A First Approach to Individual-Based Modeling of the Bacterial Conjugation Dynamics
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ACM SIGACT News Distributed Computing Column 28
ACM SIGACT News Distributed Computing Column 28 Idit Keidar Dept. of Electrical Engineering, Technion Haifa, 32000, Israel [email protected] Sergio Rajsbaum, who edited this column for seven years and established it as a relevant and popular venue, is stepping down. This issue is my first step in the big shoes he vacated. I would like to take this opportunity to thank Sergio for providing us with seven years’ worth of interesting columns. In producing these columns, Sergio has enjoyed the support of the community at-large and obtained material from many authors, who greatly contributed to the column’s success. I hope to enjoy a similar level of support; I warmly welcome your feedback and suggestions for material to include in this column! The main two conferences in the area of principles of distributed computing, PODC and DISC, took place this summer. This issue is centered around these conferences, and more broadly, distributed computing research as reflected therein, ranging from reviews of this year’s instantiations, through influential papers in past instantiations, to examining PODC’s place within the realm of computer science. I begin with a short review of PODC’07, and highlight some “hot” trends that have taken root in PODC, as reflected in this year’s program. Some of the forthcoming columns will be dedicated to these up-and- coming research topics. This is followed by a review of this year’s DISC, by Edward (Eddie) Bortnikov. For some perspective on long-running trends in the field, I next include the announcement of this year’s Edsger W. -
A Study on Asynchronous Randomized Consensus Title Algorithms for Byzantine Fault Tolerant Replication
A Study on Asynchronous Randomized Consensus Title Algorithms for Byzantine Fault Tolerant Replication Author(s) 中村, 純哉 Citation Issue Date Text Version ETD URL https://doi.org/10.18910/34568 DOI 10.18910/34568 rights Note Osaka University Knowledge Archive : OUKA https://ir.library.osaka-u.ac.jp/ Osaka University A Study on Asynchronous Randomized Consensus Algorithms for Byzantine Fault Tolerant Replication Submitted to Graduate School of Information Science and Technology Osaka University January 2014 Junya NAKAMURA iii List of Major Publications Journal Papers 1. Junya Nakamura, Tadashi Araragi, Toshimitsu Masuzawa, and Shigeru Masuyama, \A method of parallelizing consensuses for accelerating byzantine fault tolerance," IEICE Trans- actions on Information and Systems, vol. E97-D, no. 1, 2014. (to appear). 2. Junya Nakamura, Tadashi Araragi, Shigeru Masuyama, and Toshimitsu Masuzawa, “Effi- cient randomized byzantine fault-tolerant replication based on special valued coin tossing," IEICE Transactions on Information and Systems, vol. E97-D, no. 2, 2014. (to appear). Conference Papers 3. Junya Nakamura, Tadashi Araragi, and Shigeru Masuyama, \Asynchronous byzantine request- set agreement algorithm for replication," in Proceedings of the 1st AAAC Annual Meeting, p. 35, 2008. 4. Junya Nakamura, Tadashi Araragi, and Shigeru Masuyama, \Acceleration of byzantine fault tolerance by parallelizing consensuses," in Proceedings of the 10th International Conference on Parallel and Distributed Computing, Applications and Technologies, PDCAT '09, pp. 80{ 87, Dec. 2009. Technical Reports 5. Junya Nakamura, Tadashi Araragi, and Shigeru Masuyama, \Byzantine agreement on the order of processing received requests is solvable deterministically in asynchronous systems," in IEICE Technical Report, vol. 106 of COMP2006-35, pp. 33{40, Oct. -
Auto-Stabilisation : Solution Elégante Pour Lutter Contre Les Fautes Sylvie
Auto-stabilisation : Solution Elégante pour Lutter contre Les Fautes Sylvie Delaët Rapport scientifique présenté en vue de l’obtention de l’Habilitation à Diriger les Recherches. Soutenu le 8 novembre 2013 devant le jury composé de : Alain Denise, Professeur, Université Paris Sud, France Shlomi Dolev, Professeur, Ben Gurion University of the Negev, Israël Pierre Fraigniaud, Directeur de recherche CNRS, France Ted Herman, Professeur, University of Iowa, Etats Unis d’Amérique Nicolas Thiéry, Professeur, l’Université Paris Sud, France Franck Petit, Professeur, Université Paris Pierre et Marie Curie, France Après avis des rapporteurs : Ted Herman, Professeur, University of Iowa, Etats Unis d’Amérique Rachid Guerraoui, Professeur, Ecole Polytechnique Fédérale de Lausanne, Suisse Franck Petit, Université Paris Pierre et Marie Curie, France ii Sommaire Remerciements iii 1 Ma vision de ce document 1 1.1 Organisation du document . .1 2 Un peu de cuisine(s) 3 2.1 L'auberge espagnole de l'algorithmique r´epartie. .4 2.2 Exemples de probl`emes`ar´esoudreet quelques solutions . .8 3 Comprendre le monde 15 3.1 Comprendre l'auto-stabilisation . 15 3.2 Comprendre l'algorithmique r´epartie . 30 3.3 Comprendre mes contributions . 34 4 Construire l'avenir 43 4.1 Perspectives d'am´eliorationdes techniques . 43 4.2 Perspective d'ouverture `ala diff´erence . 45 4.3 Perspective de diffusion plus large . 47 4.4 Perspective de l'ordinateur auto-stabilisant . 48 A Agrafage 51 A.1 Cerner les probl`emes . 51 A.2 D´emasquerles planqu´es . 59 A.3 Recenser les pr´esents . 67 A.4 Obtenir l'auto-stabilisation gratuitement . -
Comprehensive Analysis of Mobile Genetic Elements in the Gut Microbiome Reveals Phylum-Level Niche-Adaptive Gene Pools
bioRxiv preprint doi: https://doi.org/10.1101/214213; this version posted December 22, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Comprehensive analysis of mobile genetic elements in the gut microbiome 2 reveals phylum-level niche-adaptive gene pools 3 Xiaofang Jiang1,2,†, Andrew Brantley Hall2,3,†, Ramnik J. Xavier1,2,3,4, and Eric Alm1,2,5,* 4 1 Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, 5 Cambridge, MA 02139, USA 6 2 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA 7 3 Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard 8 Medical School, Boston, MA 02114, USA 9 4 Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General 10 Hospital and Harvard Medical School, Boston, MA 02114, USA 11 5 MIT Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 12 02142, USA 13 † Co-first Authors 14 * Corresponding Author bioRxiv preprint doi: https://doi.org/10.1101/214213; this version posted December 22, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 15 Abstract 16 Mobile genetic elements (MGEs) drive extensive horizontal transfer in the gut microbiome. This transfer 17 could benefit human health by conferring new metabolic capabilities to commensal microbes, or it could 18 threaten human health by spreading antibiotic resistance genes to pathogens. Despite their biological 19 importance and medical relevance, MGEs from the gut microbiome have not been systematically 20 characterized. -
Section 4. Guidance Document on Horizontal Gene Transfer Between Bacteria
306 - PART 2. DOCUMENTS ON MICRO-ORGANISMS Section 4. Guidance document on horizontal gene transfer between bacteria 1. Introduction Horizontal gene transfer (HGT) 1 refers to the stable transfer of genetic material from one organism to another without reproduction. The significance of horizontal gene transfer was first recognised when evidence was found for ‘infectious heredity’ of multiple antibiotic resistance to pathogens (Watanabe, 1963). The assumed importance of HGT has changed several times (Doolittle et al., 2003) but there is general agreement now that HGT is a major, if not the dominant, force in bacterial evolution. Massive gene exchanges in completely sequenced genomes were discovered by deviant composition, anomalous phylogenetic distribution, great similarity of genes from distantly related species, and incongruent phylogenetic trees (Ochman et al., 2000; Koonin et al., 2001; Jain et al., 2002; Doolittle et al., 2003; Kurland et al., 2003; Philippe and Douady, 2003). There is also much evidence now for HGT by mobile genetic elements (MGEs) being an ongoing process that plays a primary role in the ecological adaptation of prokaryotes. Well documented is the example of the dissemination of antibiotic resistance genes by HGT that allowed bacterial populations to rapidly adapt to a strong selective pressure by agronomically and medically used antibiotics (Tschäpe, 1994; Witte, 1998; Mazel and Davies, 1999). MGEs shape bacterial genomes, promote intra-species variability and distribute genes between distantly related bacterial genera. Horizontal gene transfer (HGT) between bacteria is driven by three major processes: transformation (the uptake of free DNA), transduction (gene transfer mediated by bacteriophages) and conjugation (gene transfer by means of plasmids or conjugative and integrated elements). -
The Obscure World of Integrative and Mobilizable Elements Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget
The obscure world of integrative and mobilizable elements Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget To cite this version: Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget. The obscure world of integrative and mobilizable elements: Highly widespread elements that pirate bacterial conjugative systems. Genes, MDPI, 2017, 8 (11), pp.337. 10.3390/genes8110337. hal- 01686871 HAL Id: hal-01686871 https://hal.archives-ouvertes.fr/hal-01686871 Submitted on 26 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License G C A T T A C G G C A T genes Review The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems Gérard Guédon *, Virginie Libante, Charles Coluzzi, Sophie Payot and Nathalie Leblond-Bourget * ID DynAMic, Université de Lorraine, INRA, 54506 Vandœuvre-lès-Nancy, France; [email protected] (V.L.); [email protected] (C.C.); [email protected] (S.P.) * Correspondence: [email protected] (G.G.); [email protected] (N.L.-B.); Tel.: +33-037-274-5142 (G.G.); +33-037-274-5146 (N.L.-B.) Received: 12 October 2017; Accepted: 15 November 2017; Published: 22 November 2017 Abstract: Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements. -
Population Protocols: Expressiveness, Succinctness and Automatic Verification
Fakultat¨ fur¨ Informatik Technische Universitat¨ Munchen¨ Population Protocols: Expressiveness, Succinctness and Automatic Verification. Stefan Jaax Vollst¨andigerAbdruck der von der Fakult¨atf¨urInformatik der Technischen Universit¨at M¨unchen zur Erlangung des akademischen Grades eines Doktor der Naturwissenschaften (Dr. rer. nat.) genehmigten Dissertation. Vorsitzender: Prof. Dr. Helmut Seidl Pr¨ufendeder Dissertation: 1. Prof. Dr. Francisco Javier Esparza Estaun 2. Prof. Rupak Majumdar, Ph.D., Technische Universit¨atKaiserslautern Die Dissertation wurde am 03.03.2020 bei der Technischen Universit¨atM¨unchen eingereicht und durch die Fakult¨atf¨urInformatik am 04.06.2020 angenommen. Abstract Population protocols (Angluin et al., PODC, 2004) are a model of distributed computa- tion in which identical, finite-state, passively mobile agents interact in pairs to achieve a common goal. In the basic model of population protocols, agents compute number predicates by reaching a stable consensus. It is well known that population protocols compute precisely the semilinear predicates, or, equivalently, the predicates definable in Presburger arithmetic, the first-order theory of the natural numbers equipped with addition and the standard linear order. This thesis investigates three fundamental questions of the theory of population pro- tocols: Space complexity, verification complexity, and expressiveness of reasonable ex- tensions. Space Complexity. We show that every quantifier-free Presburger predicate ' aug- mented with remainder predicates is computable by a population protocol with poly(j'j) states, where j'j denotes the size of ' in binary encoding. Further, the protocol can be constructed in polynomial time. This is a major improvement to the previously known construction, which requires 2poly(j'j) states. As a special case, we consider predicates of the form 'c(x) = x ≥ c, where c is a positive integer constant. -
Population Protocols Are Fast
Population Protocols Are Fast Adrian Kosowski1 and Przemysław Uznanski´ 2 1Inria Paris, France 2 ETH Zürich, Switzerland Abstract A population protocol describes a set of state change rules for a population of n indistinguish- able finite-state agents (automata), undergoing random pairwise interactions. Within this very basic framework, it is possible to resolve a number of fundamental tasks in distributed computing, includ- ing: leader election, aggregate and threshold functions on the population, such as majority compu- tation, and plurality consensus. For the first time, we show that solutions to all of these problems can be obtained quickly using finite-state protocols. For any input, the designed finite-state proto- cols converge under a fair random scheduler to an output which is correct with high probability in expected O(poly log n) parallel time. In the same setting, we also show protocols which always reach a valid solution, in expected parallel time O(nε), where the number of states of the interacting automata depends only on the choice of ε > 0. The stated time bounds hold for any semi-linear predicate computable in the population protocol framework. The key ingredient of our result is the decentralized design of a hierarchy of phase-clocks, which tick at different rates, with the rates of adjacent clocks separated by a factor of Θ(log n). The construction of this clock hierarchy relies on a new protocol composition technique, combined with an adapted analysis of a self-organizing process of oscillatory dynamics. This clock hierarchy is used to provide nested synchronization primitives, which allow us to view the population in a global manner and design protocols using a high-level imperative programming language with a (limited) capacity for loops and branching instructions. -
Of Lactococcus Garvieae
CORE Metadata, citation and similar papers at core.ac.uk Provided by PubMed Central Characterization of Plasmids in a Human Clinical Strain of Lactococcus garvieae Mo´ nica Aguado-Urda1., Alicia Gibello1*., M. Mar Blanco1, Guillermo H. Lo´ pez-Campos2,M. Teresa Cutuli1, Jose´ F. Ferna´ndez-Garayza´bal1,3 1 Faculty of Veterinary Sciences, Department of Animal Health, Complutense University, Madrid, Spain, 2 Bioinformatics and Public Health Department, Health Institute Carlos III, Madrid, Spain, 3 Animal Health Surveillance Center (VISAVET), Complutense University of Madrid, Spain Abstract The present work describes the molecular characterization of five circular plasmids found in the human clinical strain Lactococcus garvieae 21881. The plasmids were designated pGL1-pGL5, with molecular sizes of 4,536 bp, 4,572 bp, 12,948 bp, 14,006 bp and 68,798 bp, respectively. Based on detailed sequence analysis, some of these plasmids appear to be mosaics composed of DNA obtained by modular exchange between different species of lactic acid bacteria. Based on sequence data and the derived presence of certain genes and proteins, the plasmid pGL2 appears to replicate via a rolling- circle mechanism, while the other four plasmids appear to belong to the group of lactococcal theta-type replicons. The plasmids pGL1, pGL2 and pGL5 encode putative proteins related with bacteriocin synthesis and bacteriocin secretion and immunity. The plasmid pGL5 harbors genes (txn, orf5 and orf25) encoding proteins that could be considered putative virulence factors. The gene txn encodes a protein with an enzymatic domain corresponding to the family actin-ADP- ribosyltransferases toxins, which are known to play a key role in pathogenesis of a variety of bacterial pathogens. -
Biological Circuits with Small RNA Switches
Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Stealth regulation: biological circuits with small RNA switches Susan Gottesman Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA So you thinkyou finally understand the regulation of temporal RNAs (stRNAs) or microRNAs, and that these your favorite gene? The transcriptional regulators have RNAs are processed by some of the same protein cofac- been identified; the signaling cascades that regulate syn- tors as is RNAi, have put regulatory RNAs in the spot- thesis and activity of the regulators have been found. light in eukaryotes as well. Recent searches have con- Possibly you have found that the regulator is itself un- firmed that flies, worms, plants, and humans all harbor stable, and that instability is necessary for proper regu- significant numbers of small RNAs likely to play regu- lation. Time to lookfor a new project, or retire and rest latory roles. on your laurels? Not so fast—there’s more. It is rapidly Along with the rapid expansion in RNAs doing inter- becoming apparent that another whole level of regula- esting things, has come a proliferation of nomenclature. tion lurks, unsuspected, in both prokaryotic and eukary- Noncoding RNAs (ncRNA) has been used recently, as otic cells, hidden from our notice in part by the tran- the most general term (Storz 2002). Among the noncod- scription-based approaches that we usually use to study ing RNAs, the subclass of relatively small RNAs that gene regulation, and in part because these regulators are frequently act as regulators have been called stRNAs very small targets for mutagenesis and are not easily (small temporal RNAs, eukaryotes) and sRNAs (small found from genome sequences alone. -
Genetic Exchange in Bacteria
Systems Microbiology Monday Oct 16 - Ch 10 -Brock Genetic Exchange in Bacteria •• HomologousHomologous recombinationrecombination •• TransformationTransformation •• PlasmidsPlasmids andand conjugationconjugation •• TransposableTransposable elementselements •• TransductionTransduction (virus(virus mediatedmediated xchangexchange)) Gene exchange in bacteria • Transfer of DNA from one bacterium to another is a common means of gene dispersal. It has a big effect on bacterial evolution, and tremendous practical implications. For example, lateral transfer is responsible for the spread drug resistance determinants between bacterial species. • Three common mechanisms of lateral gene exchange : – Transformation (extracellular DNA uptake) – Conjugation (bacterial mating systems) – Transduction (viral mediated gene exchange) RecA mediated Homologous recombination Images removed due to copyright restrictions. See Figures 10-9 and 10-10 in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms.11th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291. Gene exchange in bacteriaTransformation The Griffith Experiment S Injection Dead mouse; • Discovered by Griffith in yields S1 cells 1928 during the course of his Live "smooth" (encapsulated) studies of virulence in type 1 pneumococci (S1) Streptococcus pneumoniae. Dead S Live mouse Heat-killed S1 • S=smooth colony Live mouse morphotype Live "rough" (unencapsulated) pneumococci (R1 or R2) derived by subculture from S1 or S2, respectively • R=rough colony Dead mouse; yields S cells morphotype R1 + Dead S + 1 Live R1 Killed S1 R2 + Dead S + Dead mouse; yields S1 cells Live R2 Killed S2 Figure by MIT OCW. Gene exchange mechanisms in bacteria Transformation The Griffith Experiment Injection Dead mouse; S yields S cells Avery, MacLeod, and McCarthy (1944) 1 fractionation studies led to conclusion that Live "smooth" (encapsulated) type 1 pneumococci (S ) transformation principle is DNA. -
ISBN # 1-60132-514-2; American Council on Science & Education / CSCE 2021
ISBN # 1-60132-514-2; American Council on Science & Education / CSCE 2021 CSCI 2021 BOOK of ABSTRACTS The 2021 World Congress in Computer Science, Computer Engineering, and Applied Computing CSCE 2021 https://www.american-cse.org/csce2021/ July 26-29, 2021 Luxor Hotel (MGM Property), 3900 Las Vegas Blvd. South, Las Vegas, 89109, USA Table of Contents Keynote Addresses .................................................................................................................... 2 Int'l Conf. on Applied Cognitive Computing (ACC) ...................................................................... 3 Int'l Conf. on Bioinformatics & Computational Biology (BIOCOMP) ............................................ 6 Int'l Conf. on Biomedical Engineering & Sciences (BIOENG) ................................................... 12 Int'l Conf. on Scientific Computing (CSC) .................................................................................. 14 SESSION: Military & Defense Modeling and Simulation ............................................................ 27 Int'l Conf. on e-Learning, e-Business, EIS & e-Government (EEE) ............................................ 28 SESSION: Agile IT Service Practices for the cloud ................................................................... 34 Int'l Conf. on Embedded Systems, CPS & Applications (ESCS) ................................................ 37 Int'l Conf. on Foundations of Computer Science (FCS) ............................................................. 39 Int'l Conf. on Frontiers