An Interactomics Overview of the Human and Bovine Milk Proteome Over Lactation Lina Zhang1, Aalt D
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Supplementary Data
Supplementary Data for Quantitative Changes in the Mitochondrial Proteome from Subjects with Mild Cognitive Impairment, Early Stage and Late Stage Alzheimer’s disease Table 1 - 112 unique, non-redundant proteins identified and quantified in at least two of the three analytical replicates for all three disease stages. Table 2 - MCI mitochondrial samples, Protein Summary Table 3 - MCI mitochondrial samples, Experiment 1 Table 4 - MCI mitochondrial samples, Experiment 2 Table 5 - MCI mitochondrial samples, Experiment 3 Table 6 - EAD Mitochondrial Study, Protein Summary Table 7 - EAD Mitochondrial Study, Experiment 1 Table 8 - EAD Mitochondrial Study, Experiment 2 Table 9 - EAD Mitochondrial Study, Experiment 3 Table 10 - LAD Mitochondrial Study, Protein Summary Table 11 - LAD Mitochondrial Study, Experiment 1 Table 12 - LAD Mitochondrial Study, Experiment 2 Table 13 - LAD Mitochondrial Study, Experiment 3 Supplemental Table 1. 112 unique, non-redundant proteins identified and quantified in at least two of the three analytical replicates for all three disease stages. Description Data MCI EAD LAD AATM_HUMAN (P00505) Aspartate aminotransferase, mitochondrial precursor (EC Mean 1.43 1.70 1.31 2.6.1.1) (Transaminase A) (Glutamate oxaloacetate transaminase 2) [MASS=47475] SEM 0.07 0.09 0.09 Count 3.00 3.00 3.00 ACON_HUMAN (Q99798) Aconitate hydratase, mitochondrial precursor (EC 4.2.1.3) Mean 1.24 1.61 1.19 (Citrate hydro-lyase) (Aconitase) [MASS=85425] SEM 0.05 0.17 0.18 Count 3.00 2.00 3.00 ACPM_HUMAN (O14561) Acyl carrier protein, mitochondrial -
University Microfilms International 300 N
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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: [email protected]; [email protected] 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. -
Deamidation of Human Proteins
Deamidation of human proteins N. E. Robinson*† and A. B. Robinson‡ *Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and ‡Oregon Institute of Science and Medicine, Cave Junction, OR 97523 Communicated by Frederick Seitz, The Rockefeller University, New York, NY, August 31, 2001 (received for review May 8, 2001) Deamidation of asparaginyl and glutaminyl residues causes time- 3D structure is known (23). This method is more than 95% dependent changes in charge and conformation of peptides and reliable in predicting relative deamidation rates of Asn residues proteins. Quantitative and experimentally verified predictive cal- within a single protein and is also useful for the prediction of culations of the deamidation rates of 1,371 asparaginyl residues in absolute deamidation rates. a representative collection of 126 human proteins have been It is, therefore, now possible to compute the expected deami- performed. These rates suggest that deamidation is a biologically dation rate of any protein for which the primary and 3D relevant phenomenon in a remarkably large percentage of human structures are known, except for very long-lived proteins. These proteins. proteins require measurement of the 400 Gln pentapeptide rates. in vivo deamidation ͉ asparaginyl residues Materials and Methods Calculation Method. The Brookhaven Protein Data Bank (PDB) eamidation of asparaginyl (Asn) and glutaminyl (Gln) was searched to select 126 human proteins of general biochem- Dresidues to produce aspartyl (Asp) and glutamyl (Glu) ical interest and of known 3D structure without bias toward any residues causes structurally and biologically important alter- known data about their deamidation, except for 13 proteins (as ations in peptide and protein structures. -
(12) Patent Application Publication (10) Pub. No.: US 2003/0082511 A1 Brown Et Al
US 20030082511A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2003/0082511 A1 Brown et al. (43) Pub. Date: May 1, 2003 (54) IDENTIFICATION OF MODULATORY Publication Classification MOLECULES USING INDUCIBLE PROMOTERS (51) Int. Cl." ............................... C12O 1/00; C12O 1/68 (52) U.S. Cl. ..................................................... 435/4; 435/6 (76) Inventors: Steven J. Brown, San Diego, CA (US); Damien J. Dunnington, San Diego, CA (US); Imran Clark, San Diego, CA (57) ABSTRACT (US) Correspondence Address: Methods for identifying an ion channel modulator, a target David B. Waller & Associates membrane receptor modulator molecule, and other modula 5677 Oberlin Drive tory molecules are disclosed, as well as cells and vectors for Suit 214 use in those methods. A polynucleotide encoding target is San Diego, CA 92121 (US) provided in a cell under control of an inducible promoter, and candidate modulatory molecules are contacted with the (21) Appl. No.: 09/965,201 cell after induction of the promoter to ascertain whether a change in a measurable physiological parameter occurs as a (22) Filed: Sep. 25, 2001 result of the candidate modulatory molecule. Patent Application Publication May 1, 2003 Sheet 1 of 8 US 2003/0082511 A1 KCNC1 cDNA F.G. 1 Patent Application Publication May 1, 2003 Sheet 2 of 8 US 2003/0082511 A1 49 - -9 G C EH H EH N t R M h so as se W M M MP N FIG.2 Patent Application Publication May 1, 2003 Sheet 3 of 8 US 2003/0082511 A1 FG. 3 Patent Application Publication May 1, 2003 Sheet 4 of 8 US 2003/0082511 A1 KCNC1 ITREXCHO KC 150 mM KC 2000000 so 100 mM induced Uninduced Steady state O 100 200 300 400 500 600 700 Time (seconds) FIG. -
MALE Protein Name Accession Number Molecular Weight CP1 CP2 H1 H2 PDAC1 PDAC2 CP Mean H Mean PDAC Mean T-Test PDAC Vs. H T-Test
MALE t-test t-test Accession Molecular H PDAC PDAC vs. PDAC vs. Protein Name Number Weight CP1 CP2 H1 H2 PDAC1 PDAC2 CP Mean Mean Mean H CP PDAC/H PDAC/CP - 22 kDa protein IPI00219910 22 kDa 7 5 4 8 1 0 6 6 1 0.1126 0.0456 0.1 0.1 - Cold agglutinin FS-1 L-chain (Fragment) IPI00827773 12 kDa 32 39 34 26 53 57 36 30 55 0.0309 0.0388 1.8 1.5 - HRV Fab 027-VL (Fragment) IPI00827643 12 kDa 4 6 0 0 0 0 5 0 0 - 0.0574 - 0.0 - REV25-2 (Fragment) IPI00816794 15 kDa 8 12 5 7 8 9 10 6 8 0.2225 0.3844 1.3 0.8 A1BG Alpha-1B-glycoprotein precursor IPI00022895 54 kDa 115 109 106 112 111 100 112 109 105 0.6497 0.4138 1.0 0.9 A2M Alpha-2-macroglobulin precursor IPI00478003 163 kDa 62 63 86 72 14 18 63 79 16 0.0120 0.0019 0.2 0.3 ABCB1 Multidrug resistance protein 1 IPI00027481 141 kDa 41 46 23 26 52 64 43 25 58 0.0355 0.1660 2.4 1.3 ABHD14B Isoform 1 of Abhydrolase domain-containing proteinIPI00063827 14B 22 kDa 19 15 19 17 15 9 17 18 12 0.2502 0.3306 0.7 0.7 ABP1 Isoform 1 of Amiloride-sensitive amine oxidase [copper-containing]IPI00020982 precursor85 kDa 1 5 8 8 0 0 3 8 0 0.0001 0.2445 0.0 0.0 ACAN aggrecan isoform 2 precursor IPI00027377 250 kDa 38 30 17 28 34 24 34 22 29 0.4877 0.5109 1.3 0.8 ACE Isoform Somatic-1 of Angiotensin-converting enzyme, somaticIPI00437751 isoform precursor150 kDa 48 34 67 56 28 38 41 61 33 0.0600 0.4301 0.5 0.8 ACE2 Isoform 1 of Angiotensin-converting enzyme 2 precursorIPI00465187 92 kDa 11 16 20 30 4 5 13 25 5 0.0557 0.0847 0.2 0.4 ACO1 Cytoplasmic aconitate hydratase IPI00008485 98 kDa 2 2 0 0 0 0 2 0 0 - 0.0081 - 0.0 -
Molecular Basis of Angiogenesis and Neuroprotection by Angiogenin By
Molecular Basis of Angiogenesis and Neuroprotection by Angiogenin By Trish T. Hoang A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Biochemistry) at the UNIVERSITY OF WISCONSIN–MADISON 2016 Date of final oral examination: May 09, 2016 The dissertation is approved by the following members of the Final Oral Committee: Ronald T. Raines, Henry Lardy Professor of Biochemistry, Biochemistry and Chemistry Jeffrey A. Johnson, Professor, Pharmaceutical Sciences David J. Pagliarini, Associate Professor, Biochemistry Samuel E. Butcher, Professor, Biochemistry Nader Sheibani, Professor, Ophthalmology and Visual Sciences ProQuest Number:10189602 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. ProQuest 10189602 Published by ProQuest LLC ( 2018). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code Microform Edition © ProQuest LLC. ProQuest LLC. 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, MI 48106 - 1346 i Molecular Basis of Angiogenesis and Neuroprotection by Angiogenin Trish Truc Hoang Under the Supervision of Professor Ronald T. Raines at the University of Wisconsin–Madison Cancer and neurodegeneration are disorders with profound impact on human health. Cancer results from uncontrolled cell growth, whereas neurodegeneration is caused by premature neuronal cell death. Although these disease mechanisms seem to be at opposite ends of a spectrum, an increasing number of cellular and molecular studies have linked the two disorders. -
Milk Allergen by the Numbers
Milk allergen component testing Bos d4 Milk Bos allergen d5 Bos by the d8 numbers Detect sensitizations to the complete milk protein to create personalized management plans for your patients. High levels of milk IgE may predict the likelihood of sensitivity, but may not be solely predictive of TC 2851 reactions to baked milk or α-lactalbumin allergy duration.1 • Susceptible to heat denaturation2 • HIGHER RISK of reaction to fresh milk1,3 • LOWER RISK of reaction Milk allergen to baked milk1,3,a • Patient likely to “outgrow” component testing milk allergy4 Measurement of specific IgE by blood test that provides objective assessment of sensitization to milk is the first step in discovering your patient’s allergy. Milk allergen component tests can help α-lactalbumin β-lactoglobulin Casein Test interpretations and next steps you determine the likelihood of reaction to baked goods, such as cookies or cheese pizza, as well as • Avoid fresh milk the likelihood of allergy persistence. + + - • Likely to tolerate baked milk products • Baked milk oral food challenge (OFC), Knowing which protein your patient is with a specialist may be appropriate sensitized to can help you develop a + - - • Likely to outgrow allergy management plan.3,5-9 - + - • Avoid all forms of milk +/- +/- + • Unlikely to become tolerant of milk over time • Avoid milk and baked milk products (yogurt, cookies, cakes), as well as products processed with milk (chocolate, sausage, potato chips) % of children with milk allergy 75 do not react to baked milk.3 Bos d4 Bos Bos d5 d8 TC 2852 TC 2853 β-lactoglobulin Casein Determine • Susceptible to heat • Resistant to heat which proteins denaturation2 denaturation3 your patient is • HIGHER RISK of reaction • HIGHER RISK of reaction to fresh milk1,3 to all forms of milk1,3,5 sensitized to. -
Protease-Activated Alpha-2-Macroglobulin Can Inhibit Amyloid Formation Via Two Distinct Mechanisms
University of Wollongong Research Online Faculty of Science, Medicine and Health - Papers: part A Faculty of Science, Medicine and Health 1-1-2013 Protease-activated alpha-2-macroglobulin can inhibit amyloid formation via two distinct mechanisms Amy R. Wyatt University of Wollongong, [email protected] Patrick Constantinescu University of Wollongong, [email protected] Heath Ecroyd University of Wollongong, [email protected] Christopher M. Dobson University of Cambridge Mark R. Wilson University of Wollongong, [email protected] See next page for additional authors Follow this and additional works at: https://ro.uow.edu.au/smhpapers Part of the Medicine and Health Sciences Commons, and the Social and Behavioral Sciences Commons Recommended Citation Wyatt, Amy R.; Constantinescu, Patrick; Ecroyd, Heath; Dobson, Christopher M.; Wilson, Mark R.; Kumita, Janet R.; and Yerbury, Justin J., "Protease-activated alpha-2-macroglobulin can inhibit amyloid formation via two distinct mechanisms" (2013). Faculty of Science, Medicine and Health - Papers: part A. 745. https://ro.uow.edu.au/smhpapers/745 Research Online is the open access institutional repository for the University of Wollongong. For further information contact the UOW Library: [email protected] Protease-activated alpha-2-macroglobulin can inhibit amyloid formation via two distinct mechanisms Abstract α2-Macroglobulin (α2M) is an extracellular chaperone that inhibits amorphous and fibrillar protein aggregation. The reaction of α2M with proteases results in an ‘activated’ conformation, where the proteases become covalently-linked within the interior of a cage-like structure formed by α2M. This study investigates, the effect of activation on the ability of α2M to inhibit amyloid formation by Aβ1–42 and I59T human lysozyme and shows that protease-activated α2M can act via two distinct mechanisms: (i) by trapping proteases that remain able to degrade polypeptide chains and (ii) by a chaperone action that prevents misfolded clients from continuing along the amyloid forming pathway. -
The Interplay Between the RNA Decay and Translation Machinery in Eukaryotes
Downloaded from http://cshperspectives.cshlp.org/ on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press The Interplay between the RNA Decay and Translation Machinery in Eukaryotes Adam M. Heck1,2 and Jeffrey Wilusz1,2 1Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80525 2Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80525 Correspondence: [email protected] RNA decay plays a major role in regulating gene expression and is tightly networked with other aspects of gene expression to effectively coordinate post-transcriptional regulation. The goal of this work is to provide an overview of the major factors and pathways of general messenger RNA (mRNA) decay in eukaryotic cells, and then discuss the effective interplay of this cytoplasmic process with the protein synthesis machinery. Given the transcript-specific and fluid nature of mRNA stability in response to changing cellular conditions, understanding the fundamental networking between RNA decay and translation will provide a foundation for a complete mechanistic understanding of this important aspect of cell biology. NA degradation plays a major role in regu- gene expression is needed to further elucidate Rlating both the quantity and quality of gene the depth of regulation that occurs in cells. expression in the cell. The abundance of an RNA The goal of this work is to provide an up-to- transcript is a reflection of both its rate of syn- date overview of the factors and mechanisms thesis and degradation. There are numerous ex- of general mRNA decay and then focus on the amples in the literature regarding the regulation interplay of this process with the translational of gene expression associated with major cellular machinery. -
Molecular Cloning of Four Novel Murine Ribonuclease Genes: Unusual Expansion Within the Ribonuclease a Gene Family Dean Batten+, Kimberly D
1997 Oxford University Press Nucleic Acids Research, 1997, Vol. 25, No. 21 4235–4239 Molecular cloning of four novel murine ribonuclease genes: unusual expansion within the Ribonuclease A gene family Dean Batten+, Kimberly D. Dyer, Joseph B. Domachowske§ and Helene F. Rosenberg* The Laboratory of Host Defenses, Building 10, Room 11N104, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA Received August 4, 1997; Revised and Accepted September 17, 1997 DDBJ/EMBL/GenBank accession numbers: U72031, U72032, AF017258–AF017261 ABSTRACT numerous somatic tissues in addition to pancreas (5). RNases 2 and 3, eosinophil-derived neurotoxin (EDN) and eosinophil cationic We have characterized four novel murine ribonuclease protein (ECP), respectively, have been characterized primarily with genes that, together with the murine eosinophil- respect to eosinophil function (6,7), although expression of EDN associated ribonucleases 1 and 2, form a distinct and [also known as RNase Us (8) or human liver ribonuclease (9)] is unusual cluster within the RNase A gene superfamily. also widespread (5). Angiogenin (RNase 5), a structurally atypical Three of these genes (mR-3, mR-4, mR-5) include member of this family, was originally identified as an agent complete open reading frames, encoding ribo- promoting blood vessel growth and development (10,11). RNase 4 nucleases with eight cysteines and appropriately (12,13) and RNase k6 (14) are also members of the RNase A spaced histidines (His11 and His124) and lysine (Lys35) superfamily, although their functions are currently obscure. that are characteristic of this enlarging protein family; Recently, Larson and colleagues (15) described cDNAs encoding the fourth sequence encodes a non-functional pseudo- two highly homologous murine ribonucleases, the murine eosino- gene (mR-6P). -
Protein Symbol Protein Name Rank Metric Score 4F2 4F2 Cell-Surface
Supplementary Table 2 Supplementary Table 2. Ranked list of proteins present in anti-Sema4D treated macrophage conditioned media obtained in the GSEA analysis of the proteomic data. Proteins are listed according to their rank metric score, which is the score used to position the gene in the ranked list of genes of the GSEA. Values are obtained from comparing Sema4D treated RAW conditioned media versus REST, which includes untreated, IgG treated and anti-Sema4D added RAW conditioned media. GSEA analysis was performed under standard conditions in November 2015. Protein Rank metric symbol Protein name score 4F2 4F2 cell-surface antigen heavy chain 2.5000 PLOD3 Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 1.4815 ELOB Transcription elongation factor B polypeptide 2 1.4350 ARPC5 Actin-related protein 2/3 complex subunit 5 1.2603 OSTF1 teoclast-stimulating factor 1 1.2500 RL5 60S ribomal protein L5 1.2135 SYK Lysine--tRNA ligase 1.2135 RL10A 60S ribomal protein L10a 1.2135 TXNL1 Thioredoxin-like protein 1 1.1716 LIS1 Platelet-activating factor acetylhydrolase IB subunit alpha 1.1067 A4 Amyloid beta A4 protein 1.0911 H2B1M Histone H2B type 1-M 1.0514 UB2V2 Ubiquitin-conjugating enzyme E2 variant 2 1.0381 PDCD5 Programmed cell death protein 5 1.0373 UCHL3 Ubiquitin carboxyl-terminal hydrolase isozyme L3 1.0061 PLEC Plectin 1.0061 ITPA Inine triphphate pyrophphatase 0.9524 IF5A1 Eukaryotic translation initiation factor 5A-1 0.9314 ARP2 Actin-related protein 2 0.8618 HNRPL Heterogeneous nuclear ribonucleoprotein L 0.8576 DNJA3 DnaJ homolog subfamily