chromosome map See cytogenetic map, genetic map. chromosome painting a variation of fluorescence in situ hybridization (FISH) (q.v.) technique using fluorescent dye-tagged DNA segments that can hy- bridize to numerous sites along each human chromo- some. Because there are too few known fluorescent dyes to distinctively mark each human chromosome, a combinatorial approach is taken. Since the total combinations given by a number of dyes (N) is 2N − 1, as few as five dyes can give enough combinations to produce probes that will individually label each chromosome.
The fluorochrome colors cannot be distinguished by the unaided eye but can be de- tected by using a series of filters or an interferometer linked with computers to analyze the various dye combinations assigned to each chromosome. Chro- mosome painting is also known as multicolor fluo- rescence in situ hybridization (MFISH). Cross spe- cies-chromosomal painting and digital imaging are now commonly used in studies of the evolution of mammalian karyotypes. See Appendix C, 1997, Yang et al.
chromosome polymorphism the presence in the same interbreeding population of one or more chro- mosomes in two or more alternative structural forms. chromosome puff See chromosomal puff. chromosome rearrangement a chromosomal ab- erration involving new juxtapositions of chromo- somal segments; e.g., inversions, translocations. chromosome scaffold when histones are removed from isolated metaphase chromosomes and these are centrifuged onto electron microscope grids, ex- tremely long loops of DNA can be seen to project from an irregular mass (the scaffold) whose dimen- sions are similar to the original intact chromosome. chromosome set a group of chromosomes repre- senting a genome (q.v.), consisting of one represen- tative from each of the pairs characteristic of the so- matic cells in a diploid species. See polyploidy. chromosome sorting See flow cytometry.
chromosome substitution replacement by a suit- able crossing program of one or more chromosomes by homologous or homoeologous chromosomes from another source. This may be a different strain of the same species or a related species that allows hybrid- ization. See homoeologous chromosomes, homolo- gous chromosomes. chromosome theory of heredity the theory put forth by W. S. Sutton in 1902 that chromosomes are the carriers of genes and that their meiotic behavior is the basis for Mendel’s laws (q.v.). chromosome walking the sequential isolation of clones carrying overlapping restriction fragments to
span a segment of chromosome that is larger than can be carried in a phage or a cosmic vector. The technique is generally needed to isolate a locus of interest for which no probe is available but that is known to be linked to a gene that has been identified and cloned. This probe is used to screen a genome library. As a result, all fragments containing the marker gene can be selected and sequenced. The fragments are then aligned, and those segments far- thest from the marker gene in both directions are subcloned for the next step. These probes are used to rescreen the genome library to select new collec- tions of overlapping sequences.
As the process is re- peated, the nucleotide sequences of areas farther and farther away from the marker gene are identi- fied, and eventually the locus of interest will be en- countered. If a chromosomal aberration is available that shifts a particular gene that can serve as a molecular marker to another position on the chro- mosome or to another chromosome, then the chro- mosome walk can be shifted to another position in the genome. The use of chromosome aberrations in experiments of this type is referred to as chromosome jumping. See Appendix C, 1978, Bender, Spierer, and Hogness. chromotrope a substance capable of altering the color of a metachromatic dye (q.v.). chronic exposure radiation exposure of long dura- tion.
Applied to experimental conditions in which the organism is given either a continuous low level exposure or a fractionated dose. chronocline in paleontology, a character gradient in the time dimension. chronospecies a species that can be studied from its fossil remains through a defined period of time. chrysalis the pupa of a lepidopteran that makes no cocoon (q.v.). chrysomonads fresh water members of the Chromista (q.v.).
They are called golden algae be- cause their cytoplasm contains yellow plastids. An example is any species belonging to the genus Ochro- monas. Each cell has two undulipodia attached to its anterior pole. One is long and hairy, and the one behind it is shorter with fewer lateral fibers. Ochro- monas also contains a chloroplast ER. chymotrypsin a proteolytic enzyme from the pan- creas that hydrolyzes peptide chains internally at peptide bonds on the carboxyl side of various amino acids, especially phenylalanine, tyrosine, and trypto- phan. Ci abbreviation for curie (q.v.).
cichlid fishes cichlids (pronounced ‘sick-lid’) are a family of freshwater fishes distributed throughout the tropics and subtropics. There are about 1,300 species described so far, but almost 1,000 are found in the rift lakes of East Africa (Lakes Victoria, Ma- lawi, and Tanganyika). Speciation in the Rift Lake cichlids has been extremely rapid and has resulted in part from sexual selection (q.v.). See Appendix A, Chordata, Osteichythes, Neopterygii, Perciformes. cilia (singular, cilium) populations of thin, motile processes found covering the surface of ciliates or the free surface of the cells making up a ciliated epi- thelium.
Each cilium arises from a basal granule in the superficial layer of cytoplasm. The movement of cilia propels ciliates through the liquid in which they live. The movement of cilia on a ciliated epithelium serves to propel a surface layer of mucus or fluid. See axoneme. ciliate a protozoan belonging to the phylum Cilio- phora. See Appendix A, Protoctista. Ciona intestinalis a species of ascidians, com- monly called sea squirts. As adults they are her- maphrodites that live as filter feeders in shallow seas. They are sometimes called tunicates because each is enclosed in a tough tunic made up of tunicin, a cel- lulose-like fiber.
Fertilized eggs develop into free- swimming larvae, and each tadpole has a prominent notochord and dorsal nerve tube. For this reason, they are classified as Urochordates, a primitive branch of the Acraniata (q.v.). Ciona has 14 chro- mosomes and a genome size of about 156 mbp. Its 15,900 ORFs are more closely packed than those of most vertebrates. About 1/6 of the Ciona genes have vertebrate homologs.
The Ciona homologs are gen- erally present in only a few copies compared to the multiple copies found in vertebrate gene families (i.e., actin genes or myosin genes). See Appendix A, Eumetazoa, Deuterostomia, Chordata, Acraniata, Urochordata; Appendix C, 2002, Dehal et al.; iso- forms, tunicin. circadian rhythm an oscillation in the biochemis- try, physiology, or behavior of an organism that has a natural period of exactly 24 hours.
If the organism is placed under constant conditions, the rhythm will continue with a period that is close to, but not ex- actly, 24 hours. For example, in Neurospora the number of hours between peaks of conidiation is 21.5 hours under constant conditions. This endoge- nous periodicity can be reset to 24 hours by a change in light level (e.g., a shift from constant darkness to
a 12-hour light : 12-hour dark cycle). See clock mu- tants, entrainment, frequency. circular dichroism the property of molecules to show differences in absorption between the clock- wise and counterclockwise component vectors of a beam of circularly polarized light.
Since helical molecules in solution often exhibit these properties, circular dichroism spectra have been used to study coiling changes of physiological significance, which various proteins can undergo. In the cases of chro- matin fragments oriented in electric fields and ex- posed to circularly polarized ultraviolet light, mea- surements of circular dichroism allow conclusions to be drawn as to the way nucleosomes (q.v.) are stacked in 30-nanometer fibers. circular linkage map the linkage map characteris- tic of Escherichia coli.
In preparation for genetic transfer during conjugation, the ring-shaped chro- mosome of an Hfr bacterium breaks in such a way that when the ring opens the F factor is left attached to the region of the chromosome destined to enter the F− cell last.
Circular linkage maps have been con- structed for several other bacteria and for certain vi- ruses. See also linkage map. circularly permuted sequences See cyclically per- muted sequences. circular overlap the phenomenon in which a chain of continuous and intergrading populations of one species curves back until the terminal links over- lap each other.
Individuals from the terminal popu- lations are then found to be reproductively isolated from each other; that is, they behave as if they be- longed to separate species. A ring of races so formed is referred to as a Rassenkreis. circumsporozoite protein See sporozoite. cis-acting locus a genetic region affecting the ac- tivity of genes on that same DNA molecule. Cis-act- ing loci generally do not encode proteins, but rather serve as attachment sites for DNA-binding proteins.
Enhancers, operators, and promoters are examples of cis-acting loci. Contrast with trans-acting locus. cis dominance the ability of a genetic locus to in- fluence the expression of one or more adjacent loci in the same chromosome, as occurs in lac operator mutants of E.
coli. cis face See Golgi apparatus. cisplatin one of the most widely used antitumor drugs, especially effective for the management of testicular and ovarian cancers. When cisplatin binds to DNA, it loses two chloride ions and forms two platinum-nitrogen bonds with the N7 atoms of adja- cent guanines on the same strand. This localized dis- ruption of the double helix inhibits replication.
cis-splicing the splicing together of the exons within the same gene that occurs during the modifi- cation of the primary RNA transcript in the nucleus. Compare with trans-splicing and see posttranscrip- tional processing. cisterna a flattened, fluid-filled reservoir enclosed by a membrane.
See endoplasmic reticulum. cis, trans configurations terminology that is cur- rently used in the description of pseudoallelism. In the cis configuration both mutant recons are on one homolog and both wild-type recons are on the other (a1a2/++). The phenotype observed is wild type.
In the trans configuration each homolog has a mutant and a nonmutant recon (a1+/+a2), and the mutant phenotype is observed. In the case of pseudoallelic genes, the terms cis and trans configurations corre- spond to the coupling and repulsion terminology used to refer to nonallelic genes. See transvection effect. cis-trans test a test used to determine whether two mutations of independent origin affecting the same character lie within the same or different cis- trons. If the two mutants in the trans position yield the mutant phenotype, they are alleles.
If they yield the wild phenotype, they represent mutations of dif- ferent cistrons. However, different mutated alleles may represent cistrons with mutations at different sites. If these mutons are separable by crossing over, it is possible to construct a double mutant with the mutant sites in the cis configuration (m1m2/++). Indi- viduals of this genotype show the wild phenotype. See pseudoalleles. cistron originally the term referred to the DNA segment that specified the formation of a specific polypeptide chain (see Appendix C, 1955, Benzer).
The definition was subsequently expanded to in- clude the transcriptional start and stop signals. In cases where an mRNA encodes two or more pro- teins, it is referred to as polycistronic. The proteins specified by a polycistron are often enzymes that function in the same metabolic pathway. See gene, transcription unit. citrate cycle a synonym for citric acid cycle (q.v.).