Dictionary of DNA and Genome Technology, Second Edition

403 Pages·2010·8.068 MB·English

by  Paul Singleton(auth.)

Dictionary of
DNA and Genome Technology
Second Edition
Dictionary of DNA and Genome Technology, Second Edition Paul Singleton
© 2010 Paul Singleton. ISBN: 978-0-470-74732-2
Dictionary of
DNA and Genome Technology
Second Edition
Paul Singleton
AJohn Wiley & Sons, Ltd., Publication
(cid:2)2010PaulSingleton
Firstedition2008
Secondedition2010
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For Mobby
Contents
Preface ix
Notesfortheuser xi
Readyreference xv
Dictionary 1
Appendix:alphabeticallistofgenera 405
vii
Preface
This edition has been written to accomodate the recent spate of innovations and developments in DNA
technology. It covers a wide range of new methods and adaptations, as well as terminology, and reflects
currentthinkinginbothinvitroandinvivostudies.Theopportunitywasalsotakentoupdateandextend
entriesfromthe1stedition.Everyefforthasbeenmadetopresentup-to-dateinformation–muchofitnewly
publishedinmainstreamjournalswithinthelast6–12months.
Thedictionaryisdesignedforusethroughoutthebiomedicalsciences,particularlyinareassuchas:
(cid:129) biotechnology
(cid:129) diagnosis(hereditaryandinfectiousdiseases)
(cid:129) drugdevelopment
(cid:129) epidemiology
(cid:129) forensicscience
(cid:129) genetherapy
(cid:129) geneticallymodified(GM)foods
(cid:129) genomics
(cid:129) industrialenzymes
(cid:129) microbiology
(cid:129) molecularbiology
(cid:129) oncology
(cid:129) systemsbiology
(cid:129) taxonomy
(cid:129) vaccinedevelopment
References to published papers and reviews are cited throughout the dictionary. Some of these are the
source(s) of information on which particular entries are based; they can provide additional details (e.g.
protocols), and they also permit the reader to make his or her own assessment of a given source. Other
referencesareincludedinordertoindicatefurtherinformationwhichisrelevanttoagivenentry.
Some pervasive topics – for example, PCR, gene fusion, forensics, phages, overexpression, retroviruses,
typing, microarrays, stem cells – are treated more extensively. These essay-style entries are intended to
offerthenewcomerabroadworkingknowledgeofthearea.Suchentriesmayalsobeofusetotheover-
specializedresearcher.
Commercial systems and materials are widely used in DNA technology, and a range of entries describe
theseproducts.Thiskindofentrymaybeuseful,forexample,whenapaperoffersnoinformationabout
ix
Preface
a given product other than ‘‘used according to the manufacturer’s instructions’’ – leaving unanswered
questionsontheproduct,theprotocolortheprinciple.Accordingly,theseentriesgivebriefoverviewsof
products–andtheiruses–andinmanycasestheyalsociterelevantpapersdescribingworkinwhichagiven
producthasbeenused.Wherethenamesofproductsandsystemsareknowntobetrademarksthishasbeen
indicated.
Notesfortheuseronthefollowingpageswillfacilitateuseofthedictionary.Theattentionofthereaderis
drawn,inparticular,totheitemonalphabetization.
PaulSingleton
Clannaborough(UK),September1st2009
x
Notes for the user
Alphabetization
Theheadwordsinanydictionarycanbelistedineitheroftwodistinctways:
1. Accordingtothewayinwhichthetermsareactuallywritten.Thisapproach,whichiscalledthe‘word-
by-word’approach,isusedinthisdictionary.
2. Accordingtothewayinwhichthetermswouldappearifallthespacesandhyphensetc.weredeleted.
Thisisthe‘letter-by-letter’approach.
The order in which headwords are listed in any dictionary depends on the particular approach used; for
example:
Approach1 Approach2
Asite AAS
A-tract abacavir
AAS abasicsite
abacavir ABCexcinuclease
abasicsite Asite
ABCexcinuclease A-tract
blagene black–whitescreening
black–whitescreening blagene
blue–whitescreening Bluescript(cid:2)
Bluescript(cid:2) blue–whitescreening
branchmigration branchedDNAassay
branchedDNAassay branchmigration
colplasmid colchicine
colchicine colplasmid
cossite cosmid
cosmid cossite
Cre–loxPsystem CREB
CREB Cre–loxPsystem
Notethataone-letterdescriptor(suchasthe‘A’in‘Asite’)istreatedasawordforthepurposesofalpha-
betizationinapproach1.
xi
Notesfortheuser
Inpractice,neitherapproachisfoolproof.Forexample,inthefirstapproach,theorderinwhichagiventerm
is listed may depend on whether or not a hyphen is regarded as a necessary part of the term. Thus, on
deleting a hyphen – and closing-up the intervening space – the characters on either side of the hyphen
become contiguous; in this case, the character which followed the hyphen is important as a primary
determinant of alphabetical order. In the second approach, strict adherence to the basic ‘letter-by-letter’
rulewouldlead–forexample–tothefollowingorder:
factorI (1)
factorII (2)
factorIII (3)
factorIV (4)
factorIX (9)
factorV (5)
factorVI (6)
factorVII (7)
factorVIII (8)
factorX (10)
To some, this order may seem reasonable, even preferable. To others, it runs counter to common sense:
Roman numerals are generally seen (and used) as the equivalent of numbers – and ought therefore to be
arrangedinnumericalorder.
WhenaGreekletterisasignificantcomponentofanentryheading–ase.g.inlphage–itistreatedasa
wordandis listedintherelevantalphabetical positionindicated bytheEnglishname(i.e.alpha,lambda
etc.).However,b-galactosidaseandb-lactamasesarelistedunderGandL,respectively;thisruleapplies
alsotoentry headings starting with letters such asL-,p-,N-,O-etc.which precede thenamesofcertain
chemicals.Insomecasesaheadwordisgiveninbothpossiblelocations,withsuitablecross-referencing;
thishasbeendonesimplyinordertoassistreaders.
Cross references
WordsinSMALLCAPITALSreferthereadertoentrieselsewhereinthedictionary.Suchcrossreferencesare
included e.g. to extend the reader’s knowledge into related fields or topics. Cross references may be
particularly useful for directing the reader to allied, or parallel, subjects whose relationship to the entry
beingreadmaynotbeimmediatelyobvious.
Insomecasesacompleteunderstandingofagivenentry,orafullappreciationofitscontext,dependson
information contained inotherentries – which are indicated by cross reference(s).Dictionaries are often
arrangedinthiswaybecauseitavoidstheneedtorepeatinformation.Ifitisespeciallyimportanttofollow-
upacrossreference,thenthecrossreferenceisfollowedby‘(q.v.)’.Inothercases,inwhichthepurposeofa
cross reference is simply to link one topic with another, the cross reference may be preceded by ‘See
also....’or‘cf.’.
xii
Notesfortheuser
External references
Referencestopapers,articlesorreviewsinjournalsaregiveninsquarebrackets.Thenamesofjournalsare
abbreviatedtosavespace.Theabbreviatedjournalnameisfollowedbytheyearofpublication,thevolume
number(andfrequentlytheissuenumber),andpagenumber(s).Thisinformationissufficienttoenablethe
reader to obtain any given reference. (When a paper has been cited as an advance publication it may be
referredtobyitsdigitalobjectidentifier(doi)number;thisnumberallowsthereferencetobefollowed-up.)
Commercial products
Manyofthecommercialproductsarelistedundertheirtradenames.Ingeneral,theseproductsarewidely
usedinstudiesonallaspectsofDNA-basedtechnologyandarecitedinmanyresearchpapers.Itshouldbe
notedthattheinclusionofanygivenproductinthedictionaryisnotbasedonanevaluationofthatproduct,
andimpliesnocomparisonofthatproductwithanysimilarproduct(s)marketedbyothercompanies.Itis
obviously not possible to include every product currently on the market. Importantly, any details of a
product given in the dictionary are those details which are to hand at the time of writing; companies are
continually modifying and updating their products, so that the reader should refer to the manufacturer’s
literaturefordetailsofanymodifications.
xiii