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(12) Patent Application Publication (10) Pub. No.: US 2013/0089535 A1 Yamashiro Et Al
US 2013 0089535A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2013/0089535 A1 Yamashiro et al. (43) Pub. Date: Apr. 11, 2013 (54) AGENT FOR REDUCING ACETALDEHYDE Publication Classification NORAL CAVITY (51) Int. Cl. (75) Inventors: Kan Yamashiro, Kakamigahara-shi (JP); A68/66 (2006.01) Takahumi Koyama, Kakamigahara-shi A638/51 (2006.01) (JP) A61O 11/00 (2006.01) A638/44 (2006.01) Assignee: AMANOENZYME INC., Nagoya-shi (52) U.S. Cl. (73) CPC. A61K 8/66 (2013.01); A61K 38/44 (2013.01); (JP) A61 K38/51 (2013.01); A61O II/00 (2013.01) (21) Appl. No.: 13/703,451 USPC .......... 424/94.4; 424/94.5; 435/191: 435/232 (22) PCT Fled: Jun. 7, 2011 (57) ABSTRACT Disclosed herein is a novel enzymatic agent effective in (86) PCT NO.: PCT/UP2011/062991 reducing acetaldehyde in the oral cavity. It has been found S371 (c)(1), that an aldehyde dehydrogenase derived from a microorgan (2), (4) Date: Dec. 11, 2012 ism belonging to the genus Saccharomyces and a threonine aldolase derived from Escherichia coli are effective in reduc (30) Foreign Application Priority Data ing low concentrations of acetaldehyde. Therefore, an agent for reducing acetaldehyde in the oral cavity is provided, Jun. 19, 2010 (JP) ................................. 2010-140O26 which contains these enzymes as active ingredients. Patent Application Publication Apr. 11, 2013 Sheet 1 of 2 US 2013/0089535 A1 FIG 1) 10.5 1 0 9.9.5 8. 5 CONTROL TA AD (BSA) ENZYME Patent Application Publication Apr. 11, 2013 Sheet 2 of 2 US 2013/0089535 A1 FIG 2) 110 the CONTROL (BSA) 100 354. -
Bacterial Oxidases of the Cytochrome Bd Family: Redox Enzymes of Unique Structure, Function, and Utility As Drug Targets
Published in "Antioxidants & Redox Signaling doi: 10.1089/ars.2020.8039, 2020" which should be cited to refer to this work. Bacterial Oxidases of the Cytochrome bd Family: Redox Enzymes of Unique Structure, Function, and Utility As Drug Targets Vitaliy B. Borisov,1 Sergey A. Siletsky,1 Alessandro Paiardini,2 David Hoogewijs,3 Elena Forte,2 Alessandro Giuffre`,4 and Robert K. Poole5 Abstract Significance: Cytochrome bd is a ubiquinol:oxygen oxidoreductase of many prokaryotic respiratory chains with a unique structure and functional characteristics. Its primary role is to couple the reduction of molecular oxygen, even at submicromolar concentrations, to water with the generation of a proton motive force used for adenosine triphosphate production. Cytochrome bd is found in many bacterial pathogens and, surprisingly, in bacteria for- mally denoted as anaerobes. It endows bacteria with resistance to various stressors and is a potential drug target. Recent Advances: We summarize recent advances in the biochemistry, structure, and physiological functions of cytochrome bd in the light of exciting new three-dimensional structures of the oxidase. The newly discovered roles of cytochrome bd in contributing to bacterial protection against hydrogen peroxide, nitric oxide, perox- ynitrite, and hydrogen sulfide are assessed. Critical Issues: Fundamental questions remain regarding the precise delineation of electron flow within this multihaem oxidase and how the extraordinarily high affinity for oxygen is accomplished, while endowing bacteria with resistance to other small ligands. Future Directions: It is clear that cytochrome bd is unique in its ability to confer resistance to toxic small molecules, a property that is significant for understanding the propensity of pathogens to possess this oxidase. -
Reconstitution of Active Transport in Proteoliposomes Containing Cytochrome O Oxidase and Lac Carrier Protein Purified from Esch
Proc. Natl Acad. Sci. USA Vol. 80, pp. 4889-4893, August 1983 Biochemistry Reconstitution of active transport in proteoliposomes containing cytochrome o oxidase and lac carrier protein purified from Escherichia coli (chemiosmotic hypothesis/proton electrochemical gradient/carbocyanine/octyl glucoside/detergent dilution) KAZUNOBU MATSUSHITA*, LEKHA PATEL*, ROBERT B. GENNISt, AND H. RONALD KABACK*t *Roche Institute of Molecular Biology, Roche Research Center, Nutley, New Jersey 07110; and tDepartment of Chemistry, University of Illinois, Urbana, Illinois 61801 Communicated by B. L. Horecker, April 29, 1983 ABSTRACT Most active transport across the bacterial cell flux with appropriately directed lactose concentration gra- membrane is driven by a proton electrochemical gradient dients, and accumulate lactose against a concentration gradient (AJAH+, interior negative and alkaline) generated via electron when AOH+ (interior negative or alkaline or both) is imposed transfer through a membrane-bound respiratory chain. This phe- (2-5). Furthermore, the turnover number of purified lac car- nomenon is now reproduced in vitro with proteoliposomes con- rier in proteoliposomes is similar to that observed in right-side- taining only two proteins purified from the membrane of Esch- out membrane vesicles, as is the Km for lactose (1). In addition, erichia coli. An o-type cytochrome oxidase was extracted from a secondary structure model for the lac carrier protein has been membranes of a cytochrome d terminal oxidase mutant with octyl proposed (6), monoclonal antibodies against the purified pro- 8-D-glucopyranoside after sequential treatment with urea and tein have been prepared and characterized (7), and it has been cholate and was purified to homogeneity by ion-exchange chro- the matography. -
Clinical Molecular Genetics in the Uk C.1975–C.2000
CLINICAL MOLECULAR GENETICS IN THE UK c.1975–c.2000 The transcript of a Witness Seminar held by the History of Modern Biomedicine Research Group, Queen Mary, University of London, on 5 February 2013 Edited by E M Jones and E M Tansey Volume 48 2014 ©The Trustee of the Wellcome Trust, London, 2014 First published by Queen Mary, University of London, 2014 The History of Modern Biomedicine Research Group is funded by the Wellcome Trust, which is a registered charity, no. 210183. ISBN 978 0 90223 888 6 All volumes are freely available online at www.history.qmul.ac.uk/research/modbiomed/ wellcome_witnesses/ Please cite as: Jones E M, Tansey E M. (eds) (2014) Clinical Molecular Genetics in the UK c.1975–c.2000. Wellcome Witnesses to Contemporary Medicine, vol. 48. London: Queen Mary, University of London. CONTENTS What is a Witness Seminar? v Acknowledgements E M Tansey and E M Jones vii Illustrations and credits ix Abbreviations xi Ancillary guides xiii Introduction Professor Bob Williamson xv Transcript Edited by E M Jones and E M Tansey 1 Appendix 1 Photograph, with key, of delegates attending The Molecular Biology of Thalassaemia conference in Kolimbari, Crete, 1978 88 Appendix 2 Extracts from the University of Leiden postgraduate course Restriction Fragment Length Polymorphisms and Human Genetics, 1982 91 Appendix 3 Archival material of the Clinical Molecular Genetics Society 95 Biographical notes 101 References 113 Index 131 Witness Seminars: Meetings and Publications 143 WHAT IS A WITNESS SEMINAR? The Witness Seminar is a specialized form of oral history, where several individuals associated with a particular set of circumstances or events are invited to meet together to discuss, debate, and agree or disagree about their memories. -
Supplemental Methods
Supplemental Methods: Sample Collection Duplicate surface samples were collected from the Amazon River plume aboard the R/V Knorr in June 2010 (4 52.71’N, 51 21.59’W) during a period of high river discharge. The collection site (Station 10, 4° 52.71’N, 51° 21.59’W; S = 21.0; T = 29.6°C), located ~ 500 Km to the north of the Amazon River mouth, was characterized by the presence of coastal diatoms in the top 8 m of the water column. Sampling was conducted between 0700 and 0900 local time by gently impeller pumping (modified Rule 1800 submersible sump pump) surface water through 10 m of tygon tubing (3 cm) to the ship's deck where it then flowed through a 156 µm mesh into 20 L carboys. In the lab, cells were partitioned into two size fractions by sequential filtration (using a Masterflex peristaltic pump) of the pre-filtered seawater through a 2.0 µm pore-size, 142 mm diameter polycarbonate (PCTE) membrane filter (Sterlitech Corporation, Kent, CWA) and a 0.22 µm pore-size, 142 mm diameter Supor membrane filter (Pall, Port Washington, NY). Metagenomic and non-selective metatranscriptomic analyses were conducted on both pore-size filters; poly(A)-selected (eukaryote-dominated) metatranscriptomic analyses were conducted only on the larger pore-size filter (2.0 µm pore-size). All filters were immediately submerged in RNAlater (Applied Biosystems, Austin, TX) in sterile 50 mL conical tubes, incubated at room temperature overnight and then stored at -80oC until extraction. Filtration and stabilization of each sample was completed within 30 min of water collection. -
C12) United States Patent (IO) Patent No.: US 9,441,253 B2 San Et Al
IIIIII IIIIIIII Ill lllll lllll lllll lllll lllll lllll lllll lllll 111111111111111111 US009441253B2 c12) United States Patent (IO) Patent No.: US 9,441,253 B2 San et al. (45) Date of Patent: Sep.13,2016 (54) METABOLIC TRANSISTOR IN BACTERIA 114/13027 (2013.01); C12Y 205/01001 (2013.01); C12Y 205/01032 (2013.01); C12Y (71) Applicant: William Marsh Rice University, 205/01093 (2013.01); C12Y 305/01022 Houston, TX (US) (2013.01); C12Y 305/99002 (2013.01); C12Y 401/01024 (2013.01); C12Y 602/01011 (72) Inventors: Ka-Yiu San, Houston, TX (US); (2013.01); Y02E 50/17 (2013.01); Y02P 20/52 George N. Bennett, Houston, TX (US); (2015.11) Hui Wu, Houston, TX (US) (58) Field of Classification Search CPC .................................. C12P 7/56; C12N 15/70 (73) Assignee: William Marsh Rice University, Houston, TX (US) USPC .................... 435/108, 111, 115, 116, 252.33 See application file for complete search history. ( *) Notice: Subject to any disclaimer, the term ofthis patent is extended or adjusted under 35 (56) References Cited U.S.C. 154(b) by 130 days. U.S. PATENT DOCUMENTS (21) Appl. No.: 14/176,008 2004/0152159 Al 8/2004 Causey (22) Filed: Feb. 7, 2014 OTHER PUBLICATIONS (65) Prior Publication Data Wu et al. Biotechnology and bioengineering, (Aug. 2015) vol. 112, US 2014/0227745 Al Aug. 14, 2014 No. 8, pp. 1720-1726.* Alper H., Miyaoku K., Stephanopoulos G., (2005) Construction of Related U.S. Application Data lycopene overproducing E. coli strains by combining systematic and combinatorial gene knockout targets. Nat. Biotechnol. 23,612-616. -
Chemistry of Proteins and Amino Acids • Proteins Are the Most Abundant Organic Molecules of the Living System
Chemistry of Proteins and Amino Acids • Proteins are the most abundant organic molecules of the living system. • They occur in the every part of the cell and constitute about 50% of the cellular dry weight. • Proteins form the fundamental basis of structure and function of life. • In 1839 Dutch chemist G.J.Mulder while investing the substances such as those found in milk, egg, found that they could be coagulated on heating and were nitrogenous compounds. • The term protein is derived from a Greek word proteios, meaning first place. • Berzelius ( Swedish chemist ) suggested the name proteins to the group of organic compounds that are utmost important to life. • The proteins are nitrogenous macromolecules composed of many amino acids. Biomedical importance of proteins: • Proteins are the main structural components of the cytoskeleton. They are the sole source to replace nitrogen of the body. • Bio chemical catalysts known as enzymes are proteins. • Proteins known as immunoglobulins serve as the first line of defense against bacterial and viral infections. • Several hormones are protein in nature. • Structural proteins like actin and myosin are contractile proteins and help in the movement of muscle fibre. Some proteins present in cell membrane, cytoplasm and nucleus of the cell act as receptors. • The transport proteins carry out the function of transporting specific substances either across the membrane or in the body fluids. • Storage proteins bind with specific substances and store them, e.g. iron is stored as ferritin. • Few proteins are constituents of respiratory pigments and occur in electron transport chain, e.g. Cytochromes, hemoglobin, myoglobin • Under certain conditions proteins can be catabolized to supply energy. -
Product Sheet Info
Master Clone List for NR-19279 ® Vibrio cholerae Gateway Clone Set, Recombinant in Escherichia coli, Plates 1-46 Catalog No. NR-19279 Table 1: Vibrio cholerae Gateway® Clones, Plate 1 (NR-19679) Clone ID Well ORF Locus ID Symbol Product Accession Position Length Number 174071 A02 367 VC2271 ribD riboflavin-specific deaminase NP_231902.1 174346 A03 336 VC1877 lpxK tetraacyldisaccharide 4`-kinase NP_231511.1 174354 A04 342 VC0953 holA DNA polymerase III, delta subunit NP_230600.1 174115 A05 388 VC2085 sucC succinyl-CoA synthase, beta subunit NP_231717.1 174310 A06 506 VC2400 murC UDP-N-acetylmuramate--alanine ligase NP_232030.1 174523 A07 132 VC0644 rbfA ribosome-binding factor A NP_230293.2 174632 A08 322 VC0681 ribF riboflavin kinase-FMN adenylyltransferase NP_230330.1 174930 A09 433 VC0720 phoR histidine protein kinase PhoR NP_230369.1 174953 A10 206 VC1178 conserved hypothetical protein NP_230823.1 174976 A11 213 VC2358 hypothetical protein NP_231988.1 174898 A12 369 VC0154 trmA tRNA (uracil-5-)-methyltransferase NP_229811.1 174059 B01 73 VC2098 hypothetical protein NP_231730.1 174075 B02 82 VC0561 rpsP ribosomal protein S16 NP_230212.1 174087 B03 378 VC1843 cydB-1 cytochrome d ubiquinol oxidase, subunit II NP_231477.1 174099 B04 383 VC1798 eha eha protein NP_231433.1 174294 B05 494 VC0763 GTP-binding protein NP_230412.1 174311 B06 314 VC2183 prsA ribose-phosphate pyrophosphokinase NP_231814.1 174603 B07 108 VC0675 thyA thymidylate synthase NP_230324.1 174474 B08 466 VC1297 asnS asparaginyl-tRNA synthetase NP_230942.2 174933 B09 198 -
Kin Discrimination Promotes Horizontal Gene Transfer Between Unrelated Strains in Bacillus Subtilis
ARTICLE https://doi.org/10.1038/s41467-021-23685-w OPEN Kin discrimination promotes horizontal gene transfer between unrelated strains in Bacillus subtilis ✉ Polonca Stefanic 1,5,6 , Katarina Belcijan1,5, Barbara Kraigher 1, Rok Kostanjšek1, Joseph Nesme2, Jonas Stenløkke Madsen2, Jasna Kovac 3, Søren Johannes Sørensen 2, Michiel Vos 4 & ✉ Ines Mandic-Mulec 1,6 Bacillus subtilis is a soil bacterium that is competent for natural transformation. Genetically 1234567890():,; distinct B. subtilis swarms form a boundary upon encounter, resulting in killing of one of the strains. This process is mediated by a fast-evolving kin discrimination (KD) system consisting of cellular attack and defence mechanisms. Here, we show that these swarm antagonisms promote transformation-mediated horizontal gene transfer between strains of low related- ness. Gene transfer between interacting non-kin strains is largely unidirectional, from killed cells of the donor strain to surviving cells of the recipient strain. It is associated with acti- vation of a stress response mediated by sigma factor SigW in the donor cells, and induction of competence in the recipient strain. More closely related strains, which in theory would experience more efficient recombination due to increased sequence homology, do not upregulate transformation upon encounter. This result indicates that social interactions can override mechanistic barriers to horizontal gene transfer. We hypothesize that KD-mediated competence in response to the encounter of distinct neighbouring strains could maximize the probability of efficient incorporation of novel alleles and genes that have proved to function in a genomically and ecologically similar context. 1 Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia. -
Distribution of Cytochromes in Bacteria: Relationship to General Physiology DAVID J
INTERNATIONAL JOURNAL of SYSTEMATIC BACTERIOLOGY Vol. 23, No. 4 October 1973, p. 459-467 Prin ted in U.S.A. Copyright 0 1973 International Association of Microbiological Societies Distribution of Cytochromes in Bacteria: Relationship to General Physiology DAVID J. MEYER' and COLIN W. JONES Department of Biochemistry, The University of Leicester, England A review of cytochrome occurrence in bacteria is presented which gives the taxonomic distribution of cytochromes and which relates this to general physiological characteristics. Data obtained from published research and recent experimental studies on a total of 169 species of bacteria suggested the existence of four major groupings: (i) the aerobic and facultatively anaerobic, heterotrophic gram positives (cytochrome pattern aa3.0. b.c); (ii) the aerobic and facultatively anaerobic, heterotrophic gram negatives (cytochrome pattern either al.d.o.b.c, a1.o.b.c or aa3.o.b.c); (iii) anaerobic and microaerophilic hetero- trophs (cytochrome pattern b sometimes with al /d/o), and (iv) the ch'emo- and photo-autotrophs (cytochrome pattern c plus czl /aa3/o/b). The absence or minor presence of cytochrome c in facultatively anaerobic and anaerobic heterotrophs was confirmed and was also observed in plant and animal pathogens. Cytochrome d was confined in occurrence mainly to a small taxonomic group of organisms characterized by a high degree of adaptability to unstable habitats. This group was considered for further subdivision dependent upon the conditions causing the production of cytochrome d. As part of an investigation into the occur- ilated on organisms in the three major bacterial orders: rence of more than one spectral type of (i) the taxonomic status of the species according to cytochrome oxidase in many bacteria, a survey Bergey 's Manual of Determinative Bacteriology (13) of published data was carried out. -
![[Thesis Title]](https://docslib.b-cdn.net/cover/6937/thesis-title-1296937.webp)
[Thesis Title]
RICE UNIVERSITY By Anna Guseva A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE Master of Science APPROVED, THESIS COMMITTEE Jonathon Silberg Jonathon Silberg (Jun 8, 2020 14:43 CDT) Joff Silberg George Bennett George Bennett (Jun 11, 2020 21:17 CDT) George Bennett Caroline Ajo-Franklin HOUSTON, TEXAS June 2020 ABSTRACT Flavodoxin protein electron carriers: bioinformatic analysis and interactions with sulfite reductases by Anna Guseva Flavodoxins (Flds) are oxidoreductases that distribute electrons to different metabolic pathways through interactions with an array of partner proteins. The aim of my thesis is to understand Fld evolution, establish whether Flds are encoded within the same genomes as Fd-dependent sulfite reductases (SIRs), and demonstrate that a cellular assay can monitor Fld electron transfer (ET) to SIRs. Using bioinformatics, I identify numerous microbes whose genomes encode both Fld and SIR genes. Additionally, I show that Flds can support ET to SIR using a synthetic pathway where protein-mediated ET is monitored using the growth of an Escherichia coli auxotroph that depends upon Fld transferring electrons from a Fd:NADP+ reductase to SIR. My results represent the first evidence that Flds support ET to assimilatory SIRs. Additionally, they show how a synthetic ET pathway in cells can be leveraged to rapidly compare the ET efficiencies of different Flds. ii Acknowledgments While my advisor, Dr. Joff Silberg, is known for saying that PhD is not a sprint but a marathon, my accelerated Master’s program sometimes felt like a marathon that you run as if it were a sprint. Balancing my research with classes and other activities in order to complete this thesis would not be possible without the support of many mentors, members of the lab, friends, and family. -
Formalizing Common Sense Reasoning for Scalable Inconsistency-Robust Information Integration Using Direct Logictm Reasoning and the Actor Model
Formalizing common sense reasoning for scalable inconsistency-robust information integration using Direct LogicTM Reasoning and the Actor Model Carl Hewitt. http://carlhewitt.info This paper is dedicated to Alonzo Church, Stanisław Jaśkowski, John McCarthy and Ludwig Wittgenstein. ABSTRACT People use common sense in their interactions with large software systems. This common sense needs to be formalized so that it can be used by computer systems. Unfortunately, previous formalizations have been inadequate. For example, because contemporary large software systems are pervasively inconsistent, it is not safe to reason about them using classical logic. Our goal is to develop a standard foundation for reasoning in large-scale Internet applications (including sense making for natural language) by addressing the following issues: inconsistency robustness, classical contrapositive inference bug, and direct argumentation. Inconsistency Robust Direct Logic is a minimal fix to Classical Logic without the rule of Classical Proof by Contradiction [i.e., (Ψ├ (¬))├¬Ψ], the addition of which transforms Inconsistency Robust Direct Logic into Classical Logic. Inconsistency Robust Direct Logic makes the following contributions over previous work: Direct Inference Direct Argumentation (argumentation directly expressed) Inconsistency-robust Natural Deduction that doesn’t require artifices such as indices (labels) on propositions or restrictions on reiteration Intuitive inferences hold including the following: . Propositional equivalences (except absorption) including Double Negation and De Morgan . -Elimination (Disjunctive Syllogism), i.e., ¬Φ, (ΦΨ)├T Ψ . Reasoning by disjunctive cases, i.e., (), (├T ), (├T Ω)├T Ω . Contrapositive for implication i.e., Ψ⇒ if and only if ¬⇒¬Ψ . Soundness, i.e., ├T ((├T) ⇒ ) . Inconsistency Robust Proof by Contradiction, i.e., ├T (Ψ⇒ (¬))⇒¬Ψ 1 A fundamental goal of Inconsistency Robust Direct Logic is to effectively reason about large amounts of pervasively inconsistent information using computer information systems.