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Big Steve’s Mouse Glossary

 

Stephen W. Barthold, D.V.M, Ph.D.

Center for Comparative Medicine

University of California, Davis

 

AAALAC International.  Association for Assessment and Accreditation of Laboratory Animal Care International.  A voluntary accreditation program for laboratory animal facilities and programs.

AALAS. American Association for Laboratory Animal Science.

Acetylation.  Biochemical process involving addition of acetyl groups to DNA, favoring gene expression. 

Acrocentric chromosome. Chromosome pattern in which the centromere is assymetrically toward one end and the telomeres are at the ends (in contrast to telocentric and metacentric). Mice do not have acrocentric chromosomes. 

Acrosome.  The cap-like structure structure investing the anterior portions of the head of spermatozoa.

Agouti.  Pelage characteristics composed of black hairs with subapical yellow bands.

Allele.  Alternate forms of an autosomal gene or locus situated at the same locus on the maternal or paternal chromosomes.  A randomly inserted transgene is not an allele. A targeted mutation of the endogenous locus is an allele.

Alleleic series. An array of possible mutant forms of a gene, which usually cause multiple phenotypes.

Allogeneic.  Strains or individuals that express different alleles of the same gene among 2     otherwise genetically similar mice.

Antimorph.  A mutant allele that antagonizes the function of another gene and acts in a semi-dominant manner.

Autosomes.  All chromosomes other than the sex (X and Y) chromosomes.

Axenic.  Not contaminated by or associated with any foreign organisms (excepting endogenous retroviruses). A.k.a. germfree.

BAC.  Bacterial artificial chromosome.  A vector for cloning large segments of genome.

Backcross.  Cross of a hybrid (F1) mouse to one of its homozygous parents. Also the cross of an F1 heterozygote with a partner that has the same genotype as one of its parents (when working with non-inbred systems).

Barrier reared.   Population maintained behind a microbiological barrier.  Does           not necessarily mean that the animals behind the barrier are pathogen free.  Read fine print.

Base pair.  A pair of nitrogenous bases (usually one purine and one pyrimidine) held together by hydrogen bonds in a double-stranded region of nucleic acid molecule. Commonly used interchangeably with nucleotide pair. Normal base pairs in DNA are

A-T and G-C; in RNA, A-U and G-C. 

Blastocyst.  The spherical structure produced by cleavage of the fertilized ovum, consisting of a single layer of cells (blastoderm) surrounding a fluid-filled    cavity (blastocoele). 

Bruce effect.  The pheromone-driven effect of male urine (especially that of a dominant stranger) on breeding females, in which early pregancy is blocked by fetal resorption and estrus resumes.

Carrier. Heterozygote for a recessive allele.

Centimorgan.  Metric used to describe linkage distances. 1 cM = 1% chance that a marker at one genetic locus will be separated from a marker at a second locus due to crossing over in a single generation.  In humans, 1 cM=1,000,000 bp.  See linkage map.

Centromere.  The clear region where the arms of the chromosomes meet.  They are highly specialized structural elements that function to segregate eukaryotic chromosomes during mitosis and meiosis.

Chiasma.  The cross-shaped exchange configuration between non sister chromatids of homologous chromosomes that is visible during prophase I of meiosis.

Chimera.  An individual mouse composed of distinct cell populations derived from genetically different mice, usually via injection of embryonic stem cells into a recipient blastocyst.

Chromatid.  Either of the longitudinal subunits produced by chromosomal replication.

Chromatin.  The aggregate DNA and histone proteins that makes up a eukaryotic chromosome.

Chromosome.  A unit of genetic material (chromatin) in which the genome is arranged.  The mouse has 20 pairs of chromosomes, including 19 autosomal pairs and the X and Y chromosomes. 

Chromosome map.  A diagragm showing the locations and relative spacing of genes along a chromosome.

Chromosome painting. Use of differentially labeled, chromosome-specific DNA strands for hybridization with chromosomes to label each chromosome with a different color.

Cis configuration.  The arrangement of linked genes in a double heterozygote in which both mutations are present on the same chromosome.

Cistron. A nucleotide sequence coding for a single polypeptide.

Clone.  Organisms derived from a single parent and genetically identical to the parent. The term is also used in genetic engineering, meaning the linking of a specific gene or DNA fragment to a replicable DNA molecule, such as a plasmid or phage DNA.

Cloned gene or DNA fragment.  A DNA sequence incorporated into a vector and transformed into a host organism.

Codon.  A sequence of three adjacent nucleotides in an mRNA molecule, specifying either an amino acid or a stop signal in protein synthesis. 

Coisogenic.  Genetically identical, except for a difference at a single locus. More          precise than congenic, referring to a strain that differs from another by a single gene mutation from the control strain.

Commensal. Populations of house mice that depend upon human-built habitats or food production for survival. 

Compensatory genes.  One or more genes that compensate for gain or loss of function of another gene, including transgene, thereby influencing phenotype.

Complementation.  When two mutations are combined in an organism and the phenotype is wild type, the mutations are said to complement each other.

Complex trait. A multifactorial trait (phenotype) influenced by multiple genetic and environmental factors, each of relatively small effect, and their interactions.

Conditional mutant.  Conditional expression of genes created by transgenic insertion of genetic material under control of tissue specific promotors.

Congenic.  Strain that differs from another in the region of a single gene locus.  Produced by > 10 successive backcrosses or intercrosses to the control strain.

Conplastic.  Mice in which the mitochondrial genome from one strain is transferred onto a different genetic background so that the two genetically different strains have identical mitochondrial genomes.

Consomic.  Strain that differs from another in an entire chromosome.

Contig. A set of contiguous, overlapping genomic clones that span a larger region of the genome. 

Coprophagy.  Ingestion of feces.  Nearly 1/3 of the mouse’s diet is re-ingested feces, allowing acquisition of B vitamins that are generated in the hind gut by microflora to be absorbed in the small intestine. 

Copulatory plug.  Male ejaculate that is a coagulum resulting from mixing of seminal vesicle secretions with coagulating gland secretions. The coagulum is retained in the vagina of females for several hours after intercourse, and can be used as a marker for successful breeding and timed pregnancy.

Copy number.  The number of transgenes incorporated into the genome.

CRE-LoxP.  Phage-derived CRE recombinase targets specific sites that have been flanked with LoxP, allowing genomic excision (gene knock outs). This is usually achieved by crossing a CRE transgenic mouse with a mouse containing a targeted gene that has been “flanked” with LoxP sites.

Cross.  Matings among unlike (genetically distinct) homozygotes.

Crossing over.  Breaking during meiosis of one maternal and one paternal chromosome, the exchange of corresponding sections of DNA, and the rejoining of the chromosomes.  Can result in exchange of alleles between chromosomes.

Cytoplast.  Enucleated oocyte or zygote (fertilized embryo) used as a nuclear transfer recipient (as in cloning).

Delila effect.  Trichotillomania, or hair plucking behavior.

Deme. A social unit.  Can represent an entire genetically-related wild population or a population within a single cage.

Differential segment.  The region of donor flanking genetic material surrounding a selected locus in a congenic mouse that has been transferred by selective backcrossing onto a recipient mouse.

Diploid. A cell or organism with two complete sets of homologous chromosomes.

Dominant. Nature of inheritance of a phenotype, not a gene.  A dominant phenotype is detectable when only one variant allele can be detected. If both alleles are detected, then co-dominant.

Ecotropic retrovirus.  Retrovirus, either leukemia virus or mammary tumor virus, with tropism for mouse cells.  The most notable ecotropic leukemia virus is the AKR provirus, with homologues and multiple copies among many of the inbred strains.

Embryonic carcinoma cells (EC cells).  Cells derived from embryonic carcinoma (teratoma) of 129 mice.  Generally replaced by embryonic stem cells.

Embryonic stem cells (ES cells).  Early embryo cells that can replicate indefinitely and which can differentiate into other cells (pluripotential). 129 strain generally used because ES cells of this strain are conducive to manipulation.

Endogenous provirus.  Retrovirus sequences, entire or partial, occult or expressed, that are inserted within the genome and transmitted as Mendelian characteristics.  Some are replication-competent, others are defective.  Refers to both mammary tumor virus and leukemia virus sequences.        

Enhancer element.  A base sequence that increases the rate of transcription of nearby genes; the element need not be adjacent to the transcribed gene and enhancing activity is independent of orientation with respect to the gene.

ENU.  Chemical mutagen, N-ethyl-N-nitrosourea.

Epigenetic.  Inherited changes in gene expression resulting from altered chromatin structure or DNA modification (usually methylation) rather than from changes in DNA sequence.

Epistasis.  Interactions between non-allelic genes in their effects on a trait. Any type of interaction in which the genotype at one locus affects the phenotypic expression of a genotype at another locus.

ETN’s. Endogenous replication-incompetent murine retrovirus early transposon elements.

Euchromatin.  Regions of chromosomes that have normal staining characteristics and undergo a normal cycle of condensation; relatively uncoiled regions of chromatin in the interphase nucleus and contains most of the functional genes.

Exogenous retrovirus. Retrovirus that is transmitted in a conventional, horizontal (contagious) means. 

Exon.  Sequences in the gene that are retained in the messenger RNA after the introns are removed from the primary transcript.

Expressed sequence tag (EST). Partial or complete cDNA sequence.

Expressivity.  The observed quantitative differences in the expression of a phenotype among individuals that have the same mutant genotype.  When quantitative differences are observed, the phenotype has variable expressivity.

F generation.  Filial generation (generations of brother x sister matings)

F1 hybrid.  First generation of a hybrid cross between 2 different parental inbred          strains.  Genetically identical mice that are heterozygous at all loci. 

F2 hybrid.  Progeny of F1 b x s matings.  Genetically dissimilar.

F3, etc.  Subsequent b x s hybrid matings.

Feral.  Wild populations of commensal species (mice) that have become independent of human habitats or human food.

Fixation.  A genetic term in which a low frequency of heterozygosity is attained at a given locus through repeated incrossing. 

Flanking genes.  Genes that flank a specific region of interest, such as a transgene.  Important issue in incompletely backcrossed mice derived from two parental strains.

Forward genomics.  Genomic approaches in which the outcome is predicted from the alteration or introduction of a known gene.

Founder.  First generation mice derived from genetically altered eggs or embryos.

Fv-1.  A host resistance gene, with different alleles, that regulates intracellular retrovirus integration and replication.  Different alleles (b and n) determine host tropism of ecotropic retroviruses.

Fv-4.  A defective (replication-incompetent) endogenous retrovirus envelope gene (provirus) that is expressed on the cell surface and blocks entry of other ecotropic retroviruses.  Thus, expression of Fv-4, in combination with other ecotropic retroviruses, is a major determinant of retrovirus-related phenotype (neoplasia, etc.).

G.  Generation:  G1, G2, G3, etc.

Gene.  If you don’t know this, you shouldn’t be reading this glossary.  A functional unit encoding protein or RNA whose inheritance can be assayed in genetic crosses, mapping, or inference through sequence.

Gene dosage.  The number of genes.  Many genes are duplicated within the genome, and transgenes often have tandem repeats.  

Gene targeting.  Creation of a null or mutant allele by homologous recombination or targeted gene placement.

Genetic code.  The set of 64 triplets of bases (codons) that correspond to the 20 amino acids in proteins and the signals for initiation and termination of peptide synthesis.

Gene trapping.  A mutation strategy that uses random integration of a reporter gene construct into the genome such that productive integration events bring the reporter gene under the transcriptional regulation of an endogenous gene.  The inserted sequence acts as a tag from which to clone the trapped or mutated (if insertional mutagenesis occurs) gene.

Genome. The entire genetic composition of an organism.

Genomic library.  A collection of genomic clones that collectively represent the entire genome.  Any sequence of interest within the genome is likely to be present in at least one member of the library.

Genotype.  Genetic composition of the mouse, usually in terms of particular alleles, genes, or loci.  Can refer to single genes or loci, or to many.

Germfree.  Born and raised in a sterile environment free of microbes.  No mouse is technically germ free, as all laboratory mice have vertically transmitted retroviruses.

Germline mutation.  A mutation that takes place in a reproductive cell, and thereby is genetically transmitted as a Mendelian characteristic.

GLN’s.  Endogenous replication-incompetent retrovirus tRNA glutathione like sequences.

Gnotobiotic.  Population associated and maintained with known microflora.

H-2 complex. The major histocompatibility  complex (MHC) of the mouse, located on chromosome 17.

Haploid.   A cell or organism containing the set of chromosomes normally found in gametes.

Haplotype.  A number of functionally related loci that are closely linked genetically.  Alternative sates of such complexes are termed haplotypes.

Hemizygous.  Contains 1 unique genetic determinant, introduced as a transgene.

Heterochromatin.  Chromatin that remains condensed and heavily stained during interphase; commonly present adjacent to centromere and telomeres. 

Heterosis.  The superiority of hybrids over either inbred parent; a.k.a. hybrid vigor.

Heterozygous.  Contains 2 different alleles of the same gene(s). 

Histone.  Small basic proteins that bind to DNA in chromatin.

Homeobox. A DNA sequence motif found in the coding region of many regulatory genes; the encoded amino acid structure has a helix-loop-helix structure.

Homeotic (HOX) gene.  Any of a group of genes in which mutation results in the replacement of one body structure by another body structure.

Homolog. Genes are homologous if they evolved from a common ancestor.  There is NO DEGREE of homology.

Homozygous.   Contains 2 identical alleles of the same gene(s).

Hotspot.  A site in DNA molecule at which the mutation rate is much higher than the rate for most other sites.

Housekeeping gene.  A gene that is expressed at the same level in all cells and whose product participates in basic metabolic processes.

Hybrid strain. Derived by mating 2 inbred strains together.

Hybrid vigor.  Heterosis.

Hypomorph.  A mutant allele that does not eliminate the wild-type function of a gene and may give a less severe phenotype than a loss-of-function mutant.

IAP’s.  Endogenous replication-incompetent retrovirus-like elements that form intracisternal A particles.

ICSI (intracytoplasmic sperm injection).  Microinjection of an ovum with spermatozoa or precursors as a means of fertilization. Can be accomplished with non-viable spermatozoa.

ICNI (intracytoplasmic nucleus injection).  Microinjection of an ovum with a somatic or germ cell nucleus (karyoplast), a method used for cloning.

ILAR.  Institute of Laboratory Animal Resources.  ILAR is a branch of the National Science Foundation of the National Academy of Sciences which acts as an advisor to the federal government on policies relating to laboratory animals.

Imprinting.  The expression or repression of genes under male or female parental control that vary from standard genetic mechanisms (dominance and recessive).

Incipient congenic.  A new term devised by Jax labs for transgenic and targeted mutations in the process of backcrossing onto an inbred background strain, but with generations less than N10.

Incross. Matings among like homozygotes.

Inbred strain.  Derived by b x s matings for >20 consecutive generations and maintained by continuous b x s matings.  Parent x offspring may be substituted for b x s matings if in consecutive matings to younger of the 2 parents.  There are over 2,400 inbred strains of mice.

Induced mutant stocks/strains.  Stocks/strains carrying targeted mutations (knock outs, knock ins), retroviral or chemically induced mutations.

Inducible mutant. Inducible expression of genes created by transgenic insertion of genetic material under control of tetracycline, neomycin or other regulators.  Inducers inactivate a repressor, usually by binding to it and thereby altering the ability of a repressor to bind to an operator.

Inner cell mass . The mass of cells within the blastocyst which develop into the corpus of the embryo, including embryonic stem cells.  Foreign ES cells are microinjected into the blastocyst, and become incorporated into the inner cell mass, creating a chimera.

Insertional mutagenesis.  Alteration (mutagenesis) of the genome by insertion of foreign DNA so that the genome is disrupted by homologous recombination or random insertion.

Intercross.  Matings among two identically heterozygous individuals (F1 hybrids).

Interspecific cross.  A cross between mice from two different species, such as between M. musculus and M. spretus, for the purpose of linkage analysis (in order to obtain high level of polymorphism between two parents).

Intersubspecific cross.  A cross between mice from two different subspecies, such as between M. musculus domesticus and M. musculus castaneus (a natural intersubspecific cross is M. molossinus).

Intron.  A noncoding DNA sequence in a gene that is transcribed but is then excised from the primary transcript in forming a mature mRNA molecule.

Isogenic.  Genetically identical.

IVF.  In vitro fertilization. 

Karyotype. The number of chromosomes present in a given genome and the morphologic form that they assume (banding patterns, etc.) under microscopic examination. The laboratory mouse has 20 pairs of chromosomes (19 autosomal pairs and the X and Y sex chromosomes).

Karyoplast.  Isolated donor nucleus, together with its nuclear membrane and envelope of cytoplasm (as in cloning).

Kilobase (kb).  Unit of length of a duplex DNA molecule equal to 1,000 base pairs.

Knock out.  A mouse with a null mutant gene created by homologous recombination.

Knock in.  A mouse with a functional, usually mutated, gene placed into its genome by homologous recombination.

Laboratory mouse.  Domesticated Mus of mixed genetic heritage.  Genome heavily Mus domesticus, with varying degrees of M. mollosinus, M. musculus, M. castaneus, and possibly others, depending upon genotype. Cannot be called M. domesticus (sensu stricto) so must use M. musculus, the sensu lato designation for the M. musculus complex.

Lee-Boot effect.  The hormonal effect within a group of females maintained in the absence of males, leading to pseudopregnancy and anestrus. 

Ligand.  The molecule that binds to a specific receptor.

LINE element.  A type of transposable element that lacks long terminal repeats and undergoes transposition via an RNA intermediate; long interspersed element.

Linkage.  Proximity of 2 or more markers with high probability of being inherited together.  The chances of recombination between them is significantly less than 50%.

Linkage group.  The set of genes present together in a chromosome.

Linkage map.  Map of relative positions of genetic loci on a chromosome, determined on the basis of how often loci are inherited together.  Distance      between loci measured in centimorgans (cM).

Linkage group.  A set of loci in which all members are linked to all other members of the group.

Locus.  Position on a chromosome of a gene or other chromosome marker (or DNA at that position).

LTR.  Long terminal repeat region of retroviruses which encode promoter, enhancer and other biologic functions used in genomic constructs and vectors.

LTR retrotransposon.  A type of transposable element that transposes via an RNA intermediate and that has long terminal repeats in direct orientation at its ends.

Map units.  Centimorgans.

Marker.  An identifiable physical location on a chromosome (restriction enzyme           site, gene, etc.) whose inheritance can be monitored by an assay such as enzyme activity, protein band, or DNA fragment.

Megabase (Mb).  Unit of length of a duplex DNA molecule equal to 1 million base pairs.

Meiosis.  The process by which diploid germ cells segregate their chromosomes into haploid nuclei within eggs and sperm.  One replication of the chromosomes is followed by two successive divisions of the nucleus to produce four haploid nuclei.

Mendelian genetics.  The mechanism of inheritance in which the statistical relations betweent he distribution of traits in successive generations result from genes, random union of gametes, and segregation of hereditary determinants in the reproductive cells.

Metacentric chromosome. Chromosome pattern in which the centromere is in the middle of the chromosome and the telomeres are at the ends.  Metacentric chromosomes occur in mice with Robertsonian translocations. 

Methylation. Biochemical process involving addition of methyl groups to DNA, silencing a gene or cluster of genes. 

Microinjection.  The process of inserting a fine needle into the pronucleus of a fertilized ovum for the purpose of transferring foreign DNA.

Microsatellite markers. Highly polymorphic, genetically stable 2-4 base pair nucleotide repeats (n=10-60) that are scattered throughout the genome.  Length variation of these regions can be detected by PCR, allowing pedigree analysis due to polymorphism among different inbred strains of mice. A.k.a. SSLPs.

Mitochondrial heteroplasmy.  Presence of more than one genetic origin of mitochondrial DNA within a cell.

Mitosis.  The process of nuclear division in which the replicated chromosomes divide and the daughter nuclei have the same chromosome number and genetic composition as the parent nucleus.

MMTV. Murine mammary tumor virus.

Mobile DNA.  Transposable elements.

Modifier genes.  One or more genes of the genome which influence the expression of a gene, including transgenes, thereby modifying phenotype.

Morula.   The solid mass of blastomeres formed by cleavage of a fertilized ovum, filling all the space occupied by the ovum before cleavage.

Morula aggregation.  A process for creation of chimeras, in which cells are mixed in the morula stage.

Mosiac (mosaism). An organism composed of two or more genetically different types of cells. Specifically used to refer to a mouse consisting of cells with and without a gene alteration, arising from delayed integration of a transgene after the embryonic 2-cell stage.

MuLV.  Murine leukemia virus.

Murine.  Relating to rat or mouse.

MuRRS.  Endogenous replication-incompetent murine retrovirus-related DNA sequences.

MuRVY.  Endogenous retrovirus replication-incompetent murine repeated virus sequences on the Y chromosome.

Mutagenesis.  Intentional induction of gene mutations with a mutagen, such as a chemical (such as ENU) or radiation treatment of the germline.

Mutant. Any heritable feature that differs from the wild type. Used in context of mutant DNA, allele, gene, chromosome, cell, organism, or phenotype.

Mutation. A new allele that arises in an individual that is not present in the genome of either of its parents.  Somatic or germ line. 

N.  Backcross generation:  N1, N2, N3, etc.

N1 hybrid.  Backcross of F1 hybrid to one of the parental strains. 

NOD. Non-obese diabetic mouse strain, which develops diabetes due to immune-mediated islet cell destruction.

Non-LTR retrotransposon.  A type of transposable element that transposes via an RNA intermediate and that lacks terminal repeats at its ends, such as LINE elements.

Nuclear transfer.  Process by which a donor nucleus (karyplast) is inserted into an enucleated egg or zygote (cytoplast).

Null mutation.  A mutation that results in loss of gene function.

OLAW.  Office of Laboratory Animal Welfare, National Institutes of Health. Develops and monitors, enforces compliance, and provides oversight of Public Health Service policies relating to laboratory animal welfare.

Oncogene.  A gain-of-function mutation in a cellular gene called a proto-oncogene, whose normal function is to promote cellular proliferation or inhibit apoptosis; oncogenes are often associated with tumor formation and progression.

Open reading frame (ORF).  A region of DNA or mRNA containing a series of codons uninterrupted by stop codons and therefore capable of coding for a polypeptide chain.

Ooplasmic transfer.  Process by which healthy cytoplasm from a donor egg is used to enhance the cytoplasmic environment of a recipient egg.

Operator.  A regulatory region in DNA that interacts with a specific repressor protein in controlling the transcription of adjacent structural genes.

Operon.  A collection of adjacent structural genes regulated by an operator and a repressor.

Ortholog.  Genes in two species that have evolved from a single common ancestral gene.

Outbred.  Stocks of mice maintained by nonstandardized matings.  Outbred mice          have considerable genetic variability. The term is often used synonymously for randombred.

P.      Parental generation

Paralog.  Genes within the same species that have arisen from a common ancestor by duplication and subsequent divergence.

Penetrance.  The degree to which a mutant genotype is expressed as a phenotype. Incomplete penetrance is usually due to modifiers in the genetic background.

Phenotype.  Observable characteristics of a cell or organism.

Pleiotropic effect.  Any phenotype that is a secondary manifestation of a mutant gene. Pleiotropy is the condition in which a single mutant gene affects two or more distinct and seemingly unrelated traits.

Polygenic. A genetic characteristic (phenotype) that results from interactions among products of two or more genes with alternative alleles.

Polymorphism.  Differences among alleles, microsatellites, or SNPs that define different strains of mice.

Polytropic retrovirus. Retrovirus, either leukemia virus or mammary tumor virus, with tropism for mouse cells and cells from other species.

Promoter.  A DNA sequence at which RNA polymerase binds and initiates transcription. Transgene which promotes the expression of a native gene or transgene, either within the context of specific tissues, or ubiquitously. 

Pronucleus.  Either of the 2 haploid gamete nuclei just pror to fusion into a fertilized ovum.  Transgenics are generated by microinjection of the transgene into the pronucleus.

Proteome.  The set of all proteins encoded in a genome.

Proto-oncogene.   A eukaryotic gene that functions to promote cellular proliferation or inhibit apoptosis, in which gain-of-function mutations (oncogenes) are associated with cancer.

Provirus.  The genetic sequence of a retrovirus that has been incorporated in the mouse genome.

Pseudogene. A gene or sequence that is derived from, and therefore partially homologous to a normal gene, but is not transcribed and does not create a functional protein.

Pseudopregnant.  Females mated to vasectomized males.  Ability to maintain eggs transferred to them without uterine competition from naturally ovulated/fertilized eggs.

Quantitative trait.  A trait that is usually measured on a continuous scale that results from the combined action of several or many genes in conjunction with environmental factors.

QTL.  Quantitative trait loci, in which linkage of a particular phenotype is quantatively and statistically determined.

Randombred.  Stocks of mice maintained by systematic scheme of randomization.  Randombred mice are genetically heterogeneous, but genetically stable compared to outbred mice.

Recessive trait. Nature of inheritance of a phenotype, not a gene.  A recessive phenotype is detectable when both alleles have a particular variant or mutation and can be detected. Recipient.   Surrogate dam by embryo transfer.  Does not influence the genetic makeup of the introduced embryos.  Mated with vasectomized males.  Chose strains of mice prone to large litters and with good fostering skills.

Recombinant congenic strains.  Inbred strain derived by backcrossing one inbred strain onto another for 4 generations, then intercrossing filial generations to create recombinant inbred lines that are dominated by the initial backcrossed recipient line.

Recombinant inbred strain.  Inbred strain derived by mating pairs of F2 hybrid mice (derived from 2 parental inbred strains), then continuously (>20) b x s mating their descendants to create “recombinant” inbred lines.

Repressor.  A protein that binds specifically to a regulatory sequence adjacent to a gene and blocks transcription of the gene.

Reprogramming.  “Resetting” of genetic expression program of donor nucleus so as to assume a program typical of the zygote genome (undoing methylation, imprinting, etc.).

Reporter gene.  A gene sequence that is introduced into a transgenic construct that “reports” the integration of the contruct within the genome and its subsequence expression, such as LacZ, green fluorescence protein (GFP) etc.

Restriction fragment.  A segment of duplex DNA produced by cleavage of a larger DNA molecule by a restriction endonuclease enzyme.

Restriction fragment length polymorphism (RFLP).  Genetic variation in a population associated with the size of restriction fragments remaining after cutting with restriction enzymes and that contain sequences homologous to a particular probe DNA; the polymorphism results from the positions of restriction sites flanking the probe, and each variant represents a different allele. RFLPs are used to determine allelic variation in a gene or locus.

Restriction map. A diagram of a DNA molecule showing the positions of cleavage by one or more restriction enzymes.

Restriction site. The base sequence at which a particular restriction enzyme makes a cut.

Retrotransposon. An inserted genomic element that originated from reverse transcribed mRNA produced from another region of the genome. Proviral sequences can function as retrotransposons, thereby contributing to genetic drift.  

Reverse genomics. Genomic approaches in which the outcome is not predicted, such as chemical mutagenesis.  Phenotypes are identified, then genes are subsequently incriminated. Also a procedure in which mutations are made in cloned genes, then introduced back into the genome to determine effect.

Robertsonian translocation.  A fusion between the centromeres of two chromosomes to produce a single chromosome (whole arm translocations).  Some wild populations of M.domesticus poschiavinus, for example, have karyotypes with only 13 sets of chromosomes, seven of which are metacentric.   Strains of inbred mice with single Robertsonian translocations are available for experimental use. 

SCID. Severe combined immunodeficiency.  SCID mice have a spontaneous mutation of the Prk gene (therefore an allelic variant), resulting in global immunodeficiency.  SCID is NOT a strain; it is a mutation with a phenotype. SCID mice are available on various strain genetic backgrounds.

Segregation.  Separation of pairs of alleles into different gametes during meisosis.

Selfish DNA.  Transcribable elements that do not benefit the organism, and whose sole function appears to be self-propagation. These sequences do not contribute to the fitness of an organism, and are maintained by their ability to replicate and transpose.

Sib (sibling).  A brother or sister, each having the same parents. In mice, sibs can occur among multiple litters of the same parents.

SINE element.  A type of transposable element lacking long terminal repeats that undergoes transposition via an RNA intermediate; short interspersed element (in contrast to LINE elements, long interspersed elements).

Sister chromatids.  Chromatids produced by replication of a single chromosome.

SNPs.  Often referred to as “snips,” single nucleotide polymorphisms, like microsatellites, can be used for pedigree analysis.  SNPs represent minor, but stable variations in nucleotide sequences.

Somatic cell.  Any cell of a multicellular organism other than the gametes and germ cells from which gametes develop.

Somatic mutation. Mutation in the genome of a somatic cell.  Somatic mutations are not germ-line transmitted, but are responsible for genetic events within a cell population, such as cancer cells.

Specific pathogen free.  SPF.  Population free of a specific list of pathogens.  Does not necessarily mean that all pathogens are on the list.  Read the fine print!

Speed congenics. A method for accelerating the process of backcrossing of one inbred strain onto another by purposely selecting for maximal recipient strain genetic characteristics using microsatellite or SNP markers.

Splice acceptor and donor.  The 5’ and 3’ ends of an exon, respectively.

SSLPs. Simple sequence length polymorphisms. A.k.a. microsatellites.

Start codon.  An mRNA codon, usually AUG, at which polypeptide synthesis begins.

Stereotypy.  Non-purposeful, repetitive acts of behavior.

Stock.  Outbred or randombred line of mice.  Genetically heterogeneous.

Stop codon.  One of three mRNA codons…UAG< UAA, and UGA…at which polypeptide synthesis stops.

Stereotypy. Repetitive sequences of motor behavior that are topographically and morphologically invariant, often rhythmical, and apparently purposeless.

Substrain.  An inbred strain that was separated from an inbred ancestor before F40, or separated by greater than 100 generations from a common inbred ancestor, or possesses a known genetic characteristic (mutation or contamination) that distinguishes the substrain from the parental inbred strain.

Superovulation.  Above-normal ovulation induced by administration of gonadotropins to females prior to mating.

Swiss mouse.  Any mouse that is genetically derived from a progenitor pool of two female and seven male mice obtained from Andre de Coulon in Lausanne, Switzerland by Clara Lynch at the Rockefeller Institute in 1926.  Many Swiss mice are outbred stocks (CD-1, CF-1, CFW, NIH, etc.), but others are inbred (SJL, SWR, FVB, NFS, etc.). 

Sympatric. Closely related species that have overlapping natural ranges, but do not interbreed, such as Mus domesticus and Mus spretus.

Syngeneic.  Genetically identical at every locus.  Identical genotypes.

Syntenic (synteny). Two loci known to be in the same linkage group.  Conserved synteny is a situation in which two linked loci in one species have homologs that are also linked in another species.

Targeted genomics. A process of introducing foreign genetic material into targeted locations within the genome by homologous recombination for the purposes of introducing a gain- or loss-of-function mutation of a particular allele.

TATA box.  The base sequence of 5’-TATA-3’ in the DNA of a promoter region. TATA box binding proteins bind in this region.

Telocentric.  The chromosome pattern in which the centromere is at one end and the telomere is at the other.  All autosomal chromosomes and the X chromosome of the mouse are telocentric.

Telomere.  “Caps” of repeated DNA sequences that protect the ends of chromosomes from degradation.  Telomeres shorten at each round of cell division.  Mouse telomeres are very long, relative to other species, such as humans.

Tg.  Abbreviation for “transgenic” used in mouse nomenclature. Refers to random insertion of foreign transgene.

Tm.  Abbreviation for “targeted mutation” used in mouse nomenclature. Refers to insertion of foreign genetic material by homologous recombination.

Trait.  Any aspect of the appearance, behavior, development, biochemistry, or other feature of an organism. Phenotype.

Trans configuration.  The arrangement in linked inheritance in which a genotype that is heterozygous for two mutant sites has received one from each parent.

Transcription.  The process by which the information encoded in a template strand of DNA is copied into a single stranded RNA of complementary base sequence.

Transcriptional activator protein.  Positive control element that stimulates transcription by binding with particular sites in DNA.

Transfection.  The uptake, incorporation and expression of recombinant DNA by eukaryotic cells.

Transgene.  A foreign gene introduced by transfection.

Transgenic.   Organism with genes from another organism placed into its genome through recombinant techniques, usually by microinjection of the pronucleus of fertilized eggs.  DNA integration is random. 

Transgenic line.  A transgenic mouse strain in which the transgene has been stably integrated into the germline and inherited as a Mendelian characteristic.

Translation.  The process by which the amino acid sequence of a polypeptide is synthesized on a ribosome according to the nucleotide sequence of an mRNA molecule.

Translocation. Interchange of parts between nonhomologous chromosomes. 

Transposable element.  A DNA sequence capable of moving (transposing ) from one location to another in the genome.

Transomic.  Transgenic mouse created by microinjection of chromosome fragments into the embryonic nucleus (transfer of intact gene clusters).

Tumor suppressor gene.  A gene that normally controls cell proliferation or that activates the apoptotic pathway, in which loss-of-function mutations are associated with cancer progression.

Variegation.  Variable expression of a transgene  in the same cell type or tissue within a mouse.

Vector.  A DNA molecule, capable of replication, into which a gene or DNA segment can be inserted by recombinant DNA techniques; a cloning vehicle.

VL30.  Replication-incompetent retrovirus-like 30S RNA sequences.

vSAg.  MMTV superantigen gene.

Whitten effect.  The pheromone-related effect of male urine on breeding females, in which the estrus cycle is shortened, cycles among females are synchronized, and onset of puberty in young females is accelerated.  Used to advantage for timed breeding.

Wildtype.  The most common phenotype or genotype in a natural population; a phenotype or genotype arbitrarily designated as a standard for comparison. Wildtype can refer to single alleles or whole genomes. 

Xenotropic retrovirus. Retrovirus, either leukemia virus or mammary tumor virus, with tropism for cells from other species, but not mouse.

YAC. Yeast artificial chromosome. A cloning vector that can accept very large genomic inserts; a chromosome introduced to yeast derived from such a vector and containing DNA from another organism.

Zygote. The fertilized egg containing both sire and dam pronuclei; a fertilized egg.

 

March, 2003