I. the Retinofugal Pathway of Chick
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
The Extracellular Matrix: an Accomplice in Gastric Cancer Development and Progression
cells Review The Extracellular Matrix: An Accomplice in Gastric Cancer Development and Progression Ana Margarida Moreira 1,2,3, Joana Pereira 1,2,4, Soraia Melo 1,2,4 , Maria Sofia Fernandes 1,2, Patrícia Carneiro 1,2 , Raquel Seruca 1,2,4 and Joana Figueiredo 1,2,* 1 Epithelial Interactions in Cancer Group, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; [email protected] (A.M.M.); [email protected] (J.P.); [email protected] (S.M.); [email protected] (M.S.F.); [email protected] (P.C.); [email protected] (R.S.) 2 Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal 3 Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal 4 Medical Faculty, University of Porto, 4200-319 Porto, Portugal * Correspondence: jfi[email protected]; Tel.: +351-220408800; Fax: +351-225570799 Received: 15 January 2020; Accepted: 6 February 2020; Published: 8 February 2020 Abstract: The extracellular matrix (ECM) is a dynamic and highly organized tissue structure, providing support and maintaining normal epithelial architecture. In the last decade, increasing evidence has emerged demonstrating that alterations in ECM composition and assembly strongly affect cellular function and behavior. Even though the detailed mechanisms underlying cell-ECM crosstalk are yet to unravel, it is well established that ECM deregulation accompanies the development of many pathological conditions, such as gastric cancer. Notably, gastric cancer remains a worldwide concern, representing the third most frequent cause of cancer-associated deaths. Despite increased surveillance protocols, patients are usually diagnosed at advanced disease stages, urging the identification of novel diagnostic biomarkers and efficient therapeutic strategies. -
Bruch's Membrane Abnormalities in PRDM5-Related Brittle Cornea
Porter et al. Orphanet Journal of Rare Diseases (2015) 10:145 DOI 10.1186/s13023-015-0360-4 RESEARCH Open Access Bruch’s membrane abnormalities in PRDM5-related brittle cornea syndrome Louise F. Porter1,2,3, Roberto Gallego-Pinazo4, Catherine L. Keeling5, Martyna Kamieniorz5, Nicoletta Zoppi6, Marina Colombi6, Cecilia Giunta7, Richard Bonshek2,8, Forbes D. Manson1 and Graeme C. Black1,9* Abstract Background: Brittle cornea syndrome (BCS) is a rare, generalized connective tissue disorder associated with extreme corneal thinning and a high risk of corneal rupture. Recessive mutations in transcription factors ZNF469 and PRDM5 cause BCS. Both transcription factors are suggested to act on a common pathway regulating extracellular matrix genes, particularly fibrillar collagens. We identified bilateral myopic choroidal neovascularization as the presenting feature of BCS in a 26-year-old-woman carrying a novel PRDM5 mutation (p.Glu134*). We performed immunohistochemistry of anterior and posterior segment ocular tissues, as expression of PRDM5 in the eye has not been described, or the effects of PRDM5-associated disease on the retina, particularly the extracellular matrix composition of Bruch’smembrane. Methods: Immunohistochemistry using antibodies against PRDM5, collagens type I, III, and IV was performed on the eyes of two unaffected controls and two patients (both with Δ9-14 PRDM5). Expression of collagens, integrins, tenascin and fibronectin in skin fibroblasts of a BCS patient with a novel p.Glu134* PRDM5 mutation was assessed using immunofluorescence. Results: PRDM5 is expressed in the corneal epithelium and retina. We observe reduced expression of major components of Bruch’s membrane in the eyes of two BCS patients with a PRDM5 Δ9-14 mutation. -
Temporary Disruption of the Retinal Basal Lamina and Its Effect on Retinal Histogenesis
Developmental Biology 238, 79–96 (2001) doi:10.1006/dbio.2001.0396, available online at http://www.idealibrary.com on Temporary Disruption of the Retinal Basal Lamina and Its Effect on Retinal Histogenesis Willi Halfter,*,1 Sucai Dong,* Manimalha Balasubramani,* and Mark E. Bier† *Department of Neurobiology, University of Pittsburgh, 1402 E Biological Science Tower, Pittsburgh, Pennsylvania 15261; and †Department of Chemistry, Mellon Institute, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-2683 An experimental paradigm was devised to remove the retinal basal lamina for defined periods of development: the basal lamina was dissolved by injecting collagenase into the vitreous of embryonic chick eyes, and its regeneration was induced by a chase with mouse laminin-1 and ␣2-macroglobulin. The laminin-1 was essential in reconstituting a new basal lamina and could not be replaced by laminin-2 or collagen IV, whereas the macroglobulin served as a collagenase inhibitor that did not directly contribute to basal lamina regeneration. The regeneration occurred within 6 h after the laminin-1 chase by forming a morphologically complete basal lamina that included all known basal lamina proteins from chick embryos, such as laminin-1, nidogen-1, collagens IV and XVIII, perlecan, and agrin. The temporary absence of the basal lamina had dramatic effects on retinal histogenesis, such as an irreversible retraction of the endfeet of the neuroepithelial cells from the vitreal surface of the retina, the formation of a disorganized ganglion cell layer with an increase in ganglion cells by 30%, and the appearance of multiple retinal ectopias. Finally, basal lamina regeneration was associated with aberrant axons failing to correctly enter the optic nerve. -
In Normal Conditions After Heat Stress
1 Transcriptome analysis of yamame (Oncorhynchus masou) in normal conditions after heat stress Waraporn Kraitavin1, Kazutoshi Yoshitake1, Yoji Igarashi1, Susumu Mitsuyama1, Shigeharu Kinoshita1, Daisuke Kambayashi2, Shugo Watabe3 and Shuichi Asakawa1* 1 Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan; [email protected] (S.A.) 2 Kobayashi Branch, Miyazaki Prefectural Fisheries Research Institute, Kobayashi, Miyazaki 886-0005, Japan 3 School of Marine Biosciences, Kitasato University, Minami, Sagamihara, Kanagawa 252-0313, Japan; [email protected] * Correspondence: [email protected] (S.A.) 2 A B *HT represents high-temperature tolerant, NT represents non-high-temperature tolerant Figure S1. The pheatmap repeatability analysis of mRNA libraries between samples using the Pearson correlation, (A) gill and (B) fin 3 A B *HT represents high-temperature tolerant, NT represents non-high-temperature tolerant Figure S2. The PCA analysis of mRNA libraries between samples, (A) gill and (B) fin. 4 Table S1. List of the differentially expressed genes of the gill in yamame Gene_id Annotation HT_TPM NT_TPM log2(FoldChange) P - value TRINITY_DN100000_c0_g1_i2 VDAC2 27.57 17.15 0.71 0.00 TRINITY_DN100006_c4_g1_i1 0.65 2.69 -1.93 0.00 TRINITY_DN100021_c0_g1_i2 CXL14 0.13 4.06 -4.96 0.00 TRINITY_DN100027_c4_g2_i1 PEAK1 1.31 4.44 -1.77 0.00 TRINITY_DN100027_c4_g3_i1 0.17 2.38 -3.18 0.00 TRINITY_DN100035_c6_g6_i2 2.13 13.97 -2.68 0.00 TRINITY_DN100055_c1_g2_i1 3BHS 0.22 -
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, -
140503 IPF Signatures Supplement Withfigs Thorax
Supplementary material for Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis Daryle J. DePianto1*, Sanjay Chandriani1⌘*, Alexander R. Abbas1, Guiquan Jia1, Elsa N. N’Diaye1, Patrick Caplazi1, Steven E. Kauder1, Sabyasachi Biswas1, Satyajit K. Karnik1#, Connie Ha1, Zora Modrusan1, Michael A. Matthay2, Jasleen Kukreja3, Harold R. Collard2, Jackson G. Egen1, Paul J. Wolters2§, and Joseph R. Arron1§ 1Genentech Research and Early Development, South San Francisco, CA 2Department of Medicine, University of California, San Francisco, CA 3Department of Surgery, University of California, San Francisco, CA ⌘Current address: Novartis Institutes for Biomedical Research, Emeryville, CA. #Current address: Gilead Sciences, Foster City, CA. *DJD and SC contributed equally to this manuscript §PJW and JRA co-directed this project Address correspondence to Paul J. Wolters, MD University of California, San Francisco Department of Medicine Box 0111 San Francisco, CA 94143-0111 [email protected] or Joseph R. Arron, MD, PhD Genentech, Inc. MS 231C 1 DNA Way South San Francisco, CA 94080 [email protected] 1 METHODS Human lung tissue samples Tissues were obtained at UCSF from clinical samples from IPF patients at the time of biopsy or lung transplantation. All patients were seen at UCSF and the diagnosis of IPF was established through multidisciplinary review of clinical, radiological, and pathological data according to criteria established by the consensus classification of the American Thoracic Society (ATS) and European Respiratory Society (ERS), Japanese Respiratory Society (JRS), and the Latin American Thoracic Association (ALAT) (ref. 5 in main text). Non-diseased normal lung tissues were procured from lungs not used by the Northern California Transplant Donor Network. -
WES Gene Package Multiple Congenital Anomalie.Xlsx
Whole Exome Sequencing Gene package Multiple congenital anomalie, version 5, 1‐2‐2018 Technical information DNA was enriched using Agilent SureSelect Clinical Research Exome V2 capture and paired‐end sequenced on the Illumina platform (outsourced). The aim is to obtain 8.1 Giga base pairs per exome with a mapped fraction of 0.99. The average coverage of the exome is ~50x. Duplicate reads are excluded. Data are demultiplexed with bcl2fastq Conversion Software from Illumina. Reads are mapped to the genome using the BWA‐MEM algorithm (reference: http://bio‐bwa.sourceforge.net/). Variant detection is performed by the Genome Analysis Toolkit HaplotypeCaller (reference: http://www.broadinstitute.org/gatk/). The detected variants are filtered and annotated with Cartagenia software and classified with Alamut Visual. It is not excluded that pathogenic mutations are being missed using this technology. At this moment, there is not enough information about the sensitivity of this technique with respect to the detection of deletions and duplications of more than 5 nucleotides and of somatic mosaic mutations (all types of sequence changes). HGNC approved Phenotype description including OMIM phenotype ID(s) OMIM median depth % covered % covered % covered gene symbol gene ID >10x >20x >30x A4GALT [Blood group, P1Pk system, P(2) phenotype], 111400 607922 101 100 100 99 [Blood group, P1Pk system, p phenotype], 111400 NOR polyagglutination syndrome, 111400 AAAS Achalasia‐addisonianism‐alacrimia syndrome, 231550 605378 73 100 100 100 AAGAB Keratoderma, palmoplantar, -
Supporting Information for Proteomics DOI 10.1002/Pmic.200400942
Supporting Information for Proteomics DOI 10.1002/pmic.200400942 Wei-Jun Qian, Jon M. Jacobs, David G. Camp II, Matthew E. Monroe, Ronald J. Moore, Marina A. Gritsenko, Steve E. Calvano, Stephen F. Lowry, Wenzhong Xiao, Lyle L. Moldawer, Ronald W. Davis, Ronald G. Tompkins and Richard D. Smith Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry ã 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.de Supplemental Table 1: List of 804 identified plasma proteins. Note: Reference IDs correspond to either SwissProt, NCBI, or PIR database entries. For each protein, one representive peptide sequence and the peptide charge_state, SEQUEST Xcorr, and Delcn are listed. The number of different peptides identifying each specific protein is also indicated. To facilitate comparison of protein abundances between the untreated and treated samples, the numbers of peptide hit, the protein abundance ratio (treated/untreated) calculated from peptide peak area ratios, and the standard deviation of peptide peak area ratios for each protein are also listed. No abundance ratio is shown if the protein has no common peptide identified in the two samples. Whether the same protein ID was reported in reference 16 and reference 27 (195 proteins observed from two different sources) is also indicated. Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard -
Vesicoureteral Reflux and the Extracellular Matrix Connection
Vesicoureteral reflux and the extracellular matrix connection Fatima Tokhmafshan, Patrick D. Brophy, Rasheed A. Gbadegesin & Indra R. Gupta Pediatric Nephrology Journal of the International Pediatric Nephrology Association ISSN 0931-041X Pediatr Nephrol DOI 10.1007/s00467-016-3386-5 1 23 Your article is protected by copyright and all rights are held exclusively by IPNA. This e- offprint is for personal use only and shall not be self-archived in electronic repositories. If you wish to self-archive your article, please use the accepted manuscript version for posting on your own website. You may further deposit the accepted manuscript version in any repository, provided it is only made publicly available 12 months after official publication or later and provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer's website. The link must be accompanied by the following text: "The final publication is available at link.springer.com”. 1 23 Author's personal copy Pediatr Nephrol DOI 10.1007/s00467-016-3386-5 REVIEW Vesicoureteral reflux and the extracellular matrix connection Fatima Tokhmafshan1 & Patrick D. Brophy 2 & Rasheed A. Gbadegesin3,4 & Indra R. Gupta1,5 Received: 22 October 2015 /Revised: 18 March 2016 /Accepted: 21 March 2016 # IPNA 2016 Abstract Primary vesicoureteral reflux (VUR) is a common Introduction pediatric condition due to a developmental defect in the ureterovesical junction. The prevalence of VUR among indi- The ureterovesical junction (UVJ) is a critical structure in the viduals with connective tissue disorders, as well as the impor- urinary tract. It protects the low-pressure upper urinary tract from tance of the ureter and bladder wall musculature for the anti- the intermittent high pressure in the bladder. -
Binding of Tenascin-X to Decorin Provided by Elsevier - Publisher Connector
FEBS Letters 495 (2001) 44^47 FEBS 24793 View metadata, citation and similar papers at core.ac.uk brought to you by CORE Binding of tenascin-X to decorin provided by Elsevier - Publisher Connector Florent Elefteriou, Jean-Yves Exposito, Robert Garrone, Claire Lethias* Institut de Biologie et Chimie des Prote¨ines, CNRS UMR 5086, Universite¨ Claude Bernard, 7 passage du Vercors, 69367 Lyon Cedex 07, France Received 10 March 2001; accepted 20 March 2001 First published online 3 April 2001 Edited by Veli-Pekka Lehto arrangement of modules characteristic of TNs [10^13] and a Abstract Tenascin-X (TN-X) is an extracellular matrix protein whose absence results in an alteration of the mechanical widespread expression during embryonic and adult life, where properties of connective tissue. To understand the mechanisms it appears more speci¢cally in striated muscles, tendon and of integration of TN-X in the extracellular matrix, overlay blot ligament sheaths, dermis, adventitia of blood vessels, periph- assays were performed on skin extracts. A 100 kDa molecule eral nerves and digestive tract [11,12,14^16]. By immunoelec- interacting with TN-X was identified by this method and this tron microscopy, we have shown that TN-X is associated with interaction was abolished when the extract was digested by collagen ¢brils in the dermis and in the mesangium of kidney chondroitinase. By solid-phase assays, we showed that dermatan glomeruli [14]. The major functions of TN-X are not clearly sulfate chains of decorin bind to the heparin-binding site included understood at present, though some hypotheses have emerged within the fibronectin-type III domains 10 and 11 of TN-X. -
Table SI. a Total of 643 Proteins Were Identified by Tandem Mass Spectrometry in the Microvesicles/Exosomes from Patients with ABE
Table SI. A total of 643 proteins were identified by tandem mass spectrometry in the microvesicles/exosomes from patients with ABE. Accession Description Coverage PS Unique AAs Molecular Calc. pI Abundance ratio: Abundance ratio: Score Sequest no. Peptides Ms Peptides weight (kDa) Moderate/ Severe/ control HT control P01024 Complement C3 85.68851 132 228 127 1663 187.03 6.4 1.12 1.131 8141.004593 1 P0C0L5 Complement C4-B 66.80046 89 128 1 1744 192.631 7.27 2.106 1.249 4859.406727 9 P01023 Alpha-2-macroglobulin 63.83989 76 140 76 1474 163.188 6.46 1.021 0.972 5149.27648 2 P02751 Fibronectin 56.03521 87 960 87 2386 262.46 5.71 0.805 1.005 3458.332983 P02768 Serum albumin 79.31034 54 104 54 609 69.321 6.28 1.157 1.086 3705.267895 4 P08603 Complement factor H 58.4078 60 544 55 1231 139.005 6.61 1.02 0.979 1917.082723 Q9Y6R7 IgGFc-binding protein 27.71508 68 305 68 5405 571.639 5.34 1.527 1.04 981.3557811 P04114 Apolipoprotein B-100 33.66206 124 255 124 4563 515.283 7.05 1.055 1.057 753.3890735 Q12860 Contactin-1 56.87623 46 242 46 1018 113.249 5.9 0.747 0.963 816.1462975 A0A0A0M Immunoglobulin heavy 55.6391 23 124 12 399 43.884 6.96 1.206 1.104 4833.498744 S08 constant gamma 1 (Fragment) 7 P01031 Complement C5 44.98807 66 254 66 1676 188.186 6.52 1.224 1.241 804.1478994 P23142 Fibulin-1 57.32575 26 297 10 703 77.162 5.22 0.812 0.946 1110.052139 O00533 Neural cell adhesion molecule 42.88079 38 220 37 1208 134.987 5.76 0.789 0.827 804.1383946 L1-like protein B4DPQ0 cDNA FLJ54471, highly 53.82476 30 278 30 719 81.837 6.37 0.995 0.971 923.9868439 -
NIH Public Access Author Manuscript J Prosthodont Res
NIH Public Access Author Manuscript J Prosthodont Res. Author manuscript; available in PMC 2015 October 11. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: J Prosthodont Res. 2014 October ; 58(4): 193–207. doi:10.1016/j.jpor.2014.08.003. Mechano-regulation of Collagen Biosynthesis in Periodontal Ligament Masaru Kaku1,* and Mitsuo Yamauchi2 1Division of Bioprosthodontics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan 2North Carolina Oral Health Institute, University of North Carolina at Chapel Hill, NC, USA Abstract Purpose—Periodontal ligament (PDL) plays critical roles in the development and maintenance of periodontium such as tooth eruption and dissipation of masticatory force. The mechanical properties of PDL are mainly derived from fibrillar type I collagen, the most abundant extracellular component. Study selection—The biosynthesis of type I collagen is a long, complex process including a number of intra- and extracellular post-translational modifications. The final modification step is the formation of covalent intra- and intermolecular cross-links that provide collagen fibrils with stability and connectivity. Results—It is now clear that collagen post-translational modifications are regulated by groups of specific enzymes and associated molecules in a tissue-specific manner; and these modifications appear to change in response to mechanical force. Conclusions—This review focuses on the effect of mechanical loading on collagen biosynthesis and fibrillogenesis in PDL with emphasis on the post-translational modifications of collagens, which is an important molecular aspect to understand in the field of prosthetic dentistry. Keywords Periodontal ligament; Mechanical loading; Collagen; Fibrillogenesis; Post-translational modification © 2014 Japan Prosthodontic Society.