Hypermedia Glossary Of Genetic Terms – Birgid Schlindwein’s

Birgid Schlindwein’s

Hypermedia Glossary Of Genetic Terms

Alphabetical list of all 670 items of the glossary

A
Acentric
Acrocentric
Adaptation
Adaptive landscape
Adaptive peak
Adaptive radiation
Adaptive surface
Adaptive value
Addition line
Additive genetic variance
Adenine
Adenosine
AFLP
Alien addition line
Allele
Allele frequency
Allele specific associated primer
Allele specific oligo
Allele specific polymerase chain reaction
Alloenzyme
Allogamy
Alloploidy
Allopolyploidy
Allosome
Allosyndesis
Allotetraploidy
Allozygote
Alpha helix
Altruism
Amino acid
Amphidiploidy
Amphimixis
Amplification
Amplified fragment length polymorphism
Anagenesis
Anaphase
Aneuploidy
Anlage
Anneal
Anticodon
Antisense strand
Apogamy
Apomixis
AP-PCR
Arbitrarily primed polymerase chain reaction
Arbitrary primer
Arrayed library
ARS
ASAP
ASO
AS-PCR
Assortative mating
Autogamy
Autonomous replication sequence
Autopolyploidy
Autoradiography
Autosome
Autozygote
BAC
Back-cross
Bacterial artificial chromosome
Bacteriophage
Base pair
Base sequence
Base sequence analysis
Bioinformatics
Biotechnology
Bivalent
Blotting
bp
Breakpoint
Breed
Breeding line
Bridging cross
Bud
Budding
Bulk selection
Bulked segregant analysis
C
CAPS
Carboxyl terminus
CCAAT box
cDNA
cDNA library
Cell cycle
Cell division
Centimorgan
Central dogma
Centromere
Centromere interference
Character
Chiasma
Chiasma interference
Chimera
Chloroplast
Chloroplast DNA
Chromatid
Chromatin
Chromomere
Chromoneme
Chromosomal address
Chromosome
Chromosome jumping
Chromosome walking
Cis
Cistron
Clade
Cladogenesis
Class
Cleaved amplified polymorphic sequence
Clone
Clone bank
Cloning
Cloning vector
cM
Code
Codominance
Codon
Coefficient of coancestry
Coefficient of inbreeding
Coefficient of parentage
Coefficient of relationship
Comparative mapping
Complementary DNA
Complementary RNA
Complementary sequence
Complementation
Complementation test
Complete linkage
Compound heterozygote
Conjugation
Consanguinity
Consensus sequence
Conserved sequence
Contig
Contig map
Contiguous gene syndrome
Convergence
Convergent evolution
Conversion
COP
Co-segregation
Cosmid
Coupling
cpDNA
CpG island
Cre-loxP system
cRNA
Cross breeding
Crossing
Crossing over
Cultivar
Cytogenetics
Cytology
Cytoplasm
Cytosine
DAF
DAMD
Darwinian fitness
Deficiency
Deletion
Deme
Denature
Denaturing gradient gel electrophoresis
Denaturing high-performance liquid chromatography
Deoxyribonucleic acid
Deoxyribonucleotide
DGGE
DHPLC
Diakinesis
Dicentric
Dichogamy
Dihybrid cross
Dioecious
Diploid
Diplotene
Directed amplification of minisatellite region DNA
Disassortative mating
DNA
DNA amplification fingerprinting
DNA clone
DNA fingerprinting
DNA polymerase
DNA probes
DNA replication
DNA sequence
DNA typing
Domain
Dominance variance
Dominant
Double helix
Downstream
Duplication
Dysgenic
Ectopic
Electrophoresis
Electroporation
Endonuclease
Endosperm
Enhancer
Environment
Environmental variance
Enzyme
Epigenesis
Epigenetic
Episome
Epistasis
Epistatic
Escherichia coli
EST
Euchromatin
Eugenics
Eukaryote
Euploidy
Evolution
Evolutionarily conserved
Exogenous DNA
Exon
Exonuclease
Expressed gene
Expressed sequence tag
Expressivity
F1
F2
Family
Family selection
Fecundity
Fecundity selection
Fertilization
Filial generation
FISH
Fitness
Fixed allele
Flanking region
Flow cytometry
Flow karyotyping
Fluorescence in situ hybridization
Founder effect
Frameshift
Frameshift mutation
G
Gamete
Gametic selection
GBA
G-banding
Geitonogamy
Gene
Gene cluster
Gene dose
Gene expression
Gene family
Gene flow
Gene interaction
Gene library
Gene map
Gene mapping
Gene pool
Gene product
Gene targeting
Gene transfer
Genetic bit analysis
Genetic code
Genetic distance
Genetic diversity
Genetic drift
Genetic engineering
Genetic engineering technologies
Genetic fine structure
Genetic interference
Genetic map
Genetic material
Genetic variance
Genetics
Genome
Genome project
Genomic DNA
Genomic in situ hybridization
Genomic library
Genoplasm
Genotype
Genus
Germ line
Germ line mosaicism
Germplasm
Giemsa banding
Giemsa stain
GISH
Guanine
Haploid
Haploinsufficiency
Haplotype
Hardy-Weinberg equilibrium
Hemizygous
Hereditary
Heredity
Heritability
Herkogamy
Hermaphrodite
Heterochromatin
Heterochromosome
Heteroduplex analysis
Heteroduplex DNA
Heterokaryon
Heteroplasmy
Heterosome
Heterostyly
Heterozygosity
Heterozygote
Histone
Homeobox
Homoduplex DNA
Homokaryon
Homologous chromosome
Homologous recombination
Homology
Homoplasy
Homozygosity
Homozygote
Human gene therapy
Human Genome Initiative
Hybrid
Hybridization
Hydrogen bond
Hypostasis
Hypostatic
Identity
Imprinting
in silico
In situ hybridization
In vitro
In vivo
Inbreeding
Inbreeding coefficient
Inbreeding depression
Incomplete dominance
Informatics
Inheritance
Insert
Insertion
Insertion sequence
Interchange
Interference
Intergenic
Intergenic DNA
Intergenic region
Interkinesis
Interphase
Inter-simple sequence repeat
Intragenic
Intron
Intron boundary skidding
Inverse polymerase chain reaction
Inversion
Inverted repeat
IPCR
IS element
Isoenzyme
Isozyme
ISSR
Karyotype
kb
Kilobase
Kinetochore
Large single copy
Leptotene
Lethal gene
Library
Ligation
Lineage
Linkage
Linkage disequilibrium
Linkage equilibrium
Linkage group
Linkage map
Localize
Loci
Locus
LOD score
m.u.
MAAL
MAAP
Macroevolution
Macrorestriction map
Map Unit
Mapping
Marker
Maternal inheritance
Mating
Mating frequency
Mating system
Mating type
Matroclinous inheritance
Mb
Megabase
Meiosis
Meme
Mendel
Mendel’s first law
Mendel’s second law
Messenger RNA
Metacentric
Metaphase
Methylation
Microsatellite
Migration
Minisatellite
Mispairing
Mitochondria
mitochondrial DNA
Mitosis
Monoclonal
Monoecious
Monogenic
Monohybrid cross
Monosom
Mosaicism
Motif
mRNA
mtDNA
Multifactorial disorder
Multigenic disorder
Multiple allelism
Multiple arbitrary amplicon profiling
Multiplexing
Mutation
Mutator mutation
Natural selection
Negative interference
Neo-darwinism
Nick translation
Nitrogenous base
Nondisjunction
Non-linkage
Nonsense mutation
Northern blotting
Nuclease
Nucleic acid
Nucleolus
Nucleoside
Nucleosome
Nucleotide
Nucleus
Offspring
Oligonucleotide
Oncogene
Ontogeny
Open reading frame
Operator
Operon
Order
ORF
Origin
Orthology
Outbreeding
Overlapping clones
Ovum
P1-derived artificial chromosome
PAC
Pachytene
packaging RNA
Paired box
Panmixia
Parallel evolution
Parallelism
Paralogy
Parthenogenesis
Partial linkage
PCR
PCR-RFLP
Pedigree
Penetrance
Peptide
Permutation
Phage
Phenotype
Phenotypic variance
Phylogenesis
Phylon
Physical map
Plasmid
Plastid
Pleiotropy
Point mutation
Pollination
Poly A RNA
Polyamine
Polygenic
Polygenic disorders
Polymerase chain reaction
Polymorphism
Polypeptide
Polyploid
Polytene
Population
Positional cloning
Positive interference
Postmeiotic Segregation
Preformation
Pribnow box
Primer
Primordium
pRNA
Probability
Probe
Progeny
Prokaryote
Promoter
Prophase
Protein
Proteome
Proteomics
Pseudogene
Pure-breeding
Purine
Pyrimidine
QTL
Quantitative trait
Quantitative trait loci
Random mating
Randomly amplified polymorphic DNA
RAPD
Rare-cutter enzyme
Reading frame
Recessive
Reciprocal cross
Recombinant clone
Recombinant DNA molecule
Recombinant DNA techniques
Recombinase
Recombination
Recombination frequency
Regulatory region
Regulatory sequence
repetitive DNA
Replication
Replicon
Reproduction
Repulsion
Resolution
Restriction enzyme
Restriction enzyme cutting site
Restriction fragment
Restriction fragment length polymorphism
Restriction landmark genomic scanning
Restriction map
Restriction site
Retrotransposon
Retrovirus
Reversal
Reverse transcriptase
Reverse transcription
RFLP
Ribonucleic acid
Ribonucleotides
Ribosomal RNA
Ribosome
RLGS
RNA
RNA polymerase
RNA splicing
rRNA
Satellite DNA
SCAR
SDS-PAGE
Segregation
Segregation distortion
Selection
Self-incompatibility
Selfing
Self-pollination
Self-sterility
Semi-conservative
Sequence
Sequence characterised amplified region
Sequence tagged microsatellite
Sequence tagged site
Sequencing
Sex chromosome
Shotgun method
Similarity
Simple sequence repeat
Single nucleotide polymorphism
Single primer amplification reaction
Single stranded conformational polymorphism
Single-gene disorder
Site
Small single copy
SNP
Somaclonal variation
Somatic cell
Somatic hybrid
Southern blotting
SPAR
Speciation
Species
Sperm
Spireme
Spore
SSCP
SSR
Stasigenesis
STMS
Stop codon
Strain
Strand
Structural change
Strucutural gene
STS
Survival
Synapsis
Synapton
Synaptonemal complex
Syndesis
Synteny
T
Tandem repeat sequence
TATA box
Taxon
Technology transfer
Telomerase
Telomere
Telophase
Template
Termination codon
Terminator
Test-cross
Tetrad
TGGE
Thermal gel gradient electrophoresis
Thymine
Trait
Trans
Transcript
Transcription
Transcription start site
Transduction
Transfection
Transfer RNA
Transformation
Transgenic
Transition
Translation
Translocation
Transposable element
Transposase
Transposition
Transposon
Transversion
Trisomy
tRNA
True-breeding
U
Undermethylation
Upstream
Uracil
Variable-number tandem-repeat
Variation
Variety
Vector
Viability
Virus
VNTR
Western blotting
Wild-type
Xenogamy
YAC
Yeast artificial chromosome
Zygote
Zygotene

Web source : http://hal.weihenstephan.de/genglos/asp/genreq.asp?list=1

Abortive transduction

An event where the fragment of DNA introduced by transduction fails to be recombined into the recipient chromosome and because the DNA fragment lacks an origin of replication it is only inherited by one of the daughter cells at each cell division.

Acrylamide

Used to make polyacrylamide gels for separation of macromolecules by electrophoresis. Polyacrylamide gels are produced by polymerization of acrylamide into linear chains and cross-linking the acrylamide chains with bis-acrylamide (N,N’-methylene-bis-acrylamide). Polymerization is initiated by adding ammonium persulfate and the reaction is accelerated by TEMED (N,N,N’,N’-tetramethylethylenediamine) which catalyzes the formation of free radicals from ammonium persulfate. Acrylamide gels are generally poured between glass plates because oxygen inhibits the polymerization because oxygen radicals formed can interact with acrylamide and terminate chain elongation.

Activator

A gene product (usually protein) that positively regulates transcription. Activators may either increase binding of RNA polymerase to the promoter (closed complex formation) or stimulate RNA polymerase to begin transcription (open complex formation).

Active site

The region of an enzyme responsible for catalysis.

Adaption

The ability to physiologically adjust to a new environment while exposed to that particular environment. Typically cells de-adapt when transferred to different growth conditions.

Adenosine triphosphate (ATP)

A compound with high energy phosphate bonds that provide the energy for many cellular processes.

Aerobic

The presence of oxygen. Often used to describe an organism that requires oxygen for growth or growth conditions with oxygen.

Affinity

The strength of an interaction between two molecules, such as the binding of an antigen to an antibody.

Agarose

An uncharged polysaccharide purified from agar. Agarose melts when heated to 100 C and resolidifies when cooled below about 50°C. When it solidifies agarose forms a matrix. The size of the pores in the gel matrix can be varied by using different concentrations of agarose: the higher the concentration of agarose, the smaller the pore size.

Alkylating agent

An organic compound able to transfer an alkyl group to nucleotides.

Alleles

Alternative forms of a gene. For example, the mutants putA601 and putA736 each have a different mutation in the putA gene.

Allele specific suppressor

A second-site mutation that repairs the mutant phenotype but only in strains with certain, specific mutations at the first-site.

Allosteric

The stereospecific modification of a protein by an effector to influence the activity of another site of the protein.

Alpha-complementation

The ability of a short N-terminal fragment of beta-galactosidase to interact with the C-terminal portion of beta-galactosidase to form a functional enzyme.

Amber codon

The UAG nonsense codon. This is one of the three normal chain termination or stop codons that does not code for any amino add in the universal code.

Amber mutation

A mutation that creats an amber codon (UAG) from a different codon.

Amber suppressor

A mutant tRNA gene that recognizes the UAG codon but is aminoacylated and inserts the amino acid at the corresponding position in the growing polypeptide.

Ames test

A genetic test for the identification of carcinogens based upon their mutagenic activity initially developed by Bruce Ames. The test relies upon the ability of a chemical or physical agent to promote the reversion of different classes of mutations that cause histidine auxotrophy.

Amino acid analog

See analog.

Ampicillin (Amp)

An antibiotic that inhibits crosslinking of peptidoglycan chains in the cell wall of eubacteria. Cells growing in the presence of ampicillin synthesize weak cell walls, causing them to burst due to the high internal osmotic pressure. Amp resistance encoded by most transposons and plasmids is due to a periplasmic Beta-lactamase that breaks the Beta-lactam ring of ampicillin. Ampicillin is a derivative of penicillin.

Anaerobic

The absence of oxygen. Often used to describe an organism that is sensitive to oxygen or growth conditions without oxygen.

Analog (or the British spelling Analogue)

A chemical that is similar, but not identical, to another chemical. For example, thioproline is an analog of the amino acid proline, and azaguanine is an analog of the nucleotide guanine. Certain analogs are toxic and can be used to select for mutants that affect the synthesis or metabolism of the corresponding compound.

Angstrom

A unit of measurement that was widely used until recently to describe molecular dimensions, but the unit nanometer (nm) is now more commonly used. One angstrom equals 10 nm.

Antigenic drift

The accumulation of mutations that modify a molecule on the cell surface of a pathogen and thereby alters recognition by the host immune system. These changes prevent preexisting antibodies from recognizing the invading pathogen. This process is most often used to describe viruses. (See Antigenic variation below)

Antigenic variation

A change in the types or amounts of a molecule on the cell surface of a pathogen that alters recognition by the host immune system. Antigenic variation can occur by altering a variety of surface molecules including proteins and carbohydrates. There are many molecular mechanisms for antigenic variation, including inversion, recombination between multiple casettes, and hypermutation. Antigenic variation occurs in eukaryotic microbes (e.g. Trypanosomes), bacteria (e.g. Neisseria gonorrhoeae, and Salmonella enterica), and viruses. The change in surface antigens due to mutation, recombination, or chromosome reassortment in viruses is called antigenic drift.

Annealing

Pairing of a single-stranded nucleic acid with the complementary strand to form a duplex.

Antibiotic

A substance that interfers with a particular step of cellular metabolism, causing either bactericidal or bacteriostatic inhibition; sometimes restricted to those having a natural biological origin.

Antibody

A protein complex that specifically interacts with an antigen.

Anticodon

The three bases in a tRNA that are complementary to those in the codon of the mRNA.

Antigen

A substance that interacts with an antibody.

Antimutator

A mutation that decreases the overall mutation rate, often by modifying DNA polymerase.

Antisense RNA

An RNA molecule that can hybridize to an mRNA molecule. Hybridization of an antisense RNA molecule to the translation start sites on an mRNA prevents the initiation of translation. For example, an antisense RNA is involved in the regulation of transposase expression from Tn10.

Anti-terminator

A protein that allows RNA polymerase to continue transcription through a transcription termination site.

AP endonuclease

An endonuclease which recognizes an AP site and cuts the defective strand on the 5′ side of the missing base.

AP site

A molecule of single-stranded or double-stranded DNA missing a purine or pyrimidine base.

Aporepressor

A protein that requires binding of a small molecule co-repressor to negatively regulate gene expression.

Apurinic or apyrimidinic (AP) site

A molecule of single-stranded or double-stranded DNA missing a purine or pyrimidine base.

Apoptosis

Cell death due to a intracellular developmental program or induced by other cells.

A priori

Deduced from first principles; without prior knowledge.

Archae

One of the three domains of living organisms: Archae, Bacteria, and Eukarya. Although they share a basic morphology with bacteria and they are also prokaryotes (i.e. they lack a nuclear membrane), in many molecular details they resemble eukaryotes more than bacteria. Previously called Archaebacteria. First described by Carl Woese at the University of Illinois.

A site

The binding site for the aminoacyl-tRNA on the ribosome.

Atoll

A region of DNA that is absent on the chromosome of an organism but absent from closely related organisms (i.e., the opposite of a genetic island). The loss of such genetic material may confer a distinctive phenotype. For example, absence of certain genes from E. coli enhances virulence.

Attachment site (att)

The specific sequences on phage (attP) and bacterial (attB) chromosomes between which site-specific recombination occurs in order to integrate the phage genome into the bacterial chromosome.

Attenuation

A mechanism of regulating the level of transcription by interfering with mRNA elongation. Slowed translation through a regulatory region allows formation of a RNA secondary structure that promotes transcription termination. Requires coupled transcription and translation and thus is restricted to prokaryotes. Two examples of genes regulated by attenuation include the trp and his operons in E. coli.

Attenuator

A region of leader mRNA that can form alternative secondary structures that determine whether transcription is terminated or proceeds into downstream genes. See Attenuation.

Att site

See attachment site.

Autogenous regulation (autoregulation)

The gene product that controls its own expression. See autogenous repressor.

Autogenous repressor

The product of a regulator gene which binds to its own operator and prevents transcription of the associated structural genes.

Autoradiography

A photographic image produced exposing photographic film to a radiolabeled molecule (e.g. DNA, RNA, or protein). The emissions from the radioactive label expose the photographic film.

Autoregulation

See autogenous regulation.

Autotroph

An organism which does not require any organic carbon for its energy source or for its growth.

Auxotroph

A mutant that will only grow when a particular nutritional requirement (e.g. amino acid, nucleotide, or vitamin) is provided.

Auxotrophic requirement

A nutritional supplement required for growth of an auxotrophic strain.

Avidin

A protein that binds biotin with a very high affinity. Used for the detection of biotinylated probes.

ß-galactosidase

An enzyme that catalyzes the cleavage of lactose into glucose + galactose. In E. coli this enzyme is encoded by the lacZ gene. Often used as a reporter for assaying gene expression (see X-gal).

ß-lactam antibiotics

Antibiotics taht contain a ß-lactam ring and act by inhibiting peptidoglycan synthesis. For example, penicillins, cephalosporins, and related antibiotics.

ß-lactamase

An enzyme that cleaves the ß-lactam ring of ß-lactam antibiotics, thus inactivating the antibiotics. The ampicillin resistance encoded by many common plasmids is due to a secreted ß-lactamase.

BAC

An acronym for Bacterial Artifical Chromosome. Low copy number plasmid vectors that allow stable cloning very large DNA fragments (often 100 Kb or more).

Backcross

A genetic cross between an offspring and one of its parents or an organism genetically identical to one of its parents.

Back mutation

A reversion event which restores the original DNA sequence.

Bacteriophage (or simply Phage)

A virus that infects a bacterium.

Bacteriostatic

A condition which prevents the growth of bacteria without killing them.

Baculovirus

A virus that has been used as a cloning vector for the production of recombinant protein in insect cells.

Base analog

A purine or pyrimidine base that differs slightly in structure from the normal bases found in DNA or RNA. Some analogs may be incorporated into nucleic acids in place of the normal base, often resulting in a base substitution mutation. Some examples include aminopurine, azaguanine, azauracil, and 5-bromodeoxyuridine.

Base pair

A complementary purine and pyrimidine that are hydrogen-bonded to form double-stranded DNA or RNA.

Base substitution mutation

A mutation resulting in the replacement of one base for a different base.

Batch culture

Growth of bacteria in a fixed volume of liquid medium in a closed vessel, with no additions or removals made during the period of incubation.

Bidirectional replication

Two replication forks proceed in opposite directions from the same origin of replication. Sometimes called omega-replication.

Bioinformatics

The management and analysis of data (especially DNA sequence data) using advanced computing techniques. Bioinformatics is an important field of genomics research, because of the complexity of searching and comparing the large number of DNA sequences generated.

Biolistics

A means of introducing DNA into cells that involves bombardment with high-velocity microprojectiles coated with DNA.

Biological containment

One of the precautionary measures taken to prevent the replication of recombinant DNA molecules in microorganisms in the natural environment. Biological containment involves the use of vectors and host organisms that have been modified so that they will not survive outside of the laboratory.

Biotechnology

The use of living organisms (often microbes) in industrial processes.

Biotin

A molecule that can be incorporated into dUTP and used as a non-radioactive label for a DNA probe.

Blunt (flush) end

The end of a DNA molecule at which both strands terminate at the same nucleotide position with no single-stranded extension.

Branch migration

A “zipper-like” pairing of two homologous DNA strands during genetic recombination.

Broad host range

The ability to infect and reproduce in a wide variety of different organisms. For example, a phage or plasmid that can grow in many different bacterial species, or a bacterium that can produce disease in many different eukaryotic hosts.

Broth culture

Microorganisms grown in a liquid medium.

Buoyant density

The density possessed by a molecule or particle when suspended in an aqueous salt or sugar solution.

Burst size

The average number of phage released from a single infected bacterium during lytic growth. The burst size depends upon both the phage itself and the growth conditions of the bacteria. The burst size for characterized phage varies from only a few progeny phage per bacterium to over a hundred progeny phage per bacterium.

Bypass suppressor

A second site mutation that activates a new pathway that eliminates the need for the original mutant pathway. For an example of bypass suppression, see the argE suppression of proline biosynthesis mutants.

CAP (Catabolite activator protein)

See CRP.

Capsduction

A DNA transfer system in Rhodobacter capsulatus where the donor DNA is carried in a phage-like structure known as a gene transfer agent (GTA). The donor DNA derived from the GTA-producing cells can enter a recipient cell and recombine with th e recipient genome.

Capsid

The protein layer that encloses the nucleic acid of a phage or virus and protects it from the environment.

Carbon source

A nutrient which provides the carbon required for cellular biosynthesis.

Carcinogen

A physical or chemical agent that causes cancer.

Cascade

A series of events that result in transmission and usually amplification of a weak signal.

Cassette

A gene fragment that can be cloned into a site to confer some property. For example, cassettes encoding antibiotic resistance are often used to disrupt a cloned gene.

Catabolite repression

A global regulatory system resulting in decreased expression of many genes due to the addition of an efficient carbon source such as glucose. Characteristically mediated by a complex between the CRP protein and cAMP in enteric bacteria.

Catenane

A circular DNA molecule with two or more interlinked rings.

CCC

An abbreviation for “circular, covalently closed” DNA molecules.

cDNA Cloning

A technique involving reverse transcription of purified mRNA into the corresponding complementary DNA prior to insertion into a vector.

Cell extract

A preparation consisting of a large number of broken cells and their released contents.

Cell-free translation system

A cell extract containing all the components required for protem synthesis (i.e. ribosomal subunits, tRNAs, amino acids, enzymes and cofactors) and able to translate added mRNA molecules.

Centromere

The region of a eukaryotic chromosome responsible for attachment to the mitotic or meiotic spindle leading to controlled partitioning of chromosomes during nuclear division.

Chain-termination (“nonsense” or “stop”) codon

A codon signalling the termination of polypeptide synthesis. The three standard stop codons are UAG (amber), UAA (ochre), and UGA (opal).

Chaperone

A protein that facilitates the folding of other proteins or assembly of multi-protein complexes.

Chelator

A substance that binds particular ions, removing them from solution. Some chelators are relatively nonspecific, binding to a variety of ions with similar charge, and other chelators bind much more strongly to specific ions. A few examples include the divalent ion chelators citrate and EDTA, the calcium chelator EGTA, and the iron chelator desferrioxamine. For more about chelators, see: http://www.sigmaaldrich.com/Brands/Fluka___Riedel_Home/Bioscience/BioChemika_Ultra/Chelators.html.

Chemotaxis

A behavorial response of cells resulting in movement toward or away from to a chemical stimulus.

Chi site

An 8-nucleotide DNA sequence (5′ GCTGGTGG 3′) which is a hot-spot for homologous recombination. When the RecBCD exonuclease encounters a chi site the RecD subunit is released and the RecBC complex then functions as a helicase, unwinding the DNA and providing single stranded which can invade a homologous region of double-stranded DNA. Chi sites typically occur about once every 5 kb on the chromosomes of enteric bacteria and most are oriented in the same direction as DNA replication.

Chiasma

A cross-over between strands of two non-sister chromatids during recombination. The junction where two homologous chromosomes appear to exchange genetic material during recombination. (Chi is the greek letter c which resembles a genetic cross-over.)

Chimeric plasmid

A plasmid used in gene cloning and constructed from two or more different plasmids.

Chloramphenicol (Cam)

An antibiotic that inhibits protein synthesis by binding to the 50s ribosomal subunit and blocking the peptidyltransferase reaction. Chloramphenicol resistance encoded by many plasmids (e.g. pBR328) is due to a cytoplasmic chloramphenicol acyltransferase which inactivates chloramphenicol by covalently acetylating it.

Chromatid

One of the two identical strands of a newly replicated chromosome.

Chromogenic substrate

A substrate that changes color when modified by a specific enzyme.

Chromosome

A self-replicating DNA molecule that carries essential genetic information for growth and replication of a cell or virus. The DNA organized into a tightly packaged structure by associated histone-like proteins in bacteria and histones in eukaryotes. (The chromosomes of some viruses contain RNA instead of DNA.)

Chromosome walking

A technique used to identify a series of overlapping restriction fragments, often to determine the relative positions of genes on large chromosomes.

Circularly permuted DNA

A population of linear DNA molecules produced as if by breaking open circular molecules at different points.

cis

Two genes located are on the same molecule of DNA (commonly refers to genes that are located very close to each other on the same DNA molecule).

Cis-trans test

A genetic test to determine whether two mutations are in the same or in different genes.

Cis-dominance

A mutation that prevents the expression of downstream genes. Polar mutations in an operon are typically cis-dominant.

Cistron

An obsolete term for a gene. Often used to refer to the number of genes encoded by a single transcript; monocistronic refers to a transcript that encodes one gene, and polycistronic refers to a transcript that encodes multiple genes.

Cleared lysate

A cell extract that has been centrifuged to remove cell debris, subcellular particles, and much of the chromosomal DNA.

Clonal

A population of cells derived from a single cell and thus expected to be genetically identical. Genetic differences in a “clonal” population may arise from random spontaneous mutations during growth of the cells.

Clone

Cells derived from a single cell and thus expected to be genetically identical.

Cloning

The production of multiple, genetically identical molecules of DNA, cells, or organisms.

Cloning vector

A DNA molecule that is capable of replication in a suitable host cell, that has suitable site(s) for the insertion of DNA fragments by recombinant DNA techniques, and that has genetic markers that allow selection for the vector in a host cell.

Coding region

A sequence of DNA that encodes a polypeptide.

Codominance

The observation of a phenotype caused by independent expression of both alleles of a gene in a diploid.

Codon

The three consecutive nucleotides (triplets) in DNA or RNA that encode a particular amino acid or signal the termination of polypeptide synthesis.

Cohesive ends

Single-stranded complementary sequences at two ends of a DNA molecule (examples include the ends of the linear phage lambda chromosome, and the ends resulting from digestion of DNA with many restriction endonucleases).

Coinheritance frequency

The ratio of recombinants that acquire both the selected and unselected marker vs the total number of recombinants.

Cointegrate

A circular molecule of DNA formed during replicative transposition by joining two separate circular replicons. The resulting structure has two copies of the transposon, one at each junction point, orientated in direct repeats.

Colinearity

The linear correspondance between the nucleotide sequence and the order of amino acids in a polypeptide chain.

Cold sensitive mutant

A mutation that results in a gene product that is active at a high temperature (e.g. 42°C) but inactive at low temperatures (e.g. 30°C). Cold sensitive mutations often affect hydrophobic interactions between protein complexes or between proteins and membrane componants.

Cold spot

Sites within a gene (or genome)Êat which mutations occur with much lower frequency than at other sites.

Colicin

A polypeptide secreted by bacteria which inhibit or prevent the growth of related bacteria which lack the corresponding colicin immunity proteins. Colicins are encoded by a group of naturally occurring plasmids first found in E. coli (e.g., the Col E1 plasmid). Colicins kill other bacteria by a variety of mechanisms depending on the type of colicin — some colicins block protein synthesis, some colicins induce the degradation of chromosomal DNA, some colicins form transmembrane holes in the cytoplasmic membrane, etc.

Colinear

Markers that occur in a sequential order in a DNA or protein sequence.

Coliphage

A phage that infects Escherichia coli.

Colony

A visible group of cells arising from a single cell plated on solid medium.

Colony blots

See Colony hybridization.

Colony hybridization

Use of in situ hybridization with a labeled nucleotide probe to identify bacterial colonies that contain DNA sequences homologous to a probe.

Colony PCR

Use of a bacterial colony for direct polymerase chain reaction to amplify a specific nucleotide sequence.

Coorperativity

For DNA binding proteins, cooperativity generally refers to the increased binding of a protein to a DNA site due to the prior binding of another protein nearby. (Note that more rigorous definations of cooperativity are sometimes used in biochemistry to refer to binding of small molecules, that can result in positive cooperativity (enhanced binding) and negative cooperativity (poorer binding) of a second molecule following binding of a first molecule.)

Coordinate gene expression

Transcription of a group of genes at the same time due to a common regulatory mechanism.

Compatibility

The ability of two different types of plasmid to coexist in the same cell.

Competence

The transient physiological state required for a bacterial cell to take up transforming DNA.

Complementary

Two polynucleotide chains that can base-pair to form a double-stranded molecule.

Complementation

The ability of a gene to produce a functional gene product which compensates for the mutant phenotype caused by a mutation in another gene. Typically, the complementing gene produces a gene product (e.g. a repressor protein or an enzyme for synthesis of a metabolite) that is diffusible and thus functions in trans.

Complex

Containing multiple macromolecules in an organized structure. For example, the RecBCD proteins form a complex that functions as an exonuclease and this activity requires all three of the proteins to function together.

Composite transposon

A transposible element flanked by two copies of an IS element.

Concatamer

An end-to-end (tandem) array of identical DNA rnolecules; a repeated polymer of DNA.

Conditional lethal mutant

A mutant that can grow under one set (permissive) of environmental conditions but dies under different (restrictive or nonpermissive) conditions.

Conditional mutant

A mutant that can grow under one set (permissive) of environmental conditions but cannot grow under different (restrictive or nonpermissive) conditions. Some conditional mutants survive under the nonpermissive conditions but others (conditional lethal mutants) die under the nonpermissive conditions.

Congenic

Strains that are identical except for a small region of the chromosome.

Congression

The uptake of more than one transforming DNA fragment by a single competent cell (occurs most often when a high concentration of transforming DNA is available).

Conjugation

The establishment of a bridge between a donor and a recipient cell and the transfer of DNA from one cell to the other. Conjugation is mediated by certain plasmids and transposons. Conjugation requires direct contact between the donor and recipient cells.

Conjugative plasmid

A bacterial plasmid that encodes functions required for conjugation.

Conjugative transposon

A transposon that encodes functions required for conjugation.

Consensus sequence

A idealized nucleotide sequence that represents a sequence that serves some particular function (e.g. a promoter) at multiple places in a genome. Each position of the consensus sequence represents the nucleotide most often found at that position in the real sequences. The precise sequence will vary from site to site, but they all are similar to the consensus sequence.

Conservative (nonreplicative) transposition

A transposition event where the transposable element is lost from its original location and inserted at a new location.

Conserved sequence

A nucleotide or protein sequence which is shared between different regions or organisms, typically because the sequence fulfills an important function (e.g. a DNA-binding site or protein motif) and thus is retained during evolution.

Constitutive gene expression

A gene or operon which is expressed at all times independant of the environmental conditions.

Contig

A set of DNA fragments that overlap to yield a continuous sequence without gaps.

Continuous culture

The culture of microorganisms in liquid medium under controlled conditions, with regular additions of depleted nutrients and removal of excreted metabolites from the medium over a lengthy period of time.

Copy number

The number of molecules of a particular plasmid present in a bacterium.

Co-repressor

A small molecule that binds to an aporepressor protein, producing a conformational change that causes it to function as a transcriptional repressor.

Cos site

The sequence that is cut to produce the cohesive, single-stranded extensions located at the ends of the linear DNA molecules of certain phages (e.g. lambda).

Cosanguine

Related by a common ancestor.

Cosmid

A cloning vector consisting of the phage lambda cos site inserted into a plasmid. Such vectors can be packaged into lambda phage or maintained as plasmids. Cosmids are often used to clone large DNA fragments (up to about 40 kilobases).

Cotransduction

Homologous recombination of two closely linked genes or two mutations within the same gene and brought into a cell on the same fragment of transducing DNA.

Cotransformation

The simultaneous uptake of two genetic markers via transformation. Cotransformation of two markers occurs at a frequency greater than 50 percent indicates that the two markers are genetically linked.

Counterselection

A condition that prevents growth of the donor in a genetic cross.

Covalently closed-circular (CCC)

A completely double-stranded circular DNA molecule, with no nicks or discontinuities, usually with a supercoiled conformation.

CRM

Cross reacting material. A molecule that reacts with an antibody. A common test for the presence of an inactive protein in cells.

Cross-feeding

Growth of a mutant stimulated by metabolites released by another cell.

Cross-over

The site where two homologous DNA strands originating from homologous chromosomes are resealed to form the recombinant chromosome. The reciprocal exchange of genetic material to produce genetic recombinants. Sometimes abbreviated as X-over.

Cross reacting material

See CRM.

CRP

Catabolite receptor protein, also called CAP or catabolite activator protein. The interaction of CRP with cAMP modulates many aspects of catabolite repression in enteric bacteria.

Cryptic

A function that is silent. For example, a cryptic gene may have an intact coding sequence but lack an active promoter. Cryptic functions can be turned on by an appropriate mutation.

C-terminus

The end of a polypeptide chain that has a free carboxylic acid (-COOH) group.

Curing

A treatment that promotes the loss of a resident prophage or plasmid from a cell. For example, acridine orange is sometimes used to cure bacteria of a plasmid.

Cut and paste

Jargon for the excision of a DNA fragment from one molecule and insertion into another DNA molecule. Commonly used to describe cloning a DNA fragment by cleavage with a restriction enzyme and ligation into a vector. Also used to describe transposition mechanisms where the transposon is excised from one DNA molecule and inserted into a second DNA molecule without replication of the transposon.

Cyclic AMP (cAMP)

An adenosine monophosphate molecule with the phosphate covalently attached to both the 3′ and 5′ carbons of the ribose.

D-loop (displacement loop)

A structure formed when one strand of a duplex DNA molecule is displaced by a single-strand of homologous invading DNA. This reaction is catalyzed by the RecA protein in bacteria.

Defective phage

A phage that lacks one or more functions that are required for reproduction.

Defined medium

A bacterial growth medium in which all the components are known. Typically only includes the minimal growth requirements.

Deletion

The loss of one or more bases or base pairs from a molecule of DNA.

Deletion mapping

The use of deletion mutations to determine the position of overlapping point mutations for fine structure mapping of a genetic locus.

Denaturation of proteins

The unfolding of a protein molecule, usually by high temperatures or ionic detergents such as sodium dodecyl sulfate (SDS).

Denaturation of DNA or RNA

Separation of the two strands of a double-stranded DNA or RNA molecule by disrupting the hydrogen bonds that join the complementary bases from the two opposite strands, usually by heat or alkali. (Often called “melting”.)

Density shift labeling

The addition of either a heavy or a light isotope to the growth medium which changes the density of the newly synthesized nucleic acids. For example, N¹⁴ is the natural isotope of nitrogen, so incorporation of N¹⁵ into DNA incr eases the density of the DNA.

Density-gradient centrifugation

Separation of molecules and particles on the basis of buoyant density, by centrifugation in a concentrated sucrose or caesium chloride solution.

Deoxyribonucleic acid

See DNA.

Derepression

The release of a gene or operon from repression so that it is expressed (or turned on).

Diauxic growth

A biphasic growth curve, typically resulting from the sequential use of multiple nutrients (e.g. glucose utilization followed by lactose utilization).

Dideoxynucleotide

A modified nucleotide that lacks the 3′ hydroxyl group, preventing further chain elongation when incorporated into a growing polynucleotide.

Diploid

An organism which contains pairs of each chromosome.

Direct repeats

Two identical (or nearly identical) nucleotide sequences sometimes separated by a sequence of non-repeated DNA. For example, 3' TAGT . . . TAGT 5' 5' ATCA . . . ATCA 3'

Directed evolution

This term is used in two ways. (i) A laboratory process using mechanisms of natural selection to produce mutants adaptated to defined environmental challenges. This approach can be used to produce adaptions in single molecules, such as a RNA molecule or an enzyme. Since chemical reaction can occur very fast, multiple “generations” of molecules can be produced quickly. Microorganisms such as bacteria can also reproduce quickly, allowing multiple generations of selection in a short period of time. This approach has been used to produce novel enzymes with industrial and biomedical applications, and to produce bacteria with potential bioremediation applications. (i) The concept that under certain stressful conditions, there is a selection for those mutational changes that favor survival. This controversial concept, also called adaptive evolution, is essentially a molecular version of Lamarkian evolution.

Double-strand break (DSB)

A cut through both strands of the DNA backbone, resulting in two exposed double-stranded ends.

DNA (deoxyribonucleic acid)

A macromolecule usually made up of two antiparallel polynucleotide strands held together by weak hydrogen bonds and with deoxyribose as the component sugar.

DNA gyrase

A topoisomerase that removes supercoils from DNA by first producing double-strand breaks and then sealing them.

DNA ligase

The enzyme that joins the 5′ and 3′ ends of polynucleotide chains by the formation of a phosphodiester bond between them.

D-loop (displacement loop)

The structure formed when ssDNA pairs with a dsDNA molecule, disrupting the pairing of the original duplex DNA to form a hybrid between the ssDNA and one of the strands of the duplex DNA, and displacing the other strand from the duplex.

DNA polymerases

Enzymes that polymerize deoxyribonucleotides onto an existing polynucleotide chain using the complementary strand of DNA as a template.

DNA primase

The enzyme that normally synthesizes the RNA primers required for initiating DNA synthesis.

DNA Repair

A variety of different mechanisms that remove or modify damaged DNA.

DNase

An enzyme that degrades DNA.

dNTP

Deoxynucleotide triphosphates used in the synthesis of DNA — deoxy-ATP, deoxy-TTP, deoxy-GTP, or deoxy-CTP.

Domain

A discrete, independantly folded region of a protein. Different functions of a multifunctional protein are usually localized in separate domains.

Dominant

The phenotype that is observed when two alleles of a gene are present in a cell. The gene whose phenotype is expressed is the dominant allele and the allele whose phenotype is masked is the recessive allele. If the phenotype of the diploid is inte rmediate between that of the two haploid genes, then the alleles are co-dominant.

Donor

The source of DNA in a genetic cross. For example, the transducing phage brought into a bacterial cell.

Downstream

A sequence located after a particular site relative to the direction of transcription and translation (i.e. located to the 3′ side of a particular site). For example, the lacZ structural gene is located downstream of the lac promoter.

Double digestion

Cleavage of a DNA molecule with two different restriction endonucleases, either concurrently or consecutively.

Duplex DNA

A double-stranded DNA molecule.

Duplication

A region of DNA that is present in two copies. The DNA is present as an adjacent, direct repeat in tandem duplications. It is also possible for the duplicated DNA to be present at distant sites on a chromosome.

dUTPase

An enzyme which degrades dUTP to prevent the incorpation of dU into DNA.

Eclipse period

The period of time after infection with a virus during which new virions are formed, but not released (contrast with latent period).

Electrophoresis

Separation of molecules on the basis of their net electric charge.

Electrophoresis of DNA

DNA fragments have a constant charge/length ratio due to the net negative charge of the phosphate backbone. Therefore, DNA migrates toward the (+) electrode. The rate of migration of linear DNA mainly depends on the pore size of the gel and length of the DNA. During electrophoresis DNA molecules seem to “snake” through the pores in the gel “head first”. As the pore size decreases (i.e. the agarose or acrylamide concentration increases) it is harder for longer DNA molecules to orient properly to snake through the pores: smaller DNA fragments snake through the pores easier and hence migrate faster. Thus, the rate of migration of linear double stranded DNA is inversely proportional to the log of its molecular weight. By using gels with different concentrations of agarose or acrylamide, a wide range of DNA fragment sizes can be separated. The shape of the DNA molecule also affects its ability to snake through the pores in the gel. In general features that make the DNA less flexible or less compact slow the migration in a gel. The rate of migration of different forms of plasmid DNA is usually: supercoiled > linear > nicked circles. In addition, secondary structure and bends in linear DNA may affect the rate of migration.

Electroporation

A method for transferring DNA (or other small molecules) into cells by exposure to a rapid pulse of high voltage, which causes the transient formation of small pores in the cell membrane.

Elongation factor

A protein that facilitates protein synthesis.

Endonuclease

An enzyme that makes breaks in a molecule of DNA by hydrolyzing internal phosphodiester bonds. An endonuclease may be specific for either single or double stranded DNA or RNA.

Endospore

A metabolically inactive, nonreplicating form of certain bacteria, including the genera Bacillus and Clostridium. Endospores tend to be highly resistant to physical and chemical damage.

Enhancer

A cis-acting regulatory sequence that can increase transcription from an adjacent promoter.

Enrichment

A condition which increases the proportion of a particular organism or mutant strain from a mixed population. For example, a penicillin enrichment kills growing cells and allows mutants unable to grow under a particular condition to survive; however, for each round of penicillin enrichment typically only 1% of the growing cells are killed, thus each round of enrichment increases the mutant ratio about 100-fold. Compare with “selection”.

Epigenetic

The inheritance of a particular trait that is not encoded in the nucleotide sequence. For example, methylation of certain DNA sequences can influence gene expression, and the methylation pattern may be maintained following DNA synthesis by preferential methylation of hemimethylated sequences.

Episome

A genetic element that can exist either as an autonomous replicating plasmid or can insert into the bacterial chromosome. This is an old term that is rarely used anymore. Such elements are simply called plasmids (for example, F-prime plasmid).

Epistasis

A condition where one gene masks the expression of another gene. For example, if there are two mutations that affect a single metabolic pathway, a mutation that disrupts the gene product which acts at an earlier step in the pathway will usually obscure the mutation that affects a later step in the pathway.

Epitope

A portion of an antigen recognized by an antibody binding site. For protein antigens the epitope is typically 5-8 amino acids. Gene fusions to epitopes can be used as a tag to recognize specific proteins.

Error prone repair

A mechanism for repair of DNA damage that often results in mutations (e.g. SOS repair).

Ethanol precipitation

Precipitation of nucleic acid molecules by ethanol plus salt. Commonly used to concentrate DNA from aqueous solutions.

Ethidium bromide

A fluorescent chemical that intercalates between base pairs in a doublestranded DNA molecule. Commonly used to detect DNA following gel electrophoresis. Ethidium bromide intercalates between the stacked bases of DNA and RNA. When excited by UV light between 254 nm (short wave) and 366 nm (long wave) it emits fluorescent light at 590 nm. Due to the decreased rotation possible when it is intercalated, the DNA-ethidium bromide complex produces about 50 times more fluorescence than free ethidium bromide. When ethidium bromide stained gels are photographed on a UV transilluminator a UV filter is required to screen out the background UV from the transilluminator. Ethidium bromide is a known carcinogen.

Eucaryote

An organism with a nuclear membrane and membrane bound organelles (e.g. mitochondria), and a mitotic spindle. This group of organisms is more correctly called Eucarya.

Excision repair

A repair system that removes nucleotides from a damaged strand of DNA and then replaces them with a new tract of DNA synthesised using the undamaged complementary strand as a template.

Exon

The sequence in a spliced gene that is retained after removal of the introns to provide the mature mRNA that is translated by the ribosome.

Exonuclease

An enzyme that digests a molecule of nucleic acid by removing successive nucleotides from the 5′ or 3′ end. Exonucleases may be specific for single or double stranded DNA or RNA, and may be specific for either 3′ or 5′ ends.

Expression vector

A cloning vector designed so that a foreign gene inserted into the vector will be expressed in the host organism. The inserted DNA is often placed under the control of a strong, regulatable promoter (e.g. the lacZ or araBAD promoter) so that expression of the gene product will only occur when desired.

Extragenic

An affect due to a second gene. For example, an extragenic suppressor is a mutation in a second gene that repairs the mutant phenotype.

Facultative

Organisms that can grow under different conditions. Commonly used to describe bacteria that can grow oxidatively under aerobic or fermentatively under anaerobic conditions.

F-factor

An E. coli plasmid that encodes conjugative transfer (“fertility”) functions. The F-plasmid may exist as an autonomous plasmid in the cytoplasm or may integrate into specific sites in the chromosome, producing an Hfr cell.

F⁺ cell

A cell that carries a F-factor as an autonomous plasmid, which enables the cell acting as a donor (male) to transfer the F-factor to a recipient (female) cell.

F^- cell

A cell which does not contain the F-factor, and hence able to act as a recipient (female) in a conjugative DNA transfer in matings with F⁺ or Hfr strains.

Fimbriae

Thin, proteinaceous filaments that extend from the cell surface of microbial cells and facilate adhesion to solid surfaces or other cells.

Fingerprinting

A common term for methods that allow the rapid identification of particular types of bacteria (also known as “typing”). For example, plasmid fingerprinting involves determining the number and types of plasmids in a particular strain of bacteria.

F-pilus

A filamentous appendage encoded by the F-plasmid. The pilus promotes adhesion of F⁺ and F^- cells and provides adsorption sites for male-specific phages.

F-prime (F’)

An extrachromosomal F-plasmid that carries a fragment of chromosomal DNA.

Filamentous phage

A group of phage with the nucleic acid surrounded by a long, tubular protein coat. Examples of filaments phage include M13 and Ff.

Filter mating

A method where conjugation between donor and recipient bacteria is done on a millipore filter. Conjugation is often much more efficient on a solid surface, probably because the donor and recipient bacteria are fixed in close proximity facilitating stable mating bridge formation.

Flagella

Long, flexible, helical protein structures that extend from the surface of the cell. Rotation of flagella in one direction results in motility, and rotation of flagella in the opposite direction results in tumbling.

Flanking sequence or flanking region

The DNA sequence located on either side of a specific genetic locus.

Fluctuation Test

An experimental approach designed by Luria and Delbruck to determine whether mutations are random or directed, and to measure mutation rates (see http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/mutations/fluctuation.html).

Footprinting

A method for identification of a protein-binding site on a DNA molecule. For example, DNase I footprinting identifies those phosphodiester bonds which are covered by a specific DNA-binding protein and thus protected from cleavage by DNase I.

Frameshift

A mutation which adds or deletes one or two base pairs (or any non-multiple of 3) from a coding sequence in a molecule of DNA, so that the genetic code is read out-of-phase. All codons translated downstream of a frameshift mutation will be misread, and frequently an out-of-frame stop codon will prematurely terminate translation.

Functional domain

A region of a polypeptide chain or RNA that performs a particular function. Functional domains are often folded into independant structures, separated from the rest of the polymer by a flexible hinge region.

Gel electrophoresis: The process of separating charged species by subjecting them to a voltage gradient. A gel (made of agarose or polyacrylamide) provides mechanical support and prevents mixing of the molecules being separated. Electrophoresis performed in a gel matrix so that molecules of similar electric charge can be separated on the basis of size.
Gel retardation: A technique that identifies a DNA fragment that has a bound protein by virtue of its decreased mobility during gel electrophoresis.
Gel shift assay: Also known as gel retardation assay or gel mobility shift assay. See the definition under Gel retardation.
GFP: See Green Flourescent Protein.
Geminivirus: One of the two groups of DNA viruses that infect plants, the members of which have potential as cloning vectors for some species of higher plants.
Gene: The genetic unit of function. A gene may encode a polypeptide or a molecule of non-translated RNA (e.g. ribosomal RNA, transfer RNA, or a regulatory RNA).
Gene amplification: Multiple copies of a single gene within a cell.
Gene conversion: An genetic event that produces abnormal segregations by non-reciprocal recombination. Gene conversion has been extensively studied in ascomycetes, where it occurs following meiosis as the result of the formation of a mismatched base pair and subseque nt repair by the mismatch repair system.
Gene expression: The process by which a a gene product is produced. For genes that encode proteins, the gene must be transcribed into mRNA and then translated into protein. For genes that encode structural RNAs (rRNA, tRNA, etc), the gene must transcribed into RNA.
Gene fusion: A construct that joins the coding region of two open reading frames such that expression of the product results in a chimeric protein. For a more detailed description, see Operon and Gene fusions. Sometimes called a translational fusion or protein fusion.
Gene library: A random collection of DNA fragments (typically representing the entire genome of an organism) that have been inserted into a cloning vector.
Gene mapping: Determination of the relative positions of different genes on a DNA molecule.
Gene transfer agent: A phage-like agent from Rhodobacter capsulates species which can transfer DNA from the donor host to recipient cells.
Gene probe: A labelled sequence of single-stranded nucleic acid (DNA or RNA) which can be used to detect the complementary nucleic acid sequence by a hybridization techniques.
General (homologous) recombination: The common cellular mechanism for genetic recombination between DNA molecules with identical or near identical (homologous) nucleotide sequences. In enteric bacteria, homologous recombination requires the RecA protein.
Generalized transduction: The transfer of any region of the host chromosome into a recipient cell packaged in phage particles. Each phage particle only carries one region of the host chromosome, but within the population of phage every region of the host chromosome is represe nted. Generalized transduction usually results from an error resulting in packaging of host DNA into a phage particle. Typically such transducing particles only carry chromosomal DNA without any phage DNA.
Generation time: The amount of time required under specific exponential growth conditions for one cell to divide, forming two daughter cells.
Genetic code: The assignment of each of the triplet codons of mRNA to amino adds and translation stop signals. See Codon table.
Genetic engineering: The use of molecular techniques to produce DNA molecules containing new genes or new combinations of genes.
Genetic map: The relative position and distance between genes determined from recombination frequencies.
Genetic marker: A locus that has a useful phenotype which can be used for genetic selections or screens.
Genetic polymorphism: The existence of two or more genetically different classes within a population.
Genetic recombination: The process by which a fragment of DNA from one molecule (chromosome, plasmid, phage genome) is exchanged with or integrated into another molecule to produce a recombinant molecule(s).
Genome: The complete genetic content of a cell or organism, including chromosomes, plasmids, and prophages. The total genetic information of an organism. [The Oxford English Dictionary attributes the term genome to Hans Winkler who wrote in 1920 "I propose the expression Genom for the haploid chromosome set, which, together with the pertinent protoplasm, specifies the material foundations of the species ...." Source: J. Lederberg and A. McCray (2001) The Scientist 15:8]
Genomic library: A collection of clones that includes essentially all the genes of a particular organism.
Genomics: The comparative analysis of genomic DNA sequences from different organisms. Genomic analysis can provide information about the evolution of genes and can make predictions about the metabolism of an organism.
Genotype: A specific description of the genetic constitution of an organism. The genotype is defined by the allelic form of each gene in an organism, but for simplicity usually only differences from the wild-type are described.
Gentamicin: A type of aminoglycoside antibiotic. Often used to study bacterial entry into eukaryotic cells because gentamicin cannot cross the eukaryotic cell membrane, thus intracellular bacteria are resistant to gentamicin but extracellular bacteria are usually sensitive to gentamicin.
GMO: An abbreviation for “genetically modified organism”. Commonly used to refer to organisms that have been developed using recombinant DNA approaches, particularly if some foreign DNA remains in the strain.
Gradient of transfer: In an Hfr mating, the decrease in the inheritance of donor markers the farther they are from the origin of transfer.
Gram-negative bacteria: A group of bacteria with a cell wall composed of an outer membrane surrounding a thin peptidoglycan layer. When stained with crystal violet then treated with organic solvents, the dye is readily removed by the organic solvent.
Gram-positive bacteria: A group of bacteria with a cell wall composed of thick peptidoglycan layer and no outer membrane. When stained with crystal violet then treated with organic solvents, the dye is retained and thus the cells appear purple colored.
Green Flourescent Protein (GFP): An intrinsically fluorescent protein from the jellyfish Aequorea victoria. Gene fusions with GFP are commonly used for determining protein localization by fluorescence microscopy.
Growth rate: The rate of increase of cellular density per unit time.
GUS: An abbreviation for Beta-glucuronidase (encoded by the uidA gene). Commonly used for constructing operon or gene fusions in organisms with high endogenous Beta-galactosidase activity. A variety of analogs exist that make it easy to detect GUS expression on solid medium and to assay the activity of the enzyme in cells.
Gyrase: See DNA gyrase.

Glossary