DOCSLIB.ORG

Tables Index

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Tables Index Receptor proteins 1337 Ligand-gated ion channels 1337 Receptors with intrinsic enzyme function 1339 Receptor tyrosine kinases (RTKs) 1339 Receptor serine/threonine kinases 1341 Receptor tyrosine phosphatases 1342 Receptor-linked guanylyl cyclases 1342 G-protein coupled receptors (GPCRs) 1343 Cytokine receptors (Jak/STAT-coupled) 1353 TNF receptor superfamily 1354 IL-1/toll-like receptors 1355 Other cell surface receptors 1356 Plexins 1356 LDL receptor family 1357 Nuclear receptors 1357 Membrane transport proteins 1359 Channel proteins 1359 Sodium-channels 1359 Potassium channels 1360 Voltage-dependent Ca2+-channels 1363 Chloride channels 1364 Cation channels 1365 TRP channels 1365 Cyclic nucleotide-gated cation channels 1366 Calcium release channels 1366 Water channels 1367 Solute carriers 1367 Transport ATPases (ATP-powered pumps) 1383 P-type ATPases 1383 V-type ATPases 1384 F-type ATPases 1385 ABC-transporter 1385 Adhesion molecules 1387 Cadherins 1387 Classic cadherins 1387 Protocadherins 1388 Integrins 1389 Selectins 1390 Syndecans 1391 Immunoglobulin superfamily 1391 1334 Enzymes 1393 Oxidoreductases 1393 Cyclooxygenases (EC 1.14.99.1) 1393 Lipoxygenases (EC 1.13.11.-) 1393 Nitric oxide synthases (NOS; EC 1.14.13.39) 1393 Cytochrome P450 monooxygenases (EC 1.14.-) 1394 Amino acid hydroxylases (NOS; EC 1.14.16.-) 1396 Transferases 1396 Lipid kinases 1396 PI-3-kinases (EC 2.7.1.137) 1396 PI-4-kinases (EC 2.7.1.67) 1396 PI-5-kinases (EC 2.7.1.68) 1397 PI-5P-kinases (EC 2.7.1.149) 1397 Sphingosine kinases (EC 2.7.1.91) 1397 Diacyl glycerol kinases (EC 2.7.1.107) 1397 Serine/threonine kinases 1397 AGC group (containing PKA, PKG and PKC families) 1397 CAMK group 1399 CK1 group (casein kinase 1) 1400 CMGC group (containing Cdk, MAPK, GSK3, Clk families) 1401 RGC group (Receptor Guanylyl Cyclases; Guanylyl Cyclases) 1402 STE Group (homologues of yeast Sterile-7, -11, -20 kinases; MAP kinase cascades) 1402 TKL group (Tyrosine kinase-like families) 1403 Atypical group 1404 Other groups 1405 Tyrosine kinases 1406 RTK group (Receptor Tyrosine Kinases; see also under “Receptors”) 1406 NRTK group (Non-Receptor Tyrosine Kinases; tyrosine kinases) SH2 domain proteins 1408 PTB domain proteins 1411 Transglutaminases (EC 2.3.2.13) 1413 Hydrolases 1413 GTPases 1413 Heterotrimeric G-proteins 1413 RGS proteins 1414 Small GTPases 1415 GTPase activating proteins (GAPs) 1419 Guanine nucleotide exchange factors (GEFs) 1422 Phosphodiester hydrolases 1424 Phosphodiesterases (EC 3.1.4.17) 1424 Phospholipases 1425 Lyases 1426 Phosphatases 1426 Non-protein phosphatases 1426 Protein phosphatases 1428 Protein serine/threonine phosphatases (EC 3.1.3.16) 1428 Protein tyrosine phosphatases 1429 Dual specificity phosphatases (PSP) or VH1-like 1430 Cyclases 1432 Adenylyl cyclases (EC 4.6.1.1) 1432 Guanylyl cyclases (EC 4.6.1.2.) 1432 1335 Peptidases 1433 Aspartic acid peptidases 1433 Cysteine proteases 1434 Metallopeptidases 1437 Serine proteases 1442 Threonine peptidases 1447 Decarboxylases (EC 4.1.1.-) 1447 Isomerases 1448 Prostanoid synthases (EC 5.3.99.-) 1448 Transcription factors 1449 Superclass: basic domains 1449 Leucine zipper factots (bZIP) 1449 Helix-loop-helix factors (bHLH) 1450 Helix-loop-helix/leucine zipper factors (bHLH-ZIP) 1452 NF-1 1453 RF-X 1453 Helix-span-helix factors (bHSH) 1453 Zinc-coordinating DNA-binding domains 1453 Cys4 zinc finger of nuclear type 1453 Diverse Cys4 zinc fingers 1454 Cys2His2 zinc finger domain 1455 Superclass: helix-turn-helix 1456 Homeo domain 1456 Paired box 1460 Fork head/winged helix 1460 Heat shock factors 1461 Tryptophan clusters 1461 TEA domain 1462 Beta-scaffold factors with minor groove contacts 1463 RHR (Rel homology region) 1463 STAT 1463 p53 1463 MADS-box 1463 TATA-binding-proteins 1464 HMG 1464 Heteromeric CCAAT factors 1464 Grainyhead 1464 Cold-shock domain factors 1465 Runt 1465 Other transcription factors HMGI(Y) 1465 HMGI(Y) 1465 Pocket domain 1465 List of established drugs 1467 Receptor Proteins Receptor proteins are specialized structures, which are Receptors without intrinsic effector function interact able to recognize mostly but not exclusively diffusible with proteins, which are effectors themselves, or which molecules with very high specifity and to bind them can regulate effectors. The largest group of these reversibly with high affinity. Binding of a ligand to the receptors are the G-protein coupled receptors (GPCRs), receptor initiates a signal transduction process, which which via heterotrimeric G-proteins are able to regulate propagates the message of the ligand. There are many the activity of a variety of effector proteins (enzymes, different types of receptors, which differ especially in ion channels). Other receptors like the cytokine their mode of signal propagation. Most receptors are receptors interact with and activate cytosolic protein cell-surface receptors, which respond to ligands, which kinases (Jak-family) upon ligand binding. Another usually cannot enter the cell. Lipophilic molecules (e.g. group of receptors (TNF-receptor superfamily, IL-1/ steroids), in contrast, enter the cell and can act on Toll-like receptors) recruit adaptor proteins (e.g. intracellular receptors. TRADD, MyD88) after ligand-dependent activation, The group of ▶cell-surface receptors can be which then serve as a platform for the formation of an subdivided in those, which have an intrinsic effector effector complex consisting of various other proteins. function (enzymes, ion channels) and others without The majority of ▶intracellular receptors are so-called intrinsic effector function. The first group consists of “nuclear receptors,” which are transcription factors, receptor operated ion channels or receptors with which reside in the cytoplasm or nucleus and upon intrinsic enzymatic activity. In both cases the intrinsic ligand binding translocate to the nucleus and become effector function is regulated by ligand binding. transcriptionally active. Receptors linked to an intrinsic enzymatic activity are receptor tyrosine kinases, receptor serine/threonine kinases or receptor guanylyl cyclases. Ligand-Gated Ion Channels Ligand-operated ion channels generate electrical sig- pentamer contains different subunits of which two are nals in response to specific chemical neurotransmitters. ligand-binding. Each subunit has four transmembrane They are specialized for mediating the fast chemical regions. Heteropentameric channels are formed by synaptic transmission. Depending on their ion selectiv- GABAA-, glycine- nicotinic acetylcholine and, 5-HT3- ity, ligand-gated ion channels are either excitatory receptors. In contrast, the cation-selective ionotropic (glutamate-, P2X-, nicotinic, 5-HT3-receptors) or inhib- glutamate receptors have four subunits. Each subunit is itory (GABAA-, glycine-receptors). Ligand-gated ion able to bind glutamate. Finally, P2X purinoceptors channels can be grouped in three distinct families based subunits, which have two transmembrane segments, on the architecture of the channel. Most known ligand- form trimeric channels. operated ion channels consist of five subunits. This Cation Channels Receptor-subunit Ion selectivity Endogenous ligand Ionotropic glutamate receptors NMDA receptors (tetrameric) NR1 Na+/K+/(Ca2+) Glutamate, glycine NR2A Na+/K+/(Ca2+) Glutamate, glycine NR2B Na+/K+/(Ca2+) Glutamate, glycine NR2C Na+/K+/(Ca2+) Glutamate, glycine 1338 Receptor Proteins Cation Channels (Continued) Receptor-subunit Ion selectivity Endogenous ligand NR2D Na+/K+/(Ca2+) Glutamate, glycine NR3 Na+/K+/(Ca2+) Glutamate, glycine AMPA receptors (tetrameric) GluR1 (GluR-A) Na+/K+ Glutamate GluR2 (GluR-B) Na+/K+ Glutamate GluR3 (GluR-C) Na+/K+ Glutamate GluR4 (GluR-D) Na+/K+ Glutamate Kainate receptors (tetrameric) GluR5 Na+/K+ Glutamate GluR6 Na+/K+ Glutamate GluR7 Na+/K+ Glutamate KA1 Na+/K+ Glutamate KA2 Na+/K+ Glutamate Purinoceptors (P2X) (trimeric) + + 2+ P2X1 Na /K /(Ca )ATP + + 2+ P2X2 Na /K /(Ca )ATP + + 2+ P2X3 Na /K /(Ca )ATP + + 2+ P2X4 Na /K /(Ca )ATP + + 2+ P2X5 Na /K /(Ca )ATP + + 2+ P2X6 Na /K /(Ca )ATP + + 2+ P2X7 Na /K /(Ca )ATP Nicotinic acetylcholine receptors (nAChR) (pentameric) Ligand-binding α1Na+/K+ Acetylcholine α2Na+/K+ Acetylcholine α3Na+/K+ Acetylcholine α4Na+/K+ Acetylcholine α6Na+/K+ Acetylcholine α7Na+/K+ Acetylcholine α8Na+/K+ Acetylcholine α9Na+/K+ Acetylcholine α10 Na+/K+ Acetylcholine Non-ligand-binding β1Na+/K+ β2Na+/K+ β3Na+/K+ β4Na+/K+ γ Na+/K+ δ Na+/K+ ε Na+/K+ Ionotropic serotonin receptors (5-HT3) (pentameric) + + 5-HT3A Na /K Serotonin + + 5-HT3B Na /K Serotonin Anion Channels Receptor-subunit Ion selectivity Endogenous ligand GABAA receptors (pentameric) Ligand-binding α1 Cl¯ γ-Aminobutyric acid, (benzodiazepines) α2 Cl¯ γ-Aminobutyric acid, (benzodiazepines) α3 Cl¯ γ-Aminobutyric acid, (benzodiazepines) Receptor Proteins 1339 Anion Channels (Continued) Receptor-subunit Ion selectivity Endogenous ligand α4 Cl¯ γ-Aminobutyric acid α5 Cl¯ γ-Aminobutyric acid, (benzodiazepines) α6 Cl¯ γ-Aminobutyric acid Non-ligand-binding β1 Cl¯ β2 Cl¯ β3 Cl¯ γ1 Cl¯ γ2 Cl¯ γ3 Cl¯ δ Cl¯ ε Cl¯ θ Cl¯ ρ1 Cl¯ ρ2 Cl¯ ρ3 Cl¯ Glycine receptors (GlyR) (pentameric) Ligand-binding α1 Cl¯ Glycine α2 Cl¯ Glycine α3 Cl¯ Glycine α4 Cl¯ Glycine Non-ligand-binding β Cl¯ Receptors with Intrinsic Enzyme Function Receptor Tyrosine Kinases (RTKs) Receptor tyrosine kinases (RTKs) are a group of results in autophosphorylation of their cytoplasmic transmembrane receptors which are endowed with an domains. Tyrosine autophosphorylation of RTKs induces intrinsic tyrosine kinase activity.
Recommended publications
  • Proteomic Analyses Reveal a Role of Cytoplasmic Droplets As an Energy Source During Sperm Epididymal Maturation

    Proteomic Analyses Reveal a Role of Cytoplasmic Droplets As an Energy Source During Sperm Epididymal Maturation

    Proteomic analyses reveal a role of cytoplasmic droplets as an energy source during sperm epididymal maturation Shuiqiao Yuana,b, Huili Zhenga, Zhihong Zhengb, Wei Yana,1 aDepartment of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, NV, 89557; and bDepartment of Laboratory Animal Medicine, China Medical University, Shenyang, 110001, China Corresponding author. Email: [email protected] Supplemental Information contains one Figure (Figure S1), three Tables (Tables S1-S3) and two Videos (Videos S1 and S2) files. Figure S1. Scanning electron microscopic images of purified murine cytoplasmic droplets. Arrows point to indentations resembling the resealed defects at the detaching points when CDs come off the sperm flagella. Scale bar = 1µm Table S1 Mass spectrometry-based identifiaction of proteins highly enriched in murine cytoplasmic droplets. # MS/MS View:Identified Proteins (105) Accession Number Molecular Weight Protein Grouping Ambiguity Dot_1_1 Dot_2_1 Dot_3_1 Dot_4_1Dot_5_1 Dot_1_2 Dot_2_2 Dot_3_2 Dot_4_2 Dot_5_2 1 IPI:IPI00467457.3 Tax_Id=10090 Gene_Symbol=Ldhc L-lactate dehydrogenase C chain IPI00467457 36 kDa TRUE 91% 100% 100% 100% 100% 100% 100% 100% 100% 2 IPI:IPI00473320.2 Tax_Id=10090 Gene_Symbol=Actb Putative uncharacterized protein IPI00473320 42 kDa TRUE 75% 100% 100% 100% 100% 89% 76% 100% 100% 100% 3 IPI:IPI00224181.7 Tax_Id=10090 Gene_Symbol=Akr1b7 Aldose reductase-related protein 1 IPI00224181 36 kDa TRUE 100% 100% 76% 100% 100% 4 IPI:IPI00228633.7 Tax_Id=10090 Gene_Symbol=Gpi1 Glucose-6-phosphate
  • Establishing the Pathogenicity of Novel Mitochondrial DNA Sequence Variations: a Cell and Molecular Biology Approach

    Establishing the Pathogenicity of Novel Mitochondrial DNA Sequence Variations: a Cell and Molecular Biology Approach

    Mafalda Rita Avó Bacalhau Establishing the Pathogenicity of Novel Mitochondrial DNA Sequence Variations: a Cell and Molecular Biology Approach Tese de doutoramento do Programa de Doutoramento em Ciências da Saúde, ramo de Ciências Biomédicas, orientada pela Professora Doutora Maria Manuela Monteiro Grazina e co-orientada pelo Professor Doutor Henrique Manuel Paixão dos Santos Girão e pela Professora Doutora Lee-Jun C. Wong e apresentada à Faculdade de Medicina da Universidade de Coimbra Julho 2017 Faculty of Medicine Establishing the pathogenicity of novel mitochondrial DNA sequence variations: a cell and molecular biology approach Mafalda Rita Avó Bacalhau Tese de doutoramento do programa em Ciências da Saúde, ramo de Ciências Biomédicas, realizada sob a orientação científica da Professora Doutora Maria Manuela Monteiro Grazina; e co-orientação do Professor Doutor Henrique Manuel Paixão dos Santos Girão e da Professora Doutora Lee-Jun C. Wong, apresentada à Faculdade de Medicina da Universidade de Coimbra. Julho, 2017 Copyright© Mafalda Bacalhau e Manuela Grazina, 2017 Esta cópia da tese é fornecida na condição de que quem a consulta reconhece que os direitos de autor são pertença do autor da tese e do orientador científico e que nenhuma citação ou informação obtida a partir dela pode ser publicada sem a referência apropriada e autorização. This copy of the thesis has been supplied on the condition that anyone who consults it recognizes that its copyright belongs to its author and scientific supervisor and that no quotation from the
  • Calpain-5 Gene Expression in the Mouse Eye and Brain

    Calpain-5 Gene Expression in the Mouse Eye and Brain

    Schaefer et al. BMC Res Notes (2017) 10:602 DOI 10.1186/s13104-017-2927-8 BMC Research Notes RESEARCH NOTE Open Access Calpain‑5 gene expression in the mouse eye and brain Kellie Schaefer1, MaryAnn Mahajan1, Anuradha Gore1, Stephen H. Tsang3, Alexander G. Bassuk4 and Vinit B. Mahajan1,2* Abstract Objective: Our objective was to characterize CAPN5 gene expression in the mouse central nervous system. Mouse brain and eye sections were probed with two high-afnity RNA oligonucleotide analogs designed to bind CAPN5 RNA and one scramble, control oligonucleotide. Images were captured in brightfeld. Results: CAPN5 RNA probes were validated on mouse breast cancer tumor tissue. In the eye, CAPN5 was expressed in the ganglion cell, inner nuclear and outer nuclear layers of the retina. Signal could not be detected in the ciliary body or the iris because of the high density of melanin. In the brain, CAPN5 was expressed in the granule cell layers of the hippocampus and cerebellum. There was scattered expression in pons. The visual cortex showed faint signal. Most signal in the brain was in a punctate pattern. Keywords: CAPN5, Calpain, In situ hybridization, Retina, Brain, Gene expression Introduction pigmentosa, retinal neovascularization, and proliferative Calpain-5 (CAPN5) is a member of the calpain family of retinopathy. Which ultimately leads to blindness [20]. calcium-activated proteases that target a variety of path- Currently there is no treatment. ways to exert control over numerous processes, includ- An important question to understanding how CAPN5 ing tissue necrosis, cytoskeletal remodeling, cell-cycle leads to disease is identifying which tissues CAPN5 is control, cell migration, myofbril turnover, regulation expressed in and the levels of CAPN5 in those tissues.
  • Molecular Mechanisms Involved Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis

    Molecular Mechanisms Involved Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis

    Virginia Commonwealth University VCU Scholars Compass Theses and Dissertations Graduate School 2010 Molecular Mechanisms Involved Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis Ryan Fassnacht Virginia Commonwealth University Follow this and additional works at: https://scholarscompass.vcu.edu/etd Part of the Physiology Commons © The Author Downloaded from https://scholarscompass.vcu.edu/etd/2246 This Thesis is brought to you for free and open access by the Graduate School at VCU Scholars Compass. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of VCU Scholars Compass. For more information, please contact [email protected]. Ryan C. Fassnacht 2010 All Rights Reserved Molecular Mechanisms Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science at Virginia Commonwealth University. by Ryan Christopher Fassnacht, B.S. Hampden Sydney University, 2005 M.S. Virginia Commonwealth University, 2010 Director: Valeria Mas, Ph.D., Associate Professor of Surgery and Pathology Division of Transplant Department of Surgery Virginia Commonwealth University Richmond, Virginia July 9, 2010 Acknowledgement The Author wishes to thank his family and close friends for their support. He would also like to thank the members of the molecular transplant team for their help and advice. This project would not have been possible with out the help of Dr. Valeria Mas and her endearing
  • Structure of Human Aspartyl Aminopeptidase Complexed With

    Structure of Human Aspartyl Aminopeptidase Complexed With

    Chaikuad et al. BMC Structural Biology 2012, 12:14 http://www.biomedcentral.com/1472-6807/12/14 RESEARCH ARTICLE Open Access Structure of human aspartyl aminopeptidase complexed with substrate analogue: insight into catalytic mechanism, substrate specificity and M18 peptidase family Apirat Chaikuad1, Ewa S Pilka1, Antonio De Riso2, Frank von Delft1, Kathryn L Kavanagh1, Catherine Vénien-Bryan2, Udo Oppermann1,3 and Wyatt W Yue1* Abstract Backround: Aspartyl aminopeptidase (DNPEP), with specificity towards an acidic amino acid at the N-terminus, is the only mammalian member among the poorly understood M18 peptidases. DNPEP has implicated roles in protein and peptide metabolism, as well as the renin-angiotensin system in blood pressure regulation. Despite previous enzyme and substrate characterization, structural details of DNPEP regarding ligand recognition and catalytic mechanism remain to be delineated. Results: The crystal structure of human DNPEP complexed with zinc and a substrate analogue aspartate-β- hydroxamate reveals a dodecameric machinery built by domain-swapped dimers, in agreement with electron microscopy data. A structural comparison with bacterial homologues identifies unifying catalytic features among the poorly understood M18 enzymes. The bound ligands in the active site also reveal the coordination mode of the binuclear zinc centre and a substrate specificity pocket for acidic amino acids. Conclusions: The DNPEP structure provides a molecular framework to understand its catalysis that is mediated by active site loop swapping, a mechanism likely adopted in other M18 and M42 metallopeptidases that form dodecameric complexes as a self-compartmentalization strategy. Small differences in the substrate binding pocket such as shape and positive charges, the latter conferred by a basic lysine residue, further provide the key to distinguishing substrate preference.
  • Table 2. Significant

    Table 2. Significant

    Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S.
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
  • 1 Metabolic Dysfunction Is Restricted to the Sciatic Nerve in Experimental

    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.
  • To Study Mutant P53 Gain of Function, Various Tumor-Derived P53 Mutants

    To Study Mutant P53 Gain of Function, Various Tumor-Derived P53 Mutants

    Differential effects of mutant TAp63γ on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science By Shama K Khokhar M.Sc., Bilaspur University, 2004 B.Sc., Bhopal University, 2002 2007 1 COPYRIGHT SHAMA K KHOKHAR 2007 2 WRIGHT STATE UNIVERSITY SCHOOL OF GRADUATE STUDIES Date of Defense: 12-03-07 I HEREBY RECOMMEND THAT THE THESIS PREPARED UNDER MY SUPERVISION BY SHAMA KHAN KHOKHAR ENTITLED Differential effects of mutant TAp63γ on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression BE ACCEPTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Master of Science Madhavi P. Kadakia, Ph.D. Thesis Director Daniel Organisciak , Ph.D. Department Chair Committee on Final Examination Madhavi P. Kadakia, Ph.D. Steven J. Berberich, Ph.D. Michael Leffak, Ph.D. Joseph F. Thomas, Jr., Ph.D. Dean, School of Graduate Studies 3 Abstract Khokhar, Shama K. M.S., Department of Biochemistry and Molecular Biology, Wright State University, 2007 Differential effect of TAp63γ mutants on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression. p63, a member of the p53 gene family, known to play a role in development, has more recently also been implicated in cancer progression. Mice lacking p63 exhibit severe developmental defects such as limb truncations, abnormal skin, and absence of hair follicles, teeth, and mammary glands. Germline missense mutations of p63 have been shown to be responsible for several human developmental syndromes including SHFM, EEC and ADULT syndromes and are associated with anomalies in the development of organs of epithelial origin.
  • Serine Proteases with Altered Sensitivity to Activity-Modulating

    Serine Proteases with Altered Sensitivity to Activity-Modulating

    (19) & (11) EP 2 045 321 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 08.04.2009 Bulletin 2009/15 C12N 9/00 (2006.01) C12N 15/00 (2006.01) C12Q 1/37 (2006.01) (21) Application number: 09150549.5 (22) Date of filing: 26.05.2006 (84) Designated Contracting States: • Haupts, Ulrich AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 51519 Odenthal (DE) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • Coco, Wayne SK TR 50737 Köln (DE) •Tebbe, Jan (30) Priority: 27.05.2005 EP 05104543 50733 Köln (DE) • Votsmeier, Christian (62) Document number(s) of the earlier application(s) in 50259 Pulheim (DE) accordance with Art. 76 EPC: • Scheidig, Andreas 06763303.2 / 1 883 696 50823 Köln (DE) (71) Applicant: Direvo Biotech AG (74) Representative: von Kreisler Selting Werner 50829 Köln (DE) Patentanwälte P.O. Box 10 22 41 (72) Inventors: 50462 Köln (DE) • Koltermann, André 82057 Icking (DE) Remarks: • Kettling, Ulrich This application was filed on 14-01-2009 as a 81477 München (DE) divisional application to the application mentioned under INID code 62. (54) Serine proteases with altered sensitivity to activity-modulating substances (57) The present invention provides variants of ser- screening of the library in the presence of one or several ine proteases of the S1 class with altered sensitivity to activity-modulating substances, selection of variants with one or more activity-modulating substances. A method altered sensitivity to one or several activity-modulating for the generation of such proteases is disclosed, com- substances and isolation of those polynucleotide se- prising the provision of a protease library encoding poly- quences that encode for the selected variants.
  • Genome-Wide Association and Transcriptome Studies Identify Candidate Genes and Pathways for Feed Conversion Ratio in Pigs

    Genome-Wide Association and Transcriptome Studies Identify Candidate Genes and Pathways for Feed Conversion Ratio in Pigs

    Miao et al. BMC Genomics (2021) 22:294 https://doi.org/10.1186/s12864-021-07570-w RESEARCH ARTICLE Open Access Genome-wide association and transcriptome studies identify candidate genes and pathways for feed conversion ratio in pigs Yuanxin Miao1,2,3, Quanshun Mei1,2, Chuanke Fu1,2, Mingxing Liao1,2,4, Yan Liu1,2, Xuewen Xu1,2, Xinyun Li1,2, Shuhong Zhao1,2 and Tao Xiang1,2* Abstract Background: The feed conversion ratio (FCR) is an important productive trait that greatly affects profits in the pig industry. Elucidating the genetic mechanisms underpinning FCR may promote more efficient improvement of FCR through artificial selection. In this study, we integrated a genome-wide association study (GWAS) with transcriptome analyses of different tissues in Yorkshire pigs (YY) with the aim of identifying key genes and signalling pathways associated with FCR. Results: A total of 61 significant single nucleotide polymorphisms (SNPs) were detected by GWAS in YY. All of these SNPs were located on porcine chromosome (SSC) 5, and the covered region was considered a quantitative trait locus (QTL) region for FCR. Some genes distributed around these significant SNPs were considered as candidates for regulating FCR, including TPH2, FAR2, IRAK3, YARS2, GRIP1, FRS2, CNOT2 and TRHDE. According to transcriptome analyses in the hypothalamus, TPH2 exhibits the potential to regulate intestinal motility through serotonergic synapse and oxytocin signalling pathways. In addition, GRIP1 may be involved in glutamatergic and GABAergic signalling pathways, which regulate FCR by affecting appetite in pigs. Moreover, GRIP1, FRS2, CNOT2,andTRHDE may regulate metabolism in various tissues through a thyroid hormone signalling pathway.
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD

    Supplementary Table S4. FGA Co-Expressed Gene List in LUAD

    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase