Coliform | Kickoff

Coliform

27 Mar

Coliform

coliform designating a Gram-negative, lactose-fer- menting rod related to E. coli. colinearity correspondence between the location of mutant sites within a bacterial cistron and the lo- cation of amino acid substitutions in its translational product. This correspondence is not complete in most eukaryotic genes because of the presence of nontranslated introns (q.v.). See Appendix C, 1964, Sarabhai et al., Yanofsky et al. coliphage a bacteriophage (q.v.) that parasitizes E. coli.

See lambda phage. collagen the most abundant of all proteins in mam- mals; the major fibrous element of skin, bone, ten- don, cartilage, and teeth, representing one-quarter of the body’s protein. The protein consists of a triple helix 3,000 A˚ngstroms long and 15 A˚ngstroms across. Five types of collagen are known, differing in amino acid sequence of the three polypeptide chains.

In some molecules of collagen, the three chains are identical; in others, two of the chains are identical and the third contains a different amino acid se- quence. The individual polypeptide chains are trans- lated as longer precursors to which hydroxyl groups and sugars are attached.

A triple helix is formed and secreted into the space between cells. Specific en- zymes trim the ends of each helix. Type 5 collagen is a minor collagen component present in adult skin. It is encoded by the COL5A1 gene located on hu- man chromosome 9 at q34.

The gene contains at least 750 kb of DNA and is made up of 66 exons. Mutations in COL5A1 cause one form of Ehlers- Danlos syndrome (q.v.). Mutations in collagen genes also cause hereditary blistering diseases. See carti- lage, dominant negative mutation, epidermolysis bul- losa. Compare with keratin. collagenase an enzyme that digests collagen. collenchyma plant tissue composed of cells that fit closely together and have thickened walls; in meta- zoans, undifferentiated mesenchyme cells lying in a gelatinous matrix.

collision, inelastic the event occurring when a moving electron passes close to an atom. There is repulsion between the moving electron and an atomic electron sufficient to dislodge the latter from its nucleus. colony in bacteriology, a contiguous group of sin- gle cells derived from a single ancestor and growing on a solid surface. colony bank See gene library. colony hybridization an in situ hybridization (q.v.) technique used to identify bacteria carrying chimeric vectors whose inserted DNA is homologous with the sequence in question.

Colony hybridization is ac- complished by transferring bacteria from a petri plate to a nitrocellulose filter. The colonies on the  filter are then lysed, and the liberated DNA is fixed to the filter by raising the temperature to 80°C. After hybridization with a labeled probe, the posi- tion of the colonies containing the sequence under study is determined by autoradiography (q.v.). See Appendix C, 1975, Grunstein and Hogness.

color blindness defective color vision in humans due to an absence or reduced amount of one of the three visual pigments. The pigments chlorolabe, erythrolabe, and cyanolabe absorb green, red, and blue light, respectively. The pigments are made of three different opsins combined with vitamin A al- dehyde.

The green-blind individual suffers from deu- teranopia and cannot make chlorolabe. The red- blind individual suffers from protanopia and cannot make erythrolabe. The blue-blind individual suffers tritanopia and cannot make cyanolabe. Deuteranom- aly, protanomaly and tritanomaly are conditions caused by reduced amounts of the visual pigments in question, rather than their complete absence.

The protan and deutan genes for red and green blindness, respectively, occupy different loci on the X chromo- some. Blue blindness is quite rare and due to an au- tosomal gene. The famous physicist John Dalton was color blind, and he gave the earliest account of this condition. For this reason, protanopia is sometimes called daltonism. See cone pigment genes (CPGs), dal- ton, opsin, retina. Colton blood group antigens produced by a gene at human chromosome 7p14.

The gene product be- longs to the aquaporin (q.v.) family of water channel proteins. For this reason, the gene is symbolized AQP1. The gene has been cloned and is 13 kb long and contains 4 exons. See Appendix C, Preston and Agre. Columba livia the domesticated pigeon. In nature the species is called the rock dove. Its haploid chro- mosome number is 40, and its C value is 1.46 pg of DNA. Charles Darwin bred pigeons, and in his Ori- gin of Species described the numerous variations that had been selected by pigeon fanciers. There are cur- rently at least 200 breeds, including those selected for homing and racing. See Appendix A, Aves, Col- umbiformes.

Compartmentalization

column chromatography the separation of or- ganic compounds by percolating a liquid containing the compounds through a porous material in a cylin- der. The porous material may be an ion exchange resin. See chromatography. combinatorial association within a pool of im- munoglobulin molecules, the association of mole- cules from any class of heavy chain with molecules from any type of light chain.

Within a given immu- noglobulin molecule, however, there is only one class of heavy and one type of light chain. See immu- noglobulin. combinatorial translocation for an immunoglob- ulin chain (heavy or light), the association of any variable region gene with any constant region gene within that same multigene family (q.v.). The two genes are brought together by interstitial transloca- tion that may involve deletion of intervening genetic material. See immunoglobulin.

combining ability 1. general: average performance of a strain in a series of crosses. 2. specific: deviation of a strain’s performance in a given cross from that predicted on the basis of its general combining ability. comb shape a character influenced by two nonal- lelic gene pairs, Rr and Pp, in the chicken.

One of the early examples of gene interaction (q.v.). See Gallus domesticus. commaless genetic code successive codons that are contiguous and not separated by noncoding bases or groups of bases. Bacterial genes do not have in- trons (q.v.), and therefore the sequences of amino acids in polypeptides and of codons in the gene are colinear. Most eukaryotic genes contain coding re- gions called exons (specifying amino acids) inter- rupted by noncoding regions called introns, and in these situations the code is said to contain commas. commensalism the association of organisms of dif- ferent species without either receiving benefits es- sential or highly significant to survival. The species may live in the same shell or burrow, or one may be attached to or live within the other.

See parasitism, symbiosis. community interacting populations of individuals belonging to different species and occupying a given region or a distinctive range of habitat conditions. community genome sequencing the simultane- ous sequencing of the genomes present in a specified community of microorganisms. A sample is taken of the species living in specific habitat, and the DNA isolated from that sample is subjected to shotgun se- quencing (q.v.).

Advanced computer programs then allow the sequenced fragments to be assembled into groupings that represent the genomes of the most common species in the sample. About 99% of all known bacteria have never been cultured in labora- tories, and genomes have been constructed for only a small subset of the cultured species. Community genome sequencing allows the construction of ge- nomes for species that have never been cultured.

Such a study was made of samples from a biofilm in a California mine. The film forms a scum on the sur- face of a pool that has formed in a shaft that extends 1,400 feet into Iron Mountain. The water is hot (106°F), very acidic, and rich in toxic metals.

There is little light or oxygen. Eighty mbp of DNA was recovered from a sample of this biofilm and as- sembled into five genomes. The two most complete genomes belonged to extremophiles (q.v.). These species were placed in the Leptospirillum and Fer- roplasma groups of the Archaea. See Appendix C, 2004, Tyson et al., Venter et al.; Appendix F.

compartmentalization a phenomenon discovered in Drosophila by Garcia-Bellido during investigations of the distribution of genetically marked clones of

Compatibility test
cells during the development of imaginal discs (q.v.). When such clones are analyzed it is found that they do not randomly overlap any area of the disc, but are confined to compartments and never cross the borders between compartments. A compartment contains all the descendants of a small number of founder cells called a polyclone. As development pro- ceeds, large compartments are progressively split into smaller ones.

The founder cells are related to each other by position, not ancestry; the progeny of the founder cells form the compartment under con- sideration, and no other cells contribute to it. The developmental prepattern (q.v.) of each compart- ment is controlled by a selector gene. When selector genes mutate, the cells in a compartment may de- velop a pattern of cell types appropriate for another compartment.

The homeotic mutants (q.v.) are ex- amples of mutated selector genes. See Appendix C, 1973, Garcia-Bellido et al.; 1975, Morata and Law- rence; engrailed. compatibility test any serological assay designed to detect whether blood or tissue from a prospective donor(s) can be transfused or transplanted without immunological rejection.

See cross matching, major histocompatibility complex. compensator genes sex-linked genes in Drosoph- ila that when present in the female (in double dose) reduce the activity of her two doses of a given “pri- mary sex-linked gene” so as to make the total pheno- typic effect equivalent to that seen in the male (which has one dose of both the primary gene and the compensator gene).

competence 1. the state of a part of an embryo that enables it to react to a given morphogenetic stimulus by determination and subsequent differen- tiation, in a given direction. 2. in bacterial or eukary- otic cells, the ability of cells to bind and internalize exogenous DNA molecules, thereby allowing trans- formation (q.v.). Many bacteria are naturally compe- tent at some stage of their life cycle, while others are not.

Bacteria in the latter category and eukaryotic cells can be induced to become competent through biochemical or physical treatments, such as expo- sure to high concentration of calcium (Ca2+) ions or electroporation (q.v.). competition 1. the mutually exclusive use of the same limited resources (for example, food or a place to live, to hide, or to breed) by two or more organ- isms; 2. the mutually exclusive binding of two differ- ent molecules to the same site on a third molecule.

For example, folic acid and aminopterin compete for combination sites on various folic acid-dependent enzymes. competitive exclusion principle the assumption that two species with identical ecological require- ments cannot coexist in the same niche in the same location indefinitely. One species will eventually supplant the other, unless they evolve adaptations that allow them to partition the niche and thereby reduce competition.

complement a group of at least nine proteins (C1, C2, . . . C9) normally found in vertebrate blood se- rum that can be activated immunologically (by anti- bodies of immunoglobulin classes IgG or IgM) or nonimmunologically (by bacterial lipopolysaccha- rides and other substances) through an alternate (properdin) pathway. Activation of the system in- volves sequential conversion of proenzymes to en- zymes in a manner analogous to the formation of fibrin through the blood-clotting sequence. Some ac- tivated complement components enhance phagocy- tosis (opsonic activity), some make antigen-anti- body-complement complexes “sticky” and cause them to become affixed to endothelial tissues or blood cells (serological adhesion or immune adherence), some cause release of vasoactive amines from blood basophils or tissue mast cells (anaphylotoxins), and some cause dissolution of bacterial cells (bacterioly- sis).

See HLA complex, immune response. complementarity-determining region the seg- ment of the variable region of an immunoglobulin or T cell receptor molecule that contains the amino acid residues that determine the specificity of bind- ing to the antigen. See paratope. complementary base sequence a sequence of polynucleotides related by the base-pairing rules. For example, in DNA a sequence A-G-T in one strand is complementary to T-C-A in the other strand.

A given sequence defines the complementary sequence. See deoxyribonucleic acid. complementary DNA See cDNA. complementary factors complementary genes. complementary genes nonallelic genes that com- plement one another. In the case of dominant com- plementarity, the dominant alleles of two or more genes are required for the expression of some trait. In the case of recessive complementarity, the domi- nant allele of either gene suppresses the expression of some trait (i.e., only the homozygous double re- cessive shows the trait). complementary interaction the production by two interacting genes of effects distinct from those produced by either one separately.

Concerted evolution
complementary RNA See cRNA. complementation appearance of wild-type phe- notype in an organism or cell containing two dif- ferent mutations combined in a hybrid diploid or a heterokaryon.

See allelic complementation, comple- mentation test. complementation group mutants lying within the same cistron; more properly called a noncomplemen- tation group. complementation map a diagrammatic represen- tation of the complementation pattern of a series of mutants occupying a short chromosomal segment. Mutually complementing mutants are drawn as non- overlapping lines, and noncomplementing mutants are represented by overlapping, continuous lines.

Complementation maps are generally linear, and the positions of mutants on the complementation and genetic maps usually agree. A complementation map is thought to show sites where lesions have been in- troduced into the polypeptides coded for by the DNA segment under study. complementation test the introduction of two mutant chromosomes into the same cell to see if the mutations in question occurred in the same gene.

If the mutations are nonallelic, the genotype of the hy- brid may be symbolized (a+/+b). The wild pheno- type will be expressed, since each chromosome “makes up for” or “complements” the defect in the other. See also allelic complementation, cis-trans test. complete dominance See dominance. complete linkage a condition in which two genes on the same chromosome fail to be recombined and therefore are always transmitted together in the same gamete. complete medium in microbiology a minimal me- dium supplemented with nutrients (such as yeast extract, casein hydrolysate, etc.) upon which nutri- tional mutants can grow and reproduce.

complete metamorphosis See Holometabola. complete penetrance the situation in which a dominant gene always produces a phenotypic effect or a recessive gene in the homozygous state always produces a detectable effect. complete sex linkage See sex linkage.

complexity in molecular biology, the total length of different sequences of DNA present in a given preparation as determined from reassociation kinet- ics; usually expressed in base pairs, but the value may also be given in daltons or any other mass unit. complex locus a closely linked cluster of function- ally related genes: e.g., the human hemoglobin gene complex or the bithorax locus in Drosophila. See pseudoalleles.

composite a plant of the immense family Com- positae, regarded as comprising the most highly de- veloped flowering plants. The family has over 25,000 species including asters, chrysanthemums, dandelions, daisies, lettuce, sunflowers, and thistles. See Appendix A, Angiospermae, Dicotyledonae, Asterales. composite transposon a DNA segment flanked on each end by insertion sequences (q.v.), either or both of which allow the entire element to transpose.

compound eye the multifaceted kind of eye of in- sects. In Drosophila each compound eye contains nearly 800 ommatidia. See Bar, eyeless. compound heterozygote an individual that carries two different recessive mutations at the same locus, one on each homolog. An example would be an in- dividual with a different mutation in each beta chain gene. See hemoglobin genes. compound X See attached X chromosomes.

Compton effect an attenuation process observed for x- or gamma-radiation. An incident photon in- teracts with an orbital electron of an atom to eject an electron and a scattered photon of less energy than the incident photon. A. H. Compton discov- ered the phenomenon in 1923. concanavalin A a lectin (q.v.) derived from Ca- navalia ensiformis, the jack bean; abbreviated conA. The compound stimulates T lymphocytes to enter mitosis.

Compare with pokeweed mitogen. concatemer the structure formed by concatena- tion of unit-sized components. concatenation linking of multiple subunits into a tandem series or chain, as occurs during replication of genomic subunits of T7 phage.

conception See syngamy. concerted evolution the production and mainte- nance of homogeneity within families of repetitive DNAs. An example of concerted evolution would be the maintenance of the pattern of nucleotide se- quences in each of the hundreds of tandemly ar- ranged, rRNA genes of Xenopus laevis. These repeti- tive DNAs differ in sequence from the rRNA genes of X. borealis, which are also homogeneous within

Concordance
this species. See Appendix C, 1972, Brown, Wensink and Jordan; Xenopus. concordance the identity of traits displayed by members of matched pairs of individuals. Twins, for example, are said to be concordant for a given trait if both exhibit the trait. Monozygotic twins are ex- pected to show 100% concordance for genetically determined traits. If the trait is influenced by envi- ronmental factors, the degree of concordance will be lowered.

See twin studies. consilience the bringing together of knowledge from diverse disciplines to elucidate a complex problem. For example, determining the history of the domestication of maize requires the consilience of archaeology, biochemistry, botany, computer technology, evolutionary theory, and genetics.

conditional gene expression See gene expression. conditional mutation a mutation that exhibits wild phenotype under certain (permissive) environ- mental conditions, but exhibits a mutant phenotype under other (restrictive) conditions.

Some bacterial mutants are conditional lethals that cannot grow above 45°C, but grow well at 37°C. conditional probability the probability of an event that depends upon whether or not some other event has occurred previously or simultaneously. For example, the probability of a second crossover be- tween two linked genes is usually greater as its dis- tance from the first crossover increases. See positive interference.

conditioned dominance referring to an allele that may or may not express itself depending upon envi- ronmental factors or the residual genotype. Thus, under different conditions the gene may behave as a dominant or as a recessive in heterozygotes. cone 1. one of the elongate, unicellular photore- ceptors in the vertebrate retina (q.v.) involved with vision in bright light and color recognition. 2. ovule- or pollen-bearing scales, characteristic of conifers. cone pigment genes (CPGs) the genes that en- code the opsins (q.v.) synthesized by the cone cells of the retina (q.v.). The table compares the three CPGs of humans.

The green and red CPGs differ by only 15 codons. The genes lie in tandem, with the red CPG farther away from the telomere of Xq. The green CPG may be present in two or three copies, the result of unequal crossing over (q.v.). This has also produced hybrid genes that contain coding se- quences from both red and green CPGs. An upstream sequence, 4 kilobases from the red gene and 43 kilo- bases from the green gene, is essential for the activity of both. Deletions of this 580 base pair element result in a rare form of X-linked color blindness that is char- acterized by the absence of both red and green cone sensitivities.

The blue opsin shows about 40% amino acid sequence identity with either green or red opsins, and the identity value is similar when the blue opsin and the rod cell opsin are compared. All catarrhine primates (q.v.) have the three cone pigment genes mentioned. In contrast, platyrrhine monkeys (q.v.) have only one X-linked and one autosomal color pho- topigment gene. See Appendix C, 1986, Nathans et al.; color blindness, rhodopsin (RHO). confidence limits the range of values about the true value of a population parameter (such as the mean) within which sample values (e.g., means) may fall and from which inferences may be made, with any desired degree of confidence, such that it is unlikely that a disproportionate number of rejec- tions of a true hypothesis should occur.

Convention- ally, the 95% confidence limits (also known as fidu- cial limits) around the mean are ±1.96 s√n, where s is the standard deviation (q.v.) and √n is the stan- dard error (q.v.). See statistical errors. confocal microscopy a form of light microscopy that allows successively deeper layers of a fixed or living specimen to be viewed with astonishing clar- ity. In conventional light microscopy, the specimen is illuminated throughout its depth, while the objec- tive lens is focused only on a narrow plane within the specimen.

Therefore, an out-of-focus blur gener- ated by regions above and below the focal plane of interest reduces the contrast and resolution of the image. Confocal microscopes are designed so that mainly signals from the elements in the focal plane

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