第一章概述誘導(dǎo)多功能干細(xì)胞隨機(jī)模型Totipotentfertilizedeggsdifferentiateintovariouslineagesthroughthepluripotentstatus.HereIdepictthisprocessinthecontextoftheepigeneticlandscapeproposedbyConradWaddington26.TheiPScellislikeaballrollingdowntheslopeofavalley.Thereprogrammingfactorscooperativelypushcellsuptheslopetothepluripotentzone.Somecellsareblockedbyanepigeneticbump(closedrectangle)ontheslopeandthusbecomeabletoself-renew(1).Othercellsareonlypartiallyreprogrammedandarenotblockedbythebump;therefore,withouttheexogenousreprogrammingfactors,theywouldrolldownagain(2).Whentheexpressionofthereprogrammingfactorsisnotappropriate,cellsmaytransformtoothertypesofcell,orevenundergoapoptosisorsenescence.Forcellsthatarelocatedonthemiddleofthevalley(thatis,somaticstemcells)itmightbeeasiertogobacktothepluripotentstate.(Inthestochasticmodel,most,ifnotall,differentiatedcellshavethepotentialtobecomeiPScellsaftertheintroductionofthefourfactors.Celldifferentiationisoftendescribedasaballrollingdownanepigeneticlandscape,firstdepictedbyConradWaddingtonin1957,startingfromthetotipotentstate,goingthroughthepluripotentstate,androllingdowntoalineage-committedstate26(Fig.2).Innormaldevelopment,pluripotentcellsappeartransiently.Theycannotstopontheslopeandarepulledbygravitytorapidlydifferentiateintovariouslineages.Incontrast,EScellscanself-renewandmaintainpluripotencyforalongtime.Thus,itisasifEScellsareblockedbyabumporaroadblockformedbytheirparticularepigeneticstatus.Inthismetaphor,thefourreprogrammingfactorscooperativelypushthecellsupintothepluripotentstate.(Inthestochasticmodel,most,ifnotall,differentiatedcellshavethepotentialtobecomeiPScellsaftertheintroductionofthefourfactors.Celldifferentiationisoftendescribedasaballrollingdownanepigeneticlandscape,firstdepictedbyConradWaddingtonin1957,startingfromthetotipotentstate,goingthroughthepluripotentstate,androllingdowntoalineage-committedstate26(Fig.2).Innormaldevelopment,pluripotentcellsappeartransiently.Theycannotstopontheslopeandarepulledbygravitytorapidlydifferentiateintovariouslineages.Incontrast,EScellscanself-renewandmaintainpluripotencyforalongtime.Thus,itisasifEScellsareblockedbyabumporaroadblockformedbytheirparticularepigeneticstatus.Inthismetaphor,thefourreprogrammingfactorscooperativelypushthecellsupintothepluripotentstate.Thereareatleasttworequirementsforcompletereprogramming.First,thefourfactorsmustbeexpressedinapatternthatprovidesasufficientpushintherightdirection.Becauseavailabletechnologiescannotpreciselycontroltheexpressionlevelsofthefourtransgenes,thisfirstrequirementcanonlybeachievedstochastically.Second,cellsmustbeblockedbytheepigeneticbumpsothattheycanremaininthepluripotentzoneevenwhenthetransgeneexpressiondisappears.Becausethefourreprogrammingfactorsalonecannotconstitutesuchanepigeneticroadblock,stochasticeventsagainarerequiredduringiPScellgeneration.Ashasbeendemonstratedinreprogrammingbynucleartransfer,DNAmethylationandhistonemodificationsprobablyhaveimportantrolesiniPScellgeneration.)細(xì)胞自動機(jī)是一種離散模型，在可算性理論、數(shù)學(xué)及理論生物學(xué)都有相關(guān)研究。它是由無限個有規(guī)律、堅硬的方格組成，每格均處于一種有限狀態(tài)。整個格網(wǎng)可以是任何有限維的。同時也是離散的。每格于t時的態(tài)由t-1時的一集有限格（這集叫那格的鄰域）的態(tài)決定。每一格的“鄰居”都是已被固定的。（一格可以是自己的鄰居。）每次演進(jìn)時，每格均遵從同一規(guī)矩一齊演進(jìn)。細(xì)胞自動機(jī)有三個特征：平行計算（parallelcomputation）：每一個細(xì)胞個體都同時同步的改變局部的（local）：細(xì)胞的狀態(tài)變化只受周遭細(xì)胞的影響。一致性的（homogeneous）：所有細(xì)胞均受同樣的規(guī)則所支配Thesimplestnontrivialcellularautomatonwouldbeone-dimensional,withtwopossiblestatespercell,andacell'sneighborsdefinedtobetheadjacentcellsoneithersideofit.Acellanditstwoneighborsformaneighborhoodof3cells,sothereare23=8possiblepatternsforaneighborhood.Aruleconsistsofdeciding,foreachpattern,whetherthecellwillbea1ora0inthenextgeneration.Therearethen28=256possiblerules.ProtnetThegraphinpanelAisbasedonthehighconfidenceinteractomethatwasusedasinputinoursimulations.Pinkspheresrepresentproteinsthat,attheendof50000steps,werenotfoundtobeinvolvedintheformationofanycomplexinaspecificsimulationrun.Largehighlyconnectedprotein"clusters"thatcanbemappedtophysiologicallyrelevantcomplexesareoutlinedwithabrownbackgroundandidentified.InpanelBwehavefilteredtheinputgraph(panelA)byeliminatingtheedgesrepresentinginteractionsinwhichthepartnerproteinsarefoundlessthan10%ofthetimes.Catastrophetheory突變理論從牛頓和G.W.萊布尼茲時代以來得到很大發(fā)展的微積分學(xué)，一般只考慮光滑的連續(xù)變化的過程，而突變論則研究跳躍式轉(zhuǎn)變、不連續(xù)過程和突發(fā)的質(zhì)變。突變論的基礎(chǔ)是結(jié)構(gòu)穩(wěn)定性。結(jié)構(gòu)穩(wěn)定性反映同種物體在形態(tài)上千差萬別中的相似性。例如，人的面貌雖因歲月流逝而發(fā)生變化，但仍存在區(qū)別于他人的特征。結(jié)構(gòu)穩(wěn)定的喪失，就是突變的開始。突變論的創(chuàng)始人是法國數(shù)學(xué)家雷內(nèi)托姆，他于1972年發(fā)表的《結(jié)構(gòu)穩(wěn)定性和形態(tài)發(fā)生學(xué)》一書闡述了突變理論，榮獲國際數(shù)學(xué)界的最高獎菲爾茲獎?wù)?。突變論的出現(xiàn)引起各方面的重視，被稱之為“是牛頓和萊布尼茨發(fā)明微積分三百年以來數(shù)學(xué)上最大的革命”。MassivegenomicrearrangementacquiredinaSingleCatastrophicEventduringCancerDevelopmentCancerisdrivenbysomaticallyacquiredpointmutationsandchromosomalrearrangements,conventionallythoughttoaccumulategraduallyovertime.Usingnext-generationsequencing,wecharacterizeaphenomenon,whichwetermchromothripsis,wherebytenstohundredsofgenomicrearrangementsoccurinaone-offcellularcrisis.Rearrangementsinvolvingoneorafewchromosomescrisscrossbackandforthacrossinvolvedregions,generatingfrequentoscillationsbetweentwocopynumberstates.Thesegenomichallmarksarehighlyimprobableifrearrangementsaccumulateovertimeandinsteadimplythatnearlyalloccurduringasinglecellularcatastrophe.Thestampofchromothripsiscanbeseeninatleast2%–3%ofallcancers,acrossmanysubtypes,andispresentin25%ofbonecancers.Wefindthatone,orindeedmorethanone,cancer-causinglesioncanemergeoutofthegenomiccrisis.Thisphenomenonhasimportantimplicationsfortheoriginsofgenomicremodelingandtemporalemergenceofcancer.分級系統(tǒng)ageneraltheoryfortheoptimisationoftwo-levelhierarchicalsystemshasbeenintroduced.Thistheorycanbeappliedonawiderangeofapplications,examplesbeingeconomics,organisationtheoryandlargescaleindustrialplants.Inthistheorythesystemisdividedintosub-systems,whereeachsub-systemtriestoachieveitsownobjectiveswithoutconsideringwhetherornottheycontradictwithothersub-systems.Inordertorectifythe’selfishness’ofthesub-systemdecisionmaking,anupper-leveldecisionmakingsystemhastobeintroduced.Theobjectiveoftheupper-leveldecisionmakingunitistocoordinatethedecisionmakingofeachsub-system,sothatanoverallharmonyisachieved.Aspecialemphasiswasputonthesocalledbalancingtechnique,becauseitcanbeimplementednumericallywiththewell-knownLangrangetechnique.Notethatinthisreportnorigorousconvergencetheorywaspresentedfortheiterativebalancingtechnique.Adiagramofastandardtwo-levelhierarchicalsystemisshowninFig.12.1,where,asexpected,twolevelscanbefound,namelythelowerlevelandtheupperlevel.Thelowerlevelconsistsoftheprocesslevel,wheretheprocesslevelhasbeendividedintoNsub-systems.Thesub-systemsareconnectedtoeachotherbecausethereiseithermaterialorinformationflowsbetweenthesesub-systems.Eachsub-systemhasitsowndecisionunit,whichtriestocontrolthebehaviourofthesub-systemsothattheobjectivesofthisparticularsub-systemwouldbemet.Thedecisionunitcanalsousefeedbackinformationfromthesub-systemtoimproveits’controlpolicy’.However,quiteoftentheobjectivesofthesub-systemsareconflicting,resultinginapooroverallperformance.Henceanupper-leveldecisionunitoracoordinatorhastobeintroduced,andtheobjectiveofthisdecisionunitistocoordinatethedecisionmakingofthesub-systemssothattheoverallperformanceofthesystemwouldbeimproved.Thecoordinatorreceivesinformationfromthesub-systemssothatitcanmonitortheperformanceoftheoverallsystem.Notethatthisapproachisnotasrestrictiveasitsounds,becauseifanewhigherlevelisaddedintoatwo-levelsystem,inmostofcasesthenewlevelcanbechosentobethehigherlevelofthemodifiedsystem,andtheoriginaltwo-levelsystembecomesthelower-levelofthemodifiedsystem.OscillationsinNF-kBSignalingControltheDynamicsofGeneExpressionNF-kBSignaling的震動控制基因表達(dá)動力學(xué)SignalingbythetranscriptionfactornuclearfactorkappaB(NF-.B)involvesitsreleasefrominhibitorkappaB(I.B)inthecytosol,followedbytranslocationintothenucleus.NF-.BregulationofI.B!transcriptionrepresentsadelayednegativefeedbackloopthatdrivesoscillationsinNF-.Btranslocation.Singlecelltime-lapseimagingandcomputationalmodelingofNF-.B(RelA)localizationshowedasynchronousoscillationsfollowingcellstimulationthatdecreasedinfrequencywithincreasedI.B!transcription.Transcriptionoftargetgenesdependedonoscillationpersistence,involvingcyclesofRelAphosphorylationanddephosphorylation.ThefunctionalconsequencesofNF-.Bsignalingmaythusdependonnumber,period,andamplitudeofoscillations.1-50.例如，為了從表達(dá)譜推導(dǎo)基因調(diào)控網(wǎng)絡(luò)，需要全面測量基因表達(dá)譜。野生型的表達(dá)數(shù)據(jù)往往難以滿足要求。它需要每個基因缺失突變和過表達(dá)所產(chǎn)生的完整數(shù)據(jù)集。所有敲除基因的數(shù)據(jù)集使用基因芯片測量。如果因?yàn)閮r格或時間的限制，僅僅有限個基因被敲除，那么敲除緊密關(guān)聯(lián)的基因比在整個調(diào)控網(wǎng)絡(luò)上稀疏地敲除一些基因要好的多。稀疏數(shù)據(jù)點(diǎn)給可能的網(wǎng)絡(luò)結(jié)構(gòu)留下了很多不確定因素。即使是使用相同數(shù)量的數(shù)據(jù)，測量密切相關(guān)的基因所產(chǎn)生的網(wǎng)絡(luò)也較上述方法更可靠。這就是要素完備性。1-51時序完備性則對時序現(xiàn)象是必須的。時間序列數(shù)據(jù)需要特別謹(jǐn)慎，保證樣本同步測量。在傳統(tǒng)生物學(xué)實(shí)驗(yàn)中往往是這樣的情況：只有兩個測量點(diǎn)，一個在事件前，一個在事件后。例如，許多關(guān)于細(xì)胞衰老的研究測量年輕細(xì)胞、年老細(xì)胞以及永生細(xì)胞的衰老相關(guān)的基因表達(dá)，而不按精細(xì)的時間序列來記錄表達(dá)水平的變化。很多情況下，表達(dá)水平隨時間的變化對于提出或否定假設(shè)可能是十分重要的。除了需要在感興趣的生物學(xué)時間前后測量外，還必須進(jìn)行固定時間間隔的采樣測量。具有可靠的采樣時間同步性和恒定的時間間隔的表達(dá)譜數(shù)據(jù)對計算算法擬合模型、參數(shù)與實(shí)驗(yàn)數(shù)據(jù)十分有益。1-52來自蛋白質(zhì)之間相互作用的信息，譬如酵母雙雜交實(shí)驗(yàn)，對推導(dǎo)蛋白質(zhì)水平的交互，從而填補(bǔ)基因調(diào)控研究的空白就十分有用。1-53這一點(diǎn)就是說并非系統(tǒng)的所有部分必須使用相同的準(zhǔn)確度。例如噴氣式引擎的組件需要高準(zhǔn)確度，但是座椅綁帶顯然就無須和引擎同樣的精度。在未來的研究中，實(shí)驗(yàn)的類型以及準(zhǔn)確度要求可以通過理論條件來確定。1-55蛋白質(zhì)相互作用及表達(dá)譜必須在相同制備的樣本上進(jìn)行測量。這個系統(tǒng)測量的要求現(xiàn)在是非常難以滿足的，因?yàn)楹苌儆醒芯拷M可以提供多種測量技術(shù)。線蟲C.elegansisaveryfamousorganisminthefieldoflifescience.Since1998itswholegenomehasbeensuccessfullysequenced,thereare5scientistswintheNobelPrizesbecauseoftheirworkonC.elegans.Therecanbe4vocabulariesdescribingthissmartanimal,simple,open,cleverandcorrelative.Itissimple:itis1mminlengthandabout50micrometerindiameter.Thewholebodyiscomposedofonlyseveralthousandsofcells.Itisveryopen:Itisbisexual,andthebodyistotallytransparent.Wecanidentifyeachcellunderthemicroscope.Itisclever:Itcanhavesensitiveresponsestoenvironmentalchangesandlearnsomething.Itiscorrelative,because40%ofgenomeissimilartohumanbeing,andover70%genescouldbeidentifiedtheircounterpartanaloguesinotheranimals.So,itiscurrentlythemodelspeciesingenetics,neuroscienceanddevelopmentalbiology.1-59如果該項目成功的話，就可以用于早期胚胎發(fā)生時所有RNAi敲除后細(xì)胞系的自動鑒定。隨著不斷的努力，這些技術(shù)的增強(qiáng)將用于細(xì)胞之間接觸、蛋白質(zhì)定位等的自動檢測。結(jié)合整體原位雜交和將來可能進(jìn)行的單細(xì)胞表達(dá)譜，基因調(diào)控網(wǎng)絡(luò)的完全鑒定在不久的將來將成為可能1-69SimplifiedversionofthephageldecisioncircuitthatdetermineswhetherinfectedEscherichiacolicellsfollowthelyticorlysogenicpathway.Boldhorizontallinesindicatestretchesofdouble-strandedDNA.Arrowsingenesindicatethedirectionoftranscription.TheboxesR1–R3indicatenon-geneticproteinreactionsubsystems.Thethreeoperatorsites,OR1–R3,ofthe‘lswitch’implementaconcentration-dependent‘logic’,controllingpromotersPRMandPR.CroandCIdimersbindtothethreesiteswithdifferentaffinitiesandinoppositeordertocontroltheactivationlevelofthePRMandPRpromoters40,41.TheCIdimeractsaseitherarepressororactivatorofpromoterPRM,dependingonitsconcentration.Theresultisamutuallyexclusivelockingmechanism,sothateitherPRMorPRendsupbeingactivatedwiththeotherpromoterlockedoff.StrongproductionofCIrelativelysoonafterinfectionisnecessaryforlockingonthePRMlooptoselectthelysogenicpathway.ThisoccursonlywhenthestrongpromoterPREisactivatedbyCIIto‘jumpstart’CIproduction.DegradationofCIIisinhibitedbyCIII,soproductionofCIIIincreasestheprobabilityofCI‘winning’therace.EnvironmentalsignalsinfluencetheoutcomebyaffectingtherateofCIIdegradation.Duetothestochasticcharacterofproteinproductionandtheotherreactionsinvolved,boththelyticandthelysogenicoutcomecanoccurwithsomeprobability,sothattwoalternativephenotypesresult.1-73如何改變自身以適應(yīng)環(huán)境的變化？如何消除DNA損傷和突變對系統(tǒng)的潛在影響以維持穩(wěn)定？特定回路如何展示出觀察到的功能？為了獲得系統(tǒng)層次的理解，需要理解系統(tǒng)魯棒性、穩(wěn)定性和回路功能性背后的機(jī)制。1-74基因與代謝網(wǎng)絡(luò)行為的仿真在系統(tǒng)生物學(xué)研究中扮演著重要的角色，仿真不僅僅是理解系統(tǒng)行為的基本工具，而且是設(shè)計過程的基本工具。仿真是生物系統(tǒng)研究的可行方法，因此需要開發(fā)高實(shí)用化、精確、用戶界面友好的仿真系統(tǒng)。仿真系統(tǒng)需要與參數(shù)優(yōu)化工具、假設(shè)生成器以及分析工具結(jié)合，然而這些軟件后面的算法需要針對生物學(xué)研究精確設(shè)計1-75系統(tǒng)生物學(xué)研究需要開發(fā)和整合一系列軟件系統(tǒng)，包括：存儲實(shí)驗(yàn)數(shù)據(jù)的數(shù)據(jù)庫細(xì)胞與組織仿真系統(tǒng)參數(shù)優(yōu)化軟件分叉和系統(tǒng)分析軟件假設(shè)生成器和實(shí)驗(yàn)設(shè)計專家系統(tǒng)數(shù)據(jù)可視化軟件1-79來自復(fù)雜工程系統(tǒng)的經(jīng)驗(yàn)在工程系統(tǒng)與生物系統(tǒng)之間有很多有趣的相似之處：二者都通過一些進(jìn)化過程來增量設(shè)計對給定的問題一般獲得次優(yōu)解為了獲得更高的魯棒性和穩(wěn)定性，系統(tǒng)復(fù)雜度也隨之遞增。1-81前饋控制中預(yù)定義了一系列受特定刺激觸發(fā)的動作，是一種開環(huán)而且簡單的系統(tǒng)，僅僅在可能情形與對策都高度可預(yù)見的情況下使用。反饋控制，如負(fù)反饋控制，廣泛應(yīng)用于工程中。它將期望值和實(shí)際值之間的誤差取負(fù)后反饋給輸入，使輸入信號受到正比于誤差的調(diào)整。其基本形式中，表現(xiàn)為最小化輸出誤差值的效果。反饋在生物過程中的很多方面扮演著重要角色，如大腸桿菌的趨化性和熱休克響應(yīng)、生理節(jié)律、細(xì)胞周期以及發(fā)育的各個方面。1-82最典型的例子是細(xì)菌趨化性中的整體反饋回路。細(xì)菌表現(xiàn)出對很大濃度范圍下化學(xué)試劑的適應(yīng)性，因此可以感知化學(xué)濃度變化來決定其行為。這是通過一個包含閉環(huán)反饋的回路實(shí)現(xiàn)的。如圖所示，趨化性中的配體和特定的受體MCP結(jié)合形成了包含CheA和CheW的穩(wěn)定復(fù)合體。CheA磷酸化CheB及CheY。磷酸化的CheB使MCP復(fù)合體去甲基化，磷酸化的CheY觸發(fā)紊亂行為。實(shí)驗(yàn)和仿真都表明這形成了一個反饋回路從而適應(yīng)配體濃度變化。特別是對配體濃度的突然變化，通過紊亂頻率來表征的平均活動水平可以迅速收斂到一穩(wěn)態(tài)值。這意味著系統(tǒng)僅僅可以探測到?jīng)Q定紊亂頻率的配體濃度的變化，而對濃度絕對值不敏感。因此，不管絕對濃度