Linkage disequilibrium

30 Mar

Linkage disequilibrium
cause they reside on the same chromosome. See Ap- pendix A, 1906, Bateson and Punnett; 1913, Sturte- vant; 1915, Haldane et al.; 1951, Mohr. linkage disequilibrium the nonrandom distribu- tion into the gametes of a population of the alleles of genes that reside on the same chromosome. The simplest situation would involve a pair of alleles at each of two loci. If there is random association be- tween the alleles, then the frequency of each gamete type in a randomly mating population would be equal to the product of the frequencies of the alleles it contains. The rate of approach to such a random association or equilibrium is reduced by linkage and hence linkage is said to generate a disequilibrium. See gametic disequilibrium.

linkage group the group of genes having their loci on the same chromosome. See Appendix C, 1919, Morgan. linkage map a chromosome map showing the rela- tive positions of the known genes on the chromo- somes of a given species. linked genes See linkage. linker DNA 1. a short, synthetic DNA duplex con- taining the recognition site for a specific restriction endonuclease. Such a linker may be connected to ends of a DNA fragment prepared by cleavage with some other enzyme. 2. a segment of DNA to which histone H1 is bound. Such linkers connect the adja- cent nucleosomes of a chromosome. linking number the number of times that the two strands of a closed-circular, double-helical molecule cross each other.

The twisting number (T) of a re- laxed closed-circular DNA is the total number of base pairs in the molecule divided by the number of base pairs per turn of the helix. For relaxed DNA in the normal B form, L is the number of base pairs in the molecule divided by 10. The writhing number (W) is the number of times the axis of a DNA molecule crosses itself by supercoiling.

The linking number (L) is determined by the formula: L=W+T. For a relaxed molecule, W=0, and L= T. The linking number of a closed DNA molecule cannot be changed except by breaking and rejoining of strands. The utility of the linking number is that it is related to the actual enzymatic breakage and re- joining events by which changes are made in the to- pology of DNA. Any changes in the linking number must be by whole integers. Molecules of DNA that are identical except for their linking numbers are called topological isomers. Linnean Society of London a society that takes its name from Carl Linne´, the Swedish naturalist and “Father of Taxonomy.” The Society was founded in 1788 (ten years after Linne´’s death) for “the cultiva- tion of the Science of Natural History in all its branches.” Subsequently the first president of the Society purchased Linne´’s botanical and zoological collections, and they are held in the Society’s mu- seum.

An early publication of the Society contains Brown’s discovery of the cell nucleus. In 1858 essays by Darwin and Wallace presenting the theory of evolution by natural selection were first published in the Society’s Proceedings. The next year another es- say by Wallace was published by the Society. In this account of the zoological geography of the Malay Archipelago, the first description of the Wallace line (q.v.) was given. See Appendix C, 1735, Linne´;1831, Brown; 1858, Darwin and Wallace; 1859, Wallace. Linnean system of binomial nomenclature a naming system in which each newly described or- ganism is given a scientific name consisting of two Latin words. For example, in the case of the fruitfly, Drosophila melanogaster Meigen, the first name (the genus) is capitalized and the second (the species) is not. The scientific name is italicized, and the author who named and described the species is sometimes given.

In instances where the scientific name is fol- lowed by an “L” (e.g., Canis familiaris L), the species not the first to use binomial names, he was the first to employ them in constructing a taxonomy of plants and animals. When two plants or animals are accidently given the same species name, it remains valid for only the first one named. However, the same name has been allowed for a plant and an ani- mal. A good example is Cereus, a name for a well- known genus of sea anemonies and cacti. See Appen- dix C, 1735, Linne´; Hyracotherium, Linnean Society of London, Takifugu ruripes. Linum usitatissimum the cultivated flax plant, the source of fiber for linen and stationery and flax- seed for linseed oil. Classic studies on coevolution (q.v.) have utilized the genes of flax and its parasite, the rust fungus Melampsora lini. See Appendix A, Plantae, Tracheophyta, Angiospermae, Dicotyle- donae, Linales; gene-for-gene hypothesis. lipase an enzyme that breaks down fats to glycerol and fatty acids. LIPED See lod. lipid any of a group of biochemicals that are vari- ably soluble in organic solvents like alcohol and barely soluble in water (fats, oils, waxes, phospho- lipids, sterols, carotenoids, etc.).

Local population

lipid bilayer model a model for the structure of cell membranes based upon the hydrophobic prop- erties of interacting phospholiplids. The polar head groups face outward to the solvent, whereas the hy- drophobic tails face inward. Proteins (p) are embed- ded in the bilayer, sometimes being exposed on the outer surface, sometimes on the inner surface, and sometimes penetrating both surfaces. The proteins exposed on the outer surfaces of cells commonly serve as distinctive antigenic markers. Membrane proteins may serve a variety of functions such as communication, energy transduction, and transport of specific molecules across the membrane. See fluid mosaic concept.

lipopolysaccharide the active component of bac- terial endotoxins associated with the cell walls of many Gram-negative species; a B-cell mitogen in some animal species. liposomes synthetic vesicles surrounded by bi- layers of phospholipids. They have been used as models of cell membranes and as therapeutic deliv- ery systems in which the drugs employed are encap- sulated within liposomes. In studies of genetic trans- formation, the synthetic vesicles are used to protect naked DNA molecules and to allow their passage into tissue-cultured animal cells or into protoplasts from plants or bacteria. This technique is called lipo- some-mediated gene transfer. lipovitellin a lipoprotein of relative molecular mass 150,000 found in amphibian yolk platelets. See phosvitin. liquid-holding recovery a special form of dark re- activation (q.v.) in which repair of ultraviolet dam- age to DNA is enhanced by delaying bacterial growth and DNA replication through postirradiation incubation of cells in a warm, nutrient-free buffer for several hours before plating them on nutrient agar.

liquid hybridization formation of double helical nucleic acid chains (DNA with DNA, DNA with RNA, or RNA with RNA) from complementary sin- gle strands in solution. Compare with filter hybridiza- tion. liquid scintillation counter an electronic instru- ment for measuring radioisotopes dissolved in a sol- vent containing a fluorescent chemical that emits a flash of light (a scintillation) when struck by an ion- izing particle or photon of electromagnetic radia- tion. The flash is captured by a photomultiplier tube, transformed into an electric pulse, amplified, routed through a scaler, and counted. liter standard unit of capacity in metric system, equal to 1 cubic decimeter. lithosphere See plate tectonics. lithotroph a prokaryote that uses an inorganic sub- stance as a substrate in its energy metabolism. For example, energy may be obtained by the oxidation of H2, NH3, sulphur, sulphide, thiosulphate, or Fe++.

Lithotrophic metabolism is independent of light. However, a photolithotroph can use its inorganic sub- strates as electron donors in photosynthesis. See chemolithoautotroph. litter animals of one multiple birth. littoral pertaining to the shore. Liturgosa a genus of mantid. The evolution of karyotype has been extensively studied in this genus. living fossil literally referring an organism that be- longs to a group recognized on the basis of fossils and only subsequently found to be extant. The clas- sic example of such a living fossil would be Latime- ria chalumnae, the sole living representative of an ancient group of bony fishes called coelacanths. These belong to the Crossopterygii and are allies of the lung fishes and near the ancestry of the amphibi- ans. The first fossil Permian Coelacanthus was named in 1839, while the first specimen of Latimeria was captured in 1938. The term is also used to refer to a living organism that is regarded as morphologically similar to a hypothetical ancestral missing link, even though the group has little or no fossil record.

Peri- patus is such an example, since it and other onyco- phorans have characteristics of both arthropods and annelids. Finally, living fossil is used to refer to the end member of a clade that has survived a long time and undergone little morphological change. This is what Charles Darwin had in mind when he coined the term back in 1859. The externally shelled cepha- lopod, Nautilus, would be an example of a living fossil by this criterion. See Mesostigma viride. load See genetic load. local population a group of conspecific individu- als together in an area within much most of them find their mates; synonymous with deme, and Men- delian population. See subpopulations.

locus (plural loci) the position that a gene occu- pies in a chromosome or within a segment of geno- mic DNA. Locusta migratoria the Old World “plague” lo- cust. lod the abbreviation for “logarithm of the odds fa- voring linkage.” The lod score method is employed in the statistical analyses of linkage. In the calcula- tions, a pedigree is analyzed to determine the likeli- hood or probability (Pr) that two genes show a spec- ified recombination value (r). Next, the likelihood (Pi) is calculated under the assumption that the genes assort independently.

The lod score Z = log10(Pr/Pi). The advantage of using logarithms is that the scores from new pedigrees can be added to earlier Z values as they become available. A Z score of +3 is considered evidence for linkage. A computer program such as LIPED makes laborious manual computations unnecessary and is generally used in analyzing a collection of complex pedigrees. See Ap- pendix C, 1955, Morton; 1974, Ott. logarithmic phase the growth stage during which organisms are doubling their number each time a specified period of time elapses. long-day plant a plant in which the flowering pe- riod is initiated and accelerated by a daily exposure to light exceeding 12 hours. long period interspersion a genomic pattern in which long segments of moderately repetitive and nonrepetitive DNA sequences alternate.

long terminal repeats (LTRs) domains of several hundred base pairs at the ends of integrated ret- roviruses. Each retrovirus has to be copied by a re- verse transcriptase, and the DNA strand is then rep- licated to form a double-stranded DNA. It is this segment that is integrated into the chromosome of the mammalian host cell. LTRs are required for both the replication of the viral DNA and its integration. long-term memory See CREBs, spaced training. Lophotrochozoa a clade that contains the phyla Platyhelminthes, Annelida, and Mollusca.

These ani- mals all have quite similar nucleotide sequences in their 18S rRNA genes (q.v.), and they share a cluster of HOX genes (q.v.) quite different from the clusters found in ecdysozoans (q.v.) and deuterostomes (q.v.). loss of function mutation a genetic lesion that prevents the normal gene product from being pro- duced or renders it inactive. An example of a loss of function mutation would be a nonsense mutation that causes polypeptide chain termination during translation. Loss of function mutations are generally recessive. Contrast with gain of function mutation. loss of heterozygosity the loss of the normal al- lele, as the result of a deletion or inactivating muta- tion, in a heterozygous cell which already carries a mutant allele in the other homolog. Since there is now no functioning allele in the cell, it and its de- scendents will show the mutant phenotype.

Lou Gehrig disease See amyotrophic lateral sclero- sis (ALS). low-density lipoprotein receptor (LDLR) See fa- milial hypercholesterolemia. low-energy phosphate compound a phosphory- lated compound yielding relatively little energy upon hydrolysis. lozenge a sex-linked gene in Drosophila named for its effect on the compound eyes. These have a dis- turbed surface because of the fusion of adjacent fac- ets. However, various alleles also show defects in the differentiation of hemocytes and abnormalities in the development of antennae, claws, and reproduc- tive systems. Molecular studies show that the gene is made up of two regions. Mutations in the anterior controlling region influence the tissue-specific be- havior of the gene, while the posterior region en- codes a protein with a DNA-binding domain that functions as a transcription factor (q.v.). See runt (run). LTH lactogenic hormone (q.v.).

luciferase an enzyme, produced in the abdomen of lightning bugs (Photinus pyralis), whose gene has been used to determine when a target gene has been inserted into plant genomes. In the presence of oxy- gen, ATP, and a substrate called luciferin, plants genetically engineered to contain the luciferase gene glow in the dark. Compare with green fluorescent protein (GFP). See fireflies. Lucilia cuprina the Australian blowfly, a major pest of the sheep industry in Australia. Good poly- tene chromosome preparations can be obtained from pupal trichogen cells (q.v.), and extensive cytoge- netic studies have been made of chromosome re- arrangements. The concept of pest control through the introduction into the field of chromosomally al- tered strains whose descendants manifest sterility has been tested in this species. ´ virus a virus causing renal cancer in frogs.

Lucy See Australopithecine. Ludwig effect a generalization offered by W. Ludwig in 1950 that a species tends to be more di- versified (polymorphic) both morphologically and chromosomally in the center of an old established range than at its margins. luminescence light emission that cannot be attrib- uted to the temperature of the emitting body. The light energy emitted may result from a chemical re- action going on within the emitter or it may be initi- ated by the flow of some form of energy into the body from the outside. The slow oxidation of phos- phorus at room temperature is an example of the former, while luminescence resulting from electron bombardment of’gaseous atoms in a mercury vapor lamp is an example of the latter. Fluorescence is de- fined as a luminescence emission that continues after the source of exciting energy is shut off. This after- glow is temperature independent. In the case of phosphorescence, the afterglow duration becomes shorter with increasing temperature.

lungfish a group of lobed finned fishes belonging to the order Dipnoi (see Appendix A, Osteichthyes, Crossopterygii). They flourished during the Paleo- zoic but are now represented by only three genera, Lepidosiren of South America, Neoceratodus of Australia, and Protopterus of Africa. P. aethiopicus has a C value of 127 gbp of DNA, a record for an animal. Lungfish have gills and also lungs and can breathe air.

lupus erythematosus a connective tissue disorder characterized by autoantibody production against cellular components that are abundant and highly conserved. Among the antibodies produced by pa- tients with lupus are those that recognize U 1 RNA. See autoimmune disease, Usn RNAs. luteinizing hormone a glycoprotein hormone that stimulates ovulation, growth of the corpus luteum, and secretion of estrogen. LH is secreted by the ade- nohypophysis of vertebrates. Identical to ICSH. luteotropin lactogenic hormone (q.v.). Lutheran blood group a blood group determined by a red cell antigen specified by the Lu gene on human chromosome 19. Autosomal linkage in hu- mans was first demonstrated between Lu and Le. The eponym Lutheran arose from a misinterpreta- tion of the name of the patient (Luteran) who pro- vided the antigen. See blood group, Lewis blood group. luxuriance a high degree of vegetative develop- ment, often seen in species hybrids; a special feature of heterosis (q.v.). luxury genes genes coding for specialized (rather than “household”) functions.

Their products are usu- ally synthesized in large amounts only in particular cell types (e.g., hemoglobin in erythrocytes; immu- noglobulins in plasma cells). Luzula a genus of plants containing the wood rushes. Many species in this genus have diffuse cen- tromeres. See centromere. lyases enzymes that catalyze the addition of groups to double bonds or the reverse. Lycopersicon esculentum the cultivated tomato. The haploid chromosome number is 12. There are extensive linkage maps for each chromosome and also cytological maps for pachytene chromosomes. See Appendix A, Angiospermae, Dicotyledonae, Solanales. lycopods the most primitive trees. They arose in the Devonian and were the dominant plants in the Carboniferous coal swamps.

The only lycopods that survived to the present are tiny club mosses like Lycopodium. Lymantria dispar the Gypsy moth. Classical stud- ies on sex determination were performed on this species. See Appendix A, Arthropoda, Insecta, Lepi- doptera; Appendix C, 1915, Goldschmidt. lymphatic tissue tissues in which lymphocytes are produced and/or matured, including the thymus, spleen, lymph nodes and vessels, and the bursa of Fabricius (q.v.).

lymphoblast the larger, cytoplasm-rich cell that differentiates from antigenically stimulated T lym- phocytes. lymphocyte a spherical cell about 10 micrometers in diameter found in the lymph nodes, spleen, thy- mus, bone marrow, and blood. Lymphocytes, which are the most numerous cells in the body, are divided into two classes: B cells, which produce antibodies, and T cells, which are responsible for a variety of immunological reactions, including graft rejections. See Appendix C, 1962, Miller, Good et al., Warner et al.; B lymphocyte, cytotoxic T lymphocyte, helper T lymphocyte, immunoglobulin, lymphokines, T lym- phocyte, tumor necrosis factors. lymphokines a heterogeneous group of glycopro- teins (relative molecular mass 10,000-200,000) re- leased from T lymphocytes after contact with a cog-

nate antigen. Lymphokines affect other cells of the host rather than reacting directly with antigens. Var- ious lymphokines serve several major functions: (1) recruitment of uncommited T cells; (2) retention of T cells and macrophages at the site of reaction with antigen; (3) amplification of “recruited” T cells; (4) activation of the retained cells to release lympho- kines; and (5) cytotoxic effects against cells bearing foreign antigens (including foreign tissue grafts and cancer cells). Examples of lymphokines produced by T cells following in vitro antigenic stimulation are as follows: migration inhibition factor (MIF) prevents migration of macrophages; lymphotoxins (LT) kill target cells; mitogenic factor (MF) stimulates lym- phocyte division; interleukin 2 (IL2) is required for T helper activity; interferons (IFN) promote antivi- ral immunity; chemotactic factors attract neutro- phils, eosinophils, and basophils; macrophage activa- tion factor (MAF) stimulates macrophages.

See histocompatibility molecules. lymphoma cancer of lymphatic tissue. Lyon hypothesis the hypothesis that dosage com- pensation (q.v.) in mammals is accomplished by the random inactivation of one of the two X chromo- somes in the somatic cells of females. See Appendix C, 1961, Lyon and Russell; 1962, Beutler et al.; XIST. Lyonization a term used to characterize heterozy- gous females that behave phenotypically as if they were carrying an X-linked recessive in the hemizy- gous condition. An example would be a hemophilic mother that has produced nonhemophilic sons.

It is assumed, according to the Lyon hypothesis, that oc- casionally a particular tissue comes to be made up entirely of cells that contain inactivated X chromo- somes carrying the normal allele. The phenotype of such a female heterozygote would then resemble that of mutant males. See manifesting heterozygote. lyophilize to render soluble by freeze drying. lys lysine. See amino acid. lysate a population of phage particles released from host cells via the lytic cycle. Lysenkoism a school of pseudoscience that flour- ished in the Soviet Union between 1932 and 1965. Its doctrines were advanced by T. D. Lysenko (1898-1976), who did not accept the gene concept and believed in the inheritance of acquired charac- teristics.

Lysenko became the dominant figure in Soviet agriculture, after winning the support of Sta- lin. N. V. Vavilov, the great geneticist and leader of Soviet agriculture who Lysenko replaced, was later arrested for “sabotaging Soviet science” and thrown into prison, where he died of starvation in 1943. See Appendix C, 1926, Vavilov. lysine See amino acid. lysis See cell lysis. lysochrome a compound that colors lipids by dis- solving in them. See Nile blue, Sudan black B. lysogen a lysogenic bacterium. lysogenic bacterium one carrying a temperate vi- rus in the prophage state. lysogenic conversion the change in phenotype of a bacterium (in terms of its morphology or synthetic properties) accompanying lysogeny (q.v.).

Lysogenic cells exhibit immunity to superinfection by the same phage as that in the prophage state. Toxin produc- tion by Corynebacterium diphtheriae only occurs in strains that are lysogenic for phage beta. lysogenic cycle a method of temperate phage re- production in which the phage genome is integrated into the host chromosome as a prophage and repli- cates in synchrony with the host chromosome. Un- der special circumstances (e.g., when growth condi- tions for the host are poor), the phage may leave the host chromosome (deintegration or excision) and enter the vegetative state or the lytic cycle that produces progeny phage. In lambda (λ) bacterio- phage (q.v.), the OR region of the genome acts as a genetic switch between the lytic and lysogenic life cycles. OR contains operator sites for C1 and cro genes, which encode the lambda repressor (q.v.) and the cro repressor (q.v.), respectively.

At any given time the developmental pathway followed by the vi- rus depends on the relative concentrations of these repressors. See Appendix C, 1950, Lwoff and Gut- man; lambda phage genome. lysogenic immunity a phenomenon in which a prophage prevents another phage of the same type from becoming established in the same cell. lysogenic repressor a phage protein responsible for maintenance of a prophage and lysogenic immu- nity. lysogenic response the response following infec- tion of a nonlysogenic bacterium with a temperate phage. The infecting phage does not multiply but rather behaves as a prophage. See lytic response. lysogenic virus a virus that can become a pro- phage. lysogenization the experimental production of a lysogenic strain of bacteria by exposing sensitive bac- teria to a temperate phage.

Lytic virus

lysogenized bacterium a bacterium harboring an experimentally introduced, temperate phage. lysogeny the phenomenon in which genetic mate- rial of a virus and its bacterial host are integrated. lysosomal storage diseases hereditary diseases characterized by abnormal lipid storage due to de- fects in lysosomal enzymes. The accumulation of the trapped intermediates of catabolism results in the cytoplasmic storage of these complex molecules. The storage material is often desposited in myriads of concentrically arranged lamellar structures that accumulate throughout the cytoplasm of certain cell types. For example, in Tay-Sachs disease (q.v.) the targets are ganglion cells, while in Gaucher disease (q.v.) macrophages are the storage sites. See Ashken- azi, lysosomes, Wolman disease. lysosomal trafficking regulator human gene residing at 1q 42.1-2 that contains 55 exons and is thought to undergo a complex pattern of alternative RNA splicing. One 13.5 kb mRNA en- codes a protein containing 3,801 amino acids. Muta- tions which cause truncations of this protein result in severe Che´diak-Higashi syndrome (q.v.). Proteins encoded by the LYST gene play a role in the sorting of resident proteins within lysosomes and melano- somes (both of which see). lysosome a membrane-enclosed intracellular vesi- cle that acts as the primary component for intracel- lular digestion in all eukaryotes. Lysosomes are known to contain at least 50 acid hydrolases, includ- ing phosphatases, glycosidases, proteases, sulfatases, lipases, and nucleases.

Lysosomes primarily process exogenous proteins that are taken into the cell by endocytosis (q.v.) and proteins of the cell surface that are used in receptor-mediated endocytosis (q.v.). See Appendix C, 1955, deDuve et al.; lyso- somal storage diseases, protein sorting, sorting signals, ubiquitin-proteasome pathway (UPP). lysozyme an enzyme digesting mucopolysaccha- rides. Lysozymes having a bacteriolytic action have been isolated from diverse sources (tears, egg white, etc.). An important lysozyme is the enzyme synthe- sized under the direction of a phage that digests the cell wall of the host from within and thus allows the escape of the phage progeny. Lysozyme was the first enzyme whose three-dimensional structure was de- termined by x-ray crystallography.

See Appendix C, 1966, Terzaghi; 1967, Blake et al. lytic cycle the vegetative life cycle of a virulent phage, by which progeny phage are produced and the host is lysed. Temperate phage (q.v.) have the option of becoming a prophage (usually when growth conditions for its host cell are good) or enter- ing the lytic cycle when growth conditions for its host are poor. See cro repressor. lytic response lysis following infection of a bacte- rium by a virulent phage, as opposed to lysogenic response (q.v.). lytic virus a virus whose intracellular multiplica- tion leads to lysis of the host cell.

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