Plasmin Reduces Fibronectin Deposition by Mesangial Cells in a Protease-Activated Receptor-1 Independent Manner
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A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases
International Journal of Molecular Sciences Review Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases Peter Goettig Structural Biology Group, Faculty of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria; [email protected]; Tel.: +43-662-8044-7283; Fax: +43-662-8044-7209 Academic Editor: Cheorl-Ho Kim Received: 30 July 2016; Accepted: 10 November 2016; Published: 25 November 2016 Abstract: Posttranslational modifications are an important feature of most proteases in higher organisms, such as the conversion of inactive zymogens into active proteases. To date, little information is available on the role of glycosylation and functional implications for secreted proteases. Besides a stabilizing effect and protection against proteolysis, several proteases show a significant influence of glycosylation on the catalytic activity. Glycans can alter the substrate recognition, the specificity and binding affinity, as well as the turnover rates. However, there is currently no known general pattern, since glycosylation can have both stimulating and inhibiting effects on activity. Thus, a comparative analysis of individual cases with sufficient enzyme kinetic and structural data is a first approach to describe mechanistic principles that govern the effects of glycosylation on the function of proteases. The understanding of glycan functions becomes highly significant in proteomic and glycomic studies, which demonstrated that cancer-associated proteases, such as kallikrein-related peptidase 3, exhibit strongly altered glycosylation patterns in pathological cases. Such findings can contribute to a variety of future biomedical applications. Keywords: secreted protease; sequon; N-glycosylation; O-glycosylation; core glycan; enzyme kinetics; substrate recognition; flexible loops; Michaelis constant; turnover number 1. -
Towards Therapy for Batten Disease
Towards therapy for Batten disease Mariana Catanho da Silva Vieira MRC Laboratory for Molecular Cell Biology University College London PhD Supervisor: Dr Sara E Mole A thesis submitted for the degree of Doctor of Philosophy University College London September 2014 Declaration I, Mariana Catanho da Silva Vieira, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. 2 Abstract The gene underlying the classic neurodegenerative lysosomal storage disorder (LSD) juvenile neuronal ceroid lipofuscinosis (JNCL) in humans, CLN3, encodes a polytopic membrane spanning protein of unknown function. Several studies using simpler models have been performed in order to further understand this protein and its pathological mechanism. Schizosaccharomyces pombe provides an ideal model organism for the study of CLN3 function, due to its simplicity, genetic tractability and the presence of a single orthologue of CLN3 (Btn1p), which exhibits a functional profile comparable to its human counterpart. In this study, this model was used to explore the effect of different mutations in btn1 as well as phenotypes arising from complete deletion of the gene. Different btn1 mutations have different effects on the protein function, underlining different phenotypes and affecting the levels of expression of Btn1p. So far, there is no cure for JNCL and therefore it is of great importance to identify novel lead compounds that can be developed for disease therapy. To identify these compounds, a drug screen with btn1Δ cells based on their sensitivity to cyclosporine A, was developed. Positive hits from the screen were validated and tested for their ability to rescue other specific phenotypes also associated with the loss of btn1. -
Serine Proteases with Altered Sensitivity to Activity-Modulating
(19) & (11) EP 2 045 321 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 08.04.2009 Bulletin 2009/15 C12N 9/00 (2006.01) C12N 15/00 (2006.01) C12Q 1/37 (2006.01) (21) Application number: 09150549.5 (22) Date of filing: 26.05.2006 (84) Designated Contracting States: • Haupts, Ulrich AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 51519 Odenthal (DE) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • Coco, Wayne SK TR 50737 Köln (DE) •Tebbe, Jan (30) Priority: 27.05.2005 EP 05104543 50733 Köln (DE) • Votsmeier, Christian (62) Document number(s) of the earlier application(s) in 50259 Pulheim (DE) accordance with Art. 76 EPC: • Scheidig, Andreas 06763303.2 / 1 883 696 50823 Köln (DE) (71) Applicant: Direvo Biotech AG (74) Representative: von Kreisler Selting Werner 50829 Köln (DE) Patentanwälte P.O. Box 10 22 41 (72) Inventors: 50462 Köln (DE) • Koltermann, André 82057 Icking (DE) Remarks: • Kettling, Ulrich This application was filed on 14-01-2009 as a 81477 München (DE) divisional application to the application mentioned under INID code 62. (54) Serine proteases with altered sensitivity to activity-modulating substances (57) The present invention provides variants of ser- screening of the library in the presence of one or several ine proteases of the S1 class with altered sensitivity to activity-modulating substances, selection of variants with one or more activity-modulating substances. A method altered sensitivity to one or several activity-modulating for the generation of such proteases is disclosed, com- substances and isolation of those polynucleotide se- prising the provision of a protease library encoding poly- quences that encode for the selected variants. -
Review Article Molecular Functions of Thyroid Hormones and Their Clinical Significance in Liver-Related Diseases
Hindawi Publishing Corporation BioMed Research International Volume 2013, Article ID 601361, 16 pages http://dx.doi.org/10.1155/2013/601361 Review Article Molecular Functions of Thyroid Hormones and Their Clinical Significance in Liver-Related Diseases Hsiang Cheng Chi,1 Cheng-Yi Chen,1 Ming-Ming Tsai,2 Chung-Ying Tsai,1 and Kwang-Huei Lin1 1 Department of Biochemistry, School of Medicine, Chang-Gung University, Taoyuan 333, Taiwan 2 Department of Nursing, Chang-Gung University of Science and Technology, Taoyuan 333, Taiwan Correspondence should be addressed to Kwang-Huei Lin; [email protected] Received 4 February 2013; Revised 14 May 2013; Accepted 28 May 2013 Academic Editor: Elena Orlova Copyright © 2013 Hsiang Cheng Chi et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Thyroid hormones (THs) are potent mediators of several physiological processes, including embryonic development, cellular differentiation, metabolism, and cell growth. Triiodothyronine3 (T ) is the most biologically active TH form. Thyroid hormone receptors (TRs) belong to the nuclear receptor superfamily and mediate the biological functions of T3 via transcriptional regulation. TRs generally form heterodimers with the retinoid X receptor (RXR) and regulate target genes upon T3 stimulation. Research over the past few decades has revealed that disruption of cellular TH signaling triggers chronic liver diseases, including alcoholic or nonalcoholic fatty liver disease and hepatocellular carcinoma (HCC). Animal model experiments and epidemiologic studies to date imply close associations between high TH levels and prevention of liver disease. -
UC San Francisco Electronic Theses and Dissertations
UCSF UC San Francisco Electronic Theses and Dissertations Title Protease-activated receptor-2 (PAR2) in epithelial biology Permalink https://escholarship.org/uc/item/2b49z9sm Author Barker, Adrian Publication Date 2013 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California ii To my nephews for being the light of my life To my parents for showing me the way To Philip, your love knows no bounds iii ACKNOWLEDGEMENTS Wow, what a journey! First, I’d like to thank my mentor and advisor, Dr. Shaun Coughlin, for giving me the encouragement and wisdom that I needed to succeed in your lab. One thing I will take away from this experience is how powerful collaboration can be. Having encountered labs that have not been willing to collaborate, you are an inspiration and role-model in your willingness to share your resources and knowledge with the scientific community and the academic world is a better place because of it. To my thesis committee members, Dr. Charly Craik & Dr. Zena Werb. Thank you for the conversations and encouragement. You have given me motivation and kind words in pivotal moments in my career and they have helped me tremendously; more than you’ll ever know. To all the members of the Coughlin lab. We’ve been through so much together, and many of you have been around since the first day I stepped foot into the lab. Extra special thanks to: Dr. Hilary Clay, for help with the zebrafish work and for fighting for my project when it felt like no one else cared; Dr. -
Cathepsins and Their Involvement in Immune Responses
Review article: Medical intelligence | Published 20 July 2010, doi:10.4414/smw.2010.13042 Cite this as: Swiss Med Wkly. 2010;140:w13042 Cathepsins and their involvement in immune responses Sébastien Conus, Hans-Uwe Simon Institute of Pharmacology, University of Bern, Bern, Switzerland Correspondence to: cleaving proteases (= caspases) which cleave a wide range Sébastien Conus Ph.D. of cellular substrates [5]. Institute of Pharmacology Besides caspases, cathepsins have recently been shown University of Bern to be associated with cell death regulation [6–12] and vari- Friedbühlstrasse 49 3010 Bern ous other physiological and pathological processes, such as Switzerland maturation of the MHC class II complex, bone remodel- [email protected] ling, keratinocyte differentiation, tumour progression and metastasis, rheumatoid arthritis and osteoarthritis, as well Summary as atherosclerosis [13, 14] (table 1). Thus, cathepsins ap- pear to play a significant role in immune responses. In this The immune system is composed of an enormous variety of review we discuss recent advances addressing the role of cells and molecules that generate a collective and coordin- lysosomal proteases in the diverse aspects of the immune ated response on exposure to foreign antigens, called the response, and also the involvement of cathepsins in the immune response. Within the immune response, endo-lyso- pathogenesis of diseases in which these proteases seem not somal proteases play a key role. In this review we cover to be properly under control. specific roles of cathepsins in innate and adaptive immu- nity, as well as their implication in the pathogenesis of sev- The cathepsin family eral diseases. Lysosomes are membrane-bound organelles which repres- Key words: adaptive and innate immunity; apoptosis; ent the main degradative compartment in eukaryotic cells. -
A Cysteine Protease Inhibitor Blocks SARS-Cov-2 Infection of Human and Monkey Cells
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.23.347534; this version posted October 30, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. A cysteine protease inhibitor blocks SARS-CoV-2 infection of human and monkey cells Drake M. Mellott,1 Chien-Te Tseng,3 Aleksandra Drelich,3 Pavla Fajtová,4,5 Bala C. Chenna,1 Demetrios H. Kostomiris1, Jason Hsu,3 Jiyun Zhu,1 Zane W. Taylor,2,9 Vivian Tat,3 Ardala Katzfuss,1 Linfeng Li,1 Miriam A. Giardini,4 Danielle Skinner,4 Ken Hirata,4 Sungjun Beck4, Aaron F. Carlin,8 Alex E. Clark4, Laura Beretta4, Daniel Maneval6, Felix Frueh,6 Brett L. Hurst,7 Hong Wang,7 Klaudia I. Kocurek,2 Frank M. Raushel,2 Anthony J. O’Donoghue,4 Jair Lage de Siqueira-Neto,4 Thomas D. Meek1.*, and James H. McKerrow#4,* Departments of Biochemistry and Biophysics1 and Chemistry,2 Texas A&M University, 301 Old Main Drive, College Station, Texas 77843, 3Department of Microbiology and Immunology, University of Texas, Medical Branch, 3000 University Boulevard, Galveston, Texas, 77755-1001, 4Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 5Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague, Czech Republic, 6Selva Therapeutics, and 7Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, 5600 Old Main Hill, Utah State University, Logan, Utah, 84322, 8Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA.9Current address: Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99353. -
Molecular Functions of Thyroid Hormones and Their Clinical Significance in Liver-Related Diseases
Hindawi Publishing Corporation BioMed Research International Volume 2013, Article ID 601361, 16 pages http://dx.doi.org/10.1155/2013/601361 Review Article Molecular Functions of Thyroid Hormones and Their Clinical Significance in Liver-Related Diseases Hsiang Cheng Chi,1 Cheng-Yi Chen,1 Ming-Ming Tsai,2 Chung-Ying Tsai,1 and Kwang-Huei Lin1 1 Department of Biochemistry, School of Medicine, Chang-Gung University, Taoyuan 333, Taiwan 2 Department of Nursing, Chang-Gung University of Science and Technology, Taoyuan 333, Taiwan Correspondence should be addressed to Kwang-Huei Lin; [email protected] Received 4 February 2013; Revised 14 May 2013; Accepted 28 May 2013 Academic Editor: Elena Orlova Copyright © 2013 Hsiang Cheng Chi et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Thyroid hormones (THs) are potent mediators of several physiological processes, including embryonic development, cellular differentiation, metabolism, and cell growth. Triiodothyronine3 (T ) is the most biologically active TH form. Thyroid hormone receptors (TRs) belong to the nuclear receptor superfamily and mediate the biological functions of T3 via transcriptional regulation. TRs generally form heterodimers with the retinoid X receptor (RXR) and regulate target genes upon T3 stimulation. Research over the past few decades has revealed that disruption of cellular TH signaling triggers chronic liver diseases, including alcoholic or nonalcoholic fatty liver disease and hepatocellular carcinoma (HCC). Animal model experiments and epidemiologic studies to date imply close associations between high TH levels and prevention of liver disease. -
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 ........................................................................................ -
Studies of Structure and Function of Tripeptidyl-Peptidase II
Till familj och vänner List of Papers This thesis is based on the following papers, which are referred to in the text by their Roman numerals. I. Eriksson, S.; Gutiérrez, O.A.; Bjerling, P.; Tomkinson, B. (2009) De- velopment, evaluation and application of tripeptidyl-peptidase II se- quence signatures. Archives of Biochemistry and Biophysics, 484(1):39-45 II. Lindås, A-C.; Eriksson, S.; Josza, E.; Tomkinson, B. (2008) Investiga- tion of a role for Glu-331 and Glu-305 in substrate binding of tripepti- dyl-peptidase II. Biochimica et Biophysica Acta, 1784(12):1899-1907 III. Eklund, S.; Lindås, A-C.; Hamnevik, E.; Widersten, M.; Tomkinson, B. Inter-species variation in the pH dependence of tripeptidyl- peptidase II. Manuscript IV. Eklund, S.; Kalbacher, H.; Tomkinson, B. Characterization of the endopeptidase activity of tripeptidyl-peptidase II. Manuscript Paper I and II were published under maiden name (Eriksson). Reprints were made with permission from the respective publishers. Contents Introduction ..................................................................................................... 9 Enzymes ..................................................................................................... 9 Enzymes and pH dependence .............................................................. 11 Peptidases ................................................................................................. 12 Serine peptidases ................................................................................. 14 Intracellular protein -
Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in