Encyclopedia of genetics, genomics, proteomics, and informatics. Vol. 1,2

2210 Pages·2008·42.767 MB·English

by  George P. Rédei

George P. Rédei
Encyclopedia of Genetics, Genomics,
Proteomics, and Informatics
3rd Edition
Volume 1
A–L
With 1914 figures and 94 tables
George P. Rédei
Encyclopedia of Genetics, Genomics,
Proteomics, and Informatics
3rd Edition
Volume 2
M–Z
With 1914 figures and 94 tables
Author:
GeorgeP.Rédei
ProfessorEmeritus,UniversityofMissouri,Columbia
3005WoodbineCt.Columbia,MO65203-0906
USA
[email protected]
[email protected]
www.missouri.edu/~redeig
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Acknowledgements
I thank my wife Magdi for her patience during writing and for critical reading of the text. My daughter Mari
introducedmeintowordprocessing.Myson-in-law,Kirkhasbeenverysupportive.Granddaughters,Grace,Paige
andAnnearemostinspirational.Iamgratefultocountlessnumbersofcolleaguesonwhoseworkthismaterialis
basedandtowhomIcouldnotreferbecauseoflimitationsofspace.Iamindebtedtocolleagues,especiallytoDr.
CsabaKoncz,Max-Planck-Institut,Cologne,Germanyformanyusefuldiscussions.MystudentsattheUniversity
of Missouri, Columbia, MO, and students and colleagues, particularly Dr. András Fodor, at the Eötvös Lóránd
UniversityofBasicSciences,Budapest,providedpurposeforundertakingthisproject.IamalsoindebtedtoJaneD
Phillips,DirectorofDevelopmentforLifeSciencesattheUniversityofMissouriforherinterestandencouragement.
SomeofthechemicalformulasarebasedontheMerckIndex,ontheAldrichCatalogandFlukaCatalog.
Duringthepreparationofthethirdedition,MarkJarvishasbeenmosthelpfulinresolvingavarietyofcomputer
problems.
Iappreciatedthecommentsfromthereadersonthefirstandsecondeditions.Thefirste-mailfromDr.SLCsaid:
“Thankyouforassemblingsuchconciseexplanationsofallgeneticconceptsinasinglevolume”.Similarletters
camefrommanyothers,whichforreasonsofspace,Icannotquotehere.
Iamthankfultothepublicreviewsfortheconstructivecommentsandsuggestions.
AuthorismuchindebtedtoAnilChandyforexpertadvice,friendship,cooperationandunderstandingduringall
phasesoftheproductionofthisbook.
CudweedbyKonradvonGessner(1597),thefamousSwisssavantandzoologicalandbotanicalillustrator.Von
Gessner's work has been borrowed by many, among them the German Joachim Camerarius (1500–1576) of
Tübingen, a great authority on classics, religion and science and whose descendant Rudolph Jacob Camerarius
(1665–1721)wouldbecomethefirstexperimentalgeneticist,anddiscoverthelovelifeofplants.
Preface to the First Edition
TheprimarygoalofthisManualisthefacilitationofcommunicationandunderstandingacrossthewiderangeof
biologythatisnowcalledgenetics.Theemphasisisonrecenttheoreticaladvances,newconcepts,termsandtheir
applications.Thebookincludesabout18thousandconceptsandover650illustrations(graphs,tables,equations
andformulas).Mostofthecomputationalproceduresareillustratedbyworked-outexamples.Alistofabout900,
mainlyrecentbooks,isprovidedattheendofthevolume,andadditionalreferencesarelocatedatmanyentriesand
illustrations. The most relevant databases are also listed. The cross-references following the entries connect to a
network within the book, so this is not just a dictionary or glossary. By a sequential search, comprehensive,
integratedinformationcanbeobtainedasyouprepareforexams,orlectures,ordeveloporupdateacourse,orneed
toreviewamanuscript,orjustwishtoclarifysomeproblems.Incontrasttostandardencyclopedias,Ihaveused
relativelyshortbutgreatervarietyofentriesinordertofacilitaterapidaccesstospecifictopics.ThisManualwas
designed for students, teachers, scientists, physicians, reviewers, environmentalists, lawyers, administrators, and
to all educated persons who are interested in modern biology. Concise technical information is available here
on a broad range of topics without a need for browsing an entire library. This volume can always be at your
fingertips without leaving the workbench or desk. Despite the brevity of the entries, the contents are clear even
for the beginner. Herbert Macgregor made the remarkable statement that in 1992 about 7,000 articles related
just to chromosomes were scattered among 627 journals. Since then, the situation has become worse. Many
publications—beyond a person’s specialization—are almost unreadable because of the multitude of unfamiliar
acronymsandundefinedterms.Studentsandcolleagueshaveencouragedmetoundertakethisefforttofacilitate
readingofscientificandpopulararticlesandsummarizebrieflythecurrentstatusofimportanttopics.Accordingto
RobertGraves(agoodpoem)“makescompletesenseandsaysallthatithastosaymemorablyandeconomically”.
I hope you will appreciate the sense and economy of this Manual. I will be much indebted for any comment,
suggestionandcorrection.
GPR
3005WoodbineCt.
Columbia,MO65203–0906,USA
Telephone:[phone],
e-mail:[email protected]@mchsi.com
“Ialmostforgottosaythatgeneticswilldisappearasaseparatesciencebecause,inthe21stcentury,everythingin
biologywillbecomegene-based,andeverybiologistwillbeageneticist.”SydneyBrenner,1993
Preface to the Second Edition
Themajorityoftheusersofthefirsteditionconsideredthisbookasanencyclopediabecausethecross-references
tiedtheshortentriesintocomprehensivereviewsofthetopics.Incontrastto“bigencyclopedias”inthisworkonlya
fewentriesexceedacoupleofthousandwordsandthatmakeitmuchfastertofindthespecificconceptortermof
interest.Unlikemulti-authorworksthisispracticallyfreeofredundancyanditiscompactinsizebutnotindepthof
information.Oneofthereviewerspointedoutthatmanyofthetopicscoveredcouldnotbefoundinanyothersingle
book,includingencyclopedias,dictionaries orglossaries. Anotherreviewerappreciated itasabroadresourceof
informationthatmaytakealengthysearchtouncoverwithoutit.
Sincethepublicationofthe1stedition,Ihavesteadilyupdatedandimprovedonthetopics.Ihaveaddedmany
newconcepts,illustrations,booksanddatabaseaddresses.(Thedatabaseaddressesareinanunfortunatefluxand
somemaybeoutexistencebythetimeyouwishtologin;thereforeIprovidedseveraltominimizetheproblem
beyond my control.) This second edition contains about 50% more information and more than twice as many
illustrationsthanthe1stedition.Anewfeatureisthepredominantlycurrent,over7,000textreferencestojournal
articles.Theirbibliographiesmayhelptolocateadditionalkeyandclassicalpapers.TheGeneralReferencesatthe
end include about 2,000 books. For additional medical genetics references I suggest the use of OMIM at The
National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/, see also Grivell, L 2002. EMBO
Rep.3:200).Ihavegreatlyexpandedthecross-referencesamongtheentriesbecausetheusersfoundthisfeature
especiallyuseful.Colorplateswereaddedtotheendofthebook.Attheendofthefilestherearesomehistorical
vignettes.
Since the publication of the first edition the need for such a book became even more evident. In the literature
unexplained concepts, terms and acronyms are on the increase and even a name DAS (dreaded abbreviation
syndrome)hasbeencoinedforthemalaise(Science,283:1118).TheusersofthefirsteditionagreedwiththeNobel-
laureate geneticist, HJ Muller who posed and answered the still current problem: “Must we geneticists become
bacteriologists,physiologicalchemistsandphysicists,simultaneouslywithbeingzoologistsandbotanists?Letus
hopeso.”(Amer.Nat.1922,56:32).
Thevisionofgeneticstodayisnotlessthanthecompleteunderstandinghowcellsandorganismsarebuilt,how
they function metabolically and developmentally, and how they have evolved. This requires the integration of
previouslyseparatedisciplines,basedondiverseconceptsandtongues.Whateverisyourspecializationorinterest,
Ihopeyouwillfindthissinglevolumehelpfulandaffordable.
AlthoughIhadtheaimofcomprehensivenessbeyondalltheavailablecompendiums,therewereharddecisions
ofwhattoincludeandwhattopass.Thesamesciencemayappeardifferentdependingonwho,howandwhenlooks
atit(upordown)asGeraldHFisher'sartabove(manorwomanorboth)illustratesthepoint.*
Thankyoufortheappreciationofthefirstedition.Iwillbemuchindebtedforyourcommentsandsuggestions.
GPR
[email protected]
*BypermissionofPerceptionandPsychophysics4:189(1968).
Preface to the Third Edition
“WhenIacquiredtherightwords…,itwaseasierformetounderstandwhatIwasthinking:itisdifficulttoreason
throughaproblemifyoucannotarticulatewhattheproblemis.”
(JohnFBruzzi2006NewEnglandJ.Med.354:665).
Thisvolumeisessentiallyanimprovedandenlargednew versionoftheprevious,much-acclaimed book.The
thirdeditionhasover1,000pagesmoreofnewmaterialthanthesecond.Thelatestprogressincurrenthottopics
suchasstemcells,genetherapy,smallRNAs,transcriptionfactories,chromosomalterritories,networks,genetic
networks,ENCODEproject,epigenetics,histoneandproteinbiology,prions,hereditarydiseases,andevenpatents
arecovered.Thenumberofillustrationsincreasedtonearly2,000andseveralhundredsareinfour-color.Theold
entrieshavebeenrevised,updatedandexpanded.Cross-referencesamongentrieshavebeenincreased.Retractions
and corrigenda are pointed out. Nearly 1,800 database and web server addresses, about 14,000 journal paper
referencesandmorethan3,000currentbooktitlesareincluded.Interestinghistoricalvignetteslendsomeinsight
intothelightersidesofbiology.Ihopethereaderfindstheabsenceoflaboratoryjargonrefreshing.
The encyclopedia will equip its reader to prepare journal papers, write or review research proposals or help
organizeanewcourseorupdateacurrentcourse.Studentswillfindthetopicsusefulforpreparingforexamsorfor
writingtermpapers.Itmayalsoappealtobasicandappliedbiologistsandtopractitionersofmanyotherfields.The
readers of previous editions appreciated the clarity of the basics in this book. A sample of what professional
reviewerswroteaboutthebookiscarriedforthereader'sreference.Inaddition,aboutthecurrentpublicationsin
general,theEditorofSciencehadthefollowingcomment.“Eachspecialtyhasfocusedintoapointatwhicheven
the occupants of neighboring fields have trouble understanding each others’ papers”… “The language used in
ReportsandResearchArticlesissufficientlytechnicalandarcanethattheyarehardtounderstand,evenforthosein
relateddisciplines.”(Kennedy,D2007Science318:715).
One of the most fascinating features of science is its continuous evolution. My goal was to emphasize the
principles,providenumericaldataandguidetoresourcesthataremoredifficulttoaccessfromotherpublications.
ThebookcanassistthereadertomakebetteruseoftheInternetbuttheInternetandtextbooksarenosubstitutesfor
thisbook.Unlikethemajorityofbooks,thisEncyclopediawillnotbeoutdatedbecausethecontinuouslyrenewed
andupdateddatabasesandwebsiteslistedassureitsusefulnesseveninthedistantfuture.Describingindividual
genesindifferentorganisms—withsomeexceptions—isnolongerpracticalinasinglebookorevenwiththeaidof
anexcellentresourcesuchasPubMedduetothemultitudeofabstracts(morethan15,000,000entriesfrommore
than 19,000journals). The web sites—listed inthisbook—canhowever, providegreat helpin identifying many
genes, their synonyms, functions and interacting partners as well as critical references to them. Although basic
statistical concepts are explained in simple terms, most of the theoretical mathematical models or detailed
laboratoryproceduresarenotincludedbecauseofthedifficulties ofdescribingthetechniqueswithinthelimited
spaceavailableinasinglebook.Theabundanceofreferencescanleadthereaderintherightdirection.
Selectionofpapersforinclusionisalsoacontinuouschallenge.During1992to20014,061journalspublished
morethan3.47millionpeer-reviewedarticlesinhealth-relatedareasalone(Paraje,Getal.2005Science308:959).
Althoughthisbookisquitecomplex,integrated,andreferenced,itdoesnotincludeeverythingbutitmightbea
useful guide toalmost everything oneneeds in biology. Fora proof of principle, I suggestthat you look up any
conceptwhatyouknoworwhatyouareuncertainorhavedoubtsabout.
IwelcomeallreadersandIpromisetorespondtoquestionsorcomments.
GPR
[email protected]
First to Read for the Third Edition
Theorganizationoftheexpandedandrevisedthirdeditionisslightlydifferentfromthatofthepreviousones.The
materialisstillinalphabeticalorderbutinasomewhatdifferentstyle.Numbersinvolvedwiththeentriesdonot
affecttheorder.EntriesbeginningwithGreeklettersaresortedasiftheywouldbeinRomanortheGreekletter
follows the term. Words followed by a comma and another word precede entry words without comma, e.g.,
“antibody, secondary” is followed by “antibody detection”. Hyphenated entries are sorted as single words. The
spellingofsometermsvarybecauseinthescientificliteraturesometechnicaltermsarewritteneitherwithacorkor
withaneorae.Someabbreviationsareusedintheliteraturease.g.,PGDorP.G.D.andbothmaynotbeusedinthis
book.Herethemostcommonusageisfavored.Someentriesarequalifiedbyanotherwordaddedafterandinothers
thequalifiercomesfirst.Mostentriesarefollowedbycross-referencesthatguidetorelevanttopics.Inparticular
cross-referencesqualifiersarenotseparatedbycommaevenwhentheyarewithcommainthemainlist.Incaseyou
makeelectronicsearchesitisfrequentlymorepracticaltouseonlypartofthewordsbecauseinthealphabeticallist
their ending may be different, e.g., maximum or maximal. An attempt has been made to guide the reader to the
desiredentrywhennecessary.Inrareinstancesthereadermayneedtosearchforsynonymsorrelatedtermstofind
thedesiredentry.Thankyouforyourpatience.
ThisbookcontainsalargenumberofInternetaddressesundertheheadingof“databases”andevenmoreaftermany
entries.Everyefforthasbeenmadetokeepthewebaddressescurrent.Unfortunately,theyarealteredfrequentlyand
itislikelythatsomewillceasetoexistorwillchangebythetimethebookgetstoyourhands.Insomeinstances
WordalonemaynotopentheURLsitedirectly,butInternetExplorerorSafarioreventhesearchenginesGoogle,
Yahoo,AltaVistaorotherscanbeusedtoaccessthesites.
Itmustberememberedthatdataarenotknowledge.Thedatamustbeintegratedintoscienceandtheaimofthe
authorhasbeenthefacilitationofsuchintegration.Thecontentsoftheentriesarebasedonthebestinformation
availableintheliteratureatthetimeofthecompletionofthewriting.Assourcesofinformationlikemosthuman
products,arenotalwaysperfect,theauthorandpublisherscannotclaimperfectionorassumelegalresponsibilityfor
errorsbeyondtheircontrol.
“Knowledge…builtonopiniononly,willnotstand”.Linnaeus,1735
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