Exogenote

29 Mar

Exogenote
exogenote the new chromosomal fragment do- nated to a merozygote (q.v.). exogenous DNA DNA that originates outside an organism (e.g., from another cell or virus). exogenous virus a virus that replicates vegeta- tively (productively in lytic cycle) and is not verti- cally transmitted in a gametic genome. exon a portion of a split gene (q.v.) that is in- cluded in the transcript of a gene and survives pro- cessing of the RNA in the cell nucleus to become part of a spliced messenger of a structural RNA in the cell cytoplasm. Exons generally occupy three dis- tinct regions of genes that encode proteins. The first, which is not translated into protein, signals the be- ginning of RNA transcription and contains sequences that direct the mRNA to the ribosomes for protein synthesis. The exons in the second region contain the information that is translated into the amino acid sequence of the protein.

Exons in the third re- gion are transcribed into the part of the mRNA that contains the signals for the termination of translation and for the addition of a polyadenylate tail. See Ap- pendix C, 1978, Gilbert; alternative splicing, intron, leader sequence, polyadenylation, posttranscriptional processing, terminators. exon shuffling the creation of new genes by bring- ing together, as exons of a single gene, several coding sequences that had previously specified different proteins or different domains of the same protein, through intron-mediated recombination. exonuclease an enzyme that digests DNA, begin- ning at the ends of the strands. exonuclease III an enzyme from E. coli that at- tacks the DNA duplex at the 3′ end on each strand; used together with S1 nuclease (q.v.) to create dele- tions in cloned DNA molecules. Compare with Bal 31 exonuclease. exonuclease IV an enzyme that specifically de- grades single-stranded DNA. It initiates hydrolysis at both the 3′ and 5′ ends to yield small oligonucleo- tides. This enzyme is active in the presence of EDTA. exopterygota hemimetabola (q.v.).

Eyeless (ey)

exoskeleton a skeleton covering the outside of the body, characteristic of arthropods. exotoxin a poison excreted into the surrounding medium by an organism (e.g., certain Gram-positive bacteria such as those causing diphtheria, tetanus, and botulism). Exotoxins are generally more potent and specific in their action than endotoxins (q.v.). experimental error 1. the chance deviation of ob- served results from those expected according to a given hypothesis; also called random sampling error. 2. uncontrolled variation in an experiment. See anal- ysis of variance.

explant an excised fragment of a tissue or an organ used to initiate an in vitro culture. exponential growth phase that portion of the growth of a population characterized by an expo- nential increase in cell number with time. See sta- tionary phase. exponential survival curve a survival curve with- out a shoulder, or threshold region, and that plots as a straight line on semilog coordinates. expressed sequence tags (ESTs) partial cDNA (q.v.) sequences, generally 200-400 base pairs in length, which are used as “tags” to isolate known or new genes from genomic DNA.

ESTs from hun- dreds of organisms, including model organisms such as the fruitfly, zebrafish, and mouse, are screened, annotated, and stored in a publicly accessible com- puter database, called dbEST. A database search us- ing tools such as BLAST (q.v.) can be undertaken for sequence similarity between the EST and a putative disease gene or between the EST’s amino acid se- quence and partial amino acid sequence from a pro- tein of interest.

If sequence similarity is found, the EST can be used as a probe (q.v.) to screen a library (q.v.) for the gene in question. ESTs are a powerful tool for quickly isolating a gene that codes for a known protein, for identifying new genes, for identi- fying transcription units in genomic sequences and on physical maps (q.v.), and for gene comparisons between organisms. See Appendix E, Individual Data- bases; sequence tagged sites (STS). expression vector cloning vehicles designed to promote the expression of gene inserts. Typically, a restriction fragment carrying the regulatory se- quences of a gene is ligated in vitro to a plasmid con- taining a restriction fragment possessing the gene but lacking its regulatory sequences. The plasmid with this new combination of DNA sequences is then cloned under circumstances that promote the expression of the gene under the control of the regu- latory sequences.

expressivity the range of phenotypes expressed by a given genotype under any given set of environmen- tal conditions or over a range of environmental con- ditions. For example, Drosophila homozygous for the recessive gene “eyeless” may have phenotypes varying from no eyes to completely normal eyes, but the usual condition is an eye noticeably smaller than normal. expressor protein the product of a regulatory gene, necessary for the expression of one or more other genes under its positive transcriptional control. extant living at the present time, as opposed to ex- tinct. exteins external protein sequences that flank an in- tein (q.v.) and are ligated during protein splicing (q.v.) to form a mature protein. extended phenotype See phenotype. extinction termination of an evolutionary lineage without descendants. See mass extinction, pseudoex- tinction, taxonomic extinction. extrachromosomal inheritance See extranuclear inheritance.

extragenic reversion a mutational change in a sec- ond gene that eliminates or suppresses the mutant phenotype of the first gene. See suppressor mutation. extranuclear inheritance non-Mendelian heredity attributed to DNA in organelles such as mitochon- dria or chloroplasts; also called extrachromosomal inheritance, cytoplasmic inheritance, maternal in- heritance. extrapolation number in target theory (q.v.) the intercept of the extrapolated multitarget survival curve with the vertical logarithmic axis specifying the survival fraction. The extrapolation number gives the number of targets that each must be hit at least once to have a lethal effect on the biological system under study.

extremophiles archaean microbes that not only can survive in environments that are too hot, cold, salty, acidic, or alkaline for most bacteria (and all eukaryotes) but also in some cases require one or more of these extremes to survive. Heat-loving mi- crobes are referred to as thermophilic (q.v.). Those that prefer both heat and acid conditions are called thermoacidophiles (q.v.). Psychrophils are cold lovers, barophils survive at high pressures, and alkaliphils survive best at a pH of about 8 (above pH 8, RNA molecules begin to break down). Salt-loving mi- crobes are termed halophiles (q.v.).

Some of the en- zymes produced by extremophiles can function well outside the range of environments in which the en- zymes of most other organisms would be inacti- vated. These catalysts are termed extremozymes. Ex- tremophiles use a variety of processes to maintain a less harsh milieu within their cells. For example, acidophils tend to prevent acid from entering the cell and may also produce some molecules that re- side on the cell wall and underlying cell membranes that provide protection from low pH in the external environment. Taq DNA polymerase (q.v.) is an ex- tremozyme that allowed automation of the poly- merase chain reaction (q.v.).

More recently, Taq polymerase has been replaced by Pfu DNA polymer- ase (q.v.) from the hyperthermophile Pyrococcus furi- osus because it works best at 100°C and has superior proofreading activity that produces high-fidelity am- plification. extremozymes See extremophiles. exuvial an adjective describing an animal in the process of molting. The word is derived from exu- viae, the cast-off exoskeletons of arthropods. See ec- dysis. ex vivo referring to experiments in which geneti- cally defective cells from an individual are removed and cultured in vitro. After a period of multiplica- tion, wild-type genes are added to the cells to cor- rect the defect.

These modified cells are then re- turned to the donor. See gene therapy. eye evolution modeling Nilsson-Pelger model of eye evolution (q.v.). eyeless (ey) a Drosophila gene located at 4-2.0 that controls eye development. Mutations result in the complete loss or the reduction in size of the compound eye. Also severe defects occur in the brain structures essential for vision, olfaction, and the coordination of locomotion. The most studied mutation, ey2, is caused by the insertion of a trans- posable element (q.v.) in the first intron of the gene. The ey2 phenotype is the result of cell death in the

eye imaginal discs (q.v.) during the third larval in- star. The ey gene is expressed in the eye primordium in the embryo during the development of the eye imaginal disc and in the pupa when rhodopsin (q.v.) is being synthesized. Also, eyeless is expressed in the cells of Bolwig organs (q.v.) which serve as larval eyes. The ey transcription unit is about 16 kb long. Two transcripts are produced by alternative splicing (q.v.). The Ey proteins are 838 and 857 amino acids long, and they function as transcription factors (q.v.). The proteins contain an N-terminal paired (q.v.) domain and a homeobox (q.v.). The wild-type allele of eyeless is a master control gene for eye mor- phogenesis in this species. This has been shown by experimentally activating the gene in imaginal discs that normally give rise to organs other than eyes. After eclosion, flies appear with organized clusters

of ommatidia on their antennae, legs, halteres, and wings. A Drosophila head that bears a “minieye” on one antenna is shown in the frontispiece. Since eye development in Drosophila is controlled by more  than 2,500 genes, most of these must be under the direct or indirect control of ey+. The Small eye (Sey) (q.v.) genes of mice and rats and the Aniridia (q.v.) gene of humans are homologs of the eyeless gene. Ey  homologs have also been found in the zebrafish, quail, chicken, sea urchin, and squid. The squid ho- mologous gene when activated in developing Dro- sophila also initiates the formation of ectopic eyes. These findings suggest that all metazoans share the same master control genes for eye morphogenesis. See Appendix C, 1995, Halder et al.; developmental control genes, downstream genes, Drosophila tar- geted gene expression technique.

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