Engineering the Substrate Specificity of Galactose Oxidase
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Itraq-Based Quantitative Proteomics Analysis Reveals the Mechanism Underlying the Weakening of Carbon Metabolism in Chlorotic Tea Leaves
Article iTRAQ-Based Quantitative Proteomics Analysis Reveals the Mechanism Underlying the Weakening of Carbon Metabolism in Chlorotic Tea Leaves Fang Dong 1,2, Yuanzhi Shi 1,2, Meiya Liu 1,2, Kai Fan 1,2, Qunfeng Zhang 1,2,* and Jianyun Ruan 1,2 1 Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; [email protected] (F.D.); [email protected] (Y.S.); [email protected] (M.L.); [email protected] (K.F.); [email protected] (J.R.) 2 Key Laboratory for Plant Biology and Resource Application of Tea, the Ministry of Agriculture, Hangzhou 310008, China * Correspondence: [email protected]; Tel.: +86-571-8527-0665 Received: 7 November 2018; Accepted: 5 December 2018; Published: 7 December 2018 Abstract: To uncover mechanism of highly weakened carbon metabolism in chlorotic tea (Camellia sinensis) plants, iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic analyses were employed to study the differences in protein expression profiles in chlorophyll-deficient and normal green leaves in the tea plant cultivar “Huangjinya”. A total of 2110 proteins were identified in “Huangjinya”, and 173 proteins showed differential accumulations between the chlorotic and normal green leaves. Of these, 19 proteins were correlated with RNA expression levels, based on integrated analyses of the transcriptome and proteome. Moreover, the results of our analysis of differentially expressed proteins suggested that primary carbon metabolism (i.e., carbohydrate synthesis and transport) was inhibited in chlorotic tea leaves. The differentially expressed genes and proteins combined with photosynthetic phenotypic data indicated that 4-coumarate-CoA ligase (4CL) showed a major effect on repressing flavonoid metabolism, and abnormal developmental chloroplast inhibited the accumulation of chlorophyll and flavonoids because few carbon skeletons were provided as a result of a weakened primary carbon metabolism. -
Generated by SRI International Pathway Tools Version 25.0, Authors S
Authors: Pallavi Subhraveti Ron Caspi Quang Ong Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000725805Cyc: Streptomyces xanthophaeus Cellular Overview Connections between pathways are omitted for legibility. -
( 12 ) United States Patent
US010195209B2 (12 ) United States Patent ( 10 ) Patent No. : US 10 , 195 ,209 B2 Gish et al. (45 ) Date of Patent: * Feb . 5 , 2019 (54 ) ANTI- HULRRC15 ANTIBODY DRUG 4 ,634 ,665 A 1 / 1987 Axel 4 ,716 , 111 A 12 / 1987 Osband CONJUGATES AND METHODS FOR THEIR 4 ,737 , 456 A 4 / 1988 Weng USE 4 , 816 ,397 A 3 / 1989 Boss 4 , 816 ,457 A 3 / 1989 Baldwin (71 ) Applicants :AbbVie Inc. , North Chicago , IL (US ) ; 4 , 968 ,615 A 11 / 1990 Koszinowski AbbVie Biotherapeutics Inc. , 5 , 168 , 062 A 12 / 1992 Stinski 5 , 179 ,017 A 1 / 1993 Axel Redwood City , CA (US ) 5 , 225 , 539 A 7 / 1993 Winter 5 , 413 , 923 A 5 / 1995 Kucherlapati ( 72 ) Inventors : Kurt C . Gish , Piedmont, CA (US ) ; 5 ,530 , 101 A 6 /1996 Queen Jonathan A . Hickson , Lake Villa , IL 5 , 545 , 806 A 8 / 1996 Lonberg (US ) ; Susan Elizabeth Morgan - Lappe , 5 , 565 ,332 A 10 / 1996 Hoogenboom Riverwoods, IL (US ) ; James W . 5 , 569 , 825 A 10 / 1996 Lonberg 5 ,585 ,089 A 12 / 1996 Queen Purcell, San Francisco , CA (US ) 5 ,625 , 126 A 4 / 1997 Lonberg 5 ,633 , 425 A 5 / 1997 Lonberg ( 73 ) Assignees: AbbVie Inc. , North Chicago , IL (US ) ; 5 ,658 , 570 A 8 / 1997 Newman AbbVie Biotherapeutics Inc . , 5 ,661 ,016 A 8 / 1997 Lonberg Redwood City , CA (US ) 5 ,681 , 722 A 10 / 1997 Newman 5 ,693 , 761 A 12 / 1997 Queen 5 ,693 , 762 A 12 / 1997 Queen ( * ) Notice : Subject to any disclaimer, the term of this 5 ,693 , 780 A 12 / 1997 Newman patent is extended or adjusted under 35 5 , 807 ,715 A 9 / 1998 Morrison U . -
A Survey of Monte Carlo Tree Search Methods
IEEE TRANSACTIONS ON COMPUTATIONAL INTELLIGENCE AND AI IN GAMES, VOL. 4, NO. 1, MARCH 2012 1 A Survey of Monte Carlo Tree Search Methods Cameron Browne, Member, IEEE, Edward Powley, Member, IEEE, Daniel Whitehouse, Member, IEEE, Simon Lucas, Senior Member, IEEE, Peter I. Cowling, Member, IEEE, Philipp Rohlfshagen, Stephen Tavener, Diego Perez, Spyridon Samothrakis and Simon Colton Abstract—Monte Carlo Tree Search (MCTS) is a recently proposed search method that combines the precision of tree search with the generality of random sampling. It has received considerable interest due to its spectacular success in the difficult problem of computer Go, but has also proved beneficial in a range of other domains. This paper is a survey of the literature to date, intended to provide a snapshot of the state of the art after the first five years of MCTS research. We outline the core algorithm’s derivation, impart some structure on the many variations and enhancements that have been proposed, and summarise the results from the key game and non-game domains to which MCTS methods have been applied. A number of open research questions indicate that the field is ripe for future work. Index Terms—Monte Carlo Tree Search (MCTS), Upper Confidence Bounds (UCB), Upper Confidence Bounds for Trees (UCT), Bandit-based methods, Artificial Intelligence (AI), Game search, Computer Go. F 1 INTRODUCTION ONTE Carlo Tree Search (MCTS) is a method for M finding optimal decisions in a given domain by taking random samples in the decision space and build- ing a search tree according to the results. It has already had a profound impact on Artificial Intelligence (AI) approaches for domains that can be represented as trees of sequential decisions, particularly games and planning problems. -
WO 2012/170711 Al 13 December 2012 (13.12.2012) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2012/170711 Al 13 December 2012 (13.12.2012) P O P C T (51) International Patent Classification: (72) Inventors; and G01N33/5 74 (2006.01) (75) Inventors/Applicants (for US only): PAWLOWSKI, Traci [US/US]; 2014 N Milkweed Loop, Phoenix, AZ (21) International Application Number: 85037 (US). YEATTS, Kimberly [US/US]; 109 E. Pierce PCT/US2012/041387 Street, Tempe, AZ 85281 (US). AKHAVAN, Ray (22) International Filing Date: [US/US]; 5804 Malvern Hill Ct, Haymarket, VA 201 69 7 June 2012 (07.06.2012) (US). (25) Filing Language: English (74) Agent: AKHAVAN, Ramin; Caris Science, Inc., 6655 N. MacArthur Blvd., Irving, TX 75039 (US). (26) Publication Language: English (81) Designated States (unless otherwise indicated, for every (30) Priority Data: kind of national protection available): AE, AG, AL, AM, 61/494,196 7 June 201 1 (07.06.201 1) AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, 61/494,355 7 June 201 1 (07.06.201 1) CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, 61/507,989 14 July 201 1 (14.07.201 1) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, (71) Applicant (for all designated States except US): CARIS HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, LIFE SCIENCES LUXEMBOURG HOLDINGS, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, S.A.R.L [LU/LU]; Rue De Maraichers, L2124 Luxem MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, bourg, Grand-Duche De Luxembourg (LU). -
WO 2012/174282 A2 20 December 2012 (20.12.2012) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2012/174282 A2 20 December 2012 (20.12.2012) P O P C T (51) International Patent Classification: David [US/US]; 13539 N . 95th Way, Scottsdale, AZ C12Q 1/68 (2006.01) 85260 (US). (21) International Application Number: (74) Agent: AKHAVAN, Ramin; Caris Science, Inc., 6655 N . PCT/US20 12/0425 19 Macarthur Blvd., Irving, TX 75039 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 14 June 2012 (14.06.2012) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, English (25) Filing Language: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, Publication Language: English DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, (30) Priority Data: KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, 61/497,895 16 June 201 1 (16.06.201 1) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 61/499,138 20 June 201 1 (20.06.201 1) US OM, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SC, SD, 61/501,680 27 June 201 1 (27.06.201 1) u s SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, 61/506,019 8 July 201 1(08.07.201 1) u s TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. -
Elegance in Game Design
IEEE TRANSACTIONS ON COMPUTATIONAL INTELLIGENCE AND AI IN GAMES, VOL. 4, NO. 2, JUNE 2012 1 Elegance in Game Design Cameron Browne, Member, IEEE Abstract—This paper explores notions of elegance and shibui in combinatorial game design, and describes simple computational models for their estimation. Elegance is related to a game’s simplicity, clarity and efficiency, while shibui is a more complex concept from Japanese aesthetics that also incorporates depth. These provide new metrics for quantifying and categorising games that are largely independent of existing measurements such as tractability and quality. Relevant ideas from Western and Eastern aesthetics are introduced, the meaning of elegance and shibui in combinatorial games examined, and methods for estimating these values empirically derived from complexity analyses. Elegance and shibui scores are calculated for a number of example games, for comparison. Preliminary results indicate shibui estimates to be more reliable than elegance estimates. Index Terms—Game design, Computational aesthetics, Elegance, Shibui, Combinatorial game, Game complexity. F 1 INTRODUCTION 1.1 Domain PCG methods are increasingly being explored for the AMES have been a favourite testbed for Artificial generation of video game content [2], [4], and even entire G Intelligence (AI) researchers since the inception of games themselves [5], [6], [7]. These studies focus on the field. This has led from the initial formalisation of systems that can adapt or change rules as necessary, in methods for planning plausible moves, to the develop- order to maximise the player’s enjoyment and increase ment of competitive artificial players as search methods replay value. However, this paper focusses on the de- improve and domains are studied with greater vigour, sign of physical board games, specifically combinatorial to today’s computer players capable of beating human games [8], which are adversarial games that are: professionals and even solving a range of difficult board • zero-sum (concrete win/loss or draw results), games [1]. -
ENZYME BASED METHODS for LACTATE DETERMINATION Andriana Surleva1, Anna Marinova1, Vladislava Ivanova2, Robert Gradinaru3, Stela Georgieva1
Andriana Surleva,Journal Annaof Chemical Marinova, Technology Vladislava and Ivanova, Metallurgy, Robert 52, Gradinaru,3, 2017, 513-525 Stela Georgieva ENZYME BASED METHODS FOR LACTATE DETERMINATION Andriana Surleva1, Anna Marinova1, Vladislava Ivanova2, Robert Gradinaru3, Stela Georgieva1 1 Analytical Chemistry Department Received 07 November 2016 University of Chemical Technology and Metallurgy Accepted 22 January 2017 8 Kl. Ohridski, 1756 Sofia, Bulgaria E-mail: [email protected] 2Physics Department University of Chemical Technology and Metallurgy 8 Kl. Ohridski, 1756 Sofia, Bulgaria 3 Biochemistry group, Faculty of Chemistry “Alexandru Ioan Cuza” University of Iasi Iasi, Romania ABSTRACT Development of biosensors for lactate determination has gained an increased research interest because of their wide application in clinical analysis and control of fermentation processes in food industry. Lactate biosensors with enzyme modified modules are a perspective alternative to the conventional methods in clinical analysis for their fast response, applicability to continuous mode of analysis, low cost and easy automation. Food and beverage indus- try can also benefit of the advantages of lactate biosensors for monitoring of fermentation processes or control of foods labeled as “low lactate content”. The quantification of low lactate levels demands for sensitive and reliable analytical methods for lactate quantification in complex matrices. This review discusses the enzymatic methods for lactate determination. Recent advances in lactate biosensors -
Go Teaching Zero * Teaching with Stones * * Teaching with Words *
Go Teaching Zero * Teaching with stones * * Teaching with words * Content of this Guide Whatever our level, experience and interest for teaching, we all learn a bit from others and we all teach a bit from time to time, for example when we comment a few moves played in a game... Here, the general goal of this guide is to spread best practices of Go pedagogy to every player, and in particular to confirmed players who are interested in Go pedagogy, whatever it is for occasional teaching or as (amateur) teachers. Because it deals about teaching in general, this guide title contains « Zero » (referring to the Artificial Intelligence “AlphaGoZero” which has become very strong by “quantitative self- practice”) and is a follow up of the guide about Go initiation. Of course many principles of Go teaching apply both for the first steps as well as for advanced play. The first part deals with “silent pedagogy” - which is about playing to teach (not to win). This technique of teaching is nowadays rather unknown and documentation is spare, but is however a very natural and powerful way to transmit knowledge in an entertaining way. The second part deals with teaching techniques and presentation in a more formal way. 1/15 Table of Contents A. Teaching with stones - pedagogic play.............................................................................3 I. Teaching game purpose................................................................................................3 II. Keep game balance......................................................................................................3 -
Regulated T Cell Pre-Mrna Splicing As Genetic Marker of T Cell Suppression
Regulated T cell pre-mRNA splicing as genetic marker of T cell suppression by Boitumelo Mofolo Thesis presented for the degree of Master of Science (Bioinformatics) Institute of Infectious Disease and Molecular Medicine University of Cape Town (UCT) Supervisor: Assoc. Prof. Nicola Mulder August 2012 University of Cape Town The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgementTown of the source. The thesis is to be used for private study or non- commercial research purposes only. Cape Published by the University ofof Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University Declaration I, Boitumelo Mofolo, declare that all the work in this thesis, excluding that has been cited and referenced, is my own. Signature Signature Removed Boitumelo Mofolo University of Cape Town Copyright©2012 University of Cape Town All rights reserved 1 ABSTRACT T CELL NORMAL T CELL SUPPRESSION p110 p110 MV p85 PI3K AKT p85 PI3K PHOSPHORYLATION NO PHOSHORYLATION HIV cytoplasm HCMV LCK-011 PRMT5-006 SHIP145 SIP110 RV LCK-010 VCL-204 ATM-016 PRMT5-018 ATM-002 CALD1-008 LCK-006 MXI1-001 VCL-202 NRP1-201 MXI1-007 CALD1-004 nucleus Background: Measles is a highly contagious disease that mainly affects children and according to the World Health Organisation (WHO), was responsible for over 164000 deaths in 2008, despite the availability of a safe and cost-effective vaccine [56]. The Measles virus (MV) inactivates T- cells, rendering them dysfunctional, and results in virally induced immunosuppression which shares certain features with thatUniversity induced by HIV. -
Development Perspective of Bioelectrocatalysis-Based Biosensors
sensors Review Development Perspective of Bioelectrocatalysis-Based Biosensors , Taiki Adachi, Yuki Kitazumi, Osamu Shirai and Kenji Kano * y Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan; [email protected] (T.A.); [email protected] (Y.K.); [email protected] (O.S.) * Correspondence: [email protected] Present address: Center for Advanced Science and Innovation, Kyoto University, Gokasho, Uji, y Kyoto 611-0011, Japan. Received: 19 July 2020; Accepted: 25 August 2020; Published: 26 August 2020 Abstract: Bioelectrocatalysis provides the intrinsic catalytic functions of redox enzymes to nonspecific electrode reactions and is the most important and basic concept for electrochemical biosensors. This review starts by describing fundamental characteristics of bioelectrocatalytic reactions in mediated and direct electron transfer types from a theoretical viewpoint and summarizes amperometric biosensors based on multi-enzymatic cascades and for multianalyte detection. The review also introduces prospective aspects of two new concepts of biosensors: mass-transfer-controlled (pseudo)steady-state amperometry at microelectrodes with enhanced enzymatic activity without calibration curves and potentiometric coulometry at enzyme/mediator-immobilized biosensors for absolute determination. Keywords: current–potential curve; multi-enzymatic cascades; multianalyte detection; mass-transfer-controlled amperometric response; potentiometric coulometry 1. Introduction Electron transfer reactions such as photosynthesis, respiration and metabolisms play an important role in all living things. A huge variety of redox enzymes catalyze the oxidation and reduction of couples of two inherent substrates. Usually, the electrons are transferred between the two substrates through a cofactor(s) that is covalently or non-covalently bound to the redox enzymes. -
Enzyme-Based Amperometric Galactose Biosensors: a Review
Microchim Acta DOI 10.1007/s00604-017-2465-z REVIEW ARTICLE Enzyme-based amperometric galactose biosensors: a review Prosper Kanyong1,2 & Francis D. Krampa1,3 & Yaw Aniweh 1 & Gordon A. Awandare 1,3 Received: 26 May 2017 /Accepted: 14 August 2017 # The Author(s) 2017. This article is an open access publication Abstract This review (with 35 references) summarizes the Introduction various strategies used in biosensors for galactose, and their analytical performance. A brief comparison of the enzyme The quantitative determination of galactose is of great impor- immobilization methods employed and the analytical perfor- tance in clinical chemistry, food and fermentation industries. mance characteristics of a range of galactose biosensors are There are two general analytical methods for the analysis of first summarized in tabular form and then described in detail. galactose in real samples, namely, separation by liquid or gas Selected examples have been included to demonstrate the var- chromatography, and enzyme-based methods using galactose ious applications of these biosensors to real samples. oxidase (GalOx) or galactose dehydrogenase (GADH) in con- Following an introduction into the field that covers the signif- junction with spectrophotometric, polarimetric, and fluo- icance of sensing galactose in various fields, the review covers rometric detection of enzymatic products [1, 2]. Several com- biosensors based on the use of galactose oxidase, with a dis- mercial assay kits based on GADH have been developed. cussion of methods for their immobilization (via cross- However, these methods are usually cumbersome and expen- linking, adsorption, covalent bonding and entrapment). This sive, time-consuming and often require skilled personnel to is followed by a short section on biosensors based on the use operate them [1–3].