Protease and Protease-Activated Receptor-2 Signaling in the Pathogenesis of Atopic Dermatitis
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Supplementary Data for Quantitative Changes in the Mitochondrial Proteome from Subjects with Mild Cognitive Impairment, Early Stage and Late Stage Alzheimer’s disease Table 1 - 112 unique, non-redundant proteins identified and quantified in at least two of the three analytical replicates for all three disease stages. Table 2 - MCI mitochondrial samples, Protein Summary Table 3 - MCI mitochondrial samples, Experiment 1 Table 4 - MCI mitochondrial samples, Experiment 2 Table 5 - MCI mitochondrial samples, Experiment 3 Table 6 - EAD Mitochondrial Study, Protein Summary Table 7 - EAD Mitochondrial Study, Experiment 1 Table 8 - EAD Mitochondrial Study, Experiment 2 Table 9 - EAD Mitochondrial Study, Experiment 3 Table 10 - LAD Mitochondrial Study, Protein Summary Table 11 - LAD Mitochondrial Study, Experiment 1 Table 12 - LAD Mitochondrial Study, Experiment 2 Table 13 - LAD Mitochondrial Study, Experiment 3 Supplemental Table 1. 112 unique, non-redundant proteins identified and quantified in at least two of the three analytical replicates for all three disease stages. Description Data MCI EAD LAD AATM_HUMAN (P00505) Aspartate aminotransferase, mitochondrial precursor (EC Mean 1.43 1.70 1.31 2.6.1.1) (Transaminase A) (Glutamate oxaloacetate transaminase 2) [MASS=47475] SEM 0.07 0.09 0.09 Count 3.00 3.00 3.00 ACON_HUMAN (Q99798) Aconitate hydratase, mitochondrial precursor (EC 4.2.1.3) Mean 1.24 1.61 1.19 (Citrate hydro-lyase) (Aconitase) [MASS=85425] SEM 0.05 0.17 0.18 Count 3.00 2.00 3.00 ACPM_HUMAN (O14561) Acyl carrier protein, mitochondrial -
Newly Developed Serine Protease Inhibitors Decrease Visceral Hypersensitivity in a Post-Inflammatory Rat Model for Irritable Bowel Syndrome
This item is the archived peer-reviewed author-version of: Newly developed serine protease inhibitors decrease visceral hypersensitivity in a post-inflammatory rat model for irritable bowel syndrome Reference: Ceuleers Hannah, Hanning Nikita, Heirbaut Leen, Van Remoortel Samuel, Joossens Jurgen, van der Veken Pieter, Francque Sven, De Bruyn Michelle, Lambeir Anne-Marie, de Man Joris, ....- New ly developed serine protease inhibitors decrease visceral hypersensitivity in a post-inflammatory rat model for irritable bow el syndrome British journal of pharmacology - ISSN 0007-1188 - 175:17(2018), p. 3516-3533 Full text (Publisher's DOI): https://doi.org/10.1111/BPH.14396 To cite this reference: https://hdl.handle.net/10067/1530780151162165141 Institutional repository IRUA NEWLY DEVELOPED SERINE PROTEASE INHIBITORS DECREASE VISCERAL HYPERSENSITIVITY IN A POST-INFLAMMATORY RAT MODEL FOR IRRITABLE BOWEL SYNDROME. Running title: Serine proteases in visceral hypersensitivity Hannah Ceuleers, Nikita Hanning, Jelena Heirbaut, Samuel Van Remoortel, Michelle De bruyn, Jurgen Joossens, Pieter van der Veken, Anne-Marie Lambeir, Sven M Francque, Joris G De Man, Jean-Pierre Timmermans, Koen Augustyns, Ingrid De Meester, Benedicte Y De Winter Hannah Ceuleers, Nikita Hanning, Jelena Heirbaut, Sven Francque, Joris G De Man, Benedicte Y De Winter, Laboratory of Experimental Medicine and Pediatrics, Division of Gastroenterology, University of Antwerp, Antwerp, Belgium. Samuel Van Remoortel, Jean-Pierre Timmermans, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium. Jurgen Joossens, Pieter van der Veken, Koen Augustyns, Laboratory of Medicinal Chemistry, University of Antwerp, Antwerp, Belgium. Sven Francque, Antwerp University Hospital, Antwerp, Belgium. Michelle De bruyn, Anne-Marie Lambeir, Ingrid De Meester, Laboratory of Medical Biochemistry, University of Antwerp, Antwerp, Belgium. -
Evaluation of Chromatin Accessibility in Prefrontal Cortex of Individuals with Schizophrenia
ARTICLE DOI: 10.1038/s41467-018-05379-y OPEN Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia Julien Bryois 1, Melanie E. Garrett2, Lingyun Song3, Alexias Safi3, Paola Giusti-Rodriguez 4, Graham D. Johnson 3, Annie W. Shieh13, Alfonso Buil5, John F. Fullard6, Panos Roussos 6,7,8, Pamela Sklar6, Schahram Akbarian 6, Vahram Haroutunian 6,9, Craig A. Stockmeier 10, Gregory A. Wray3,11, Kevin P. White12, Chunyu Liu13, Timothy E. Reddy 3,14, Allison Ashley-Koch2,15, Patrick F. Sullivan 1,4,16 & Gregory E. Crawford 3,17 1234567890():,; Schizophrenia genome-wide association studies have identified >150 regions of the genome associated with disease risk, yet there is little evidence that coding mutations contribute to this disorder. To explore the mechanism of non-coding regulatory elements in schizophrenia, we performed ATAC-seq on adult prefrontal cortex brain samples from 135 individuals with schizophrenia and 137 controls, and identified 118,152 ATAC-seq peaks. These accessible chromatin regions in the brain are highly enriched for schizophrenia SNP heritability. Accessible chromatin regions that overlap evolutionarily conserved regions exhibit an even higher heritability enrichment, indicating that sequence conservation can further refine functional risk variants. We identify few differences in chromatin accessibility between cases and controls, in contrast to thousands of age-related differential accessible chromatin regions. Altogether, we characterize chromatin accessibility in the human prefrontal cortex, the effect of schizophrenia and age on chromatin accessibility, and provide evidence that our dataset will allow for fine mapping of risk variants. 1 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177 Stockholm, Sweden. -
Data Sheet Cathepsin V Inhibitor Screening Assay Kit Catalog #79589 Size: 96 Reactions
6405 Mira Mesa Blvd Ste. 100 San Diego, CA 92121 Tel: 1.858.202.1401 Fax: 1.858.481.8694 Email: [email protected] Data Sheet Cathepsin V Inhibitor Screening Assay Kit Catalog #79589 Size: 96 reactions BACKGROUND: Cathepsin V, also called Cathepsin L2, is a lysosomal cysteine endopeptidase with high sequence homology to cathepsin L and other members of the papain superfamily of cysteine proteinases. Its expression is regulated in a tissue-specific manner and is high in thymus, testis and cornea. Expression analysis of cathepsin V in human tumors revealed widespread expression in colorectal and breast carcinomas, suggesting a possible role in tumor processes. DESCRIPTION: The Cathepsin V Inhibitor Screening Assay Kit is designed to measure the protease activity of Cathepsin V for screening and profiling applications. The Cathepsin V assay kit comes in a convenient 96-well format, with purified Cathepsin V, its fluorogenic substrate, and Cathepsin buffer for 100 enzyme reactions. In addition, the kit includes the cathepsin inhibitor E- 64 for use as a control inhibitor. COMPONENTS: Catalog # Component Amount Storage 80009 Cathepsin V 10 µg -80 °C Fluorogenic Cathepsin Avoid 80349 Substrate 1 (5 mM) 10 µl -20 °C multiple *4X Cathepsin buffer 2 ml -20 °C freeze/thaw E-64 (1 mM) 10 µl -20 °C cycles! 96-well black microplate * Add 120 µl of 0.5 M DTT before use. MATERIALS OR INSTRUMENTS REQUIRED BUT NOT SUPPLIED: 0.5 M DTT in aqueous solution Adjustable micropipettor and sterile tips Fluorescent microplate reader APPLICATIONS: Great for studying enzyme kinetics and screening small molecular inhibitors for drug discovery and HTS applications. -
Felipe Jun Fuzita Molecular Physiology of Digestion In
FELIPE JUN FUZITA MOLECULAR PHYSIOLOGY OF DIGESTION IN ARACHNIDA: FUNCTIONAL AND COMPARATIVE-EVOLUTIONARY APPROACHES Thesis presented to the Programa de Pós-Graduação Interunidades em Biotecnologia USP/Instituto Butantan/IPT, to obtain the Title of Doctor in Biotechnology. São Paulo 2014 FELIPE JUN FUZITA MOLECULAR PHYSIOLOGY OF DIGESTION IN ARACHNIDA: FUNCTIONAL AND COMPARATIVE-EVOLUTIONARY APPROACHES Thesis presented to the Programa de Pós-Graduação Interunidades em Biotecnologia USP/Instituto Butantan/IPT, to obtain the Title of Doctor in Biotechnology. Concentration area: Biotechnology Advisor: Dr. Adriana Rios Lopes Rocha Corrected version. The original electronic version is available either in the library of the Institute of Biomedical Sciences and in the Digital Library of Theses and Dissertations of the University of Sao Paulo (BDTD). São Paulo 2014 DADOS DE CATALOGAÇÃO NA PUBLICAÇÃO (CIP) Serviço de Biblioteca e Informação Biomédica do Instituto de Ciências Biomédicas da Universidade de São Paulo © reprodução total Fuzita, Felipe Jun. Molecular physiology of digestion in Arachnida: functional and comparative-evolutionary approaches / Felipe Jun Fuzita. -- São Paulo, 2014. Orientador: Profa. Dra. Adriana Rios Lopes Rocha. Tese (Doutorado) – Universidade de São Paulo. Instituto de Ciências Biomédicas. Programa de Pós-Graduação Interunidades em Biotecnologia USP/IPT/Instituto Butantan. Área de concentração: Biotecnologia. Linha de pesquisa: Bioquímica, biologia molecular, espectrometria de massa. Versão do título para o português: Fisiologia molecular da digestão em Arachnida: abordagens funcional e comparativo-evolutiva. 1. Digestão 2. Aranha 3. Escorpião 4. Enzimologia 5. Proteoma 6. Transcriptoma I. Rocha, Profa. Dra. Adriana Rios Lopes I. Universidade de São Paulo. Instituto de Ciências Biomédicas. Programa de Pós-Graduação Interunidades em Biotecnologia USP/IPT/Instituto Butantan III. -
Crystal Structure of Cathepsin X: a Flip–Flop of the Ring of His23
st8308.qxd 03/22/2000 11:36 Page 305 Research Article 305 Crystal structure of cathepsin X: a flip–flop of the ring of His23 allows carboxy-monopeptidase and carboxy-dipeptidase activity of the protease Gregor Guncar1, Ivica Klemencic1, Boris Turk1, Vito Turk1, Adriana Karaoglanovic-Carmona2, Luiz Juliano2 and Dušan Turk1* Background: Cathepsin X is a widespread, abundantly expressed papain-like Addresses: 1Department of Biochemistry and v mammalian lysosomal cysteine protease. It exhibits carboxy-monopeptidase as Molecular Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia and 2Departamento de well as carboxy-dipeptidase activity and shares a similar activity profile with Biofisica, Escola Paulista de Medicina, Rua Tres de cathepsin B. The latter has been implicated in normal physiological events as Maio 100, 04044-020 Sao Paulo, Brazil. well as in various pathological states such as rheumatoid arthritis, Alzheimer’s disease and cancer progression. Thus the question is raised as to which of the *Corresponding author. E-mail: [email protected] two enzyme activities has actually been monitored. Key words: Alzheimer’s disease, carboxypeptidase, Results: The crystal structure of human cathepsin X has been determined at cathepsin B, cathepsin X, papain-like cysteine 2.67 Å resolution. The structure shares the common features of a papain-like protease enzyme fold, but with a unique active site. The most pronounced feature of the Received: 1 November 1999 cathepsin X structure is the mini-loop that includes a short three-residue Revisions requested: 8 December 1999 insertion protruding into the active site of the protease. The residue Tyr27 on Revisions received: 6 January 2000 one side of the loop forms the surface of the S1 substrate-binding site, and Accepted: 7 January 2000 His23 on the other side modulates both carboxy-monopeptidase as well as Published: 29 February 2000 carboxy-dipeptidase activity of the enzyme by binding the C-terminal carboxyl group of a substrate in two different sidechain conformations. -
Mutations in SERPINB7, Encoding a Member of the Serine Protease Inhibitor Superfamily, Cause Nagashima-Type Palmoplantar Keratosis
REPORT Mutations in SERPINB7, Encoding a Member of the Serine Protease Inhibitor Superfamily, Cause Nagashima-type Palmoplantar Keratosis Akiharu Kubo,1,2,3,* Aiko Shiohama,1,4 Takashi Sasaki,1,2,3 Kazuhiko Nakabayashi,5 Hiroshi Kawasaki,1 Toru Atsugi,1,6 Showbu Sato,1 Atsushi Shimizu,7 Shuji Mikami,8 Hideaki Tanizaki,9 Masaki Uchiyama,10 Tatsuo Maeda,10 Taisuke Ito,11 Jun-ichi Sakabe,11 Toshio Heike,12 Torayuki Okuyama,13 Rika Kosaki,14 Kenjiro Kosaki,15 Jun Kudoh,16 Kenichiro Hata,5 Akihiro Umezawa,17 Yoshiki Tokura,11 Akira Ishiko,18 Hironori Niizeki,19 Kenji Kabashima,9 Yoshihiko Mitsuhashi,10 and Masayuki Amagai1,2,4 ‘‘Nagashima-type’’ palmoplantar keratosis (NPPK) is an autosomal recessive nonsyndromic diffuse palmoplantar keratosis characterized by well-demarcated diffuse hyperkeratosis with redness, expanding on to the dorsal surfaces of the palms and feet and the Achilles tendon area. Hyperkeratosis in NPPK is mild and nonprogressive, differentiating NPPK clinically from Mal de Meleda. We performed whole-exome and/or Sanger sequencing analyses of 13 unrelated NPPK individuals and identified biallelic putative loss-of-function mutations in SERPINB7, which encodes a cytoplasmic member of the serine protease inhibitor superfamily. We identified a major caus- ative mutation of c.796C>T (p.Arg266*) as a founder mutation in Japanese and Chinese populations. SERPINB7 was specifically present in the cytoplasm of the stratum granulosum and the stratum corneum (SC) of the epidermis. All of the identified mutants are predicted to cause premature termination upstream of the reactive site, which inhibits the proteases, suggesting a complete loss of the protease inhibitory activity of SERPINB7 in NPPK skin. -
1 No. Affymetrix ID Gene Symbol Genedescription Gotermsbp Q Value 1. 209351 at KRT14 Keratin 14 Structural Constituent of Cyto
1 Affymetrix Gene Q No. GeneDescription GOTermsBP ID Symbol value structural constituent of cytoskeleton, intermediate 1. 209351_at KRT14 keratin 14 filament, epidermis development <0.01 biological process unknown, S100 calcium binding calcium ion binding, cellular 2. 204268_at S100A2 protein A2 component unknown <0.01 regulation of progression through cell cycle, extracellular space, cytoplasm, cell proliferation, protein kinase C inhibitor activity, protein domain specific 3. 33323_r_at SFN stratifin/14-3-3σ binding <0.01 regulation of progression through cell cycle, extracellular space, cytoplasm, cell proliferation, protein kinase C inhibitor activity, protein domain specific 4. 33322_i_at SFN stratifin/14-3-3σ binding <0.01 structural constituent of cytoskeleton, intermediate 5. 201820_at KRT5 keratin 5 filament, epidermis development <0.01 structural constituent of cytoskeleton, intermediate 6. 209125_at KRT6A keratin 6A filament, ectoderm development <0.01 regulation of progression through cell cycle, extracellular space, cytoplasm, cell proliferation, protein kinase C inhibitor activity, protein domain specific 7. 209260_at SFN stratifin/14-3-3σ binding <0.01 structural constituent of cytoskeleton, intermediate 8. 213680_at KRT6B keratin 6B filament, ectoderm development <0.01 receptor activity, cytosol, integral to plasma membrane, cell surface receptor linked signal transduction, sensory perception, tumor-associated calcium visual perception, cell 9. 202286_s_at TACSTD2 signal transducer 2 proliferation, membrane <0.01 structural constituent of cytoskeleton, cytoskeleton, intermediate filament, cell-cell adherens junction, epidermis 10. 200606_at DSP desmoplakin development <0.01 lectin, galactoside- sugar binding, extracellular binding, soluble, 7 space, nucleus, apoptosis, 11. 206400_at LGALS7 (galectin 7) heterophilic cell adhesion <0.01 2 S100 calcium binding calcium ion binding, epidermis 12. 205916_at S100A7 protein A7 (psoriasin 1) development <0.01 S100 calcium binding protein A8 (calgranulin calcium ion binding, extracellular 13. -
Biochemical Characterization of Human Kallikrein 8 and Its Possible Involvement in the Degradation of Extracellular Matrix Proteins
Biochemical characterization of human kallikrein 8 and its possible involvement in the degradation of extracellular Title matrix proteins Author(s) Rajapakse, Sanath; Ogiwara, Katsueki; Takano, Naoharu; Moriyama, Akihiko; Takahashi, Takayuki Febs Letters, 579(30), 6879-6884 Citation https://doi.org/10.1016/j.febslet.2005.11.039 Issue Date 2005-12-01 Doc URL http://hdl.handle.net/2115/985 Type article (author version) File Information FL579-30.pdf Instructions for use Hokkaido University Collection of Scholarly and Academic Papers : HUSCAP Biochemical characterization of human kallikrein 8 and its possible involvement in the degradation of extracellular matrix proteins Sanath Rajapaksea, Katsueki Ogiwaraa, Naoharu Takanoa, Akihiko Moriyamab, Takayuki Takahashia,* aDivision of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810 Japan bDivision of Biomolecular Science, Institute of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan *Correspondence: Takayuki Takahashi, Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan Tel: 81-11-706-2748 Fax: 81-11-706-4851 E-mail: [email protected] 1 Abstract Human kallikrein 8 (KLK8) is a member of the human kallikrein gene family of serine proteases, and its protein, hK8, has recently been suggested to serve as a new ovarian cancer marker. To gain insights into the physiological role of hK8, the active recombinant enzyme was obtained in a pure state for biochemical and enzymatic characterizations. hK8 had trypsin-like activity with a strong preference for Arg over Lys in the P1 position, and its activity was inhibited by typical serine protease inhibitors. The protease degraded casein, fibronectin, gelatin, collagen type IV, fibrinogen, and high-molecular-weight kininogen. -
Development and Validation of a Protein-Based Risk Score for Cardiovascular Outcomes Among Patients with Stable Coronary Heart Disease
Supplementary Online Content Ganz P, Heidecker B, Hveem K, et al. Development and validation of a protein-based risk score for cardiovascular outcomes among patients with stable coronary heart disease. JAMA. doi: 10.1001/jama.2016.5951 eTable 1. List of 1130 Proteins Measured by Somalogic’s Modified Aptamer-Based Proteomic Assay eTable 2. Coefficients for Weibull Recalibration Model Applied to 9-Protein Model eFigure 1. Median Protein Levels in Derivation and Validation Cohort eTable 3. Coefficients for the Recalibration Model Applied to Refit Framingham eFigure 2. Calibration Plots for the Refit Framingham Model eTable 4. List of 200 Proteins Associated With the Risk of MI, Stroke, Heart Failure, and Death eFigure 3. Hazard Ratios of Lasso Selected Proteins for Primary End Point of MI, Stroke, Heart Failure, and Death eFigure 4. 9-Protein Prognostic Model Hazard Ratios Adjusted for Framingham Variables eFigure 5. 9-Protein Risk Scores by Event Type This supplementary material has been provided by the authors to give readers additional information about their work. Downloaded From: https://jamanetwork.com/ on 10/02/2021 Supplemental Material Table of Contents 1 Study Design and Data Processing ......................................................................................................... 3 2 Table of 1130 Proteins Measured .......................................................................................................... 4 3 Variable Selection and Statistical Modeling ........................................................................................ -
Prostatic Trypsin-Like Kallikrein-Related Peptidases
Article in press - uncorrected proof Biol. Chem., Vol. 389, pp. 653–668, June 2008 • Copyright ᮊ by Walter de Gruyter • Berlin • New York. DOI 10.1515/BC.2008.078 Review Prostatic trypsin-like kallikrein-related peptidases (KLKs) and other prostate-expressed tryptic proteinases as regulators of signalling via proteinase-activated receptors (PARs) Andrew J. Ramsay1, Janet C. Reid1, Mark N. cesses by selective cleavage of specific substrates to Adams1, Hemamali Samaratunga2, Ying Dong1, influence cell behaviour (Turk, 2006). Well known physio- Judith A. Clements1 and John D. Hooper1,* logical examples include the proteinases of the blood coagulation (e.g., thrombin) (Davie et al., 1991), digestive 1 Institute of Health and Biomedical Innovation, (e.g., trypsin) (Yamashina, 1956) and wound healing (e.g., Queensland University of Technology, 6 Musk Avenue, plasmin) (Castellino and Ploplis, 2005) cascades. It is Kelvin Grove, Queensland 4059, Australia also clear that dysregulated serine proteinase activity 2 Department of Anatomical Pathology, Sullivan facilitates progression of various diseases including can- Nicolaides Pathology, Taringa 4068, Australia cer (Dano et al., 2005; Turk, 2006; Szabo and Bugge, * Corresponding author 2008). The cleavage site specificity of these enzymes is e-mail: [email protected] indicated by the residue six amino acids before the cat- alytic serine. In the active conformation of the proteinase, this residue is located at the bottom of a pocket in which Abstract the side-chain of the scissile bond of the substrate is inserted. An aspartate or, rarely, a glutamate at this site The prostate is a site of high expression of serine pro- indicates that the serine proteinase will preferentially teinases including members of the kallikrein-related cleave after substrate arginine or lysine residues (trypsin- peptidase (KLK) family, as well as other secreted and like or tryptic substrate specificity); a small hydrophobic membrane-anchored serine proteinases. -
Sex-Specific Transcriptome Differences in Human Adipose
G C A T T A C G G C A T genes Article Sex-Specific Transcriptome Differences in Human Adipose Mesenchymal Stem Cells 1, 2, 3 1,3 Eva Bianconi y, Raffaella Casadei y , Flavia Frabetti , Carlo Ventura , Federica Facchin 1,3,* and Silvia Canaider 1,3 1 National Laboratory of Molecular Biology and Stem Cell Bioengineering of the National Institute of Biostructures and Biosystems (NIBB)—Eldor Lab, at the Innovation Accelerator, CNR, Via Piero Gobetti 101, 40129 Bologna, Italy; [email protected] (E.B.); [email protected] (C.V.); [email protected] (S.C.) 2 Department for Life Quality Studies (QuVi), University of Bologna, Corso D’Augusto 237, 47921 Rimini, Italy; [email protected] 3 Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy; fl[email protected] * Correspondence: [email protected]; Tel.: +39-051-2094114 These authors contributed equally to this work. y Received: 1 July 2020; Accepted: 6 August 2020; Published: 8 August 2020 Abstract: In humans, sexual dimorphism can manifest in many ways and it is widely studied in several knowledge fields. It is increasing the evidence that also cells differ according to sex, a correlation still little studied and poorly considered when cells are used in scientific research. Specifically, our interest is on the sex-related dimorphism on the human mesenchymal stem cells (hMSCs) transcriptome. A systematic meta-analysis of hMSC microarrays was performed by using the Transcriptome Mapper (TRAM) software. This bioinformatic tool was used to integrate and normalize datasets from multiple sources and allowed us to highlight chromosomal segments and genes differently expressed in hMSCs derived from adipose tissue (hADSCs) of male and female donors.