Enhancer trap | Kickoff

Enhancer trap

27 Mar

Enhancer trap
to loop out to bring the enhancer into physical con- tact with the promoter of the gene it enhances. This loop structure then facilitates the attachment of polymerase molecules to the transcribing gene. En- hancers that specify the type of cell in which a given gene will be expressed have been located within the first introns of genes such as those that encode the heavy-chain immunoglobin proteins and certain col- lagens.

See Appendix C, 1981, Banjerji et al.; 1983, Gillies et al.; CTCF protein, DNA looping, H19, immu- noglobin genes, insulator DNAs, intron. enhancer trap a technique used in Drosophila to demonstrate the occurrence of enhancers that switch on genes in specific groups of cells during certain de- velopmental periods. A reporter gene (q.v.) is used, which has a promoter that requires the assistance of an enhancer to be activated.

The reporter gene, to- gether with its “weak” promotor, is spliced into a transposable element (q.v.). In Drosophila, P ele- ments (q.v.) are used, and these insert themselves at various chromosomal sites. When insertion occurs near an enhancer that normally activates genes in specific areas of a developing embryo, the reporter gene intercepts the signal and reports the position of the cells by its activity. In cases where the reporter is lacZ, blue pigment appears in specific cells; for ex- ample, in localized regions of the developing central nervous system. Once insertions that generate inter- esting staining patterns are identified, stable strains of flies carrying the insertions can be produced.

Such lines are called transposants. Cytological mapping has shown that insertions occur throughout the ge- nome. Since the enhancers are generally positioned within a few hundred base pairs of the start site of their target genes, these can be subsequently cloned and sequenced. See Appendix C, 1987, O’Kane and Gehring. enkephalins pentapeptides with opiate-like activ- ity (compare with endorphins), first isolated in 1975 from pig brain. Met-enkephalin has the amino acid sequence Tyr-Gly-Gly-Phe-Met; Leu-enkephalin has the sequence Tyr-Gly-Gly-Phe-Leu. See polyprotein. enol forms of nucleotides See tautomeric shift. enrichment methods for auxotrophic mutants See filtration enrichment, penicillin enrichment technique.

Ensembl genome database a joint project be- tween the European Bioinformatics Institute, the European Molecular Biology Laboratory, and the Wellcome Trust-Sanger Institute. Ensemble contin- ues to update the annotations of the genomes of a large sample of eukaryotes including Homo sapiens, chimpanzee, mouse, rat, dog, chicken, Xenopus, pufferfish, fruitfly, mosquito, honeybee, Caenorhab- ditis, and Ciona. http://www.ensembl.org/. enterovirus a member of a group of RNA-contain- ing viruses (including poliomyelitis virus) inhabiting the human intestine. entoderm endoderm (q.v.).

entomophilous designating flowers adapted for pollination by insects. entrainment dragging along after itself. In refer- ence to circadian rhythm (q.v.), the resetting of an endogenous clock to exactly 24 hours by environ- mental cues, such as 12 hours of light (or warmth), followed by 12 hours of darkness (or cold). Entrez a powerful search engine allowing access to the databases maintained by the National Center for Biotechnology Information. See Appendix E, Master Web Sites. enucleate to remove the nucleus from a cell. enucleated lacking a nucleus. enveloped viruses viruses that have envelopes surrounding their nucleocapsids. Each viral envelope is derived from the host cell, and as a result the vi- ruses will contain lipids, as well as nucleic acids and proteins.

Spikes often project from the envelopes, and these contain virus-encoded proteins. The co- rona viruses, herpes viruses, HIVs, influenza viruses, Sendai viruses, andsmallpox viruses are examples of viruses with envelopes.

Epicotyl

environment the complex of physical and biotic factors within which an organism exists. environmental sex determination any mecha- nism of sex determination (q.v.) in which the sex of an organism is permanently established not by its genetic constitution, but by environmental condi- tions (such as temperature, local hormonal concen- trations, or population density) in which it develops.

For example, sex is determined in turtles and croco- diles by the prevailing temperature during the incu- bation of the fertilized eggs. Compare with genotypic sex determination. environmental variance that portion of the phe- notypic variance caused by differences in the envi- ronments to which the individuals in a population have been exposed. enzyme fusion See histidine operon. enzymes protein catalysts.

Enzymes differ from inorganic catalysts in their extreme specificity. They catalyze reactions involving only one or a few closely related compounds, and they are able to distinguish between stereoisomers. All chemical reactions have potential energy barriers. In order to pass this bar- rier, the reactant must be activated to reach a transi- tion state from which the products of the reaction can be released. During an enzyme-catalyzed reac- tion, an enzyme-substrate complex is formed. The E-S complex has a lowered activation energy, and this allows the reaction to occur at body tempera- ture. A systematic classification of enzymes has been established by the Commission on Enzymes of the International Union of Biochemistry.

All known en- zymes have been grouped into six classes: (1) oxido- reductases, (2) transferases, (3) hydrolases, (4) ly- ases, (5) isomerases, and (6) ligases. Each specific enzyme is given a classification code by the Enzyme Commission, which consists of EC and four figures. For example, EC 3.1.21.1 is the code designation for deoxyribonuclease 1. The first three numbers define various properties of the subfamily of enzymes to which DNase 1 belongs, while the last number uniquely specifies this enzyme. See Appendix C, 1876, Ku¨hne; 1926, Sumner; Appendix E, Individual Databases; abzymes, DNA glycosylases, DNA ligases, DNA methylase, DNA polymerase, DNA restriction enzyme, DNase, endonuclease, exonuclease, first- order kinetics, kinase, papain, pepsin, peptidyl trans- ferase, phosphodiesterase I, ribozyme, RNA ligase, RNA polymerase, RNA replicase, RNase, substrate, topoisomerase, trypsin, triptophan synthetase, tyrosi- nase, zymogen.

enzyme-linked immunosorbent assay (ELISA) an immunochemical technique that avoids the hazards of radiochemicals and the expense of fluorescence detection systems. Instead, the assay uses enzymes as indicators. This ELISA technique can be illus- trated by its use in detecting the AIDS virus in se- rum samples. First, antibodies are prepared in rab- bits against specific proteins present in the coat of the virus. Next, a reporter antibody is prepared in goats against rabbit immunoglobulins. Then, the en- zyme horseradish peroxidase attached to the goat-antirabbit Ig-antibody.

Serum from a donor is incubated in a plastic dish. The pro- teins in the serum sample bind to the surface of the dish. Now the AIDS-specific rabbit antibody is added. If virus coat proteins are present, they have been bound to the dish and the antibody now binds to them. The dish is washed to remove any unbound rabbit antibodies. Next, the goat antibody-peroxi- dase conjugate is added, and it binds to the rabbit antibody-viral protein complex. A reagent is then added, which becomes colored when dehydroge- nated by the peroxidase. The amount of color devel- oped in a specified time is a measure of the amount of virus in the serum sample.

See HIV. eobiogenesis the first instance of the generation of living matter from inorganic material. Eocene the second epoch in the Tertiary period. The angiosperms and gymnosperms were the domi- nant plants, and representatives of all mammalian orders were present. Huge flightless birds were ma- jor predators. Whales evolved in the oceans. See geologic time divisions, Hyracotherium. eocytes See sulfur-dependent thermophiles. Eohippus See Hyracotherium. eon the most inclusive of the divisions of geologic time. See geologic time divisions.

Ephestia kuhniella the Mediterranean meal moth. Numerous mutants affecting the color pattern of the forewing and eye pigmentation have been studied in this species. It is parasitized by Habrobracon jug- landis (q.v.). See Appendix C, 1935, Kuhn and Bu- tenandt. epicanthus a fold of skin extending over the inner corner of the eye characteristic of members of the Mongoloid race. epicotyl the portion of the seedling above the cot- yledons that develops into the shoot and its deriva- tives.

Epidemiology

epidemiology the study of disease epidemics, with an effort to tracing down the cause. epidermal growth factor stimulates cell proliferation in a wide variety of eu- karyotic cells. It is a protein containing 53 amino acids. The receptor for EGF is a protein kinase (q.v.), which is activated when the mitogen attaches.

Once bound to the cell surface, the complex is inter- nalized. EGF is generated by enzymatic cleavage be- tween repeated EGF domains carried in an EGF precursor protein, which is embedded in cell mem- branes by a membrane-spanning domain. The EGF precursor molecule of humans contains 1,207 amino acids. EGF repeats facilitate interactions between proteins and calcium binding, and they are found in a wide variety of proteins.

These include transmem- brane proteins like the low-density lipoprotein re- ceptor (q.v.), extracellular matrix proteins like fi- brillin (q.v.), and soluble, secreted proteins like the plasma thromboplastin component (q.v.). See Ap- pendix C, 1962, Cohen; familial hypercholesterol- emia, neuregulins (NRGs), Notch. epidermolysis bullosa a group of diseases usually showing autosomal dominant inheritance.

They are characterized by blistering owing to fragility of the skin and mucous membranes. The blistering is due to separation of epidermal tissues from the underly- ing dermis. In EB simplex, tissue separation occurs within the basal layer of the epidermis, and the de- fect arises from mutations in a gene located at 12q11-13. This encodes keratins, which are synthe- sized by basal keratinocytes. In junctional EB, the separation occurs within the basement membrane zone of the lamina lucida, and the defect arises from mutations in a gene located at 1q25-31.

This en- codes a laminin protein component of the basement membrane. In dystrophic EB, the separation is in the papillary dermis at the level of the fibrils that con- nect the lamina lucida to the dermis. The defect arises from mutations in a gene located at 3p21, which encodes a type of collagen that is a major component of the anchoring fibrils. epigamic serving to attract or stimulate members of the opposite sex during courtship.

epigamic selection See sexual selection. epigenesis the concept that an organism develops by the new appearance of structures and functions, as opposed to the hypothesis that an organism devel- ops by the unfolding and growth of entities already present in the egg at the beginning of development (preformation). epigenetics the study of the mechanisms by which genes bring about their phenotypic effects. Clones of cells may inherit phenotypic changes that are not due to changed nucleotide sequences in the genome. DNA-binding proteins encoded by regulatory genes sometimes produce epigenetic changes that can be preserved during the mitotic division of the cells of different somatic tissues in a multicellular organism.

However, meiosis seems to reset the genome to some baseline epigenetic state, so that the develop- mental program of the species unfolds anew with each new generation. epigenotype the series of interrelated develop- mental pathways through which the adult form is realized. epimers organic compounds that are partial iso- mers in that they differ from each other only in the three-dimensional positioning of atoms about a sin- gle asymmetric carbon atom. epinephrine a hormone from the adrenal medulla that elevates blood glucose by mobilizing glycogen reserves.

episome a class of genetic elements of which phage lambda and sex factor F are examples in E. coli. Episomes may behave (1) as autonomous units replicating in the host independent of the bacterial chromosome, or (2) as integrated units attached to the bacterial chromosome and replicating with it. Compare with plasmid. epistasis the nonreciprocal interaction of nonalle- lic genes. The situation in which one gene masks the expression of another.

The recessive gene apterous (ap) in Drosophila produces wingless homozygotes. In such individuals, any other recessive gene affect- ing wing morphology will have its action masked. The apterous gene is said to be epistatic to a gene like curled wing, which is hypostatic to ap. See Ap- pendix C, 1900, Bateson; Bombay blood group.

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