DOCSLIB.ORG

Bacterial Communities Associated with Healthy and Diseased

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Bacterial Communities Associated with Healthy and Diseased Nova Southeastern University NSUWorks HCNSO Student Theses and Dissertations HCNSO Student Work 7-21-2017 Bacterial Communities Associated with Healthy and Diseased Acropora cervicornis (Staghorn Coral) Using High-Throughput Sequencing Charles Walton Nova Southeastern University, [email protected] Follow this and additional works at: https://nsuworks.nova.edu/occ_stuetd Part of the Animal Diseases Commons, Environmental Microbiology and Microbial Ecology Commons, Marine Biology Commons, Oceanography and Atmospheric Sciences and Meteorology Commons, and the Other Genetics and Genomics Commons Share Feedback About This Item NSUWorks Citation Charles Walton. 2017. Bacterial Communities Associated with Healthy and Diseased Acropora cervicornis (Staghorn Coral) Using High- Throughput Sequencing. Master's thesis. Nova Southeastern University. Retrieved from NSUWorks, . (449) https://nsuworks.nova.edu/occ_stuetd/449. This Thesis is brought to you by the HCNSO Student Work at NSUWorks. It has been accepted for inclusion in HCNSO Student Theses and Dissertations by an authorized administrator of NSUWorks. For more information, please contact [email protected]. HALMOS COLLEGE OF NATURAL SCIENCES AND OCEANOGRAPHY BACTERIAL COMMUNITIES ASSOCIATED WITH HEALTHY AND DISEASED ACROPORA CERVICORNIS (STAGHORN CORAL) USING HIGH-THROUGHPUT SEQUENCING BY CHARLES J. WALTON SUBMITTED TO THE FACULTY OF NOVA SOUTHEASTERN UNIVERSITY OCEANOGRAPHIC CENTER IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE WITH A SPECIALTY IN: MARINE BIOLOGY AND COASTAL ZONE MANAGEMENT NOVA SOUTHEASTERN UNIVERSITY JULY 21, 2017 Thesis of CHARLES J. WALTON Submitted in Partial Fulfillment of the Requirements for the Degree of Masters of Science: Marine Biology and Coastal Zone Management Nova Southeastern University Halmos College of Natural Sciences and Oceanography July 2017 Approved: Thesis Committee Major Professor :______________________________ David S. Gilliam, Ph.D. Committee Member :___________________________ Jose V. Lopez, Ph.D. Committee Member :___________________________ Aurelien Tartar, Ph.D. TABLE OF CONTENTS Acknowledgements ................................................................................................................. II Abstract ..................................................................................................................................... III List of Figures ............................................................................................................................ V List of Tables ........................................................................................................................... VII List of Appendix Figures .................................................................................................... VIII List of Appendix Tables ......................................................................................................... IX Introduction ............................................................................................................................... 1 Methods ....................................................................................................................................... 7 Sample Collection ............................................................................................................................... 7 DNA Extraction .................................................................................................................................... 8 16S rRNA Gene Amplification and Sequencing ........................................................................ 8 Quality Checking and Taxonomic Assignments ....................................................................... 9 Microbial Community Statistical Analyses ............................................................................. 12 Community Diversity (Alpha Diversity) ............................................................................................ 12 Community Composition (Beta Diversity) ....................................................................................... 13 Taxonomic Differential Abundance ..................................................................................................... 15 Results ........................................................................................................................................ 17 Microbial Community Diversity (Alpha diversity) .............................................................. 17 Microbial Community Composition (Beta diversity) .......................................................... 19 All Sample Types ......................................................................................................................................... 19 Tissue ............................................................................................................................................................... 25 Taxonomic Differential Abundance .......................................................................................... 31 Discussion ................................................................................................................................. 46 Conclusions .............................................................................................................................. 54 Citations ..................................................................................................................................... 56 Appendix: Figures .................................................................................................................. 78 Appendix: Tables .................................................................................................................... 85 I Acknowledgements Thank you to my advisor Dr. David S. Gilliam for the opportunity to work in the Coral Reef Restoration and Monitoring lab and for having the confidence in my abilities to take on a project beyond the scope of the laboratory. Additionally, thank you Dave for the all of the excellent field and travel opportunities that allowed me to experience great places and meet many wonderful people. Thank you to Dr. Jose V. Lopez for his guidance and allowing me to use his laboratory for my research. I also thank Dr. Aurelien Tarter for his assistance in the project development and excellent and insightful comments. Thank you to the Nova Southeastern University President’s Faculty Research and Development Grant for providing funding for this research. Thank you to the members of the CRRAM lab past and present for their assistance with the fieldwork. Thank you to members of the Microbiology and Genetics laboratory for their assistance during my lab work and accepting me into their lab. A special thank you to Drs. Andia Chaves-Fonnegra and Cole Easson for their long chats and guidance throughout my research and their excellent comments. A huge thank you to my wife Heather for her patience, understanding, and support throughout this experience. Finally, thank you to my family for their never ending support. II Abstract Coral diseases were first noted in the 1960s and 1970s and have had major impacts globally on coral reef community structures. In the Caribbean, a major outbreak of white band disease has been considered responsible for the drastic decline of Caribbean Acroporids since the 1970s. In addition to white band disease, another more recently described condition known as rapid tissue loss (RTL) has had major impacts on Acropora cervicornis populations, specifically offshore Broward County Southeast Florida. While these diseases have contributed to the population decline, determining their etiologies has been elusive. Coral diseases have been characterized by shifts in their microbial counterparts within many levels of the coral host. While some coral diseases have had specific pathogens identified, research has not been able to determine pathogens for most. Evidence points toward bacterial causes for many diseases, but due to the complexity of the coral holobiont and the interaction with the environment, elucidating the causes has proven difficult. Many studies have examined the microbiomes of specific diseases and determined some potential pathogens or at least taxa playing important roles in the disease, although none have looked at RTL. Recognizing the local affect of RTL on A. cervicornis, this study set out to gain a baseline understanding of the healthy and RTL affected microbiome of A. cervicornis. 16S rRNA gene sequencing was used to examine the microbiome of completely healthy colonies, healthy regions of diseased colonies, and the disease margin of diseased colonies. Analysis of four microbial diversity metrics revealed marked increases in diversity with respect to declining health states. Additionally, community dissimilarity analysis and analysis of differentially abundant taxa exhibited distinct microbial community structures due to coral health. Several highly abundant (Rickettsiales, Rhodobacteraceae) and a few low abundance (Bdellovibrionales) taxa were identified as primary drivers of the differences. Additionally, Piscirickettsiaceae, a known fish pathogen, was consistently associated with RTL and warrants further investigation. All of the taxa identified with in RTL have been associated with other Acroporid and non- Acroporid diseases throughout the Caribbean and the rest of the world. The consistent III association of similar taxa for coral
Load more

Recommended publications
  • A Quick Guide to Southeast Florida's Coral Reefs
    A Quick Guide to Southeast Florida’s Coral Reefs DAVID GILLIAM NATIONAL CORAL REEF INSTITUTE NOVA SOUTHEASTERN UNIVERSITY Spring 2013 Prepared by the Land-based Sources of Pollution Technical Advisory Committee (TAC) of the Southeast Florida Coral Reef Initiative (SEFCRI) BRIAN WALKER NATIONAL CORAL REEF INSTITUTE, NOVA SOUTHEASTERN Southeast Florida’s coral-rich communities are more valuable than UNIVERSITY the Spanish treasures that sank nearby. Like the lost treasures, these amazing reefs lie just a few hundred yards off the shores of Martin, Palm Beach, Broward and Miami-Dade Counties where more than one-third of Florida’s 19 million residents live. Fishing, diving, and boating help attract millions of visitors to southeast Florida each year (30 million in 2008/2009). Reef-related expen- ditures generate $5.7 billion annually in income and sales, and support more than 61,000 local jobs. Such immense recreational activity, coupled with the pressures of coastal development, inland agriculture, and robust cruise and commercial shipping industries, threaten the very survival of our reefs. With your help, reefs will be protected from local stresses and future generations will be able to enjoy their beauty and economic benefits. Coral reefs are highly diverse and productive, yet surprisingly fragile, ecosystems. They are built by living creatures that require clean, clear seawater to settle, mature and reproduce. Reefs provide safe havens for spectacular forms of marine life. Unfortunately, reefs are vulnerable to impacts on scales ranging from local and regional to global. Global threats to reefs have increased along with expanding ART SEITZ human populations and industrialization. Now, warming seawater temperatures and changing ocean chemistry from carbon dioxide emitted by the burning of fossil fuels and deforestation are also starting to imperil corals.
    [Show full text]
  • Metagenomics and Metatranscriptomics of the Leaf-And Root-Associated Microbiomes of Zostera Marina and Zostera Japonica
    1 Metagenomics and metatranscriptomics of the leaf- and root-associated microbiomes of Zostera marina and Zostera japonica by John Michael Adrian Wojahn A THESIS submitted to Oregon State University Honors College in partial fulfillment of the requirements for the degree of Honors Baccalaureate of Science in Microbiology and Biology (Honors BS) Presented May 10, 2016 Commencement June 2016 2 3 AN ABSTRACT OF THE THESIS OF John M. A. Wojahn for the degree of Honors Baccalaureate of Science in Microbiology and Biology presented on May 10, 2016. Title: Metagenomics and Metatranscriptomics of the leaf- and root-associated microbiomes of Zostera marina and Zostera japonica . Abstract approved: _____________________________________________ Byron C. Crump A great deal of research has been focused on the microbiomes of terrestrial angiosperms (flowering plants), but much less research has been performed on the microbiomes of aquatic angiosperms (Turner et al. 2013). Eelgrass beds are extremely productive ecosystems that provide habitat for many marine organisms, such as fish, shelfish, crabs, and algae (Smith et al. 1988). Eelgrass beds contribute to storm surge damping (Spalding et al. 2009), nutrient cycling (Smith et al. 1988), and water clarification (Orth et al. 2006). We examined the metagenomics and metatranscriptomics of the leaf- and root- associated microbiomes of Zostera marina and Zostera japonica. In our study, the phylogenetic composition of plant-associated bacterial communities was not significantly different between plant species for leaf communities (ANOSIM P<0.199) and for root communities (ANOSIM P<0.091). However, leaf-, root-, and water column associated bacterial communities were significantly different from one another (ANOSIM, P<0.001).
    [Show full text]
  • Methylamine As a Nitrogen Source for Microorganisms from a Coastal Marine
    Methylamine as a Nitrogen Source for Microorganisms from a Coastal Marine Environment Martin Tauberta,b, Carolina Grobb, Alexandra M. Howatb, Oliver J. Burnsc, Jennifer Pratscherb, Nico Jehmlichd, Martin von Bergend,e,f, Hans H. Richnowg, Yin Chenh,1, J. Colin Murrellb,1 aAquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany bSchool of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK cSchool of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK dDepartment of Molecular Systems Biology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany eInstitute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Brüderstraße 32, 04103 Leipzig, Germany fDepartment of Chemistry and Bioscience, University of Aalborg, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark. gDepartment of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research – UFZ, Permoserstrasse 15, 04318 Leipzig, Germany hSchool of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK 1To whom correspondence should be addressed. J. Colin Murrell, Phone: +44 (0)1603 59 2959, Email: [email protected], and Yin Chen, Phone: +44 (0)24 76528976, Email: [email protected] Keywords: marine methylotrophs, 15N stable isotope probing, methylamine, metagenomics, metaproteomics Classification: BIOLOGICAL SCIENCES/Microbiology Short title: Methylamine as a Nitrogen Source for Marine Microbes 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: 10.1111/1462-2920.13709 This article is protected by copyright.
    [Show full text]
  • Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz
    Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 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. THÈSE Pour l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr.
    [Show full text]
  • The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro
    FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities.
    [Show full text]
  • Distinct Bacterial Communities Associated with the Coral Model Aiptasia in Aposymbiotic and Symbiotic States with Symbiodinium
    ORIGINAL RESEARCH published: 18 November 2016 doi: 10.3389/fmars.2016.00234 Distinct Bacterial Communities Associated with the Coral Model Aiptasia in Aposymbiotic and Symbiotic States with Symbiodinium Till Röthig †, Rúben M. Costa †, Fabia Simona, Sebastian Baumgarten, Ana F. Torres, Anand Radhakrishnan, Manuel Aranda and Christian R. Voolstra * Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia Coral reefs are in decline. The basic functional unit of coral reefs is the coral metaorganism or holobiont consisting of the cnidarian host animal, symbiotic algae of the genus Symbiodinium, and a specific consortium of bacteria (among others), but research is slow due to the difficulty of working with corals. Aiptasia has proven to be a tractable Edited by: model system to elucidate the intricacies of cnidarian-dinoflagellate symbioses, but Thomas Carl Bosch, characterization of the associated bacterial microbiome is required to provide a complete University of Kiel, Germany and integrated understanding of holobiont function. In this work, we characterize and Reviewed by: analyze the microbiome of aposymbiotic and symbiotic Aiptasia and show that bacterial Simon K. Davy, Victoria University of Wellington, associates are distinct in both conditions. We further show that key microbial associates New Zealand can be cultured without their cnidarian host. Our results suggest that bacteria play an Mathieu Pernice, University of Technology, Australia important role in the symbiosis of Aiptasia with Symbiodinium, a finding that underlines *Correspondence: the power of the Aiptasia model system where cnidarian hosts can be analyzed in Christian R. Voolstra aposymbiotic and symbiotic states.
    [Show full text]
  • RML Algol 60 Compiler Accepts the Full ASCII Character Set Described in the Manual
    I I I · lL' I I 1UU, Alsol 60 CP/M 5yst.. I I , I I '/ I I , ALGOL 60 VERSION 4.8C REI.!AS!- NOTE I I I I CP/M Vers1on·2 I I When used with CP/M version 2 the Algol Ifste. will accept disk drive Dames extending from A: to P: I I I ASSEMBLY CODE ROUTINES I I .'n1~ program CODE.ALG and CODE.ASe 1s an aid to users who wish ·to add I their own code routines to the runtime system. The program' produc:es an I output file which contains a reconstruction of the INPUT, OUTPUT, IOC and I ERROR tables described in the manual. 1111s file forms the basis of an I assembly code program to which users may edit in their routines... Pat:ts I not required may be removed as desired. The resulting program should I then be assembled and overlaid onto the runtime system" using DDT, the I resulti;lg code being SAVEd as a new runtime system. It 1s important that. I the CODE program be run using the version of the runtimesY$tem to. which I the code routines are to be linked else the tables produced DUly, be·\, I incompatible. - I I I I Another example program supplied. 1. QSORT. the sortiDI pro~edure~, I described in the manual. I I I I I I I I I I , I I I -. I I 'It I I I I I I I I I I I ttKL Aleol 60 C'/M Systea I LONG INTEGER ALGOL Arun-L 1s a version of the RML zao Algol system 1nwh1c:h real variables are represented, DOt in the normal mantissalexponent form but rather as 32 .bit 2 s complement integers.
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • Workplace Learning Connection Annual Report 2019-20
    2019 – 2020 ANNUAL REPORT SERVING SCHOOLS, STUDENTS, EMPLOYERS, AND COMMUNITIES IN BENTON, CEDAR, IOWA, JOHNSON, JONES, LINN, AND WASHINGTON COUNTIES Connecting today’s students to tomorrow’s careers LINN COUNTY JONES COUNTY IOWA COUNTY CENTER REGIONAL CENTER REGIONAL CENTER 200 West St. 1770 Boyson Rd. 220 Welter Dr. Williamsburg, Iowa 52361 Hiawatha, Iowa 52233 Monticello, Iowa 52310 866-424-5669 319-398-1040 855-467-3800 KIRKWOOD REGIONAL CENTER WASHINGTON COUNTY AT THE UNIVERSITY OF IOWA REGIONAL CENTER 2301 Oakdale Blvd. 2192 Lexington Blvd. Coralville, Iowa 52241 Washington, Iowa 52353 319-887-3970 855-467-3900 BENTON COUNTY CENTER CEDAR COUNTY CENTER 111 W. 3rd St. 100 Alexander Dr., Suite 2 WORKPLACE LEARNING Vinton, Iowa 52349 Tipton, Iowa 52772 CONNECTION 866-424-5669 855-467-3900 2019 – 2020 AT A GLANCE Thank you to all our contributors, supporters, and volunteers! Workplace Learning Connection uses a diverse funding model that allows all partners to sustain their participation in an equitable manner. Whether a partners’ interest are student career development, future workforce development, or regional economic development, all funds provide age-appropriate career awareness and exploration services matching the mission of WLC and our partners. Funding the Connections… 2019 – 2020 Revenue Sources Kirkwood Community College (General Fund) $50,000 7% State and Federal Grants (Kirkwood: Perkins, WTED, IIG) $401,324 54% Grant Wood Area Education Agency $40,000 5% K through 12 School Districts Fees for Services $169,142 23% Contributions,
    [Show full text]
  • Think Complexity: Exploring Complexity Science in Python
    Think Complexity Version 2.6.2 Think Complexity Version 2.6.2 Allen B. Downey Green Tea Press Needham, Massachusetts Copyright © 2016 Allen B. Downey. Green Tea Press 9 Washburn Ave Needham MA 02492 Permission is granted to copy, distribute, transmit and adapt this work under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License: https://thinkcomplex.com/license. If you are interested in distributing a commercial version of this work, please contact the author. The LATEX source for this book is available from https://github.com/AllenDowney/ThinkComplexity2 iv Contents Preface xi 0.1 Who is this book for?...................... xii 0.2 Changes from the first edition................. xiii 0.3 Using the code.......................... xiii 1 Complexity Science1 1.1 The changing criteria of science................3 1.2 The axes of scientific models..................4 1.3 Different models for different purposes............6 1.4 Complexity engineering.....................7 1.5 Complexity thinking......................8 2 Graphs 11 2.1 What is a graph?........................ 11 2.2 NetworkX............................ 13 2.3 Random graphs......................... 16 2.4 Generating graphs........................ 17 2.5 Connected graphs........................ 18 2.6 Generating ER graphs..................... 20 2.7 Probability of connectivity................... 22 vi CONTENTS 2.8 Analysis of graph algorithms.................. 24 2.9 Exercises............................. 25 3 Small World Graphs 27 3.1 Stanley Milgram......................... 27 3.2 Watts and Strogatz....................... 28 3.3 Ring lattice........................... 30 3.4 WS graphs............................ 32 3.5 Clustering............................ 33 3.6 Shortest path lengths...................... 35 3.7 The WS experiment....................... 36 3.8 What kind of explanation is that?............... 38 3.9 Breadth-First Search.....................
    [Show full text]
  • Coral 66 Language Reference Makrjal
    CORAL 66 LANGUAGE REFERENCE MAKRJAL The Centre for Computing History Nl www.CompuUngHistofy.ofg.uk \/ k > MICRO FOCUS CORAL 66 LANGUAGE REFERENCE MANUAL Version 3 Micro Focus Ltd. Issue 2 March 1982 Not to be copied without the consent of Micro Focus Ltd. This language definition reproduces material from the British Standard BS5905 which is hereby acknowledged as a source. / \ / N Micro Focus Ltd. 58,Acacia Rood, St. Johns Wbod, MICRO FOCUS London NW8 6AG Telephones: 017228843/4/5/6/7 Telex: 28536 MICROFG CX)PYRI(fflT 1981, 1982 by Micro Focus Ltd. ii CORAL 66 LANGUAGE REFERENCE MANUAL AMENDMENT RECORD AMENDMENT DATED INSERTED BY SIGNATURE DATE NUMBER iii PREFACE This manual defines the programming language CORAL 66 as implemented in Version 3 of the CORAL compilers known as RCC80 and RCC86. Now that British Standard BS5905 has become the main source for CORAL implementation its structure and style have been adopted. Con5)ared to previous version's of the RCC compilers. Version 3 incorporates 'TABLE' and 'OVERLAY', and allows additional forms of Real numbers in line with the British Standard. Coiiq}iler error reporting has been .modified slightly - in particular all error messages now have identifying numbers and are listed in appendices to the operating manuals. Micro Focus has now assumed direct responsibility for production of all RCC CORAL manuals and believes that this will offer users a better service than has been possible in the past. iv AUDIENCE This manual is intended as a description of CORAL 66 for reference and assumes familiarity with use of the language.
    [Show full text]
  • Stable-Isotope Probing Implicates Methylophaga Spp and Novel Gammaproteobacteria in Marine Methanol and Methylamine Metabolism
    The ISME Journal (2007) 1, 480–491 & 2007 International Society for Microbial Ecology All rights reserved 1751-7362/07 $30.00 www.nature.com/ismej ORIGINAL ARTICLE Stable-isotope probing implicates Methylophaga spp and novel Gammaproteobacteria in marine methanol and methylamine metabolism Josh D Neufeld1, Hendrik Scha¨fer, Michael J Cox2, Rich Boden, Ian R McDonald3 and J Colin Murrell Department of Biological Sciences, University of Warwick, Coventry, UK The metabolism of one-carbon (C1) compounds in the marine environment affects global warming, seawater ecology and atmospheric chemistry. Despite their global significance, marine micro- organisms that consume C1 compounds in situ remain poorly characterized. Stable-isotope probing (SIP) is an ideal tool for linking the function and phylogeny of methylotrophic organisms by the metabolism and incorporation of stable-isotope-labelled substrates into nucleic acids. By combining DNA-SIP and time-series sampling, we characterized the organisms involved in the assimilation of methanol and methylamine in coastal sea water (Plymouth, UK). Labelled nucleic acids were analysed by denaturing gradient gel electrophoresis (DGGE) and clone libraries of 16S rRNA genes. In addition, we characterized the functional gene complement of labelled nucleic acids with an improved primer set targeting methanol dehydrogenase (mxaF) and newly designed primers for methylamine dehydrogenase (mauA). Predominant DGGE phylotypes, 16S rRNA, methanol and methylamine dehydrogenase gene sequences, and cultured isolates all implicated Methylophaga spp, moderately halophilic marine methylotrophs, in the consumption of both methanol and methylamine. Additionally, an mxaF sequence obtained from DNA extracted from sea water clustered with those detected in 13C-DNA, suggesting a predominance of Methylophaga spp among marine methylotrophs.
    [Show full text]