Dictionary of DNA and Genome Technology

any given sequence of nucleotides in the DNA will be resistant to such modification if it is protected from the reagent by a closely bound protein. When extracted from the cell, the modified DNA is cleaved, at the sites of modified bases, into a number of fragments; the fragments are then analyzed and compared with control preparations. Analysis may be carried out by subjecting the fragments to LIGATION-MEDIATED PCR.

When the final experimental and control preparations are compared by gel electrophoresis, the absence of particular bands of fragments in the experimental preparation indicates that DNA-binding protein(s) have protected the correspond-

incompatibility groups (among plasmids) See PLASMID (Compatibility: Inc groups).

IncP group See PLASMID (Compatibility: Inc groups). IncX group See PLASMID (Compatibility: Inc groups). indel An insertion–deletion polymorphism.

indinavir See PROTEASE INHIBITORS.

indirect suppression See SUPPRESSOR MUTATION. induced FRET See IFRET.

inducer exclusion See CATABOLITE REPRESSION.

induction (of a lysogen) See LYSOGENY.

INH Isonicotinic acid hydrazide: see ISONIAZID.

INN International non-proprietary name. (rINN may be used to mean recommended international non-proprietary name.)

INNO-LiPA Mycobacteria® A PCR-based PROBE system from Innogenetics (Ghent, Belgium) which is used for identifying medically important mycobacteria (cf. ACCUPROBE). Amplification of spacers in the 16S–23S rRNA genes of the test strains (by PCR) is followed by reverse hybridization of the products to a range of membrane-bound probes [see J Clin Microbiol (2001) 39:3222–3227 and J Clin Microbiol (2004) 42:3083–3088].

INNO-LiPA Rif TB See LINE PROBE ASSAY. inorganic pyrophosphate (PPi) See PYROPHOSPHATE.

inosine A riboNUCLEOSIDE.

INSDC INTERNATIONAL NUCLEOTIDE SEQUENCE DATABASE COLLABORATION.

insect-cell-based expression systems Those systems used for the expression of recombinant proteins in either cultures of insect cells or in live insects: see BACULOVIRUS EXPRESSION

SYSTEMS and DES.

insertion sequence (IS; IS element) A type of TRANSPOSABLE ELEMENT (q.v.) which encodes only those functions that are necessary for transposition. (cf. TRANSPOSON.) The structural

gene(s) of an insertion sequence are bracketed by a pair of INVERTED REPEAT sequences; usually, these inverted repeats form the terminal parts of an insertion sequence, but in some IS elements (e.g. members of the IS1111 FAMILY) the inverted repeats are subterminal.

A specific insertion sequence is commonly designated by ‘IS’ followed by an italic number (e.g. IS1, IS2 etc.); in some cases the designation of an IS element includes an indication of the source organism – e.g. ISHP608 (q.v.), which is present in the Gram-negative bacterial pathogen Helicobacter pylori.

Insertion sequences exist in their own right, and they also form the terminal parts of class I (composite) transposons.

Insertion sequences commonly transpose by a cut-and-paste mechanism (see figure in entry TRANSPOSABLE ELEMENT) – but some transpose in the replicative mode (see e.g. IS1071) and some (see TRANSPOSABLE ELEMENT for details) transpose with the formation of a circular intermediate.

In bacteria, the chromosomal REP sequences have been reported to be common targets for insertion sequences [BMC Genomics (2006) 7:62].

Transposition frequency varies with insertion sequence and with the physiological state of the host cell. In general, the frequency of transposition ranges from ~10−9 to ~10−5 per IS per cell division.

The presence of an insertion sequence may be indicated e.g. by the effects of its insertion. For example, the presence of IS3 in the finO gene of the F plasmid inactivates the finO gene and results in the ability of this plasmid to behave as a constitutively derepressed conjugative plasmid.

Some insertion sequences are used as markers for detecting or typing particular bacteria – e.g. IS900 has been used as a specific marker for Mycobacterium paratuberculosis. IS6110 is regarded as specific for the Mycobacterium tuberculosis complex; different strains contain different numbers of copies of IS6110 – e.g. the genome of the reference strain of M. tuberculosis (H37rv) contains 16 copies, while some strains apparently lack the sequence. Strains of M. bovis generally contain a single copy.

[Diversity of insertion sequences in the Archaea: Microbiol Mol Biol Rev (2007) 71(1):121–157.]

(See also entries for some individual insertion sequences under ‘IS’.)

insertion vector A CLONING VECTOR into which target DNA can be inserted, at one restriction site, without the need to remove non-essential DNA

(cf. REPLACEMENT VECTOR.)

insertional targeting vector See VECTOR.

insulator See CHROMATIN INSULATOR.

insulin aspart The (non-commercial) name for a genetically engineered short-acting form of human insulin: see INSULINS. insulin glargine The (non-commercial) name for a genetically engineered long-acting form of human insulin in which the C-terminal residue in the A chain is replaced with a glycine residue and the B chain has two additional arginine residues.

The recombinant protein is produced in Escherichia coli.

(See also INSULINS.)

[Use of insulin glargine for studying streptozotocin-induced diabetic mice: Cardiovasc Diabetol (2007) 6:6.]

insulins (recombinant) Any of various forms of insulin, some short-acting and some long-acting, which are produced by recombinant DNA techniques in a range of commercial organizations; some of these engineered insulins are synthesized in Escherichia coli and others are synthesized in the yeast

Saccharomyces cerevisiae.

The native (human) insulin molecule consists of two polypeptide chains, A and B, of 21 and 30 amino acid residues, respectively, that are held together by two disulfide bridges. Even small changes in this molecule can cause significant changes in biological activity. For example, replacement of the proline residue at position B28 by an aspartic acid residue gives rise to a short-acting insulin (insulin aspart – compare

INSULIN GLARGINE).

(See also HUMAN INSULIN CRB and HUMAN INSULIN PRB.)

Porcine insulin differs from human insulin by only a single amino acid residue, and it has little immunogenicity in man; it can be converted enzymically/chemically to a form which has the same composition as human insulin.

Bovine insulin differs from human insulin by three amino acid residues, and it does trigger an immunological response in humans.

int gene (phage λ) See PHAGE LAMBDA.

integrase See RECOMBINASE.

integration host factor (IHF) In Escherichia coli: a multifunctional, heterodimeric protein with contributory roles that include e.g. expression of the F plasmid, on–off switching of type I fimbriae, promotion of sigma factor specificity, and integration of the phage λ genome into the host cell chromosome.

integrin Any of a specific category of cell adhesion molecules which form part of the cytoplasmic membrane in many types of eukaryotic (including mammalian) cell and which have roles in various aspects of physiology. The integrin molecule is a heterodimer consisting of α and β protein subunits linked non-covalently. There are many types of α subunit but only relatively few types of β subunit; the particular combination of α and β subunits in any given integrin determines its distribution and biological properties.

The β1 integrins, which occur e.g. in epithelial cells, have important roles in cell–cell and cell–matrix interactions; the matrix components to which these integrins bind include e.g. collagen, fibronectin and laminin. As well as the maintenance of tissue structure such binding is also involved in generation of signals that influence a range of cell functions, including aspects of the cell cycle.

Integrins of the β1 group may also act as receptors for the specific adhesins of invasive pathogenic bacteria.

The β2 integrins can be expressed by leukocytes and may also serve as receptors for bacterial adhesins. Many integrins bind, via their α subunit, to ligands containing the RGD motif (arginine–glycine–aspartic acid motif); this motif is mimick-

ed by the FHA (i.e. filamentous hemagglutinin) of the Gramnegative bacterial pathogen Bordetella pertussis – binding between FHA and the αMβ2 integrin (= Mac-1) on an activated macrophage facilitating uptake by the macrophage [see also Infect Immun (2005) 73(11):7317–7323].

Inadequate expression of β2 integrins by leukocytes results in the failure of these cells to respond normally in the process of inflammation (= leukocyte adhesion deficiency, LAD); those with this condition are more susceptible than others to infectious diseases.

A β3 integrin (αIIbβ3), found e.g. on blood platelets, binds to ligands which include fibrinogen, von Willebrand factor and fibronectin; deficiency of this integrin leads to defective platelet agglutination (GLANZMANN’S THROMBASTHENIA).

A given integrin may be denoted by two CD numbers, one number referring to the α subunit, the other to the β subunit; for example, LFA-1 (leukocyte function-associated antigen-1) is CD11a/CD18, and the Mac-1 integrin is CD11b/CD18.

integron A segment of DNA containing (i) a gene encoding a recombinase (integrase) and (ii) site(s) (att) for the insertion or excision of one or more gene cassettes – such insertion or excision being mediated by the integrase.

Resistance integrons characteristically contain genes that encode resistance to antibiotics and/or to disinfectants. These integrons are found in bacterial chromosomes and also in plasmids and transposons. They have been divided into three classes on the basis of e.g. structure and distribution; resistance integrons of class 2 are associated with transposons of the Tn7 family and are found in Gram-negative species.

Super-integrons are species-specific elements which may contain up to ~100 gene cassettes that encode a variety of functions; they are chromosomal elements.

intein In some proteins: an internal sequence of amino acids which is able to catalyze its own excision (self-splicing) and to join the flanking regions (exteins) to form a functional protein; a branched polypeptide (having two N terminals and one C terminal) is formed as an intermediate product in the splicing process.

At least some excised inteins exhibit the properties of a site-specific endonuclease (homing endonuclease). Such an intein can (in e.g. the VMA1 gene of Saccharomyces cerevisiae) mediate insertion of an intein-encoding sequence into an intein-less copy of the gene; the latter is cleaved (at the site normally occupied by an intein) and an intein sequence that is copied from the intein-containing allele is inserted. The ability of an intein to mediate the insertion of its own coding sequence into an intein-less copy of the gene is called intein homing.

(See also INTRON HOMING.)

The sequence-specific characteristic of the homing endonucleases – which are also called meganucleases – has been exploited e.g. in promoting homologous recombination in the vicinity of their specific target sequences. It was suggested that these enzymes might be useful for inserting transgenes at specific (rather than random) locations in the

context of gene therapy. However, given the limited repertoire of naturally occurring homing endonucleases, it would probably be difficult to find an enzyme that could promote the insertion of a particular, chosen transgene; for this reason, a combinatorial approach has been used to create artificial homing endonucleases that cleave specific, chosen sequences [Nucleic Acids Res (2006) Nov 27 doi: 10.1093/nar/ gkl720].

First discovered in the yeast VMA1 gene, inteins also occur e.g. in the bacterium Mycobacterium tuberculosis (recA gene [Nucleic Acids Res (2003) 31(14):4184– 4191]), the archaean Thermococcus litoralis (DNA polymerase gene) and in some algal viruses (DNA polymerase gene [Appl Environ Microbiol (2005) 71(7):3599–3607]); they have also been reported in the alga Chlamydomonas reinhardtii [BMC Biol (2006) 4: 38].

intein homing See INTEIN.

intercalating agents Molecules that contain a planar chromophore which can insert (intercalate) between adjacent base pairs in double-stranded nucleic acids; a bifunctional intercalating agent has two planar chromophores per molecule. The effects of intercalation may include e.g. local unwinding of the duplex.

In linear dsDNA, intercalation results in an increase in viscosity and a reduction in the sedimentation coefficient. In ccc dsDNA intercalation results e.g. in a local increase in pitch and changes in the viscosity of the DNA solution – and in the sedimentation coefficient of the DNA. Nicked circular (or linear) molecules of DNA can bind more molecules of an intercalating agent than can an equivalent ccc dsDNA mole-

cule (see also ETHIDIUM BROMIDE).

When one molecule of an intercalating agent inserts at a given site it inhibits the insertion of another molecule in the adjacent two or three base pairs (the neighbor exclusion principle).

Intercalation in vivo can inhibit transcription and replication and may also induce mutations. Lower concentrations of e.g. some acridines, or of ethidium bromide, may selectively block replication of small bacterial plasmids (see CURING).

Intercalating agents include ACTINOMYCIN D, anthracy-

clines, ETHIDIUM BROMIDE, PSORALENS, QUINOXALINE ANTI-

BIOTICS and tilorone.

intergenic repeat unit Syn. ERIC SEQUENCE. intergenic spacer region (ISR) See RRN OPERON. intergenic suppression See SUPPRESSOR MUTATION.

International Nucleotide Sequence Database Collaboration

A joint, collaborative project involving the DNA DataBank of Japan (DDBJ), European Molecular Biology Laboratory (EMBL) and GenBank (NCBI: National Center for Biotechnology Information).

interrupted gene Syn. SPLIT GENE.

interrupted mating A method once used to study the transfer of genes, from donor to recipient cell, during conjugation. At

time zero, a population of (Hfr) donors is mixed with a population of recipients; samples are removed from the mating mixture at regular intervals and are plated in order to select recombinants. Donor genes are transferred to recipient cells sequentially (according to their positions on the chromosome) so that a given donor gene will appear in recombinants after a characteristic interval from time zero.

In Escherichia coli the entire chromosome may be transferred in ~100 minutes, although, as time progresses, there is an increasing chance of strand breakage.

Interrupted mating has been used for genetic mapping. interstitial junction sequence See TRANSPOSABLE ELEMENT. intervening sequence Syn. INTRON.

intrabody A genetically engineered form of an antibody which remains within the cell in which it is synthesized. Intrabodies have been used in studies on GENE THERAPY (q.v.).

intragenic suppression See SUPPRESSOR MUTATION. intramer An (intracellular) APTAMER (sense 1) which has been

transcribed within a cell.

[Example of use: Proc Natl Acad Sci USA (2004) 101(31): 11221–11226.]

intron (intervening sequence) A sequence that occurs between those regions (exons) in a SPLIT GENE (q.v.) which, collectively, make up the coding sequence of that gene; introns are found in the split genes of eukaryotes, archaeans, bacteria and viruses.

Normally, the expression of a given split gene requires (i) transcription followed by (ii) excision of those sequences that correspond to the introns – and ligation (i.e. joining together) of the exonic regions to form a continuous coding sequence (i.e. a mature mRNA).

In human pre-mRNA, the excision of introns occurs by a complex process involving a SPLICEOSOME (see SPLICING).

At least some of the introns in bacteria and bacteriophages are autocatalytic (i.e. self-splicing).

(See also INTRON HOMING.)

intron homing (in bacteria) The replicative spread of a given intron to an intron-less allele. For a group I intron, homing begins with a typically double-stranded cut in the intron-less allele made by a homing endonuclease (which is encoded by the intron). During repair, the intron is used as template, so that a copy of that intron is inserted into the intron-less gene.

(See also INTEIN.)

For a group II intron, an RNA copy of the intron complexes with an intron-encoded protein. This complex makes a double-stranded cut in the target site and inserts the strand of RNA; a cDNA copy is made and the RNA is replaced by DNA. This process has been termed retrohoming (because of the involvement of an RNA intermediate).

[Review of intron homing: J Bacteriol (2000) 182:5281– 5289.]

intron retention See ALTERNATIVE SPLICING.

inv–spa genes See PATHOGENICITY ISLAND (Salmonella).

inverse affinity nested PCR (IAN-PCR) See METAGENOME. inverse PCR A form of PCR which is used e.g. for amplifying

the (unknown) DNA that flanks a known sequence (on both sides) in a circular molecule. Inverse PCR is useful e.g. for investigating the site of insertion of a transposon in a plasmid or a chromosome.

In inverse PCR the primers are complementary to the two terminal (end) regions of the known sequence. However, unlike the normal arrangement in PCR, when these primers are bound to their complementary sequences they are extended in opposite directions, i.e. outwards, into the unknown flanking sequence on each side.

If the known sequence (e.g. transposon) has inserted into a long molecule (e.g. a bacterial chromosome), the initial task is to cut the molecule (with a RESTRICTION ENDONUCLEASE) and obtain the known sequence, together with both flanking regions, on a small, linear restriction fragment. This fragment is then circularized through hybridization and ligation of the STICKY ENDS. (Circularization can be promoted by carrying out the ligation with low concentrations of the fragments; in this way, the sticky ends on a given fragment are more likely to hybridize with each other than with sticky ends on another fragment.)

The circularized fragments are amplified by PCR, using the primers as described above. The resulting amplicons contain parts of the known sequence, i.e. the primer-binding sites at each end, and also the unknown (original flanking sequences) which now form the main (continuous) central region of each amplicon. The amplicons can then be cloned and sequenced etc.

Other uses of inverse PCR include e.g. the preparation of deletion mutations (see e.g. SITE-DIRECTED MUTAGENESIS) and preparation of full-length cDNAs (see CAPfiNDER).

inverted repeat (IR) In a given, double-stranded molecule of nucleic acid, either of two sequences such as:

i.e. sequences which are identical, with the same polarity, but opposite in orientation. The two sequences may or may not be contiguous. (cf. PALINDROMIC SEQUENCE.)

In single-stranded nucleic acids an IR is equivalent to one of the two strands in a double-stranded IR; such IRs can e.g. form hairpin structures.

Typically, a pair of inverted repeats form the two terminal

sequences in each TRANSPOSON and INSERTION SEQUENCE,

although in some transposable elements (see e.g. IS1111) the inverted repeats are in subterminal locations.

IPTG Isopropyl-β-D-thiogalactoside: a synthetic inducer of the lac operon, i.e. it inhibits the repressor system of that operon. As IPTG is not a substrate for β-galactosidase it is referred to as a gratuitous inducer.

(See also ALLOLACTOSE.) IR INVERTED REPEAT.

IRES Internal ribosomal entry site: a specific segment of RNA (first obtained from the encephalomyocarditis virus, EMCV)

which, when present in mRNAs, promotes high-level, CAP- independent synthesis of proteins in mammalian cells (and in in vitro systems) in monocistronic and bicistronic vectors. (The designation IRES is also used to refer to segments from other organisms/cells which promote cap-independent translation in eukaryotes.)

Versions of the EMCV IRES, that differ in sequence, have been widely used in a range of studies. These versions do not behave in the same way (e.g. they can exhibit a requirement for different types of translation factor) and so may behave differently in different types of cell. Accordingly, the results reported in studies involving EMCV IRES should include precise details of the particular IRES sequence used. [Translational efficiency of EMCV IRES in bicistronic vectors: BioTechniques (2006) 41(3):283–292].

iRNA/DNA See OKAZAKI FRAGMENT.

IRS Internal resolution site: see TN3.

IS INSERTION SEQUENCE.

IS element Syn. INSERTION SEQUENCE.

IS1 A 768-bp INSERTION SEQUENCE present e.g. in some R plasmids (which encode antibiotic-resistance), in the chromosome of strains of Escherichia coli K12, and in the genome of phage P1.

Target sites for IS1 appear to occur preferentially in ATrich regions, and insertion may generate 9-bp or 8-bp targetsite duplication.

IS5 A 1195-bp INSERTION SEQUENCE present in the chromosome of strains of Escherichia coli K12.

IS101 A 209-bp defective (gene-less) INSERTION SEQUENCE; transposition of IS101 depends on functions encoded by the insertion sequence IS1000. (The inverted repeat sequences of IS101 are similar, but not identical, to those of IS1000.)

IS911 An INSERTION SEQUENCE which forms a circular intermediate (‘minicircle’) between excision and insertion into the target sequence. During circularization (see TRANSPOSABLE ELEMENT) juxtaposition of the inverted repeats (separated by the intervening junction sequence) brings together a −35 box and a −10 box at an optimal distance to provide an efficient promoter.

IS1000 (γδ) A 5.8-kb INSERTION SEQUENCE that has extensive homology with the DNA of transposon Tn3.

IS1071 A 3.2-kb INSERTION SEQUENCE, often associated with xenobiotic-degrading genes, in which the 110-bp terminal inverted repeats and the transposase gene are related to those of class II transposons. Transposition of IS1071 involves the formation of a cointegrate, and a 5-bp target-site duplication is produced at the site of insertion.

[Functional analysis of IS1071: Appl Environ Microbiol (2006) 72(1):291–297.]

IS1111 An atypical INSERTION SEQUENCE that is characterized by subterminal inverted repeats, the absence of target-site duplication on transposition, and the formation of a circular intermediate between excision and insertion into the target

site.

(See also ISEC11.)

IS6110 An insertion sequence apparently specific to members of the Mycobacterium tuberculosis complex – see INSERTION SEQUENCE for further details.

(See also W-BEIJING STRAIN.)

ISEc11 An INSERTION SEQUENCE, related to members of the IS1111 family, present in the chromosome (and the virulence plasmid pINV) in a strain of enteroinvasive Escherichia coli (EIEC) [J Bacteriol (2006) 188(13):4681–4689].

ISH In situ hybridization: a PROBE-based procedure for detecting a target sequence in situ (at a normal or aberrant location within cells or tissues or e.g. within an in vitro preparation of chromosomes). A probe used for ISH – or a conjugate which is subsequently bound to a hybridized probe – may exhibit any of various types of label. Radioactive labels were widely used in the early protocols; fluorescent labeling (see fiSH) is currently popular.

ISH has various applications in the study of structure and function in the biological sciences. In medicine it can be used e.g. to detect certain pathogens in clinical samples by using probes that bind to pathogen-specific sequences; in certain cases (e.g. Mycobacterium tuberculosis) a pathogen may be detected by ISH significantly earlier than it could be detected by culture. (ISH may also be able to distinguish virulent from non-virulent strains of an organism by the use of probes for specific virulence factors.)

ISHp608 An INSERTION SEQUENCE, present in a plasmid in Helicobacter pylori, which excises as a circular element; the break in the parent molecule is resealed. Transposition is sitespecific (5′-TTAC-3′) [EMBO J (2005) 24(18):3325–3338]. island rescue PCR A form of PCR which has been used e.g. for the amplification of CPG ISLAND sequences from inserts in artificial chromosomes (e.g. YACs). This approach relies on the presence, in the insert, of (i) an ALU SEQUENCE (Alu sequences are common in the human genome), and (ii) a GCrich recognition site for a RESTRICTION ENDONUCLEASE such as BSSHII; GC-rich cleavage sites are commonly found to be

associated with CpG islands.

Artificial chromosomes are cut with the restriction enzyme, and the linear fragments are ligated to vectorette linkers (see VECTORETTTE PCR). PCR is then carried out with a primer specific for an Alu sequence and a vectorette-specific primer. isochore In human genomic DNA: a long sequence of nucleotides (of the order of hundreds of kilobases in length) that is characterized by a uniform, or near-uniform, content of the bases guanine + cytosine (G + C); the G + C content differs among different isochores. Isochores can be classified in five

groups according to their G + C content.

Isochore mapping of the human genome revealed ~3200 isochores (which cover the entire genome) [Genome Res (2006) 16(4):536–541].

A web-based tool (called GC-profile) has been devised for analyzing variation in G + C content in sequences of genomic DNA [GC-profile: Nucleic Acids Res (2006) 34(Web Server

issue): W686–W691].

isoniazid (INH) Isonicotinic acid hydrazide: a synthetic antibiotic, used as an anti-tuberculosis drug, which is bactericidal for actively growing cells of e.g. Mycobacterium tuberculosis (and some other mycobacteria). The antibacterial function of isoniazid depends on its intracellular activation by a catalase (the katG gene product). The catalase-activated drug appears to inhibit synthesis of the essential cell-wall mycolic acid.

Resistance to isoniazid may result from mutation in any of several genes, including katG and ahpC.

(See also LINE PROBE ASSAY.)

isoschizomer A RESTRICTION ENDONUCLEASE whose recog-

nition site is identical to that of another restriction enzyme. In general, the restriction enzyme which is first shown to recognize a particular sequence is called the prototype (in relation to that sequence); a prototype may have many isoschizomers (which can occur in different species).

An isoschizomer whose cutting site (within the recognition site) differs from that of the prototype is referred to as a neoschizomer.

isotachophoresis (ITP) A form of ELECTROPHORESIS in which fragments of nucleic acid of different sizes can be focused into a single band, i.e. in this procedure the electrophoretic mobility of polynucleotides is independent of size. DNA has been isolated from biological fluids by ITP and then analyzed by PCR [BioTechniques (2005) 39(5):695–699]; the DNA in such fluids may contain specific mutant alleles associated with cancer, so that ITP may be useful for the diagnosis and monitoring of cancer.

isotopic labeling (of probes) See PROBE LABELING.

ISR Intergenic spacer region: see RRN OPERON.

iteron One of a series of tandemly repeated (‘reiterated’) sequences of nucleotides found e.g. in the origin of replication of certain types of PLASMID. [Example of use: Proc Natl Acad Sci USA (2005) 102(8):2856–2861.]

The term ‘iteron’ (singular) has also been used for a series of these sequences.

(See also HANDCUFfiNG.)

ITP ISOTACHOPHORESIS.

ITR Inverted terminal repeat – see e.g. ADENOVIRUS.

iutA gene In Escherichia coli: the gene encoding an outer membrane protein that acts as a receptor for the siderophore aerobactin (and for a colicin: cloacin DF13).

IVET In vivo expression technology: a method used originally to detect those genes (in a pathogen) that are expressed only during infection of the host animal; genes expressed only during infection may be virulence genes, and their identification can be followed-up e.g. with animal tests using strains of the pathogen which have mutations in the relevant genes.

The principle of IVET is shown diagrammatically in the figure.

The IVET principle is now exploited in different contexts. For example, the method was used to identify those genes of the plant pathogen Erwinia amylovora which are induced during infection of immature pear tissue [J Bacteriol (2005) 187(23):8088–8103], and has also been used to investigate in

vivo gene expression in Lactobacillus reuteri during fermentation of sourdough [Appl Environ Microbiol (2005) 71(10): 5873–5878].

[IVET for exploring niche-specific gene expression: Microbiol Mol Biol Rev (2005) 69(2):217–261.]

Jacob–Monod model An early model (~1960) for the system now known as an OPERON.

JAK kinase A member of the family of JANUS KINASES. janiemycin A polypeptide with antibacterial activity; it inhibits

transglycosylation during synthesis of the cell-wall polymer peptidoglycan.

Janus kinases A family of cell-membrane-associated tyrosine kinases – see e.g.

OF TRANSCRIPTION.

(See also TYROSINE KINASE.)

Java codon adaptation tool See CODON BIAS.

JC virus An icosahedral virus with a ccc dsDNA genome that belongs to the polyomavirus group. JC virus infects humans and other mammals; it can be oncogenic in newborn rodents, can transform certain types of cell in culture, and in immunocompromised humans (e.g. AIDS patients) it can give rise e.g. to a fatal demyelinating condition known as progressive multifocal leukoencephalopathy (PML).

JC virus is similar to another human polyomavirus, the BK virus. Detection and differentiation of these two viruses (in cerebrospinal fluid, serum and urine) has been reported with a commercial hybridization assay [J Clin Microbiol (2006) 44(4):1305–1309].

JCat See CODON BIAS.

JM109 A strain of Escherichia coli used e.g. for cloning; it has mutations in various genes, including endA, recA, relA and supE, and is suitable for blue–white screening and for singlestrand rescue.

juglone A compound, 5-hydroxy-1,4-naphthoquinone, found in leaves and roots of walnut (Juglans), with antibacterial and antifungal activity. [Transcription-blocking activity: Nucleic Acids Res (2001) 29:767–773; possible immunosuppressant activity: PLoS ONE (2007) 2(2):e226.]

jumping gene Syn. TRANSPOSABLE ELEMENT.

junction-resolving enzyme See HOLLIDAY JUNCTION.

K (1) A specific indicator of ambiguity in the recognition site of a RESTRICTION ENDONUCLEASE or in another nucleic acid sequence; for example, in CMG↓CKG (enzyme NspBII) the ‘K’ indicates G or T. (In RNA ‘K’ indicates G or U.) In this example, ‘M’ is A or C.

(2) L-Lysine (alternative to Lys). K-ras See RAS.

Kaiso protein A protein that binds to DNA containing methylCpGs; the binding involves a characteristic zinc finger motif. The protein also binds to the sequence: CTGCNA.

Mice with a null mutation in the Kaiso gene were found to show resistance to intestinal cancer; this has suggested the possibility that Kaiso may be a potential target for therapeutic intervention [Mol Cell Biol (2006) 26(1):199–208].

The Kaiso-like proteins designated ZBTB4 and ZBTB38, unlike Kaiso, can bind to single methylated CpGs [Mol Cell Biol (2006) 26(1):169–181].

(See also MBD PROTEINS.)

kanamycin An AMINOGLYCOSIDE ANTIBIOTIC used e.g. as a

selective agent for bacteria containing a vector which carries a kanamycin-resistance gene.

Kaposi’s sarcoma A form of sarcoma found e.g. in immunosuppressed patients, including those with AIDS. It has been associated with human herpesvirus 8 (HHV-8).

In vitro activation of latent HHV-8 was achieved by promoter demethylation using the reagent tetradecanoylphorbol acetate (TPA); a relationship was suggested between methylation status, transactivation, and the occurrence of HHV-8- mediated disease.

vIL-6, a form of interleukin-6 which is encoded by HHV-8, and which is apparently associated with pathogenesis, has been targeted by an intrabody [J Virol (2006) 80(17):8510– 8520].

karyogram See IDIOGRAM.

karyolysis (histopathol.) Degradation of a eukaryotic nucleus with loss of affinity for basic dyes.

(cf. KARYORRHEXIS.) karyomere See MACRONUCLEUS.

karyonide (ciliate protozool.) A clone of cells whose macronuclei are derived from the same parental macronucleus. karyopherins In eukaryotic cells: agents involved in transport

of proteins/nucleoprotein complexes between the nucleus and

the cytoplasm; they include the exportins and the importins. Exportin 1 is also called CRM1.

karyoplast An isolated eukaryotic nucleus enclosed within a sac of cytoplasmic membrane that includes a small amount of cytoplasm.

karyorrhexis (histopathol.) The fragmentation of a eukaryotic nucleus.

(See also KARYOLYSIS and PYKNOSIS.)

karyosome A nucleolus-like body, or a nucleolus.

karyotic Refers to those cells which contain a nucleus: most of the cells of eukaryotes – but not e.g. erythrocytes (red blood cells).

karyotype A representation of (all) the chromsomes in the nucleus of a given type of eukaryotic cell, showing their size and morphology (usually) at metaphase.

(cf. IDIOGRAM.)

kasugamycin An AMINOGLYCOSIDE ANTIBIOTIC which has

antibacterial activity mainly against Gram-positive species; it has also been used to control rice blast disease caused by the fungus Pyricularia oryzae.

(See also ANTIBIOTIC.)

katG gene See ISONIAZID and LINE PROBE ASSAY.

kb Kilobase, i.e. a length of 103 bases in a single-stranded (or sometimes double-stranded) nucleic acid. In double-stranded nucleic acids a length may be given in base pairs (bp) or in kilobase-pairs (kbp).

kbp Kilobase-pairs: see KB.

kDNA See KINETOPLAST.

kdpABC operon See TWO-COMPONENT REGULATORY SYSTEM.

Kemptide sequence The sequence of amino acid residues – leucine-arginine-arginine-alanine-serine-leucine-glycine (also written LRRASLG) – in a peptide tag which is used e.g. in a test system for the enzyme cAMP-dependent protein kinase A (PKA); the Kemptide sequence is phosphorylated by PKA.

The Kemptide sequence is also used as a tag that is suitable for in vitro labeling of recombinant proteins expressed in E. coli.

Kepivance® See BIOPHARMACEUTICAL (table).

Ki-ras See RAS.

Kid See PARD SYSTEM.

(See also R1 PLASMID.)

killer factor (in Saccharomyces cerevisiae) In ‘killer’ strains of S. cerevisiae: any of several secreted protein toxins encoded by a cytoplasmically inherited dsRNA element. Type 1 (or K1) killer strains form the K1 toxin – which binds initially to the cell wall of a sensitive cell and subsequently disrupts the cytoplasmic membrane.

(cf. KILLER PLASMIDS.)

killer plasmids (in yeasts) In some strains of Kluyveromyces marxianus: two linear, multicopy dsDNA plasmids (pGl1 and pGl2); cells containing these plasmids produce a glycoprotein toxin that kills (sensitive) strains of e.g. Candida, Kluyveromyces and Saccharomyces.

Killer plasmids can be transferred to other yeasts, e.g. by protoplast fusion; the recipients then exhibit the killer pheno-

type.

(cf. KILLER FACTOR.)

kilobase See KB.

Kineret® See BIOPHARMACEUTICAL (table).

kinetochore In eukaryotic chromosomes: either of the two multi-protein structures that assemble on both sides of the centromere at cell division; they are involved e.g. in attachment to the spindle and in regulating alignment of chromosomes prior to anaphase.

The outer part of a vertebrate’s kinetochore includes micro- tubule-binding proteins (such as CENP-E), while the inner part includes e.g. CENP-A, -B, -C, -H and -I proteins, which keep their positions throughout the cell cycle.

A knock-out mutation of CENP-A was reported to result in misaggregation of the kinetochore [Mol Cell Biol (2005) 25 (10):3967–3981].

kinetoplast A complex network of catenated DNA molecules (kDNA) within the mitochondrion in protozoa of the order Kinetoplastida (e.g Trypanosoma). There are ~20–50 large circular molecules (maxicircles) and several thousand small circles (minicircles).

Maxicircles appear to be equivalent to mitochondrial DNA in other eukaryotes (encoding e.g. rRNA and proteins).

Minicircles encode most of the guide RNAs (gRNAs) that are involved in RNA EDITING [kDNA: Eukaryotic Cell (2002) 1:495–502].

The mitochondrion (including the kinetoplast) divides prior to cell division.

Division of the kinetoplast can be inhibited by certain intercalating agents, e.g. some phenanthridine derivatives such as ethidium bromide.

Kis See PARD SYSTEM.

kit (KIT) An ONCOGENE present in a strain of feline sarcoma virus. The c-kit product is a transmembrane protein with tyrosine kinase activity in the cytoplasmic region; it binds to, and enhances the activity of, stem cell factor (= kit ligand; mast cell growth factor; steel factor), an agent which can e.g. stimulate the proliferation of mast cells and regulate the growth/ survival of hemopoietic precursors.

c-kit is strongly expressed in certain types of cancer. kit ligand See KIT.

Kleinschmidt monolayer technique A method used for examining molecules of nucleic acid by electronmicroscopy. Nucleic acid is first coated with e.g. cytochrome c and it then forms extended (relaxed) molecules in a monolayer of denatured protein at an air–liquid interface; part of the monolayer is transferred to a grid, shadowed with heavy metal, and examined under the electronmicroscope.

Klenow fragment See DNA POLYMERASE I.

knockdown Refers to an organism in which one or more genes have been inactivated, or to the inactivated genes themselves. knock-in mutation Any engineered change in nucleotide sequence that is designed to promote the expression of a given gene or genes – including gene(s) previously inactivated e.g.

by a KNOCK-OUT MUTATION.

knock-out mutation Any engineered mutation that is designed to nullify the expression of a given gene or genes.

[Improved method for generating knock-out and knock-in mutations in cultured human cells: Nucleic Acids Res (2005) 33(18):e158.]

Kogenate® Recombinant human factor VIII (Bayer) which is used e.g. for therapy in cases of hemophilia A.

[Use (as a standard) for the in vitro assay of factor VIII: Biochem J (2006) 396(2):355–362.]

(See also table in the entry BIOPHARMACEUTICAL.)

Kornberg enzyme Syn. DNA POLYMERASE I.

Kozak sequence A sequence of nucleotides, flanking the init-

iator codon, reported to optimize initiation of translation by eukaryotic ribosomes. In the original paper the sequence was reported as ACCATGG.

[Example of use: Clin Vaccine Immunol (2007) 14(1):28– 35.]

The Kozak sequence is also used e.g. in some vectors of the

EXCHANGER SYSTEM.

KpnI A type IIP RESTRICTION ENDONUCLEASE (see table in

Ku70 protein See GRANZYMES.