The GWAS Analysis of Body Size and Population Verification of Related
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Bioluminescent Properties of Semi-Synthetic Obelin and Aequorin Activated by Coelenterazine Analogues with Modifications of C-2, C-6, and C-8 Substituents
International Journal of Molecular Sciences Article Bioluminescent Properties of Semi-Synthetic Obelin and Aequorin Activated by Coelenterazine Analogues with Modifications of C-2, C-6, and C-8 Substituents 1, 2,3, 1 2, Elena V. Eremeeva y , Tianyu Jiang y , Natalia P. Malikova , Minyong Li * and Eugene S. Vysotski 1,* 1 Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk 660036, Russia; [email protected] (E.V.E.); [email protected] (N.P.M.) 2 Key Laboratory of Chemical Biology (MOE), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China; [email protected] 3 State Key Laboratory of Microbial Technology, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Qingdao 266237, China * Correspondence: [email protected] (M.L.); [email protected] (E.S.V.); Tel.: +86-531-8838-2076 (M.L.); +7-(391)-249-44-30 (E.S.V.); Fax: +86-531-8838-2076 (M.L.); +7-(391)-290-54-90 (E.S.V.) These authors contributed equally to this work. y Received: 23 June 2020; Accepted: 27 July 2020; Published: 30 July 2020 Abstract: Ca2+-regulated photoproteins responsible for bioluminescence of a variety of marine organisms are single-chain globular proteins within the inner cavity of which the oxygenated coelenterazine, 2-hydroperoxycoelenterazine, is tightly bound. Alongside with native coelenterazine, photoproteins can also use its synthetic analogues as substrates to produce flash-type bioluminescence. However, information on the effect of modifications of various groups of coelenterazine and amino acid environment of the protein active site on the bioluminescent properties of the corresponding semi-synthetic photoproteins is fragmentary and often controversial. -
Discovery and Protein Engineering of Baeyer-Villiger Monooxygenases
Discovery and Protein Engineering of Baeyer-Villiger monooxygenases Inauguraldissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) der Mathematisch-Naturwissenschaftlichen Fakultät der Ernst-Moritz-Arndt-Universität Greifswald vorgelegt von Andy Beier geboren am 11.10.1988 in Parchim Greifswald, den 02.08.2017 I Dekan: Prof. Dr. Werner Weitschies 1. Gutachter: Prof. Dr. Uwe T. Bornscheuer 2. Gutachter: Prof. Dr. Marko Mihovilovic Tag der Promotion: 24.10.2017 II We need to learn to want what we have, not to have what we want, in order to get stable and steady happiness. - The Dalai Lama - III List of abbreviations % Percent MPS Methyl phenyl sulfide % (v/v) % volume per volume MPSO Methyl phenyl sulfoxide % (w/v) % weight per volume MPSO2 Methyl phenyl sulfone °C Degrees Celsius MTS Methyl p-tolyl sulfide µM µmol/L MTSO Methyl p-tolyl sulfoxide aa Amino acids MTSO2 Methyl p-tolyl sulfone + AGE Agarose gel electrophoresis NAD Nicotinamide adenine dinucleotide, oxidized aq. dest. Distilled water NADH Nicotinamide adenine dinucleotide, reduced + BLAST Basic Local Alignment Search NADP Nicotinamide adenine dinucleotide Tool phosphate, oxidized bp Base pair(s) NADPH Nicotinamide adenine dinucleotide phosphate, reduced BVMO Baeyer-Villiger monooxyge- OD600 Optical density at 600 nm nase CHMO Cyclohexanone monooxyge- PAGE Polyacrylamide gel electrophoresis nase Da Dalton PAMO Phenylacetone monooxygenase DMF Dimethyl formamide PCR Polymerase chain reaction DMSO Dimethyl sulfoxide PDB Protein Data Bank DMSO2 Dimethyl sulfone rpm Revolutions per minute DNA Desoxyribonucleic acid rv Reverse dNTP Desoxynucleoside triphosphate SDS Sodium dodecyl sulfate E. coli Escherichia coli SOC Super Optimal broth with Catabolite repression ee Enantiomeric excess TAE TRIS-Acetate-EDTA FAD Flavin adenine dinucleotide TB Terrific broth Fig. -
Cloning of Firefly Luciferase Cdna and the Expression of Active
Proc. Natl. Acad. Sci. USA Vol. 82, pp. 7870-7873, December 1985 Biochemistry Cloning of firefly luciferase cDNA and the expression of active luciferase in Escherichia coli (bioluminescence/Photinus pyralis/antibody screening/expression vector/recombinant DNA) JEFFREY R. DE WET*, KEITH V. WOODt, DONALD R. HELINSKI*, AND MARLENE DELUCAt Departments of *Biology and tChemistry, University of California, San Diego, La Jolla, CA 92093 Communicated by W. D. McElroy, July 26, 1985 ABSTRACT A cDNA library was constructed from firefly library was screened with anti-P. pyralis luciferase antibody, (Photinuspyralis) lantern poly(A)I RNA, using the Escherichia using a chromogenic detection technique (8), and several coli expression vector Xgtll. The library was screened with cDNA clones were isolated and characterized. These clones anti-P. pyralis luciferase (Photinus luciferin:oxygen 4-oxidore- were found to be homologous to the mRNA that encodes ductase, EC 1.13.12.7) antibody, and several cDNA clones luciferase. The largest luciferase cDNA clone that was expressing luciferase antigens were isolated. One clone, ALucl, isolated was able to direct the synthesis of active luciferase contained 1.5 kilobase pairs of cDNA that hybridized to a 1.9- in E. coli. to 2.0-kilobase band on a nitrocellulose blot of electrophoreti- cally fractionated lantern RNA. Hybridization of the cloned MATERIALS AND METHODS cDNA to lantern poly(A)I RNA selected an RNA that directed the in vitro synthesis of a single polypeptide. This polypeptide Enzymes and Strains. Restriction endonucleases and E. coli comigrated with luciferase on NaDodSO4/PAGE and produced DNA polymerase I were purchased from New England bioluminescence upon the addition of luciferin and ATP. -
Bioluminescence Is Produced by a Firefly-Like Luciferase but an Entirely
www.nature.com/scientificreports OPEN New Zealand glowworm (Arachnocampa luminosa) bioluminescence is produced by a Received: 8 November 2017 Accepted: 1 February 2018 frefy-like luciferase but an entirely Published: xx xx xxxx new luciferin Oliver C. Watkins1,2, Miriam L. Sharpe 1, Nigel B. Perry 2 & Kurt L. Krause 1 The New Zealand glowworm, Arachnocampa luminosa, is well-known for displays of blue-green bioluminescence, but details of its bioluminescent chemistry have been elusive. The glowworm is evolutionarily distant from other bioluminescent creatures studied in detail, including the frefy. We have isolated and characterised the molecular components of the glowworm luciferase-luciferin system using chromatography, mass spectrometry and 1H NMR spectroscopy. The purifed luciferase enzyme is in the same protein family as frefy luciferase (31% sequence identity). However, the luciferin substrate of this enzyme is produced from xanthurenic acid and tyrosine, and is entirely diferent to that of the frefy and known luciferins of other glowing creatures. A candidate luciferin structure is proposed, which needs to be confrmed by chemical synthesis and bioluminescence assays. These fndings show that luciferases can evolve independently from the same family of enzymes to produce light using structurally diferent luciferins. Glowworms are found in New Zealand and Australia, and are a major tourist attraction at sites located across both countries. In contrast to luminescent beetles such as the frefy (Coleoptera), whose bioluminescence has been well characterised (reviewed by ref.1), the molecular details of glowworm bioluminescence have remained elusive. Tese glowworms are the larvae of fungus gnats of the genus Arachnocampa, with eight species endemic to Australia and a single species found only in New Zealand2. -
The Role of the X Chromosome in Embryonic and Postnatal Growth
The role of the X chromosome in embryonic and postnatal growth Daniel Mark Snell A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy of University College London. Francis Crick Institute/Medical Research Council National Institute for Medical Research University College London January 28, 2018 2 I, Daniel Mark Snell, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the work. Abstract Women born with only a single X chromosome (XO) have Turner syndrome (TS); and they are invariably of short stature. XO female mice are also small: during embryogenesis, female mice with a paternally-inherited X chromosome (XPO) are smaller than XX littermates; whereas during early postnatal life, both XPO and XMO (maternal) mice are smaller than their XX siblings. Here I look to further understand the genetic bases of these phenotypes, and potentially inform areas of future investigation into TS. Mouse pre-implantation embryos preferentially silence the XP via the non-coding RNA Xist.XPO embryos are smaller than XX littermates at embryonic day (E) 10.5, whereas XMO embryos are not. Two possible hypotheses explain this obser- vation. Inappropriate expression of Xist in XPO embryos may cause transcriptional silencing of the single X chromosome and result in embryos nullizygous for X gene products. Alternatively, there could be imprinted genes on the X chromosome that impact on growth and manifest in growth retarded XPO embryos. In contrast, dur- ing the first three weeks of postnatal development, both XPO and XMO mice show a growth deficit when compared with XX littermates. -
CSE642 Final Version
Eindhoven University of Technology MASTER Dimensionality reduction of gene expression data Arts, S. Award date: 2018 Link to publication Disclaimer This document contains a student thesis (bachelor's or master's), as authored by a student at Eindhoven University of Technology. Student theses are made available in the TU/e repository upon obtaining the required degree. The grade received is not published on the document as presented in the repository. The required complexity or quality of research of student theses may vary by program, and the required minimum study period may vary in duration. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain Eindhoven University of Technology MASTER THESIS Dimensionality Reduction of Gene Expression Data Author: S. (Sako) Arts Daily Supervisor: dr. V. (Vlado) Menkovski Graduation Committee: dr. V. (Vlado) Menkovski dr. D.C. (Decebal) Mocanu dr. N. (Nikolay) Yakovets May 16, 2018 v1.0 Abstract The focus of this thesis is dimensionality reduction of gene expression data. I propose and test a framework that deploys linear prediction algorithms resulting in a reduced set of selected genes relevant to a specified case. Abstract In cancer research there is a large need to automate parts of the process of diagnosis, this is mainly to reduce cost, make it faster and more accurate. -
Muscle Regeneration Controlled by a Designated DNA Dioxygenase
Wang et al. Cell Death and Disease (2021) 12:535 https://doi.org/10.1038/s41419-021-03817-2 Cell Death & Disease ARTICLE Open Access Muscle regeneration controlled by a designated DNA dioxygenase Hongye Wang1, Yile Huang2,MingYu3,YangYu1, Sheng Li4, Huating Wang2,5,HaoSun2,5,BingLi 3, Guoliang Xu6,7 andPingHu4,8,9 Abstract Tet dioxygenases are responsible for the active DNA demethylation. The functions of Tet proteins in muscle regeneration have not been well characterized. Here we find that Tet2, but not Tet1 and Tet3, is specifically required for muscle regeneration in vivo. Loss of Tet2 leads to severe muscle regeneration defects. Further analysis indicates that Tet2 regulates myoblast differentiation and fusion. Tet2 activates transcription of the key differentiation modulator Myogenin (MyoG) by actively demethylating its enhancer region. Re-expressing of MyoG in Tet2 KO myoblasts rescues the differentiation and fusion defects. Further mechanistic analysis reveals that Tet2 enhances MyoD binding by demethylating the flanking CpG sites of E boxes to facilitate the recruitment of active histone modifications and increase chromatin accessibility and activate its transcription. These findings shed new lights on DNA methylation and pioneer transcription factor activity regulation. Introduction Ten-Eleven Translocation (Tet) family of DNA dioxy- 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Skeletal muscles can regenerate due to the existence of genases catalyze the active DNA demethylation and play muscle stem cells (MuSCs)1,2. The normally quiescent critical roles in embryonic development, neural regen- MuSCs are activated after muscle injury and further dif- eration, oncogenesis, aging, and many other important – ferentiate to support muscle regeneration3,4. -
Relating Metatranscriptomic Profiles to the Micropollutant
1 Relating Metatranscriptomic Profiles to the 2 Micropollutant Biotransformation Potential of 3 Complex Microbial Communities 4 5 Supporting Information 6 7 Stefan Achermann,1,2 Cresten B. Mansfeldt,1 Marcel Müller,1,3 David R. Johnson,1 Kathrin 8 Fenner*,1,2,4 9 1Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, 10 Switzerland. 2Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 11 Zürich, Switzerland. 3Institute of Atmospheric and Climate Science, ETH Zürich, 8092 12 Zürich, Switzerland. 4Department of Chemistry, University of Zürich, 8057 Zürich, 13 Switzerland. 14 *Corresponding author (email: [email protected] ) 15 S.A and C.B.M contributed equally to this work. 16 17 18 19 20 21 This supporting information (SI) is organized in 4 sections (S1-S4) with a total of 10 pages and 22 comprises 7 figures (Figure S1-S7) and 4 tables (Table S1-S4). 23 24 25 S1 26 S1 Data normalization 27 28 29 30 Figure S1. Relative fractions of gene transcripts originating from eukaryotes and bacteria. 31 32 33 Table S1. Relative standard deviation (RSD) for commonly used reference genes across all 34 samples (n=12). EC number mean fraction bacteria (%) RSD (%) RSD bacteria (%) RSD eukaryotes (%) 2.7.7.6 (RNAP) 80 16 6 nda 5.99.1.2 (DNA topoisomerase) 90 11 9 nda 5.99.1.3 (DNA gyrase) 92 16 10 nda 1.2.1.12 (GAPDH) 37 39 6 32 35 and indicates not determined. 36 37 38 39 S2 40 S2 Nitrile hydration 41 42 43 44 Figure S2: Pearson correlation coefficients r for rate constants of bromoxynil and acetamiprid with 45 gene transcripts of ECs describing nucleophilic reactions of water with nitriles. -
Functions and Applications of Nmos
Functions and applications of NMOs Willem Dijkman (1606212), June 20 2009 Assisted by drs. Anette Riebel and prof. dr. ir. Marco W. Fraaije Abstract The hydroxylation of amino groups is performed by different types of enzymes. Some of these types are metal dependent whereas others need a flavin cofactor. These flavoproteins (NMOs, for N-hydroxylating monooxygenases) can be assigned to subclass B of the external flavoproteins, an enzyme class consisting of enzymes with a broad range of monooxygenating activity. NMOs are mostly found in the biosynthesis of siderophores of different bacteria. Recently a NMO has been identified in the biosynthesis of a kutzneride. NMOs have a narrow substrate range, making them less applicable in industry. NMOs in siderophore biosynthesis can however be targeted to slow down bacterial growth. Contents enzymes which perform these monooxygenations often contain metal Introduction 1 atoms. Different types of enzymes are Classification of flavoproteins 2 known. P450 enzymes as well as non-heme 2 The catalytic cycle of flavins 3 monooxygenases contain iron and copper- N-hydroxylation in nature 4 dependent enzymes also perform Characteristics of NMOs 4 monooxygenations. Not all enzymes depend - NMOs in siderophore synthesis 5 on a (metallic) cofactor for their activity: - A NMO in kutzneride synthesis 7 flavin-dependent monooxygenases make use - N-hydroxylation in valanimycin synthesis 7 of a flavin group instead of a metal ion and Recombinant NMOs 8 recently enzymes without any cofactor have 3,4 Pharmaceutical applications 8 shown monooxygenase activity . Industrial applications 9 In this article one type of monooxygenation Conclusion 10 will be described, focusing on one group of Literature 10 monooxygenating enzymes. -
Elucidation of Dose-Dependent Transcriptional Events Immediately Following Ionizing Radiation Exposure
bioRxiv preprint doi: https://doi.org/10.1101/207951; this version posted October 23, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 2 3 4 Elucidation of dose-dependent transcriptional events immediately following 5 ionizing radiation exposure 6 7 Eric C. Rouchka1,2,*, Robert M. Flight3, Brigitte H. Fasciotto4, Rosendo Estrada5, John W. 8 Eaton6,7,8, Phani K. Patibandla5, Sabine J. Waigel8, Dazhuo Li1, John K. Kirtley1, Palaniappan 9 Sethu9,10, and Robert S. Keynton5 10 11 1Department of Computer Engineering and Computer Science, University of Louisville, 12 Louisville, Kentucky, United States of America 13 14 2Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of 15 Louisville, Louisville, Kentucky, United States of America 16 17 3Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, 18 Kentucky, United States of America 19 20 4The ElectroOptics Research Institute and Nanotechnology Center, University of Louisville, 21 Louisville, Kentucky, United States of America 22 23 5Department of Bioengineering, University of Louisville, Louisville, Kentucky, United States of 24 America 25 26 6Department of Medicine, University of Louisville, Louisville, Kentucky, United States of 27 America 28 29 7Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, 30 United States of America 31 32 8James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United 33 States of America 34 35 9Division of Cardiovascular Disease, Department of Medicine, University of Alabama at 36 Birmingham, Birmingham, Alabama, United States of America 37 38 10Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, 39 Alabama, United States of America 1 bioRxiv preprint doi: https://doi.org/10.1101/207951; this version posted October 23, 2017. -
Nitric Oxide Prevents a Pathogen-Permissive Granulocytic Inflammation During Tuberculosis
ARTICLES PUBLISHED: 15 MAY 2017 | VOLUME: 2 | ARTICLE NUMBER: 17072 Nitric oxide prevents a pathogen-permissive granulocytic inflammation during tuberculosis Bibhuti B. Mishra1, Rustin R. Lovewell1,AndrewJ.Olive1, Guoliang Zhang2, Wenfei Wang2, Eliseo Eugenin3, Clare M. Smith1,JiaYaoPhuah1, Jarukit E. Long1, Michelle L. Dubuke4, Samantha G. Palace1, Jon D. Goguen1,RichardE.Baker1, Subhalaxmi Nambi1, Rabinarayan Mishra5, Matthew G. Booty1,ChristinaE.Baer1, Scott A. Shaffer4, Veronique Dartois3,BethA.McCormick1, Xinchun Chen2,6* and Christopher M. Sassetti1* Nitric oxide contributes to protection from tuberculosis. It is generally assumed that this protection is due to direct inhibition of Mycobacterium tuberculosis growth, which prevents subsequent pathological inflammation. In contrast, we report that nitric oxide primarily protects mice by repressing an interleukin-1- and 12/15-lipoxygenase-dependent neutrophil recruitment cascade that promotes bacterial replication. Using M. tuberculosis mutants as indicators of the pathogen’s environment, we inferred that granulocytic inflammation generates a nutrient-replete niche that supports M. tuberculosis growth. Parallel clinical studies indicate that a similar inflammatory pathway promotes tuberculosis in patients. The human 12/15-lipoxygenase orthologue, ALOX12, is expressed in cavitary tuberculosis lesions; the abundance of its products correlates with the number of airway neutrophils and bacterial burden and a genetic polymorphism that increases ALOX12 expression is associated with tuberculosis -
Mechanisms Underlying Platelet Function
Received Date : 09-Dec-2013 Accepted Date : 19-Feb-2014 Article type : Original Article - Platelets Mechanisms underlying platelet function defect in a pedigree with FPD/AML: potential role for candidate RUNX1-targets Glembotsky AC,* Bluteau D,†‡ Espasandin YR,* Goette NP,* Marta RF,* Marin Oyarzun CP,* Korin L,* Lev PR,* Laguens RP, § Molinas FC,* Raslova H,† Heller PG* *Departamento de Hematología Investigación. Instituto de Investigaciones Médicas Article Alfredo Lanari. Universidad de Buenos Aires. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Buenos Aires. Argentina †INSERM, UMR1009. Equipe Labellisée Ligue Contre le Cancer. Gustave Roussy. Université Paris-Sud. Villejuif. France ‡Ecole Pratique des Hautes Etudes (EPHE), Paris, France §Departamento de Patología. Universidad de Favaloro. Buenos Aires. Argentina Corresponding author: Paula G. Heller. Departamento de Hematología Investigación. Instituto de Investigaciones Médicas Alfredo Lanari. Universidad de Buenos Aires. CONICET. Combatientes de Malvinas 3150. Buenos Aires 1427. Argentina This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record. Please cite this article as an 'Accepted Article', doi: 10.1111/jth.12550 Accepted This article is protected by copyright. All rights reserved. Phone/Fax: +54 11 4523 89 47 Email address: [email protected] Short title Platelet function defect in FPD/AML Summary Background FPD/AML is an inherited platelet disorder caused by germline RUNX1 mutation and characterized by thrombocytopenia, platelet function defect and leukemia Article predisposition. The mechanisms underlying FPD/AML platelet dysfunction remain incompletely clarified. We aimed to determine the contribution of platelet structural abnormalities and defective activation pathways to the platelet phenotype.