Protein T1 C1 Accession No. Description
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Review: Microbial Transformations of Human Bile Acids Douglas V
Guzior and Quinn Microbiome (2021) 9:140 https://doi.org/10.1186/s40168-021-01101-1 REVIEW Open Access Review: microbial transformations of human bile acids Douglas V. Guzior1,2 and Robert A. Quinn2* Abstract Bile acids play key roles in gut metabolism, cell signaling, and microbiome composition. While the liver is responsible for the production of primary bile acids, microbes in the gut modify these compounds into myriad forms that greatly increase their diversity and biological function. Since the early 1960s, microbes have been known to transform human bile acids in four distinct ways: deconjugation of the amino acids glycine or taurine, and dehydroxylation, dehydrogenation, and epimerization of the cholesterol core. Alterations in the chemistry of these secondary bile acids have been linked to several diseases, such as cirrhosis, inflammatory bowel disease, and cancer. In addition to the previously known transformations, a recent study has shown that members of our gut microbiota are also able to conjugate amino acids to bile acids, representing a new set of “microbially conjugated bile acids.” This new finding greatly influences the diversity of bile acids in the mammalian gut, but the effects on host physiology and microbial dynamics are mostly unknown. This review focuses on recent discoveries investigating microbial mechanisms of human bile acids and explores the chemical diversity that may exist in bile acid structures in light of the new discovery of microbial conjugations. Keywords: Bile acid, Cholic acid, Conjugation, Microbiome, Metabolism, Microbiology, Gut health, Clostridium scindens, Enterocloster bolteae Introduction the development of healthy or diseased states. For The history of bile example, abnormally high levels of the microbially modi- Bile has been implicated in human health for millennia. -
THESIS Entitled Studies on Fraction 1 Protein of Beta Vulgaris Submitted for the Degree of DOCTOR of PHILOSOPHY by Kenneth Edwar
THESIS entitled Studies on Fraction 1 Protein of Beta vulgaris Submitted for the degree of DOCTOR OF PHILOSOPHY by Kenneth Edward Moon 1 970 TABLE OF CONTENTS Acknowledgements i Abbreviations i Summary ii Chapter 1 Introduction 1.1 Carbon Dioxide Fixation in the Calvin • 1 Cycle 1.2 Some Properties of RuDPcase and Similarity 2 to Fraction 1 Protein 1.3 Cellular Location of Fraction 1 Protein 3 1.4 The Mechanism of Action of RuDPcase 4 1.5 Structure of Fraction 1 Protein from 13 Higher Plants 1.6 Relationship of Structure to Enzymic 14 Activity and Role of Sulphydryl Groups 1.7 Studies on RuDPcase from Sources other 17 than the Higher Plants 1.8 Comparison of Some Kinetic and Physical 21 Constants of RuDPcase from Different Sources 1.9 Aim of This Research Project 23 Chapter 2 Methods and Materials 2.1 Plant Material 24 2.2 Preparation of Chloroplasts and Isolation 24 of Fraction 1 Protein 2.3 Concentrating Protein Solutions 26 2.4 Preparation of Reduced and Carboxy- 27 methylated Fraction 1 Protein 2.5 Preparation of Maleyl-carboxymethyl 28 Fraction 1 Protein 2.6 Removal of Maleyl Groups 29 2.7 Gel Electrophoresis 30 2.7 (i) Polyacrylamide Disk Electrophoresis 30 (ii) Polyacrylamide Electrophoresis in 31 the presence of SDS (iii) Slab Acrylamide Gel Electrophoresis 32 (iv) Isoelectric Focusing 33 2.8 Ribulose-1,5-diphosphate Carboxylase 3^ Assay 2.9 Preparation of the S-Sulphenylsulphanate 34 Derivative of Fraction 1 Protein 2.10 Edman Degradations 35 2.11 Hydrazinolysis 35 2.12 Isolation of Blocked N-Terminal Peptides 36 2.13 Tryptic -
The International Journal of Biochemistry & Cell Biology
The International Journal of Biochemistry & Cell Biology 41 (2009) 1685–1696 Contents lists available at ScienceDirect The International Journal of Biochemistry & Cell Biology journal homepage: www.elsevier.com/locate/biocel Cathepsin X cleaves the C-terminal dipeptide of alpha- and gamma-enolase and impairs survival and neuritogenesis of neuronal cells Natasaˇ Obermajer a,b,∗, Bojan Doljak a, Polona Jamnik c,Ursaˇ Pecarˇ Fonovic´ a, Janko Kos a,b a University of Ljubljana, Faculty of Pharmacy, Askerceva 7, 1000 Ljubljana, Slovenia b Jozef Stefan Institute, Department of Biotechnology, Jamova 39, 1000 Ljubljana, Slovenia c University of Ljubljana, Biotechnical Faculty, Jamnikarjeva 101, 1000 Ljubljana, Slovenia article info abstract Article history: The cysteine carboxypeptidase cathepsin X has been recognized as an important player in degenerative Received 22 January 2009 processes during normal aging and in pathological conditions. In this study we identify isozymes alpha- Received in revised form 17 February 2009 and gamma-enolases as targets for cathepsin X. Cathepsin X sequentially cleaves C-terminal amino acids Accepted 18 February 2009 of both isozymes, abolishing their neurotrophic activity. Neuronal cell survival and neuritogenesis are, Available online 6 March 2009 in this way, regulated, as shown on pheochromocytoma cell line PC12. Inhibition of cathepsin X activity increases generation of plasmin, essential for neuronal differentiation and changes the length distribution Keywords: of neurites, especially in the early phase of neurite outgrowth. Moreover, cathepsin X inhibition increases Cathepsin X Enolase neuronal survival and reduces serum deprivation induced apoptosis, particularly in the absence of nerve Neuritogenesis growth factor. On the other hand, the proliferation of cells is decreased, indicating induction of differ- Neuronal cell survival entiation. -
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. -
Gentaur Products List
Chapter 2 : Gentaur Products List • Rabbit Anti LAMR1 Polyclonal Antibody Cy5 Conjugated Conjugated • Rabbit Anti Podoplanin gp36 Polyclonal Antibody Cy5 • Rabbit Anti LAMR1 CT Polyclonal Antibody Cy5 • Rabbit Anti phospho NFKB p65 Ser536 Polyclonal Conjugated Conjugated Antibody Cy5 Conjugated • Rabbit Anti CHRNA7 Polyclonal Antibody Cy5 Conjugated • Rat Anti IAA Monoclonal Antibody Cy5 Conjugated • Rabbit Anti EV71 VP1 CT Polyclonal Antibody Cy5 • Rabbit Anti Connexin 40 Polyclonal Antibody Cy5 • Rabbit Anti IAA Indole 3 Acetic Acid Polyclonal Antibody Conjugated Conjugated Cy5 Conjugated • Rabbit Anti LHR CGR Polyclonal Antibody Cy5 Conjugated • Rabbit Anti Integrin beta 7 Polyclonal Antibody Cy5 • Rabbit Anti Natrexone Polyclonal Antibody Cy5 Conjugated • Rabbit Anti MMP 20 Polyclonal Antibody Cy5 Conjugated Conjugated • Rabbit Anti Melamine Polyclonal Antibody Cy5 Conjugated • Rabbit Anti BCHE NT Polyclonal Antibody Cy5 Conjugated • Rabbit Anti NAP1 NAP1L1 Polyclonal Antibody Cy5 • Rabbit Anti Acetyl p53 K382 Polyclonal Antibody Cy5 • Rabbit Anti BCHE CT Polyclonal Antibody Cy5 Conjugated Conjugated Conjugated • Rabbit Anti HPV16 E6 Polyclonal Antibody Cy5 Conjugated • Rabbit Anti CCP Polyclonal Antibody Cy5 Conjugated • Rabbit Anti JAK2 Polyclonal Antibody Cy5 Conjugated • Rabbit Anti HPV18 E6 Polyclonal Antibody Cy5 Conjugated • Rabbit Anti HDC Polyclonal Antibody Cy5 Conjugated • Rabbit Anti Microsporidia protien Polyclonal Antibody Cy5 • Rabbit Anti HPV16 E7 Polyclonal Antibody Cy5 Conjugated • Rabbit Anti Neurocan Polyclonal -
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. -
Supplementary Materials
1 Supplementary Materials: Supplemental Figure 1. Gene expression profiles of kidneys in the Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice. (A) A heat map of microarray data show the genes that significantly changed up to 2 fold compared between Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice (N=4 mice per group; p<0.05). Data show in log2 (sample/wild-type). 2 Supplemental Figure 2. Sting signaling is essential for immuno-phenotypes of the Fcgr2b-/-lupus mice. (A-C) Flow cytometry analysis of splenocytes isolated from wild-type, Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice at the age of 6-7 months (N= 13-14 per group). Data shown in the percentage of (A) CD4+ ICOS+ cells, (B) B220+ I-Ab+ cells and (C) CD138+ cells. Data show as mean ± SEM (*p < 0.05, **p<0.01 and ***p<0.001). 3 Supplemental Figure 3. Phenotypes of Sting activated dendritic cells. (A) Representative of western blot analysis from immunoprecipitation with Sting of Fcgr2b-/- mice (N= 4). The band was shown in STING protein of activated BMDC with DMXAA at 0, 3 and 6 hr. and phosphorylation of STING at Ser357. (B) Mass spectra of phosphorylation of STING at Ser357 of activated BMDC from Fcgr2b-/- mice after stimulated with DMXAA for 3 hour and followed by immunoprecipitation with STING. (C) Sting-activated BMDC were co-cultured with LYN inhibitor PP2 and analyzed by flow cytometry, which showed the mean fluorescence intensity (MFI) of IAb expressing DC (N = 3 mice per group). 4 Supplemental Table 1. Lists of up and down of regulated proteins Accession No. -
A Genetic and Developmental Analysis of Dnase-1, an Acid Deoxyribonuclease in Droso~Hila Melano~Aster
A GENETIC AND DEVELOPMENTAL ANALYSIS OF DNASE-1, AN ACID DEOXYRIBONUCLEASE IN DROSOPHILA MEL~NOGASTER A Thesis Presented to the Faculty of the Graduate School in Partial Fulfillment for the Degree of Doctor of Philosophy by Charles Roger Detwiler Hay, 1979 BIOGRAPHICAL SKETCH Charles R. Detwiler was born on December 15, 1950 in Norristown, Pennsylvania. He attended Collegeville-Trappe High School in Trappe, Pennsylvania from 1964 to 1968; Houghton College in Houghton, New York from 1968 to 1972 (B.S., Zoology); Buc~~ell University in Lewisburg, Pennsylvania from 1972 to 1974 (M.S., Biology); and Cornell University in Ithaca, New York from 1974 to 1979 (Ph.D., 1979). At Cornell he was a National Institutes of Health Genetics Trainee. He is a member of the Genetics Society of America, the American Scientific Afffiliation, and of Phi Sigma, the National Honorary Biology Society. ii - To the Designer of the fly iii ACKNOWLEDGMENTS I would like to thank all my friends 1-rho by their moral support or careful critical attention contributed to the completion of this work. First, I would like to thank my major professor, Dr. Ross MacIntyre, for his patience, generosity, and valuable ideas. I would like to thank Dr. Richard Halberg and Dr. Bruce "\{allace for their helpful comments and criticisms 1-li th regard to the thesis project. I would like to thank Margaret Dean for tireless reassurances and valuable tecrillical assistance especially at the begLnning. Lastly, Beverly my wife is aCYil101-Iledged. It would be absurd to "thank" her. Her patience and devotion have served both in brlllging these pages together, and in keeping hw people together in one beautiful relationship. -
Figure S1. Quality Control Validation of MS Data. (A‑C) Mass Error Distribution of All Peptides Identified in the Acetylome
Figure S1. Quality control validation of MS data. (A‑C) Mass error distribution of all peptides identified in the acetylome, succi- nylome and quantitative proteome, respectively. (D‑F) Length distribution of peptides identified in the acetylome, succinylome and quantitative proteome, respectively. Figure S2. Comparison of modification level between breast cancer tissue and normal tissue. Comparison of acetylation level (A) and succinylation level (B) between breast cancer tissue and normal tissue. Data are medians and were analyzed using Wilcoxon Signed Rank Test. **P<0.01. Table SI. Protein sites whose acetylation and succinylation levels were both significantly upregulated in breast cancer tissues (fold change ≥1.5 compared with normal tissues). Protein ID Protein name Modification site P54868 HMCS2 310K Q15063 POSTN 549K Q99715 COCA1 1601K P51572 BAP31 72K P07237 PDLA1 328K Q06830 PRDX1 192K P48735 IDHP 180K P30101 PDIA3 417K P0DMV9 HS71B 526K Q01995 TAGL 21K P06748 NPM1 27K Q00325 MPCP 209K P00488 F13A 69K P02545 LMNA 260K P08133 ANXA6 478K P02452 CO1A1 751K Table SII. Protein sites whose acetylation and succinylation levels were both significantly downregulated in breast cancer tissues (fold change ≥1.5 compared with normal tissues). Protein ID Protein name Modification site RET4 P02753 30K PSG2 P07585 142K HBA P69905 12K IGKC P01834 80K HBA P69905 8K Table SIII. All proteins whose expression level were significantly upregulated in breast cancer tissues (fold change ≥1.5 compared with normal tissues). Protein ID Protein description -
Datasheet: VMA00346 Product Details
Datasheet: VMA00346 Description: MOUSE ANTI AKR1C2 Specificity: AKR1C2 Format: Purified Product Type: PrecisionAb™ Monoclonal Isotype: IgG2a Quantity: 100 µl Product Details Applications This product has been reported to work in the following applications. This information is derived from testing within our laboratories, peer-reviewed publications or personal communications from the originators. Please refer to references indicated for further information. For general protocol recommendations, please visit www.bio-rad-antibodies.com/protocols. Yes No Not Determined Suggested Dilution Western Blotting 1/1000 PrecisionAb antibodies have been extensively validated for the western blot application. The antibody has been validated at the suggested dilution. Where this product has not been tested for use in a particular technique this does not necessarily exclude its use in such procedures. Further optimization may be required dependant on sample type. Target Species Human Product Form Purified IgG - liquid Preparation Mouse monoclonal antibody prepared by affinity chromatography on Protein G Buffer Solution Phosphate buffered saline Preservative 0.09% Sodium Azide (NaN3) Stabilisers Immunogen Recombinant human AKR1C2 External Database Links UniProt: P52895 Related reagents Entrez Gene: 1646 AKR1C2 Related reagents Synonyms DDH2 Specificity Mouse anti Human AKR1C2 antibody recognizes the aldo-keto reductase family 1 member C2, also known as 3-alpha-HSD3, DD-2, DD/BABP, aldo-keto reductase family 1 member C2, Page 1 of 2 chlordecone reductase homolog HAKRD, dihydrodiol dehydrogenase 2, bile acid binding protein, 3-alpha hydroxysteroid dehydrogenase, type III, pseudo-chlordecone reductase, testicular 17,20-desmolase deficiency, trans-1,2-dihydrobenzene-1,2-diol dehydrogenase and type II dihydrodiol dehydrogenase. Encoded by the AKR1C2 gene, aldo-keto reductase family 1 member C2 is a member of the aldo/keto reductase superfamily, which consists of more than 40 known enzymes and proteins. -
Summary & Conclusions
Enzymatic functionalization and degradation of natural and synthetic polymers Von der Fakultät für Mathematik, Informatik und Naturwissenschaften der RWTH Aachen University zur Erlangung des akademischen Grades einer Doktorin der Naturwissenschaften genehmigte Dissertation vorgelegt von Shohana Subrin Islam M. Sc. Biotechnologie aus Dhaka, Bangladesch Berichter: Univ. -Prof. Dr. Ulrich Schwaneberg Univ. -Prof. Dr. Lothar Elling Tag der mündlichen Prüfung: 23.01.2019 Diese Dissertation ist auf den Internetseiten der Universitätsbibliothek verfügbar. To my mom & my sister-the two persons in the world who always stand by me Table of content Table of content Table of content _______________________________________________________________ v Publications and patents ________________________________________________________ ix Abstract _____________________________________________________________________ xi 1. General introduction _______________________________________________________ 1 1.1 Enzymatic functionalization of (bio)polymers _______________________________________ 1 1.2 Enzymatic degradation of polymers _______________________________________________ 3 1.3 Protein engineering ____________________________________________________________ 5 1.3.1 Directed evolution of enzymes _________________________________________________________ 6 1.3.2 KnowVolution – Directed Evolution 2.0 __________________________________________________ 9 1.4 Aims of the dissertation _______________________________________________________ 11 2. Engineering of -
Phylogenetic Analysis, Subcellular Localization, and Expression
BMC Plant Biology BioMed Central Research article Open Access Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants Malona V Alinsug, Chun-Wei Yu and Keqiang Wu* Address: Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan Email: Malona V Alinsug - [email protected]; Chun-Wei Yu - [email protected]; Keqiang Wu* - [email protected] * Corresponding author Published: 28 March 2009 Received: 26 November 2008 Accepted: 28 March 2009 BMC Plant Biology 2009, 9:37 doi:10.1186/1471-2229-9-37 This article is available from: http://www.biomedcentral.com/1471-2229/9/37 © 2009 Alinsug et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Although histone deacetylases from model organisms have been previously identified, there is no clear basis for the classification of histone deacetylases under the RPD3/ HDA1 superfamily, particularly on plants. Thus, this study aims to reconstruct a phylogenetic tree to determine evolutionary relationships between RPD3/HDA1 histone deacetylases from six different plants representing dicots with Arabidopsis thaliana, Populus trichocarpa, and Pinus taeda, monocots with Oryza sativa and Zea mays, and the lower plants with Physcomitrella patens. Results: Sixty two histone deacetylases of RPD3/HDA1 family from the six plant species were phylogenetically analyzed to determine corresponding orthologues. Three clusters were formed separating Class I, Class II, and Class IV.