TABLE 5. Proteins Identified in Cumulus and Oocyte. GI Number

Total Page:16

File Type:pdf, Size:1020Kb

TABLE 5. Proteins Identified in Cumulus and Oocyte. GI Number TABLE 5. Proteins identified in Cumulus and Oocyte. GI Cell Protein DDF Protein name Peptides number typea categoryb fraction 30523262 100 kDa coactivator C K 5 2 2852383 14-3-3 protein beta C K 2 4 2852385 14-3-3 protein gamma C K 14 4 298639 155 kda myosin light chain kinase homolog O K 1 1 576 17,000 dalton myosin light chain CO K 5 3 8118661 17-beta-hydroxysteroid dehydrogenase type 1 C K 2 3 17864970 17-beta-hydroxysteroid dehydrogenase type 1 CO K 38 3 59857747 1-acylglycerol-3-phosphate O-acyltransferase 4 O K 1 3 30017445 2',5'-oligoadenylate synthetase 1, 40/46kDa C K 2 4,3 66792906 2'-5' oligoadenylate synthetase 2 C K 1 1 7271506 2-amino-3-ketobutyrate coenzyme A ligase O K 2 1 31414871 2-enoyl thioester reductase C K 2 4,1 45219953 5-hydroxytryptamine receptor 2A C K 2 4,1 47564115 5-oxo-L-prolinase CO K 5 1 34392345 90-kDa heat shock protein beta CO K 54 1 56967054 A Chain A, Crystal Structure Of Bosus Mitochondrial Elongation Factor TuT O K 2 3 27807141 A disintegrin-like and metalloprotease (reprolysin type) with thrombos O K 1 3 89579 A23707 aminomethyltransferase (EC 2.1.2.10) precursor C K 3 3 89381 A29600 alkaline phosphatase (EC 3.1.3.1) precursor, hepatic - bovine O K 1 1 108687 A36623 gap junction protein Cx43 C K 3 4 89346 A40981 3',5'-cyclic-nucleotide phosphodiesterase (EC 3.1.4.17), cGMP-stimulated C K 1 4 1363022 A56351 cleavage and polyadenylation specificity factor 100K chain C K 1 3 1363051 A56534 interferon-induced double-stranded RNA-activated protein kinase inhibitor C K 1 4 14194421 AAKG1_BOVIN 5'-AMP-activated protein kinase, gamma-1 subunit C K 1 4 62751897 Abhydrolase domain containing 2 CO K 2 1 61554426 Abl-philin 2 isoform 2 CO K 2 3 63092048 Acetyl-CoA carboxylase, type beta C K 1 3 6006405 Acetyl-CoA-carboxylase C K 3 1 163596 Acid phosphatase C K 1 4 1649041 Acidic ribosomal phosphoprotein C K 2 1 2293577 Acidic ribosomal phosphoprotein PO C K 6 1 600177 Acidic ribosomal protein P2 C K 9 4 1351857 ACON_BOVIN Aconitate hydratase, mitochondrial precursor CO K 27 1 58013001 Actin [Cryptosporidium sp. ex Bosus] C K 5 4 61555662 Actin related protein 2/3 complex subunit 1B C K 1 2 27806765 Actin, beta CO K 20 2 1381584 Activin receptor type I C K 4 2 59857635 Acyl-Coenzyme A dehydrogenase, short/branched chain precursor C K 9 2 27806205 Acyl-coenzyme A dehydrogenase, very long chain C K 14 3 2498104 AD50_BOVIN ADRENAL MEDULLA 50 KD PROTEIN O K 1 2 20141178 ADA_BOVIN Adenosine deaminase (Adenosine aminohydrolase) O K 1 2 29420423 Adaptor related protein complex (AP)-3 delta subunit C K 2 4 57162630 Adaptor-related protein complex 3, mu 1 subunit C K 1 1 58760446 Adenine phosphoribosyltransferase C K 1 4 61888850 Adenylate kinase 1, soluble C K 1 4 217607 Adenylate kinase 2B CO K 18 1 895754 Adipocyte-type fatty acid binding protein C K 1 4 5823591 Adipophilin C K 2 3 13162341 ADP-ribosylation factor 2 C K 1 3 6680730 ADP-ribosylation factor-like 4 O K 1 1 3041655 ADRO_BOVIN NADPH:adrenodoxin oxidoreductase, mitochondrial precursor C K 3 4 52000728 ADT2_BOVIN ADP,ATP carrier protein 2 (ADP/ATP translocase 2) CO K 40 3 399012 ADT3_BOVIN ADP,ATP carrier protein, isoform T2 (ADP/ATP translocase 3) CO K 10 1 113469 ADX2_BOVIN Adrenodoxin 2, mitochondrial precursor (Adrenal ferredoxin) C K 1 4 31324244 Aggrecanase-1 OK 1 2 6319132 Aggrecanase-1 C K 1 4 6319134 Aggrecanase-2 C K 1 3 1352248 AL1A1_BOVIN Retinal dehydrogenase 1 (RalDH1) (RALDH 1) C K 1 4 162648 Albumin CO K 67 3 60302887 Aldose reductase C K 2 4 4097475 Allele: DQB*1004 C K 1 1 240434 Alpha 1C-adrenergic receptor [cattle, Peptide, 466 aa] C K 2 4,1 61553131 Alpha 2 actin CO K 69 2 386077 Alpha B-crystallin [cattle, lens, Peptide, 175 aa] C K 1 1 2967448 Alpha2(I) collagen C K 1 1 37652865 Alpha2,3-sialyltransferase O K 1 2 56292039 Alpha-2,6-sialyltransferase ST6Gal II C K 1 1 47564072 Alpha-2,8-sialyltransferase 8D C K 1 1 498822 Alpha-2-antiplasmin C K 1 3 61553826 Alpha-N-acetylgalactosaminidase precursor C K 2 4 2506821 AMBP_BOVIN AMBP protein precursor C K 1 4 525 Amine oxidase (flavin-containing); monoamine oxidase type A (MAO-A) C K 1 2 62751707 AminoadipateAminotransferase C K 1 2 4468135 Amyloid precursor protein O K 1 3 61555206 Amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate C K 1 2 20455472 ANG1_BOVIN Angiogenin-1 precursor O K 1 3 12643645 ANGP2_BOVIN Angiopoietin-2 (ANG-2) C K 1 1 61555439 Ankyrin repeatAnd SOCS box-containing protein 14 C K 1 2 59858367 Annexin 5 C K 15 4 61554010 Annexin A8 C K 3 4,1 61553085 Annexin I C K 2 3 1842109 Annexin VI C K 25 2 1168458 ANPRB_BOVIN Atrial natriuretic peptide receptor B precursor (ANP-B) C K 1 2 432627 Anti-testosteroneAntibody CO K 4 3 113956 ANXA4_BOVIN Annexin A4 (Annexin IV) (Lipocortin IV) (Endonexin I) C K 10 4 113983 APEX1_BOVIN DNA-(apurinic or apyrimidinic site) lyase (AP endonuclease 1) CO K 7 2 162678 Apolipoprotein A-I precursor CO K 7 1 46359698 Apolipoprotein C-III C K 2 3 162680 Apolipoprotein H O K 1 3 42564208 Apoliprotein A-I binding protein O K 3 1 47681470 Apoptosis inhibitor survivin C K 1 3 26453359 Apoptosis-associated speck-like protein containing a CARD C K 1 3 114151 ARBK1_BOVIN Beta-adrenergic receptor kinase 1 (Beta-ARK-1) C K 1 4 19354187 Arf3 protein C K 2 4 46213277 Argonaute 3 C K 1 3 162642 Aromatic-L-amino acid decarboxylase C K 2 4 50978894 ARP1 actin-related protein 1 homolog A, centractin alpha C K 1 1 3004445 Arylacetyl acyl-CoA N-acyltransferase C K 1 1 3492930 Arylacetyltransferase C K 6 1 33359641 Aryl-hydrocarbon receptor-interacting protein O K 1 2 59858077 Aspartate aminotransferase 1 C K 1 4 27807467 Aspartate beta-hydroxylase C K 3 1 60391782 ASPM_BOVIN Abnormal spindle-like microcephaly-associated protein homolog C K 1 4 114617 AT5F1_BOVIN ATP synthase B chain, mitochondrial C K 1 3 124013 ATIF1_BOVIN ATPase inhibitor, mitochondrial precursor CO K 3 3 114686 ATP5H_BOVIN ATP synthase D chain, mitochondrial CO K 12 1 231615 ATP5I_BOVIN ATP synthase e chain, mitochondrial CO K 2 3 114687 ATP5J_BOVIN ATP synthase coupling factor 6, mitochondrial precursor C K 1 3 19919710 ATPase 6 C K 2 3 27807317 ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member C K 1 3 61553266 ATPase, H+ transporting, lysosomal 31kD, V1 subunit E isoform 1 C K 3 2,1 14250784 ATPase, H+ transporting, lysosomal, V0 subunit D isoform 1 C K 2 3 114543 ATPB_BOVIN ATP synthase beta chain, mitochondrial precursor CO K 116 3 67010049 ATP-binding cassette sub-family A member 1 CO K 2 3 114579 ATPD_BOVIN ATP synthase delta chain, mitochondrial precursor C K 1 4 62751919 ATP-dependent Lon protease C K 2 4 22297308 Attractin C K 1 1 56967055 B Chain B, Crystal Structure Of Bosus Mitochondrial Elongation Factor O K 1 3 1083059 B54717 palmitoyl-protein thioesterase precursor C K 5 4 162731 Bactenecin 5 precursor C K 1 3 5442448 Band 3 protein C K 3 4 913808 Band 6 polypeptide B6P C K 1 3 33327729 Barrier-to-autointegration factor C K 7 2,1 2309001 BCNT C K 7 2 22779307 Bcnt C K 1 2 6224858 Beta actin CO K 30 3 312732 Beta prime cop C K 1 3 50844501 Beta tubulin CO K 42 3 61553937 Beta-1,3-N-acetylglucosaminyltransferase bGnT-6 O K 1 3 62177160 Beta-3-glucuronyltransferase P C K 1 4 62177158 Beta-3-glucuronyltransferase-S C K 1 3 25808793 Beta-actin binding proteinBetaCAP73 CO K 2 1 47523792 Beta-catenin C K 2 4 55416130 Beta-defensin 402 C K 2 4 2388780 Beta-nerve growth factor O K 1 3 7547262 Biglycan core protein precursor O K 1 3 685045 Bone sialoprotein; BSP C K 1 2 5705922 Bovine corneal protein 54; BCP 54 C K 1 3 3057087 Bovine submaxillary mucin 1 C K 2 2 285664 Bovine T cell receptor gamma chain C K 1 1 7715053 Bradykinin receptor B2 C K 1 4 1438984 Brain-type ribonuclease CO K 3 3 59858011 Branched chain aminotransferase 2, mitochondrial C K 1 1 13195201 BRCA1 C K 2 2,4 29640734 Breast and ovarian cancer susceptibility protein O K 1 3 1710369 BSP30 OK 1 3 27807233 Butyryl Coenzyme A synthetase 1 C K 1 4 30523021 Bv8/prokineticin 2-like protein CO K 2 3 46405153 C19orf10-like C K 1 4 453109 Ca(2+)-sensing receptor C K 1 3 27807135 Calcium channel, voltage-dependent, L type, alpha 1B subunit C K 1 4 2315159 Caldesmon OK 2 3 32766614 Calm2-prov protein C K 4 4 27806049 Calmodulin-dependent phosphodiesterase type 1 C K 1 4 27806721 Calpastatin C K 1 1 287744 CaMP-gated channel CO K 2 3 38322703 Capping protein (actin filament) muscle Z-line, alpha 2 C K 2 4 1838956 Capping protein, beta3 isoform C K 6 4 28192437 Carbonic anhydrase-related XI protein C K 1 1 59676559 CaSP8 and FADD-like apoptosis regulator C K 1 2 13924448 Catecholamine binding protein C K 1 3 1707415 Cathelicidin C K 1 3 809479 Cathepsin B C K 5 4 12697815 Cathepsin D CO K 4 2 59858409 Cathepsin L2 preproprotein C K 4 4 12803555 CBX1 protein C K 1 4 4928775 Cctq C K 5 2,4 56682913 CD2 antigen C K 1 4 27806911 CD9 antigen (p24) C K 1 3 19170724 CD97 protein OK 1 2 1345706 CDC2_BOVIN Cell division control protein 2 homolog (p34 protein kinase) O K 1 2 59857651 CDC37 homolog C K 1 4 61553589 Cdc42 guanine exchange factor 9 O K 1 3 59857983 CDC45-like C K 1 3 30794346 Cellular retinoic acid binding protein 1 C K 1 4 56182498 Cellular retinoic acid binding protein 2 C K 2 4 33323485 Cellular retinol binding protein 1 C K 5 4 32481980 C-Fos C K 1 1 37780029 CGI-105 protein C K 4 3 61554294 CGI-107 protein C K 1 4 59858441 CGI-30 protein OK 1 3 204 CGMP-gated channel C K 1 1 61553710 chaperonin containing TCP1, subunit 3 (gamma) C K 4 1 58760440 Chemokine (C-X-C motif) ligand 13-like C K 2 2 33415854 Chemokine receptor 7 C K 1 4 51316067 CHIA_BOVIN Acidic mammalian
Recommended publications
  • New Concepts in Basement Membrane Biology Willi Halfter1, Philipp Oertle2, Christophe A
    REVIEW ARTICLE New concepts in basement membrane biology Willi Halfter1, Philipp Oertle2, Christophe A. Monnier2,*, Leon Camenzind2, Magaly Reyes-Lua1, Huaiyu Hu3, Joseph Candiello4, Anatalia Labilloy5,†, Manimalha Balasubramani6, Paul Bernhard Henrich1 and Marija Plodinec2,7 1 Department of Ophthalmology, University Hospital Basel, Switzerland 2 Biozentrum and the Swiss Nanoscience Institute, University of Basel, Switzerland 3 Department of Neurobiology and Physiology, Upstate University Hospital, SUNY University, Syracuse, NY, USA 4 Department of Bioengeneering, University of Pittsburgh, PA, USA 5 Department of Renal Physiology, University of Pittsburgh, PA, USA 6 Proteomics Core Facility of the University of Pittsburgh, PA, USA 7 Department of Pathology, University Hospital Basel, Switzerland Keywords Basement membranes (BMs) are thin sheets of extracellular matrix that basal lamina; basement membrane; outline epithelia, muscle fibers, blood vessels and peripheral nerves. The biomechanical properties; collagen IV; current view of BM structure and functions is based mainly on transmis- laminin; membrane asymmetry; nidogen; sion electron microscopy imaging, in vitro protein binding assays, and phe- perlecan notype analysis of human patients, mutant mice and invertebrata. Correspondence Recently, MS-based protein analysis, biomechanical testing and cell adhe- W. Halfter, Department of Ophthalmology, sion assays with in vivo derived BMs have led to new and unexpected University Hospital Basel, Mittlere insights. Proteomic analysis combined with ultrastructural studies showed Strasse 91, 4031 Basel, Switzerland that many BMs undergo compositional and structural changes with Fax: +41 61 267 21 09 advancing age. Atomic force microscopy measurements in combination Tel: +49 7624 982528 with phenotype analysis have revealed an altered mechanical stiffness that E-mail: whalfter@pitt.edu M.
    [Show full text]
  • 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
    [Show full text]
  • Ophthalmological Features Associated with COL4A1 Mutations
    OPHTHALMIC MOLECULAR GENETICS SECTION EDITOR: JANEY L. WIGGS, MD, PhD Ophthalmological Features Associated With COL4A1 Mutations Isabelle Coupry, PhD; Igor Sibon, MD, PhD; Bruno Mortemousque, MD; Franc¸ois Rouanet, MD; Manuele Mine, PharmD, PhD; Cyril Goizet, MD, PhD Objective: To investigate the wide variability of ocular Conclusions: The COL4A1 mutations may be associ- manifestations associated with mutations in the COL4A1 ated with various ophthalmologic developmental anoma- gene that encodes collagen IV␣1. lies of anterior segment dysgenesis type, which are reminiscent of Axenfeld-Rieger anomalies (ARA). Cere- Methods: We clinically evaluated 7 patients from 2 un- brovascular disorders should be added to the list of signs related families in whom ocular features segregated with potentially associated with ARA. COL4A1 mutations that were identified by direct se- quencing. Clinical Relevance: These data suggest that cerebral magnetic resonance imaging may be recommended in Results: The G2159A transition (c.2159GϾA) that leads the clinical treatment of patients with apparently iso- tothemissensemutationp.Gly720Aspwasidentifiedinfam- lated ARA, even when neurological symptoms or signs ily A. An ocular phenotype of variable severity was observed are lacking. in all affected relatives. The missense mutation c.2263GϾA, p.Gly755Arg was identified in family B. One patient from family B also displayed notable ocular features. Arch Ophthalmol. 2010;128(4):483-489 NEW FORM OF HEREDITARY constellation of ocular findings that in- cerebrovascular disorder clude anomalies of the anterior chamber was recently associated angle and aqueous drainage structures (iri- with mutations in the dogoniodysgenesis), iris hypoplasia, ec- COL4A1 gene that en- centric pupil (corectopia), iris tears (poly- Acodes collagen IV␣1.1,2 Mutations in coria), and iridocorneal adhesions COL4A1 were initially associated with ce- traversing the anterior chamber.
    [Show full text]
  • 1 Metabolic Dysfunction Is Restricted to the Sciatic Nerve in Experimental
    Page 1 of 255 Diabetes Metabolic dysfunction is restricted to the sciatic nerve in experimental diabetic neuropathy Oliver J. Freeman1,2, Richard D. Unwin2,3, Andrew W. Dowsey2,3, Paul Begley2,3, Sumia Ali1, Katherine A. Hollywood2,3, Nitin Rustogi2,3, Rasmus S. Petersen1, Warwick B. Dunn2,3†, Garth J.S. Cooper2,3,4,5* & Natalie J. Gardiner1* 1 Faculty of Life Sciences, University of Manchester, UK 2 Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK 3 Centre for Endocrinology and Diabetes, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, UK 4 School of Biological Sciences, University of Auckland, New Zealand 5 Department of Pharmacology, Medical Sciences Division, University of Oxford, UK † Present address: School of Biosciences, University of Birmingham, UK *Joint corresponding authors: Natalie J. Gardiner and Garth J.S. Cooper Email: natalie.gardiner@manchester.ac.uk; garth.cooper@manchester.ac.uk Address: University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, United Kingdom Telephone: +44 161 275 5768; +44 161 701 0240 Word count: 4,490 Number of tables: 1, Number of figures: 6 Running title: Metabolic dysfunction in diabetic neuropathy 1 Diabetes Publish Ahead of Print, published online October 15, 2015 Diabetes Page 2 of 255 Abstract High glucose levels in the peripheral nervous system (PNS) have been implicated in the pathogenesis of diabetic neuropathy (DN). However our understanding of the molecular mechanisms which cause the marked distal pathology is incomplete. Here we performed a comprehensive, system-wide analysis of the PNS of a rodent model of DN.
    [Show full text]
  • Studies on the Proteome of Human Hair - Identifcation of Histones and Deamidated Keratins Received: 15 August 2017 Sunil S
    www.nature.com/scientificreports OPEN Studies on the Proteome of Human Hair - Identifcation of Histones and Deamidated Keratins Received: 15 August 2017 Sunil S. Adav 1, Roopa S. Subbaiaih2, Swat Kim Kerk 2, Amelia Yilin Lee 2,3, Hui Ying Lai3,4, Accepted: 12 January 2018 Kee Woei Ng3,4,7, Siu Kwan Sze 1 & Artur Schmidtchen2,5,6 Published: xx xx xxxx Human hair is laminar-fbrous tissue and an evolutionarily old keratinization product of follicle trichocytes. Studies on the hair proteome can give new insights into hair function and lead to the development of novel biomarkers for hair in health and disease. Human hair proteins were extracted by detergent and detergent-free techniques. We adopted a shotgun proteomics approach, which demonstrated a large extractability and variety of hair proteins after detergent extraction. We found an enrichment of keratin, keratin-associated proteins (KAPs), and intermediate flament proteins, which were part of protein networks associated with response to stress, innate immunity, epidermis development, and the hair cycle. Our analysis also revealed a signifcant deamidation of keratin type I and II, and KAPs. The hair shafts were found to contain several types of histones, which are well known to exert antimicrobial activity. Analysis of the hair proteome, particularly its composition, protein abundances, deamidated hair proteins, and modifcation sites, may ofer a novel approach to explore potential biomarkers of hair health quality, hair diseases, and aging. Hair is an important and evolutionarily conserved structure. It originates from hair follicles deep within the der- mis and is mainly composed of hair keratins and KAPs, which form a complex network that contributes to the rigidity and mechanical properties.
    [Show full text]
  • Download The
    PROBING THE INTERACTION OF ASPERGILLUS FUMIGATUS CONIDIA AND HUMAN AIRWAY EPITHELIAL CELLS BY TRANSCRIPTIONAL PROFILING IN BOTH SPECIES by POL GOMEZ B.Sc., The University of British Columbia, 2002 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in THE FACULTY OF GRADUATE STUDIES (Experimental Medicine) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) January 2010 © Pol Gomez, 2010 ABSTRACT The cells of the airway epithelium play critical roles in host defense to inhaled irritants, and in asthma pathogenesis. These cells are constantly exposed to environmental factors, including the conidia of the ubiquitous mould Aspergillus fumigatus, which are small enough to reach the alveoli. A. fumigatus is associated with a spectrum of diseases ranging from asthma and allergic bronchopulmonary aspergillosis to aspergilloma and invasive aspergillosis. Airway epithelial cells have been shown to internalize A. fumigatus conidia in vitro, but the implications of this process for pathogenesis remain unclear. We have developed a cell culture model for this interaction using the human bronchial epithelium cell line 16HBE and a transgenic A. fumigatus strain expressing green fluorescent protein (GFP). Immunofluorescent staining and nystatin protection assays indicated that cells internalized upwards of 50% of bound conidia. Using fluorescence-activated cell sorting (FACS), cells directly interacting with conidia and cells not associated with any conidia were sorted into separate samples, with an overall accuracy of 75%. Genome-wide transcriptional profiling using microarrays revealed significant responses of 16HBE cells and conidia to each other. Significant changes in gene expression were identified between cells and conidia incubated alone versus together, as well as between GFP positive and negative sorted cells.
    [Show full text]
  • Table SD1. Patient Characteristicsa
    Table SD1. Patient characteristicsa Patient Sex Age Esophageal Treatment Maximum Cell Maximum Maximum Genotype Food SPT/Ab SPT/F b RAST b Rhinitisc Atopicc Asthmac Alternative diagnosis Dated (year) Disease eosinophils thickness in mast cells lymphocytes anaphylaxis (positive dermatitis /hpf basal layer /hpf /hpf reaction) 1 M 11 NL None 0 3 5 3 Unk No ND ND ND Yes No No Recurrent croup December 2 M 11 NL LTRA 0 3 4 3 Unk No ND ND ND No No Yes Functional abdominal pain May 3 F 9 NL None 0 3 4 3 Unk Unk ND ND ND Unk Unk Unk Functional abdominal pain March 4 M 14 NL None 0 2 6 4 Unk No ND ND ND No No No Vomiting/diarrhea Febuary 5 F 7 NL LTRA 0 3 5 6 Unk Yes 1 3 ND Unk Unk Yes Functional abdominal pain March 6 F 13 NL None 0 2 4 2 Unk No 0 4 ND No No No Functional abdominal pain August 7 M 17 CE PPI 0 4 7 12 Unk Yes 17 4 ND No No Yes None November 8 M 6 CE PPI 0 4 6 10 Unk Unk ND ND ND Unk Unk Unk None June 9 F 16 CE LTRA 3 4 6 8 Unk No ND ND ND No No Yes None January 10 F 13 CE LTRA+PPI 3 5 4 8 Unk No 0 0 ND No No No None August 11 F 11 CE LTRA+PPI 6 4 6 9 Unk Unk ND ND ND Unk Unk Unk None May 12 M 11 EE PPI 24 6 6 12 TT No 2 5 3 Yes No Yes None November 13 F 4 EE PPI 25 6 15 15 TT No 0 0 ND No No No None November 14 M 15 EE None 30 6 24 6 TG Unk 1 1 ND Unk Unk Yes None February 15 M 15 EE None 31 6 15 11 TT No 8 2 ND Yes No Yes None March 16 M 13 EE PPI 32 6 10 25 TG No 0 0 ND No No No None June 17 M 6 EE PPI 40 7 10 21 TT Yes 5 3 0 Unk Unk No None November 18 M 13 EE LTRA 42 7 10 5 TT No 4 5 2 Yes Yes Yes None November 19 F 16 EE LTRA+PPI
    [Show full text]
  • Research Article Characterization of the Equine Skeletal Muscle
    McGivney et al. BMC Genomics 2010, 11:398 http://www.biomedcentral.com/1471-2164/11/398 RESEARCH ARTICLE Open Access CharacterizationResearch article of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training Beatrice A McGivney1, Paul A McGettigan1, John A Browne1, Alexander CO Evans1,3, Rita G Fonseca2, Brendan J Loftus3, Amanda Lohan3, David E MacHugh1,3, Barbara A Murphy1, Lisa M Katz2 and Emmeline W Hill*1 Abstract Background: Digital gene expression profiling was used to characterize the assembly of genes expressed in equine skeletal muscle and to identify the subset of genes that were differentially expressed following a ten-month period of exercise training. The study cohort comprised seven Thoroughbred racehorses from a single training yard. Skeletal muscle biopsies were collected at rest from the gluteus medius at two time points: T1 - untrained, (9 ± 0.5 months old) and T2 - trained (20 ± 0.7 months old). Results: The most abundant mRNA transcripts in the muscle transcriptome were those involved in muscle contraction, aerobic respiration and mitochondrial function. A previously unreported over-representation of genes related to RNA processing, the stress response and proteolysis was observed. Following training 92 tags were differentially expressed of which 74 were annotated. Sixteen genes showed increased expression, including the mitochondrial genes ACADVL, MRPS21 and SLC25A29 encoded by the nuclear genome. Among the 58 genes with decreased expression, MSTN, a negative regulator of muscle growth, had the greatest decrease. Functional analysis of all expressed genes using FatiScan revealed an asymmetric distribution of 482 Gene Ontology (GO) groups and 18 KEGG pathways.
    [Show full text]
  • Predicting Clinical Response to Treatment with a Soluble Tnf-Antagonist Or Tnf, Or a Tnf Receptor Agonist
    (19) TZZ _ __T (11) EP 2 192 197 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 02.06.2010 Bulletin 2010/22 C12Q 1/68 (2006.01) (21) Application number: 08170119.5 (22) Date of filing: 27.11.2008 (84) Designated Contracting States: (72) Inventor: The designation of the inventor has not AT BE BG CH CY CZ DE DK EE ES FI FR GB GR yet been filed HR HU IE IS IT LI LT LU LV MC MT NL NO PL PT RO SE SI SK TR (74) Representative: Habets, Winand Designated Extension States: Life Science Patents AL BA MK RS PO Box 5096 6130 PB Sittard (NL) (71) Applicant: Vereniging voor Christelijk Hoger Onderwijs, Wetenschappelijk Onderzoek en Patiëntenzorg 1081 HV Amsterdam (NL) (54) Predicting clinical response to treatment with a soluble tnf-antagonist or tnf, or a tnf receptor agonist (57) The invention relates to methods for predicting a clinical response to a therapy with a soluble TNF antagonist, TNF or a TNF receptor agonist and a kit for use in said methods. EP 2 192 197 A1 Printed by Jouve, 75001 PARIS (FR) EP 2 192 197 A1 Description [0001] The invention relates to methods for predicting a clinical response to a treatment with a soluble TNF antagonist, with TNF or a TNF receptor agonist using expression levels of genes of the Type I INF pathway and a kit for use in said 5 methods. In another aspect, the invention relates to a method for evaluating a pharmacological effect of a treatment with a soluble TNF antagonist, TNF or a TNF receptor agonist.
    [Show full text]
  • Association of Gene Ontology Categories with Decay Rate for Hepg2 Experiments These Tables Show Details for All Gene Ontology Categories
    Supplementary Table 1: Association of Gene Ontology Categories with Decay Rate for HepG2 Experiments These tables show details for all Gene Ontology categories. Inferences for manual classification scheme shown at the bottom. Those categories used in Figure 1A are highlighted in bold. Standard Deviations are shown in parentheses. P-values less than 1E-20 are indicated with a "0". Rate r (hour^-1) Half-life < 2hr. Decay % GO Number Category Name Probe Sets Group Non-Group Distribution p-value In-Group Non-Group Representation p-value GO:0006350 transcription 1523 0.221 (0.009) 0.127 (0.002) FASTER 0 13.1 (0.4) 4.5 (0.1) OVER 0 GO:0006351 transcription, DNA-dependent 1498 0.220 (0.009) 0.127 (0.002) FASTER 0 13.0 (0.4) 4.5 (0.1) OVER 0 GO:0006355 regulation of transcription, DNA-dependent 1163 0.230 (0.011) 0.128 (0.002) FASTER 5.00E-21 14.2 (0.5) 4.6 (0.1) OVER 0 GO:0006366 transcription from Pol II promoter 845 0.225 (0.012) 0.130 (0.002) FASTER 1.88E-14 13.0 (0.5) 4.8 (0.1) OVER 0 GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism3004 0.173 (0.006) 0.127 (0.002) FASTER 1.28E-12 8.4 (0.2) 4.5 (0.1) OVER 0 GO:0006357 regulation of transcription from Pol II promoter 487 0.231 (0.016) 0.132 (0.002) FASTER 6.05E-10 13.5 (0.6) 4.9 (0.1) OVER 0 GO:0008283 cell proliferation 625 0.189 (0.014) 0.132 (0.002) FASTER 1.95E-05 10.1 (0.6) 5.0 (0.1) OVER 1.50E-20 GO:0006513 monoubiquitination 36 0.305 (0.049) 0.134 (0.002) FASTER 2.69E-04 25.4 (4.4) 5.1 (0.1) OVER 2.04E-06 GO:0007050 cell cycle arrest 57 0.311 (0.054) 0.133 (0.002)
    [Show full text]
  • List of Down-Regulated Transcripts
    Supplementary Table 1: List of down-regulated transcripts (Fold Change>1.7 and p<0.05). List of the transcipts downregulated by Tpr-Met in P27 cachectic gastrocnemius muscles. Shown are the transcripts gene annotation: Mus Musculus Entrez Gene ID, official symbol from NCBI, average (AVG) Log2 Ratio derived from Illumina microarrays (3 replicates/condition), fold change and p-value computations, Log2 ratio over AVG Log2 controls and full definition of the genes. All genes modulated with a fold change > 1.7 and p-value<0.05 are included. AVG Entrez Gene Fold Symbol Log2 T-test Ctrl Ctrl Ctrl TM TM TM Definition ID Change Ratio - - - - 26908 Eif2s3y 3.598 12.1 0.000 0.146 0.248 0.102 3.712 3.571 -3.510 eukaryotic translation initiation factor 2, subunit 3, structural gene Y-linked (Eif2s3y), mRNA. - - - 13628 Eef1a2 1.333 2.5 0.011 -0.444 0.261 0.183 1.503 0.950 -1.546 eukaryotic translation elongation factor 1 alpha 2 (Eef1a2), mRNA. - - - 13628 Eef1a2 1.298 2.5 0.031 -0.383 0.275 0.108 1.632 0.605 -1.656 eukaryotic translation elongation factor 1 alpha 2 (Eef1a2), mRNA. - - - 56222 Cited4 1.268 2.4 0.029 -0.466 0.035 0.431 1.109 0.889 -1.805 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 4 (Cited4), mRNA. - - - 18810 Plec1 1.246 2.4 0.022 -0.440 0.327 0.113 1.303 0.779 -1.657 plectin 1 (Plec1), transcript variant 10, mRNA. - - - 20741 Spnb1 1.238 2.4 0.016 -0.384 0.314 0.071 1.129 0.902 -1.684 spectrin beta 1 (Spnb1), mRNA.
    [Show full text]
  • Effet De La Cryptorchidie Sur Le Transcriptome Testiculaire Humain
    MARIE EVE BERGERON EFFET DE LA CRYPTORCHIDIE SUR LE TRANSCRIPTOME TESTICULAIRE HUMAIN Mémoire présenté à la Faculté des études supérieures et postdoctorales de l’Université Laval dans le cadre du programme de maîtrise en Physiologie-Endocrinologie pour l’obtention du grade de Maître ès sciences (M.Sc.) DÉPARTEMENT D’OBSTÉTRIQUE ET DE GYNÉCOLOGIE FACULTÉ DE MÉDECINE UNIVERSITÉ LAVAL QUÉBEC 2012 © Marie Eve Bergeron, 2012 Résumé Les niveaux d’expression de nombreux gènes peuvent être affectés par l’environnement et mener au développement de la cryptorchidie. Cette malformation congénitale est la plus commune dont une des conséquences majeures est l’infertilité masculine due au testicule non-descendu, auquel un risque plus élevé de cancer testiculaire est associé. L’expression des ARN totaux isolés à partir de biopsies testiculaires ont été analysés par micropuces, puis par une analyse bio-informatique et une validation par RT-qPCR de plusieurs gènes sélectionnés. Ces analyses m’ont permis d’identifier plus de deux milles candidats montrant une expression différente entre des sujets cryptorchides et normaux. Certains de ces gènes sélectionnés peuvent être associés à la descente testiculaire, d’autres au cancer testiculaire ou encore aux divers types cellulaires retrouvés dans cet organe. Les différences dans le transcriptome dues à la cryptorchidie vont nous aider à comprendre la cause génétique de cette maladie. ii Abstract Expression level of numerous genes may be affected by environmental condition and lead to development of cryptorchidism. The most common congenital malformation in male is cryptorchidism. One major consequence of this anomaly is infertility due to undescended testis, to which an increased risk of testicular cancer is associated.
    [Show full text]