Systematics

4 Apr

Systematics

syncytium a multinucleate tissue whose consti- tutent cells have only partial cell boundaries and are connected through a common cytoplasm. A syncy- tium arises when nucleated cells fail to completely separate from one another during meiosis or mitosis (as in sperm development) or when nucleated cells fuse with one another (as in the fetal-maternal inter- face called a syncytiotrophoblast). syndactyl having webbed digits either as a normal aspect of the species or, in man, pathologically. syndesis meiotic chromosomal synapsis. syndrome a group of symptoms that occur to- gether, characterizing a disease.

Synechocystis a genus of bacteria that belongs to the Cyanobacteria (q.v.). The cells are coccoid and divide by binary fission in two or three planes to pro- duce clusters of cells. One species from this genus (referred to as sp. strain PCC 6803) has had its ge- nome completely sequenced. It is made up of 3.57 mb of DNA and contains 3,168 ORFs. Genes ho- mologous to 45 of the ORFs from Synechocystis have been found in the chloroplasts of a wide variety of photosynthetic protoctists and land plants. See Ap- pendix C, 1996, Kaneko et al.; Appendix E; Arabidop- sis thaliana, chloroplast, serial symbiosis theory. synergid one of two haploid cells that lie beside the ovum in the embryo sac (q.v.). Synergids of an- giosperms are the source of chemical cues that guide pollen tubes to ovules. See double fertilization. synergism the phenomenon in which the action of two agents used in combination is more effective than the sum of their individual actions.

synezis the clumping of chromosomes into a dense knot that adheres to one side of the nucleus. Synezis is a common occurrence during leptonema in microsporocytes. syngamy the union of the nuclei of two gametes following fertilization to produce a zygote nucleus; karyogamy. syngen See Paramecium aurelia. syngeneic pertaining to genetically identical or- ganisms such as identical twins or the members of a highly inbred strain. Because syngeneic animals have the same antigens on their tissues, they can ex- change skin or organ grafts successfully. Compare with allogeneic, congenic strain. syngraft a graft wherein the recipient receives a graft of tissue from a genetically identical donor (e.g., from an identical twin or from a member of the same highly inbred line). Contrast with allograft, autograft, xenoplastic transplantation. synkaryon 1. the zygote nucleus resulting from the fusion of two gametic nuclei. 2. the product of nuclear fusion in somatic cell genetic experiments. synomone See allomone. synonym in taxonomy, a different name for the same species or variety. synonymous codons same-sense codons.

For ex- ample, UUU and UUC code for the same amino acid-phenylalanine. See degenerate code, genetic code. syntenic genes genes that are orthologs (q.v.) and reside on the same chromosome in two species. For example, when Drosophila melanogaster and D. pseu- doobscura are compared, the vast majority of their genes are found to be syntenic. However, the se- quences of the genes in each chromosome arm have been extensively shuffled.

See Appendix C, 2005, Richards et al. synthetase an enzyme catalyzing the synthesis of a molecule from two components, with the coupled breakdown of ATP or some other nucleoside tri- phosphate. synthetic lethal a lethal chromosome derived from normally viable chromosomes by crossing over. synthetic linkers short, chemically synthesized DNA duplexes containing sites for one or more re- striction endonucleases. Synthetic linkers are used most commonly in the cloning of blunt-ended DNA molecules. synthetic polyribonucleotides RNA molecules made without a nucleic acid template, either by en- zyme action or chemical synthesis. See Appendix C, 1961, Nirenberg and Matthaei; 1967, Khorana; po- lynucleotide phosphorylase. syphilis a sexually transmitted disease caused by the spirochaete Treponema pallidum (q.v.). systematics the study of classification; taxonomy based on evolutionary relationships.

t See symbols used in human cytogenetics. t the Student’s t statistic that is used for testing the difference between the means of two samples. See Student’s t test, and page 65. T thymine or thymidine. tachyauxesis See heterauxesis. tachytelic evolution See evolutionary rate. Takifugu rubripes in the earlier literature this ma- rine pufferfish is called Fugu rubripes. Pufferfish have the most compact genomes seen in vertebrates.

The value (400 Mb) is 7.5 times smaller than the human genome. The number of ORFs is similar in both spe- cies, but the pufferfish has genes with smaller in- trons, the intergenic sequences are smaller, and there is less repetitive DNA. The compaction of the genome appears to result from the selection of dele- tions during the evolution of the fish. Duplicate genes are common in the pufferfish genome, and a phylogenetic analysis suggests the ancestral genome was duplicated early during the evolution of the Os- teichthyes. See Appendix A, Chordata, Osteichthyes, Neopterygii, Tetraodontiformes; Appendix C, 2002, Aparicio et al.; Appendix E, Species Web Sites; Hun- tington disease (HD), Linnean system of binomial no- menclature, shotgun sequencing, Tetraodon nigrovi- ridis. TAOS1 a gene on the short arm of chromosome 11 which is amplified and overexpressed in human oral squamous cell carcinomas.

The name is an acro- nym for tumor amplified and overexpressed se- quence 1. tandem duplication an aberration in which two identical chromosomal segments lie one behind the other. The order of the genes in each segment is the same. tandem repeat See microsatellites, tandem duplica- tion. T antigen a “tumor” antigen found in the nuclei of cells infected or transformed by certain oncogenic viruses such as polyoma.

The antigen is thought to be a protein coded for by a virus cistron. Taq DNA polymerase a DNA polymerase synthe- sized by the thermophilic bacterium Thermus aqua- ticus. This enzyme, which is stable up to 95°C, is used in the polymerase chain reaction (q.v.). See li- gase chain reaction. target number See extrapolation number. target organ the receptor organ upon which a hormone has its effect. target theory a theory developed to explain some biological effects of radiation on the basis of ioniza- tion occurring in a very small sensitive region within the cell.

One or more “hits,” that is, ionizing events, within the sensitive volume are postulated to be nec- essary to bring about the effect. See Appendix C, 1936, Timofeyeff-Ressovsky and Delbru¨ck; extrapo- lation number. target tissue 1. the tissue against which antibodies are formed. 2. the tissue responding specifically to a given hormone. tassel the staminate inflorescence of corn. taste receptor gene a gene in humans which re- sides at 7q35-q36. It is symbolized TAS2R38, and human polymorphisms in the ability to taste phe- nylcarbamide (q.v.) are due to base substitutions at various sites within the gene. The gene contains a single exon 1,002 base pairs long, and it encodes a G protein-coupled receptor (q.v.). TATA box Hogness box (q.v.); pronounced “tah- tah.” TATA box-binding protein (TBP) an essential transcription factor for RNA polymerases I, II, and III of eukaryotes. TBP does not occur in eubacteria, but archaebacteria (q.v.) contain a TBP that has amino acid sequence similarities to the eukaryotic TBP. These and other data suggest that archaebacte- ria and eukaryotes are more closely related than ei- ther is to eubacteria. tautomeric shift a reversible change in the loca- tion of a hydrogen atom in a molecule that alters it from one to another isomer. Thymine and guanine are normally in keto forms, but when in the rare enol forms (see diagram on page 437) they can join by three hydrogen bonds with keto forms of guanine or thymine, respectively. Likewise, cytosine and ade-

nine are normally in amino forms, but when in the rare imino forms they can join by two hydrogen bonds with amino forms of adenine or cytosine, re- spectively. Tautomeric shifts that modify the pairing of nucleotides can result in base substitutions and, as a result, mutations.

Tautomeric forms of DNA bases

tautomerism the phenomenon in which two iso- meric forms of molecules exist in equilibrium. Taxol See paclitaxel. taxon (plural taxa) the general term for a taxo- nomic group whatever its rank. taxonomic category the rank of a taxon in the hi- erarchy of classification. See classification. taxonomic congruence the degree to which dif- ferent classifications of the same organisms postulate the same groupings. When the classifications com- pared are based on different sources of information (independent sets of data), congruence provides a measure of the degree to which the classifications remain stable as various lines of evidence are consid- ered. taxonomic extinction nonsurvival of a taxon, ei- ther by extinction or by pseudoextinction (q.v.). taxonomist a specialist in taxonomy (q.v.). taxonomy the study of the classification of living things. Classically, taxonomy is concerned with de- scription, naming, and classification on the basis of morphology. More recently, taxonomists have been concerned with the analyses of patterns of variation in order to discover how they evolved, with the identification of evolutionary units, and with the de- termination by experiment of the genetic interrela- tionships between such units. See Appendix C, 1735, Linne´;PhyloCode. Taxus brevifolia the Pacific yew, a small, slow- growing evergreen tree native to the northwestern United States.

The spindle poison paclitaxel (q.v.) is extracted from its bark. Tay-Sachs disease a lethal hereditary disease due to a deficiency of hexosaminidase A. This deficiency results in storage of its major substrate (Gm2 gangli- oside). Progressive accumulation of this compound causes developmental retardation, followed by paral- ysis, mental deterioration, and blindness. Most pa- tients die by the age of three. The alpha chain of hexosaminidase A is encoded by a gene, HEXA, on the long arm of chromosome 15 between bands 22 and 25. About 2% of all Ashkenazi Jews are hetero- zygous for a defective HEXA allele. There are two distinct common mutations, as well as other rare ones. The beta chain of hexosaminidase A is en- coded by a gene, HEXB, on autosome 5. Humans homozygous for mutant alleles of HEXB suffer from storage of gangliosides. The condition, Sandhoff dis- ease, has symptoms similar to Tay-Sachs disease.

Both HEXA and HEXB contain 14 exons and are believed to have arisen from a single ancestral gene. The disease gets its name from Warren Tay and Ber- nard Sachs, who published accounts of its patholo- gies in 1881 and 1887, respectively. See Appendix C, 1935, Klenk; Ashkenazi, ganglioside, hexosamini- dase, lysosomal storage diseases. T bacteriophages See T phages. T box genes any gene containing a conserved mo- tif encoding a DNA-binding site. In mice, amphibi- ans, and fishes, these genes encode proteins neces- sary for the development of mesodermal structures.

In humans the T box gene (TBX1) maps to 22q11.2, and the protein it encodes shares a 98% amino acid identity with the mouse TBX. In Drosophila, T box genes are expressed during eye development. See

TBP

Appendix C, 1990, Hermann et al.; 1994, Bollag et al.; brachyury, DNA-binding motifs, T complex. TBP TATA box-binding protein (q.v.). TCA trichloroacetic acid (q.v.). TCA cycle an abbreviation for tricarboxylic acid cycle (q.v.). T C loop the hairpin loop nearest the 3′ end of tRNA molecules, containing the modified base pseu- douridine (ψ). This loop is thought to interact with ribosomal RNA. See transfer RNA (tRNA). T cell T lymphocyte.

See lymphocyte. T cell receptor (TCR) a heteromeric protein on the surface of T lymphocytes (q.v.) that specifically recognizes histocompatibility molecules (q.v.). T cell receptors are made up of two different polypeptide chains that are joined by disulfide bonds and are em- bedded in the plasmalemma with their carboxyl ends extending into the cytoplasm and their amino ends reaching outside the cell. The membrane por- tion of the T cell receptor is associated with a collec- tion of CD3 proteins that transmit, from the outside of the cell to the inside, information as to whether or not the T cell receptor is occupied. The receptor recognizes as nonself the histocompatibility mole- cules on foreign cells, and it can also recognize anti- genic sites on smaller molecules, provided these are presented in association with self-histocompatibility molecules. See immunoglobulin domain superfamily.

T cell receptor genes genes that encode the com- ponent polypeptides of T cell receptors (q.v.). There are two types of receptors: those containing an alpha and a beta chain, and those containing a delta and a gamma chain. In humans, both the alpha and the gamma chains are encoded by genes on the long arm of chromosome 14. The beta chain gene is located on the long arm of chromosome 7, and the gamma chain gene resides on the short arm of chromosome 7. As in the case of the immunoglobulins, the T cell receptor polypeptide chains are encoded by gene segments that are reshuffled during the differentia- tion of the precursor cells. The rearrangement of segments occurs in thymocytes before the genes en- coding the polypeptides are expressed. As a result, T cell receptors have more than 107 different amino acid sequences. See Appendix C, 1984, Davis and Mak; V(D)J recombination. T4, T8 cells classes of helper and suppressor T lymphocytes, respectively, characterized by anti- genic markers that react with monoclonal antibodies designated anti-T4 and anti-T8, respectively.

See lymphocyte. Tc1/mariner element transposable elements that are 1,300-2,400 bp in length and contain a single gene that encodes a transposase (q.v.). The DNA segment is characterized by terminal inverted re- peats. The transposon family is named after its two best-studied members, the Tc1 transposon of Cae- norhabditis elegans and the mariner transposon of Drosophila mauritiana. See mariner elements, trans- posons. T complex a region on chromosome 17 of the mouse; it contains genes that affect tail length. Het- erozygous mice with only one functional gene have shortened or missing tails. Homozygotes (T−/T−) die as embryos with defects in mesoderm-derived tis- sues. See Appendix C, 1990, Hermann et al.; brady- ury, T box genes.

T-DNA a group of seven genes (collectively re- ferred to as transferred DNA) of the Ti plasmid (q.v.) that integrates into the nuclear DNA of the host plant during tumor induction. T-DNA is always present in crown gall cells of plants. See Agrobacter- ium tumefaciens. T4 DNA ligase an enzyme encoded by E. coli phage T4 that not only seals nicks in double- stranded DNA but also has the unique ability to join two DNA molecules that have completely base- paired (blunt) ends. This latter property is useful in forming recombinant DNA molecules. T4 DNA polymerase an enzyme encoded by coli- phage T4 that catalyzes the synthesis of DNA in the 5′ to 3′ direction and also has 3′ to 5′ exonuclease activity.

If DNA is incubated with T4 DNA poly- merase in the absence of deoxyribonucleoside tri- phosphates, the DNA will be partially degraded by the exonuclease. If the four dNTPs are now added, the degraded strand will be resynthesized by the polymerase. Thus, if the alpha phosphates of the added nucleotides are 32P-labeled, a highly radioac- tive product can be obtained. The technique serves as an alternative to nick translation (q.v.). tectonic plates See plate tectonics. tektins a class of proteins found attached to the peripheral microtubules in sperm tails. Tectin fila- ments are 2 nanometers in diameter, 50 nanometers long, and are positioned longitudinally along the walls of the outer doublet, where the A and B sub- fibers join. See axoneme, Y chromosome. teleology the explanation of a phenomenon such as evolution by the purposes or goals it serves. Tele- ological explanations usually invoke supernatural powers and are therefore nonscientific.

telomeric fusion site

teleonomy the doctrine that the existence in an organism of a structure or function implies that it has conferred an advantage on its possessor during evolution. telestability destabilization of a DNA double he- lix at a site distant from the site of binding of a pro- tein. For example, binding of the cAMP-CAP com- plex to the lac operon of E. coli facilitates the distal formation of an open promoter site in which RNA polymerase can initiate transcription. See catabolite activating protein. telocentric chromosome a chromosome with a terminal centromere. telolecithal egg one in which the yolk spheres are accumulated in one hemisphere. See centrolecithal egg, isolecithal egg, vegetal hemisphere. telomerase a reverse transcriptase containing an RNA molecule that functions as the template for the telomeric repeat. The first telomerase was isolated from Tetrahymena (q.v.).

It is a large ribonucleopro- tein complex weighing about 500 kilodaltons. The RNA of the Tetrahymena telomerase contains 159 nucleotides, and its secondary structure is shown in the drawing. The nine specific nucleotides form the templating domain, which is complementary to the G-rich strand of the telomere (q.v.). The functioning of telomerases seems to be activated in dividing em- bryonic cells and gametocytes. Telomerase function is repressed in differentiated somatic cells but reacti- vated in cancer cells. In human telomerase, the tem- plating domain is 5′-CUAACCCUAAC-3′ and the telomeric repeat is (TTAGGG) n. Antisense RNAs designed to bind with telomerases cause HeLa cells (q.v.) to die after 23 to 26 doublings. See Appendix C, 1985, Greider and Blackburn; 1994, Kim et al.; 1995, Feng et al.; RNA-dependent DNA polymerase. Ÿ

telomere a specialized DNA sequence found at the ends of eukaryotic chromosomes. The first telo- meres to be sequenced belonged to Tetrahymena thermophila. They contained an A2C4 segment in one DNA strand and a T2G4 segment in the other, re- peated in tandem about 60 times. The telomeres from all species subsequently studied showed the same pattern: a short DNA sequence, one strand G- rich and one C-rich, that is tandemly repeated many times. These telomere-specific repeats make it possi- ble to identify chromosomes that have arisen by telomere-telomere fusions. Chromosomes lose nu- cleotides from their ends each cell division, and the shortening of telomeres may provide cells with a mi- totic clock. Telomeric sequences can be added back to the chromosome ends, one base at a time by a telomerase (q.v.). The maintenance of telomeres is required for cells to escape from replicative senes- cence and to continue to multiply. In human leuco- cytes, telomeres shorten at a rate of 1,000 base pairs per year during the first 4 years of life. Then for about 20 years telomeres stay at lengths of about 12 kb. Thereafter there is a gradual loss (700 bp/yr) through old age. At the end of chromosomes, the 3′ overhang of the DNA duplex folds upon itself to form a telomeric loop (t-loop).

The sequestered ends within t-loops are protected from enzymes that might degrade them. Drosophila chromosomes do not have conventional telomeres. Instead, telomere- specific retrotransposons are present in multiple copies on normal chromosome ends, and these ret- roposons can transpose to heal terminally deleted chromosomes. Bacterial chromosomes are generally circular. The spirochaete Borrelia burgdorferi, how- ever has a linear major chromosome, and some of its plastids are also linear. Telomeric DNA forms cova- lently closed hairpin structures. See Appendix C, 1938, Muller, McClintock; 1971, Olonikov; 1972, Watson; 1978, Blackburn and Gall; 1990, Biessman et al.; 1991, Ijdo et al.; 1998, Frenck, Blackburn, and Shannon; Appendix E; bouquet configuration, centric fusion, guanine-quartet model, Hayflick limit, lamins, marginotomy, replication of DNA, sheep, telomere- led chromosome movement, Tetrahymena, tissue cul- ture. telomere-led chromosome movement the move- ment of chromosomes seen during meiotic prophase when all chromosomes associate by their telomeres, and these assume the leading position as the homol- ogous chromosomes synapse and undergo crossing over.

See Appendix C, 1994, Chikashige et al.; nucle- oporins (Nups). telomeric fusions end-to-end attachments of chromosomes during the evolution of a species which results in a reduction in the chromosome number from the ancestral value. See Muntiacus. telomeric fusion site a segment on human chro- mosome 2 that contains nucleotide sequences which once resided at or near telomeres. This region (2q13-2q14.1) is where two nonhomologous autos- omes fused end-to-end to produce a single V-shaped chromosome. This telomere fusion occurred early in human evolution, and it explains why the human diploid chromosome number is 46, not 48—the

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