Information Processing in Cells and Tissues PDF
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Information Processing in Cells and Tissues Infonnation Processing in Cells and Tissues Edited by Mike Holcombe University ofS heffield Sheffield, United Kingdom and Ray Paton University ofL iverpool Liverpool, Umted Kingdom Springer Science+Business Media, LLC Llbrary of Congress Cataloging-in-Publication Data Information processing in cells and tissues ( edited by Mike Holcombe and Ray Paton. p. cm. Includes bibliographical references and index. ISBN 978-1-4613-7438-1 ISBN 978-1-4615-5345-8 (eBook) DOI 10.1007/978-1-4615-5345-8 1. Cell interaction--Congresses. 2. Cellular signal transduction -Congresses. 3. Information theory in biology--Congresses. 4. Second messengers (Biochemistry)--Congresses. 1. Holcombe, W. M. L. (William Michael Lloyd). 1944- II. Paton, Ray. OH604.2.152 1998 571.6--dc21 98-18265 CIP Proceedings ofthe International Workshop on Information Processing in Cells and Tissues, held September 1-4, 1997, in Sheffield, United Kingdom ISBN 978-1-4613-7438-1 © 1998 Springer Science+Business Media New York Origina1Iy published by Plenum Press, New York in 1998 Softcover reprint ofthe hardcover Ist edition http://www.plenum.com 1098765432 I AII rights reserved No part ofthis book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without written permis sion from the Publisher PREFACE The Second International Workshop on Information Processing in Cells and Tissues (IPCAT) was held in Sheffield from Ist to 4th ofSeptember, 1997. The meeting took place in Halifax Hall, a former steel baron's mansion located in Broomhill, a leafy suburb of Sheffield once described byJohn Betjeman as the "prettiest suburb in England". As with the First International IPCAT in 1995 the purpose ofthe workshop was to bring together a group ofscientistsworking in the general areaofmodelling cells and tissues. The resultwas a multidisciplinary event involving over 50 biologists, physicists, computer scientists and mathematiciansfrom Europe, Japan and the USA. A central theme underlying the workshop was the nature ofbiological information and the ways it is processed in cells a.nd tissues. The workshop sought to provide a forum to report research, discuss emerging topics and gain new insights into information processing systems. As a result many areas were considered including'enzyme and gene networks, second messenger systems and signal transduction, automata models, PDP models, cellular automata models, molecular computing, single neuron computation, information processing in developmental systems, information processing in neural and non-neural systems and new insightsinto non-linear aspects ofphysiological behaviour. This post-conference proceedingshas been organised into three sections. Thefirst two sectionsconsistofpapersand aselection ofpostersthat were presented during the three and a halfdays ofthe meeting. Section I deals with the topic ofsignalling and communication and covers anumberofsubjects ranging from gapjunctionsand calcium signalsto neurones, the pituitary and the heart. The emphasis ofsection 2 is computation and information. The range ofbiological systems covered here is quite wide including embryos, gene expression, immune system, enzymes, neurones and signalling. The organisation ofthefirst two sections has notbeen straightforward and there is considerable overlap in content. Such is the nature ofthis area ofresearch. However, it is hoped that the.incorporation ofsome structure will facilitate the readability ofthe whole. The final section contains abridged notes based on discussionsthat were held duringtheworkshop. A key motivation of the IPCAT workshops is to provide a common ground for dialogue and reporting research without emphasising one particular research constituency or wayofmodelling or singular issue in this area. IPCAT '97 sought to further the meaningful dialogue and exchange ofideas started at IPCAT '95. We hope this book will reflect some ofthevaluable work that isgoing on. Ourthanksto the programmereview committee: Guenter Albrecht-Buehler(CellBiology) - Northwestern University DennisBray(Zoology) -UniversityofCambridge DavidBrown (Neurobiology) -BabrahamInstitute, Cambridge Robin CalIaI'd (Immun610g~') - University ofLondon, London ChrisCannings (Statistics) -·Univ.ersity ofSheffield TeresaChay(Biological Sciences) - University ofPittsburgh v Michael Conrad (Computer Science) -Wayne StateUniversity, Detroit JohnEasterby(Biochemistry) -UniversityofLiverpool BardErmentrout(Mathematics) - UniversityofPittsburgh LeonGlass(Biological Sciences) -McGill University AlbertGoldbeter(NonlinearSystems) - UniversityLibre, Brussels Uwean derHeiden (Mathematics)- UniversityofWitten/Herdecke MikeHolcombe(ComputerScience) - UniversityofSheffield FelixHong(physiology)- Wayne StateUniversity, Detroit TsuguchikaKaminuma(Biosciences)-NIHS, Tokyo GeorgeKampis (PhilosophyofScience)-Budapest DouglasKell (Biochemistry) -UniversityofWales, Aberystwyth RolfKoetter(Neurobiology)-UniversityofDusseldorf GarethLeng(physiology) -UniversityofEdinburgh PhilipMaini (Mathematics)- UniversityofOxford PedfOMarijuan(Electronics/Biolnfonnatics) - UniversityofZaragoza Koichiro Matsuno (BioEngineering) - UniversityofNagaoka Hiroshi Okamoto(Neurobiology)-Fuji Xerox, Kanagawa RayPaton(ComputerScience) - UniversityofLiverpool PeterSchuster(MolecularBiotechnology) - UniversityofJena Gordon Shepherd (Neurobiology)- YaleUniversity Richard Stark(Mathematics) -'universityofSouthFlorida, Tampa Rene Thomas(MolecularBiology) -UniversityLibre, Brussels ChrisTofts(Computer Science) - UniversityofLeeds RickeyWelch(Biochemistry) - UniversityofMaryland Hans Westerhoff(Math. Biochemistry) -FreeUniversity, Amsterdam GershomZajicek (Medicine) -HebrewUniversityofJerusalem We also wish to thank Matt Fairtlough and Marie Willett who were involved in local arrangements for the workshop and helped a great deal in ensuring that the event ran smoothly. Finally, our thanks to 1.Lawrence ofPlenum for her encouragement and advice duringthe production ofthis book. Theeditors also acknowledgethe help and support ofa number oforganisations: SmithKline Beecham, GPT, Unilever, Hewlett-Packard, Geomica andEPSRC. TheIPCATWWW HomePageislocated at:http://www.csc.liv.ac.uk/-biocomp/ipcat/iphome.html The IPCAT email list was set up after IPCAT '95 in order to promote dialogue among the delegates. Since that time it has grown in size. To subscribe to the IPCAT email list send an email messagetotheaddress:[email protected] containing the simple message: subscribe. Furtherinformation about IPCAT can beobtainedfrom RayPaton. Further reading Cuthbertson, R., Holcombe, M. & Paton, R. (eds) (1996) Computation in CellularandMolecularBiological Systems, Singapore: World Scientific. vi CONTENTS SIGNALLINGAND COMMUNICATION: AN INTRODUCTION TO SECTION 1 . SomeAspects ofGap JunctionDynamics inEmbryonic Systems 7 StephenBaigent, Jaroslav Stark,and Anne Warner Real TimeProcessingofNerve Signalsfor ControllingaLimbProstheses. ......... 17 MartinBodganand Wolfgang Rosentiel Stimulus-SecretionCouplinginPancreatic13-CellsExplainedbyChay's Store-OperatedModel. ............................................... 27 TeresaRee Chay TowardsComputational ModelsofChemotaxis inEscherichiacoli ................ 39 Laurence ClarkeandRay C. Paton ThreeModes ofCalcium-InducedCalciumRelease(CICR) inNeurons. ........... 47 DavidD. Friel 8-neuron, aOneDimensional SpikingModel thatReproducesin vitroandin vivo SpikingCharacteristicsofCorticalNeurons 57 Boris S. Gutkinand G. BardErmentrout ASimulationofGrowthCone FilopodiaDynamicsBasedonTuringMorphogenesis Patterns. ..................... ..................................... 69 TimA. Hely, ArjenvanOoyen, andDavidJ. Willshaw OrganFunctionandCellBehaviour: SimulatingDisturbances inVentricular Propagation. ....................................................... 75 A. V. Holden, G. P. Kremmydas, andA. Bezerianos ExtracellularSignallinginan OscillatoryYeastCulture. ........................ 85 Mark Keulers and Hiroshi Kuriyama Dopamine-mediatedDephosphorylationofN/P-TypeCalciumChannels in Striatal Neurons: AQuantitativeModel. ....................................... 95 RolfKotter, Dirk Schirok, and Karl Zilles vii The World Wide WebCytokine Database-NewTechniques ofDiagrammatic InfonnationManagementonthe Web 107 Xiao Mang Shouand SiobhanNorth InvolvementofReceptor-Kinase in the BiochemistryUpstreamfrom cAMP Synthesis in Cells III Juergen Nauroschatand Uwe an derHeiden Amplification ofSwitchingCharacteristicsofBiochemical-ReactionNetworks InvolvingCa2+/Calmodulin-DependentProteinKinase II: Implicationfor LTP Induced bya Single Burstduring the ThetaOscillation 125 Hiroshi Okamotoand Kazuhisa Ichikawa Influence ofCalciumBindingto ProteinsonCalciumOscillations and ER MembranePotential Oscillations. AMathematical Model 137 Stefan Schuster, Marko Marhl, MilanBrumen, and Reinhart Heinrich AModel ofLHRH 'Self-Priming'at the Pituitary 151 Sinead Scullion, DavidBrown, andGarethLeng COMPUTATIONAND INFO;RMATION: AN INTRODUCTIONTO SECTION2 161 Ray Paton MorphomechanicalFeedback in EmbryonicDevelopment ....................... 165 L. V. Beloussov Information ProcessinginComputational Tissues .............................. 177 Mark H. Butler,Ray C. Paton, and Paul H. Leng SemioticsofComplex Systems: A Hierarchical Notation forthe Mathematical Structureofa SingleCell 185 JerryL. R. Chandler Localisation andNonlocality inComputation 197 Ron Cottam, Nils Langloh, WillyRanson, and RogerVounckx Mining theGene ExpressionMatrix: InferringGene Relationshipsfrom Large Scale GeneExpressionData 203 PatrikD'haeseleer, XilingWen, StefanieFuhnnan,andRoland Somogyi Computational ModelsofImmunological Pathways 213 Mike Holcombeand Alex Bell Control Laws in the Mesoscopic ProcessesofBiocomputing 227 Felix T. Hong AComputerSystemthatLinksGeneExpressionto Spatial Organizationof Caenorhabditis eleg£,lns 243 TsuguchikaKaminuma,Taka,ko Igarashi, TatsuyaNakano, andJohji Miwa Verbs,Glueand Categories in theCellularEconomy 253 Ray Patonand Koichiro Matsuno Vlll AComputationalArchitecture BasedonCellularProcessing 261 Mark Shackletonand ChrisWinter Distributivity, aGeneral InformationTheoreticNetwork Measure, orWhy the Whole isMore than the SumofitsParts 273 Roland Somogyiand Stefanie Fuhrman GeNetDatabaseas aTool forthe AnalysisofRegulatoryGeneticNetworks 285 AlexanderV. Spirovand MariaG. Samsonova Cellular-Automata-likeSimulations ofDynamic Neural Fields 295 JorgWellnerand Andreas Schierwagen TowardsaMetabolicRobotControl System 305 JensZeigler, PeterDittrich, andWolfgang Banzhaf Epilogue--ConcludingDiscussions 319 Index 325 IX Information Processing in Cells and Tissues SIGNALLINGAND COMMUNICATION AN INTRODUCTIONTO SECTION 1 RayPaton DepartmentofComputerScience UniversityofLiverpool LiverpoolL69 3BX The first section ofthe book deals with papers which can be described as focusing on signalling and communication. As noted in the preface there is a degree ofarbitrariness in making this separation and so some papers which deal with this subject may be found in the second section. The paper by Steve Baigent, Jaroslav Stark and Anne Warner discusses a model built to explore the possible role of gap junctions in mediating developmentally importantsignalsinadevelopingXenopus embryo. Biophysical modelsforboththe cellsand the gapjunctions are outlined and used to build a model embryo in the form ofan arbitrary network ofcells linked together by gap junctions through which various molecular species are communicated. They outline the dynamics ofthe network model, which may be viewed as a singularly perturbed system, and discuss the model from a thermodynamic viewpoint. Finally, they outline how perturbation techniques can be used to study the steady state properties of the network and comment upon the relevance of our results to pattern formation. Following on from their IPCAT '95 contribution, Martin Bogdan and Wolfgang Rosenstiel present a paper concerned with the real time processing of nerve signals for controlling a limb prostheses. Microfabricated neural interfaces promise to become a powerful tool for applications like the control of motor/sensory limb prostheses for amputees and the direct stimulation ofspinal cord injuries (FNS). Such interfaces, which have been fabricated within the INTER-project (Intelligent Neural InTERface), have been successfullyimplanted and signals ofthe peripheral nerve system (PNS) havebeen recorded. Thegroup has proposed amodus operandi to processrecorded nerve signalsusing Artificial Neural Nets (ANNs). In the present paper they show that it is possible to process nerve signals and to direct a limb prostheses in real time using Artificial Neural Nets (ANN). After a short introduction to the INTER-project, they discuss the signal processing using recordings from the stomatogastric nervous system (STNS) ofthe crab Cancer parugus. The recording have been classified byKohonen's self-organizing map (SOM). The obtained clustershavebeenused to assignan actionto limb prostheses. Afterthetrainingofthe SOM and the assignment of the clusters to an action of the prostheses, the system is able to InformationProcessinginCellsandTissues EditedbyHolcombeandPaton,PlenumPress,NewYork, 1998
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