithaa Anandakumar1,2, Orr Shomroni4, Matthias Schmidt5, Jana Zschüntzsch5, Jens Schmidt5, Gabriela Salinas-Riester4, Andreas Unger6, Wolfgang A. Linke6, André Fischer3,7, Wolfram-Hubertus Zimmermann1,2,3,7,8*, Malte Tiburcy1,2* 1 Institute of Pharmacology and Toxicology, University Medical Center Göttingen, Göttingen, Germany. 2 DZHK (German Center for Cardiovascular Research), partner site Göttingen. 3 Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, Göttingen, Germany 4 NGS Integrative Genomics Core Unit, Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany 5 Department of Neurology, University Medical Center Göttingen, Göttingen, Germany 6 Institute of Physiology II, University of Münster, D-48149 Münster, Germany 7 Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany; 8 Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Göttingen, Germany Supplementary table 1 related to Figure 2: Biological process annotation of coexpression clusters. Cluster Biological process annotated Enriched GO terms identifier Black Migrating limb progenitors Muscle -
Multi-Trait GWAS Using Imputed High- Density Genotypes from Whole-Genome Sequencing Identifies Genes Associated with Body Traits in Nile Tilapia Grazyella M
Yoshida and Yáñez BMC Genomics (2021) 22:57 https://doi.org/10.1186/s12864-020-07341-z RESEARCH ARTICLE Open Access Multi-trait GWAS using imputed high- density genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia Grazyella M. Yoshida1 and José M. Yáñez1,2* Abstract Background: Body traits are generally controlled by several genes in vertebrates (i.e. polygenes), which in turn make them difficult to identify through association mapping. Increasing the power of association studies by combining approaches such as genotype imputation and multi-trait analysis improves the ability to detect quantitative trait loci associated with polygenic traits, such as body traits. Results: A multi-trait genome-wide association study (mtGWAS) was performed to identify quantitative trait loci (QTL) and genes associated with body traits in Nile tilapia (Oreochromis niloticus) using genotypes imputed to whole-genome sequences (WGS). To increase the statistical power of mtGWAS for the detection of genetic associations, summary statistics from single-trait genome-wide association studies (stGWAS) for eight different body traits recorded in 1309 animals were used. The mtGWAS increased the statistical power from the original sample size from 13 to 44%, depending on the trait analyzed. The better resolution of the WGS data, combined with the increased power of the mtGWAS approach, allowed the detection of significant markers which were not previously found in the stGWAS. Some of the lead single nucleotide polymorphisms -
Downloaded from Genomic Data Common Website (GDC at Accessed on 2019)
G C A T T A C G G C A T genes Article Molecular Pathways Associated with Kallikrein 6 Overexpression in Colorectal Cancer Ritu Pandey 1,2,*, Muhan Zhou 3, Yuliang Chen 3, Dalila Darmoul 4 , Conner C. Kisiel 2, Valentine N. Nfonsam 5 and Natalia A. Ignatenko 1,2 1 Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85721, USA; [email protected] 2 University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA; [email protected] 3 Bioinformatics Shared Resource, University of Arizona Cancer Center, Tucson, AZ 85724, USA; [email protected] (M.Z.); [email protected] (Y.C.) 4 Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Paris, Lariboisière Hospital, 75010 Paris, France; [email protected] 5 Department of Surgery, Section of Surgical Oncology, University of Arizona, Tucson, AZ 85724, USA; [email protected] * Correspondence: [email protected] Abstract: Colorectal cancer (CRC) remains one of the leading causes of cancer-related death world- wide. The high mortality of CRC is related to its ability to metastasize to distant organs. The kallikrein-related peptidase Kallikrein 6 (KLK6) is overexpressed in CRC and contributes to cancer cell invasion and metastasis. The goal of this study was to identify KLK6-associated markers for the CRC prognosis and treatment. Tumor Samples from the CRC patients with significantly elevated Citation: Pandey, R.; Zhou, M.; Chen, KLK6 transcript levels were identified in the RNA-Seq data from Cancer Genome Atlas (TCGA) Y.; Darmoul, D.; Kisiel, C.C.; and their expression profiles were evaluated using Gene Ontology (GO), Phenotype and Reactome Nfonsam, V.N.; Ignatenko, N.A. -
(ADAMTS9) Expression by Chondrocytes During Endochondral Ossification*
Arch Histol Cytol, 72 (3): 175-185 (2009) A disintegrin and metalloproteinase with thrombospondin motifs 9 (ADAMTS9) expression by chondrocytes during endochondral ossification* Kanae Kumagishi1, Keiichiro Nishida1, Tomoichiro Yamaai2, Ryusuke Momota1, Shigeru Miyaki3, Satoshi Hirohata4, Ichiro Naito1, Hiroshi Asahara3, Yoshifumi Ninomiya4, and Aiji Ohtsuka1 Departments of 1Human Morphology, 2Oral Function and Anatomy, and 4Molecular Biology and Biochemistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama; and 3Department of Regenerative Biology and Medicine, National Research Institute for Child Health and Development, Tokyo, Japan S u m m a r y . A d i s i n t e g r i n a n d m e t a l l o p r o t e i n a s e chondrocyte phenotypes, respectively. We found the gene with thrombospondin motifs 9 (ADAMTS9) is known expression of ADAMTS9 by ATDC5 cells as a dual mode, to influence aggrecan degradation in endochondral both before the expression of type X collagen and after ossification, but its role has not been well understood. hypertrophic differentiation. The immunoreactivity of In the present study, in vitro gene expression of ADAMTS9 ADAMTS9 was observed in chondrocytes of proliferative was investigated by RT-PCR in ATDC5 cells in which and hypertrophic zones in the growth plate. The experimentally chondrogenic differentiation had been population of ADAMTS9 positive cells decreased with age. induced. We also investigated the protein localization The results of the present study suggest that ADAMTS9 and gene expression pattern of ADAMTS9 in the tibia might have a role in aggrecan cleavage around the growth plate cartilage of male mice in a day 1 neonate, chondrocytes to allow chondrocyte proliferation and 7-week-old young adult, and a 12-week-old adult by hypertrophy.