Osteogenesis Imperfecta Types I-XI Implications for the Neonatal Nurse Jody Womack , RNC-NIC, NNP-BC, MS
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Supplemental Figure 1. Vimentin
Double mutant specific genes Transcript gene_assignment Gene Symbol RefSeq FDR Fold- FDR Fold- FDR Fold- ID (single vs. Change (double Change (double Change wt) (single vs. wt) (double vs. single) (double vs. wt) vs. wt) vs. single) 10485013 BC085239 // 1110051M20Rik // RIKEN cDNA 1110051M20 gene // 2 E1 // 228356 /// NM 1110051M20Ri BC085239 0.164013 -1.38517 0.0345128 -2.24228 0.154535 -1.61877 k 10358717 NM_197990 // 1700025G04Rik // RIKEN cDNA 1700025G04 gene // 1 G2 // 69399 /// BC 1700025G04Rik NM_197990 0.142593 -1.37878 0.0212926 -3.13385 0.093068 -2.27291 10358713 NM_197990 // 1700025G04Rik // RIKEN cDNA 1700025G04 gene // 1 G2 // 69399 1700025G04Rik NM_197990 0.0655213 -1.71563 0.0222468 -2.32498 0.166843 -1.35517 10481312 NM_027283 // 1700026L06Rik // RIKEN cDNA 1700026L06 gene // 2 A3 // 69987 /// EN 1700026L06Rik NM_027283 0.0503754 -1.46385 0.0140999 -2.19537 0.0825609 -1.49972 10351465 BC150846 // 1700084C01Rik // RIKEN cDNA 1700084C01 gene // 1 H3 // 78465 /// NM_ 1700084C01Rik BC150846 0.107391 -1.5916 0.0385418 -2.05801 0.295457 -1.29305 10569654 AK007416 // 1810010D01Rik // RIKEN cDNA 1810010D01 gene // 7 F5 // 381935 /// XR 1810010D01Rik AK007416 0.145576 1.69432 0.0476957 2.51662 0.288571 1.48533 10508883 NM_001083916 // 1810019J16Rik // RIKEN cDNA 1810019J16 gene // 4 D2.3 // 69073 / 1810019J16Rik NM_001083916 0.0533206 1.57139 0.0145433 2.56417 0.0836674 1.63179 10585282 ENSMUST00000050829 // 2010007H06Rik // RIKEN cDNA 2010007H06 gene // --- // 6984 2010007H06Rik ENSMUST00000050829 0.129914 -1.71998 0.0434862 -2.51672 -
Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
Human Oxygen Sensing May Have Origins in Prokaryotic Elongation Factor Tu Prolyl-Hydroxylation
Human oxygen sensing may have origins in prokaryotic elongation factor Tu prolyl-hydroxylation John S. Scottia, Ivanhoe K. H. Leunga,1,2, Wei Gea,b,1, Michael A. Bentleyc, Jordi Papsd, Holger B. Kramere, Joongoo Leea, WeiShen Aika, Hwanho Choia, Steinar M. Paulsenc,3, Lesley A. H. Bowmanf, Nikita D. Loika,4, Shoichiro Horitaa,e, Chia-hua Hoa,5, Nadia J. Kershawa,6, Christoph M. Tangf, Timothy D. W. Claridgea, Gail M. Prestonc, Michael A. McDonougha, and Christopher J. Schofielda,7 aChemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom; bChinese Academy of Medical Sciences, Beijing 100005, China; cDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom; dDepartment of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom; eDepartment of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom; and fDepartment of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom Edited by Gregg L. Semenza, The Johns Hopkins University School of Medicine, Baltimore, MD, and approved August 5, 2014 (received for review May 30, 2014) The roles of 2-oxoglutarate (2OG)-dependent prolyl-hydroxylases Results in eukaryotes include collagen stabilization, hypoxia sensing, and Pseudomonas spp. Contain a Functional PHD. To investigate the role translational regulation. The hypoxia-inducible factor (HIF) sensing of a putative PHD homolog in Pseudomonas aeruginosa (PPHD), system is conserved in animals, but not in other organisms. How- we initially characterized a PPHD insertional mutant strain. ever, bioinformatics imply that 2OG-dependent prolyl-hydroxy- Metabolic screening studies revealed that the PPHD mutant strain lases (PHDs) homologous to those acting as sensing components displays impaired growth in the presence of iron chelators (e.g., for the HIF system in animals occur in prokaryotes. -
Characterization of Collagen Fibers (I, III, IV) and Elastin of Normal and Neoplastic Canine Prostatic Tissues
veterinary sciences Article Characterization of Collagen Fibers (I, III, IV) and Elastin of Normal and Neoplastic Canine Prostatic Tissues Luis Gabriel Rivera Calderón 1, Priscila Emiko Kobayashi 2, Rosemeri Oliveira Vasconcelos 1, Carlos Eduardo Fonseca-Alves 3 and Renée Laufer-Amorim 2,* 1 Department of Veterinary Pathology, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, São Paulo 14884-900, Brazil; [email protected] (L.G.R.C.); [email protected] (R.O.V.) 2 Department of Veterinary Clinic, School of Veterinary Medicine and Animal Science, São Paulo State University (Unesp), Botucatu, São Paulo 18618-681, Brazil; [email protected] 3 Department of Veterinary Surgery and Anesthesiology, School of Veterinary Medicine and Animal Science, São Paulo State University (Unesp), Botucatu, São Paulo 18618-681, Brazil; [email protected] * Correspondence: [email protected]; Tel.: +55-14-3880-2076 Received: 7 January 2019; Accepted: 25 February 2019; Published: 2 March 2019 Abstract: This study aimed to investigate collagen (Coll-I, III, IV) and elastin in canine normal prostate and prostate cancer (PC) using Picrosirius red (PSR) and Immunohistochemical (IHC) analysis. Eight normal prostates and 10 PC from formalin-fixed, paraffin-embedded samples were used. Collagen fibers area was analyzed with ImageJ software. The distribution of Coll-I and Coll-III was approximately 80% around prostatic ducts and acini, 15% among smooth muscle, and 5% surrounding blood vessels, in both normal prostate and PC. There was a higher median area of Coll-III in PC when compared to normal prostatic tissue (p = 0.001 for PSR and p = 0.05 for IHC). -
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 -
Collagen Type I and Decorin Expression in Tenocytes Depend On
Wagenhäuser et al. BMC Musculoskeletal Disorders 2012, 13:140 http://www.biomedcentral.com/1471-2474/13/140 RESEARCH ARTICLE Open Access Collagen type I and decorin expression in tenocytes depend on the cell isolation method Markus U Wagenhäuser1†, Matthias F Pietschmann1*†, Birte Sievers1, Denitsa Docheva2, Matthias Schieker2, Volkmar Jansson1 and Peter E Müller1 Abstract Backround: The treatment of rotator cuff tears is still challenging. Tendon tissue engineering (TTE) might be an alternative in future. Tenocytes seem to be the most suitable cell type as they are easy to obtain and no differentiation in vitro is necessary. The aim of this study was to examine, if the long head of the biceps tendon (LHB) can deliver viable tenocytes for TTE. In this context, different isolation methods, such as enzymatic digestion (ED) and cell migration (CM), are investigated on differences in gene expression and cell morphology. Methods: Samples of the LHB were obtained from patients, who underwent surgery for primary shoulder arthroplasty. Using ED as isolation method, 0.2% collagenase I solution was used. Using CM as isolation method, small pieces of minced tendon were put into petri-dishes. After cell cultivation, RT-PCR was performed for collagen type I, collagen type III, decorin, tenascin-C, fibronectin, Scleraxis, tenomodulin, osteopontin and agreccan. Results: The total number of isolated cells, in relation to 1 g of native tissue, was 14 times higher using ED. The time interval for cell isolation was about 17 hours using ED and approximately 50 days using CM. Cell morphology in vitro was similar for both isolation techniques. Higher expression of collagen type I could be observed in tenocyte-like cell cultures (TLCC) using ED as isolation method (p < 0.05), however decorin expression was higher in TLCC using CM as isolation method (p < 0.05). -
Collagens—Structure, Function, and Biosynthesis
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of East Anglia digital repository Advanced Drug Delivery Reviews 55 (2003) 1531–1546 www.elsevier.com/locate/addr Collagens—structure, function, and biosynthesis K. Gelsea,E.Po¨schlb, T. Aignera,* a Cartilage Research, Department of Pathology, University of Erlangen-Nu¨rnberg, Krankenhausstr. 8-10, D-91054 Erlangen, Germany b Department of Experimental Medicine I, University of Erlangen-Nu¨rnberg, 91054 Erlangen, Germany Received 20 January 2003; accepted 26 August 2003 Abstract The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified so far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. This review focuses on the distribution and function of various collagen types in different tissues. It introduces their basic structural subunits and points out major steps in the biosynthesis and supramolecular processing of fibrillar collagens as prototypical members of this protein family. A final outlook indicates the importance of different collagen types not only for the understanding of collagen-related diseases, but also as a basis for the therapeutical use of members of this protein family discussed in other chapters of this issue. D 2003 Elsevier B.V. All rights reserved. Keywords: Collagen; Extracellular matrix; Fibrillogenesis; Connective tissue Contents 1. Collagens—general introduction ............................................. 1532 2. Collagens—the basic structural module......................................... -
Sources of Collagen for Biomaterials in Skin Wound Healing
bioengineering Review Sources of Collagen for Biomaterials in Skin Wound Healing Evan Davison-Kotler 1,2, William S. Marshall 1 and Elena García-Gareta 2,* 1 Biology Department, St. Francis Xavier University, Antigonish, NS B2G 2W5, Canada 2 Regenerative Biomaterials Group, The RAFT Institute, Mount Vernon Hospital, Northwood HA6 2RN, UK * Correspondence: [email protected]; Tel.: +44-(0)-1923844350 Received: 23 May 2019; Accepted: 26 June 2019; Published: 30 June 2019 Abstract: Collagen is the most frequently used protein in the fields of biomaterials and regenerative medicine. Within the skin, collagen type I and III are the most abundant, while collagen type VII is associated with pathologies of the dermal–epidermal junction. The focus of this review is mainly collagens I and III, with a brief overview of collagen VII. Currently, the majority of collagen is extracted from animal sources; however, animal-derived collagen has a number of shortcomings, including immunogenicity, batch-to-batch variation, and pathogenic contamination. Recombinant collagen is a potential solution to the aforementioned issues, although production of correctly post-translationally modified recombinant human collagen has not yet been performed at industrial scale. This review provides an overview of current collagen sources, associated shortcomings, and potential resolutions. Recombinant expression systems are discussed, as well as the issues associated with each method of expression. Keywords: collagen; collagen sources; recombinant collagen; biomaterials; regenerative medicine; tissue engineering; wound healing; skin 1. Introduction 1.1. The Molecular Structure of Collagen The 28 different collagen types of the collagen superfamily are further divided into eight subfamilies, with the majority of the collagen types belonging to the fibril-forming or fibrillar subfamily [1,2]. -
Serum Type I and Type III Procollagen Peptide Levels in Sarcoidosis
Eur Respir J, 1996, 9, 1648–1651 Copyright ERS Journals Ltd 1996 DOI: 10.1183/09031936.96.09081648 European Respiratory Journal Printed in UK - all rights reserved ISSN 0903 - 1936 Serum type I and type III procollagen peptide levels in sarcoidosis L. Bacchella*, C. Tinelli**, L.S. Gilè+, V. Peona+, C. Aprile*, M.Gorrini+, L. Pasturenzi+, G. Cetta++, M. Luisetti+ Serum type I and type III procollagen peptide levels in sarcoidosis. L. Bacchella, C. *Servizio di Medicina Nucleare, Fondazione Tinelli, L.S. Gilè, V. Peona, C. Aprile, M.Gorrini, L. Pasturenzi, G. Cetta, M. Luisetti. Clinica del Lavoro, Pavia, Italy. **Unità ERS Journals Ltd 1996. di Statistica and +Istituto di Tisiologia e ABSTRACT: Type I and type III are the most abundant collagens in the lung. Malattie Respiratorie, IRCCS Policlinico ++ The aim of our study was to compare type I and III procollagen peptides in sera San Matteo, Pavia, Italy. Dipartimento of sarcoid patients. di Biochimica, Università di Pavia, Italy. Sixty eight patients with sarcoidosis were studied (19 with newly recognized dis- Correspondence: M. Luisetti, Istituto di ease, 7 with relapsing disease, 15 with chronic disease, and 27 in stable remission). Tisiologia e Malattie Respiratorie, IRCCS Thirty healthy volunteers served as controls. The levels of procollagen I and III Policlinico San Matteo, Università degli peptides were determined by radioimmunoassay. Angiotensin-converting enzyme Studi di Pavia, Via Taramelli 5, 27100 (ACE) level was evaluated by means of a colorimetric assay. Pavia, Italy In patients with newly recognized sarcoidosis, both serum procollagen I and III peptide levels were increased with respect to controls (p=0.0014 and p<0.00001, Keywords: Angiotensin-converting enzyme, respectively). -
Proteoglycan Form and Function: a Comprehensive Nomenclature of Proteoglycans
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Matrix Biol Manuscript Author . Author manuscript; Manuscript Author available in PMC 2016 May 06. Published in final edited form as: Matrix Biol. 2015 March ; 42: 11–55. doi:10.1016/j.matbio.2015.02.003. Proteoglycan form and function: A comprehensive nomenclature of proteoglycans Renato V. Iozzo1 and Liliana Schaefer2 1Department of Pathology, Anatomy and Cell Biology and the Cancer Cell Biology and Signaling Program, Kimmel Cancer Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA 2Pharmazentrum Frankfurt/ZAFES, Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany Abstract We provide a comprehensive classification of the proteoglycan gene families and respective protein cores. This updated nomenclature is based on three criteria: Cellular and subcellular location, overall gene/protein homology, and the utilization of specific protein modules within their respective protein cores. These three signatures were utilized to design four major classes of proteoglycans with distinct forms and functions: the intracellular, cell-surface, pericellular and extracellular proteoglycans. The proposed nomenclature encompasses forty-three distinct proteoglycan-encoding genes and many alternatively-spliced variants. The biological functions of these four proteoglycan families are critically assessed in development, cancer and angiogenesis, and in various acquired and genetic diseases where their expression is aberrant. Keywords Proteoglycan; Glycosaminoglycan; Cancer growth; Angiogenesis; Growth factor modulation Introduction It has been nearly 20 years since the original publication of a comprehensive classification of proteoglycan gene families [1]. For the most part, these classes have been widely accepted. However, a broad and current taxonomy of the various proteoglycan gene families and their products is not available. -
Architectural Delineation and Molecular Identification Of
© 2017. Published by The Company of Biologists Ltd | Biology Open (2017) 6, 1383-1390 doi:10.1242/bio.026336 RESEARCH ARTICLE Architectural delineation and molecular identification of extracellular matrix in ascidian embryos and larvae Jiankai Wei1, Guilin Wang1, Xiang Li1, Ping Ren1, Haiyan Yu1 and Bo Dong1,2,3,* ABSTRACT date, 28 types of collagens and >40 distinct α-chains have been The extracellular matrix (ECM) not only provides essential physical identified in vertebrates (Ricard-Blum, 2011). Collagens play scaffolding for cellular constituents but also initiates crucial structural roles and contribute to mechanical properties, biochemical and biomechanical cues that are required for tissue organization and pattern shaping of tissues. Proteoglycans are morphogenesis. In this study, we utilized wheat germ agglutinin characterized by a core protein that is covalently linked to (WGA) staining to characterize the ECM architecture in ascidian glycosaminoglycans (GAGs), which are long, negatively charged embryos and larvae. The results showed three distinct populations of and linear chains of disaccharide repeats. The primary biological ECM presenting in Ciona embryogenesis: the outer layer localized at function of proteoglycans derives from the biochemical and the surface of embryo, an inner layer of notochord sheath and the hydrodynamic characteristics of the GAGs, which bind water to apical ECM secreted by the notochord. To further elucidate the provide hydration and compressive resistance (Mouw et al., 2014). precise structure of Ciona -
Identification and Structural Analysis of Type I Collagen Sites in Complex with Fibronectin Fragments
Identification and structural analysis of type I collagen sites in complex with fibronectin fragments Miche` le C. Erata, David A. Slatterb, Edward D. Lowec, Christopher J. Millarda, Richard W. Farndaleb, Iain D. Campbella, and Ioannis Vakonakisa,1 aDepartment of Biochemistry and cLaboratory of Molecular Biophysics, University of Oxford, Oxford OX1 3QU, United Kingdom; and bDepartment of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom Edited by John Kuriyan, University of California, Berkeley, CA, and approved January 28, 2009 (received for review December 9, 2008) Collagen and fibronectin are major components of vertebrate ments bind the same peptide sequence just C-terminal to the extracellular matrices. Their association and distribution control MMP-1 cleavage site; the tightest binding, however, is mediated 8–9 the development and properties of diverse tissues, but thus far no by the FnI domain pair that also binds ␣2(I). A 2.1-Å crystal 8–9 structural information has been available for the complex formed. structure of FnI in complex with the ␣1(I) peptide shows an ␣ Here, we report binding of a peptide, derived from the 1 chain of extended single-strand peptide conformation, which suggests type I collagen, to the gelatin-binding domain of human fibronec- that FN stabilizes a noncanonical collagen structure upon bind- tin and present the crystal structure of this peptide in complex with ing. We explore this hypothesis in thermal denaturation exper- 8–9 the FnI domain pair. Both gelatin-binding domain subfrag- iments using model triple-helical peptides. The results presented 6 1–2 7 8–9 ments, FnI FnII FnI and FnI, bind the same specific sequence show the first atomic resolution picture of the interaction ␣ on D-period 4 of collagen I 1, adjacent to the MMP-1 cleavage site.