speed up aging. In mutant yeast cells there is an ex- cessive production of small circles of ribosomal DNA. Eventually the rDNA exceeds the amounts of DNA that comprise the total genome in the normal yeast cell. See gene amplification. shadow casting the use of a vacuum evaporator (q.v.) to deposit a coating of a heavy metal on a sub- microscopic particle.
The coating is cast at an angle so that metal will build up on one side of the particle and cover the specimen support except in the shadow of the particle. The length and shape of the shadow allows calculation of the dimensions of the particle. SH domains See Src. shearing in molecular biology, the process whereby a DNA sample is broken into pieces of fairly uni- form size (e.g., by subjecting them to shearing forces in a Waring blender). sheep a mammal belonging to the genus Ovis and domesticated for its meat, milk, wool, and hide. The domestic sheep, Ovis aries (q.v.), is distributed worldwide, and common breeds are Merino, Ram- bouillet, Finn Dorset, Debouillet, Lincoln, Leicester, Cotswold, Romney, Corridale, Columbia, Romel- dale, Panama, Montadale, Polwarth, Targee, Hamp- shire, Shropshire, Southdown, Suffolk, Cheviot, Oxford, Tunis, Ryeland, and Blackface Highland.
The most famous member of this species was Dolly (q.v.). shift See translocation. shifting balance theory a theory, proposed by Sewell Wright, that maintains that biological evolu- tion proceeds most rapidly when subpopulations of a species remain isolated for a time sufficient to acquire distinctive adaptations, followed by reestablishment of gene flow, the broadening of genetic diversity, and the enhancement of evolutionary flexibility. See Ap- pendix C, Wright. Shine-Dalgarno (S-D) sequence in E. coli the mRNA consensus sequence 5′ AGGAGGU 3′ that is between 6 and 8 bases upstream from the AUG translation initiation codon. The S-D sequence forms complementary base pairs with a consensus sequence found at the 3′ end of the 16S rRNA mole- cule (q.v.) in the 30S subunit of the ribosome. The S-D sequence thus serves as the binding site for bac- terial mRNA molecules on ribosomes. See Appendix C, 1974, Shine and Dalgarno; translation. Shope papilloma virus an icosahedral particle about 53 nanometers in diameter containing 8 kbp of DNA.
The virus (q.v.) was discovered in 1933 by R. E. Shope. The virus produces papillomas in wild, cottontail, North American rabbits. short-day plant a plant with a flowering period that is accelerated by daily exposures to light of less than 12 hours. See photoperiodism. short-period interspersion a genomic pattern in which moderately repetitive DNA sequences (each about 300 base pairs in length) alternate with nonre- petitive sequences of about 1,000 base pairs. short tandem repeat (STR) See microsatellites, STR analysis. short term memory consolidation See CREBs, spaced training. shotgun cloning a technique in which the geno- mic DNA of an organism is randomly broken into smaller fragments by mechanical shearing or partial digestion with restriction endonucleases (q.v.) and cloned in appropriate vectors to produce a genomic library (q.v.).
The clones are then used in shotgun sequencing (q.v.). shotgun sequencing a method for determining the nucleotide sequence of a large stretch of DNA by randomly sequencing a genomic library (q.v.) de- rived from it containing clones with overlapping DNA fragments and using powerful computers to assemble the sequence data into a continuum. The application of this method to determine the nucleo- tide sequence of a whole genome is called whole- genome sequencing (WGS) or assembly. In this ap- proach randomly-selected inserts, whose physical lo- cation in the genome need not have been mapped, are sequenced using a primer from within the clon- ing vector. A more recent approach is to prepare more than one such library with small and large in- sert sizes and to sequence the ends of randomly se- lected inserts. When a sufficiently large number of such fragments has been sequenced, they theoreti- cally contain enough overlaps such that subsequent assembly by computational methods yields a contin- uous genomic sequence. In practice, the preliminary sequence assembled in this way contains gaps of un- known sequence. These gaps are filled in a variety of ways, such as by further sequencing using primers derived from DNA sequences flanking the gaps, or by identifying small-insert library clones that span the gaps. The final sequence is then analyzed, anno- tated, and stored in publicly accessible databases. The first free-living organism whose genome was se- quenced by WGS methodology was Haemophilus in- fluenzae. Subsequent advances in the development of large-insert vectors, sequencing, and computa- tional technology have allowed WGS of a large
signal recognition particle (SRP)
number of genomes, including those of Drosophila melanogaster, Anopheles gambiae, Takifugu rubripes, Homo sapiens, and microbial populations from spe- cific habitats. See Appendix C, 1995, Fleischmann et al.; 2000, Adams et al.; 2001, Venter et al.; 2002, Aparicio et al., Holt et al.; 2004, Venter et al., Tyson et al.; Appendix E, Individual Databases, Species Web Site Addresses; Appendix F; community ge- nome sequencing, DNA vector, genomic annotation, primer DNA, shotgun cloning. shuttle vector a cloning vector able to replicate in two different organisms—e.g., in E. coli and yeast. These DNA molecules can therefore shuttle be- tween the different hosts. Also called bifunctional vectors. sib a shortened form for sibling. siblings brothers and/or sisters; the offspring of the same parents. sibling species species that are almost identical morphologically but are reproductively isolated; also called cryptic species. sibmating a brother-sister mating. sibship all the siblings in a family. sickle-cell anemia a generally fatal form of hemo- lytic anemia seen in individuals homozygous for an autosomal, codominant gene HS. The erythrocytes of such individuals contain an abnormal hemoglobin, HbS (q.v.).
These cells undergo a reversible alter- ation in shape when the oxygen tension of the plasma falls slightly, and they assume elongate, fil- amentous, and sickle-like forms. Such red cells show a greatly shortened life span, since they tend to clump together and are rapidly destroyed. About 0.2% of ba- bies of African descent born in the United States suf- fer from sickle-cell anemia. See Appendix C, 1949, Neel, Pauling et al.; 1957, Ingram; 1978, Kan and Dozy; gene, hemoglobin C. sickle-cell hemoglobin See hemoglobin S. sickle-cell trait the benign condition shown by in- dividuals carrying both the normal gene, HA, and the sickle-cell gene, HS. The erythrocytes of such indi- viduals produce both HbA and HbS.
Such heterozy- gotes are healthy, and their erythrocytes can be caused to sickle only under conditions where the ox- ygen concentration is drastically reduced. HA/HS in- dividuals suffer far less severely from Plasmodium falciparum infections than do HA/HA individuals. This malaria plasmodium enters the erythrocyte and lives by engulfing cytoplasm into its food vacuole. Parasites are unable to feed efficiently upon HA/HS cells because HbS molecules are insoluble compared to HbA and cause a great increase in the viscosity of the cytoplasm. About 9% of the African-American population of the United States shows the sickle-cell trait.
See Appendix C, 1954, Allison; hemoglobin, he- moglobin S, malaria, Plasmodium life cycle. siderophilin plasma transferrin (q.v.). Sievert (Sv) the amount of ionizing radiation that liberates one joule of energy per kilogram of tissue. One Sv equals 100 rem. The millesievert (mSv) is often used in estimates of annual dose rates to hu- man populations. The average U.S. citizen receives approximately 4 mSv per year, with radon (q.v.) ac- counting for 55% and dental and medical x-rays about 15%. Doses of more than five Sieverts are usu- ally fatal to humans. See radiation units. Sigma ( ) the summation of all quantities follow- ing the symbol. sigma ( ) factor a polypeptide subunit of the RNA polymerase of E. coli. This molecule by itself has no catalytic function, but it serves to recognize specific binding sites on DNA molecules for the ini- tiation of RNA transcription. See Appendix C, 1969, Burgess et al.; Pribnow box, RNA polymerase. sigma replication See rolling circle. sigma virus a virus that confers CO2 sensitivity upon Drosophila melanogaster. signal hypothesis the notion that the N-terminal amino acid sequence of a secreted polypeptide is critical for attaching the nascent polypeptide to membranes.
See Appendix C, 1975, Blobel and Dob- berstein; receptor-mediated translocation, signal pep- tide. signal peptide a sequence of about 20 amino acids at or near the amino terminus of a polypeptide chain that attaches the nascent polypeptide and its ribo- some to the endoplasmic reticulum. Polypeptides thus anchored are “flagged” to be processed in the Golgi apparatus prior to release from the cell. See Appendix C, 1999, Blobel. signal recognition particle (SRP) a nucleoprotein particle that functions during receptor-mediated translocation (q.v.). The particle contains a 7S RNA molecule and six different proteins. More than 75% of the total 7S RNA in animal cells is present in SRPs. There is a high degree of homology between the 7S RNAs of different animal species. All cells analyzed thus far have SRPs that select proteins des- tined to be secreted or integrated into the plasma
membrane and target them to the endoplasmic retic- ulum (q.v.) in eukaryotic cells or to the plasma mem- brane in prokaryotic cells. In E. coli, the SRP consists of a single protein and a 4.5S RNA molecule. Other cells have SRPs that contain additional proteins and larger RNA molecules, but all share the same evolu- tionarily conserved core of nucleoprotein. See Appen- dix E, Individual Databases; protein sorting, viroid. signal sequence synonym for leader sequence (q.v.). signal transduction See cellular signal transduc- tion. significance of results if the probability values are equal to or less than .05 but greater than .01, the results are said to be significantly different; probability values ≤ .01 but > .001 are called highly significant, and those ≤ .001 are called very highly significant by convention. See P value. silent allele an allele that has no detectable prod- uct. See null allele. silent mutation a gene mutation that has no con- sequence at the phenotypic level; i.e., the protein product of the mutant gene functions just as well as that of the wild-type gene.
Functionally equivalent amino acids may sometimes substitute for one an- other (e.g., leucine might be replaced by another nonpolar amino acid such as isoleucine). See neutral mutation, samesense mutation, synonymous codons. silk the cocoon filament spun by the fifth-instar larva of Bombyx mori. Each cocoon filament contains two cylinders of fibroin, each surrounded by three layers of sericin. Fibroin is secreted by the cells of the posterior portion of the silk gland. These cells un- dergo 18 to 19 cycles of endomitotic DNA replication before they begin transcribing fibroin mRNAs. The fibroin gene is present in only one copy per haploid genome. It resides on chromosome 23 and is about 18 kilobases long. The fibroin gene is fundamentally an extensive array of 18 base-pair repeats coding for Gly-Ala-Gly-Ala-Gly-Ser. The similarity of the fi- broin gene to a satellite DNA suggests that the gene grew to its current size and continues to evolve by unequal crossing over. The sericin proteins receive their name because of the abundance of serine, which makes up over 30% of the total amino acids.
There are at least three sericins, and one of these is encoded by a gene on chromosome 11. All sericins are secreted by the cells from the middle region of the silk gland. Several mutations are known that in- fluence silk production. Some (Fib and Src-2) repre- sent mutations in the cistrons coding for fibroin and sericin molecules. Others (Nd, Nd-s, and flc) seem to have defects in the intracellular transport and se- cretion of fibroin. See Appendix C, 1972, Suzuki and Brown; 1979, Perdix-Gillot; beta pleated sheet, en- dopolyploidy. silkworm the larva of Bombyx mori (q.v.). Silurian the Paleozoic period during which the first life appeared on land. It consisted of psilophytes (q.v.) and millipedes. In the oceans, agnathans diver- sified and placoderms arose.
See geologic time divi- sions. silversword alliance a group of 30 species of plants belonging to three genera endemic to the Ha- waiian islands and most closely related to California tarweeds in the “Madia” lineage. They get their com- mon name from the visually impressive silversword, Argyroxiphium sandwicense, which lives in dry alpine habitats on the Haleakala and Mauna Kea volcanoes. Silverswords are members of the sunflower family (Asteraceae) and represent one of the world’s most spectacular examples of adaptive radiation (q.v.) on islands. They populate a variety of habitats, show a diverse range of leaf and flower morphologies, and grow as shrubs, trees, climbing vines, or herbaceous mats. Most species can be crossed and some even produce fully fertile hybrids. The entire set of taxa originated from seeds presumably caught on the feathers of migrating sea birds and transferred from North America to Kauai soon after it rose above the
The Hawaiian silversword (Argyroxiphium sandwi-cense) is an impressive sight framed by the lava back- ground of its volcanic habitat. When in flower the plant may be 3 meters tall and 75 cm wide. As many as 800 compound flower heads are carried on the inflorescense, and the individual flowers are pink or wine red.
sister chromatid cohesion
sea. Studies of chloroplast and nuclear gene se- quences show that the ancestral silversword arose as an allotetraploid (q.v.) from an interspecific cross be- tween two diploid species of tarweed. As new is- lands emerged from the Hawaiian islands hotspot and were rafted to the northwest, the silversword dispersed southeastward to successively younger is- lands. In these new habitats they evolved into new species.
See Appendix A, Plantae, Trachaeophyta, Angiospermae, Asterales; Appendix C, 1991, Bal- dwin et al.; hotspot archipelago. simian immunodeficiency viruses (SIVs) viruses that are genetically similar to the HIVs but occur in wild populations of monkeys and apes. The SIV most closely related to HIV-1 was found in the chimpanzees of Gabon. Perhaps the progenitor of HIV-1 was a zoonotic virus (q.v.) which infected na- tives that butchered chimpanzees for food. The date of origin of HIV-1 has been estimated to have been about 1931.
See Appendix C, 2000, Korber et al.. simian sarcoma virus retrovirus first found in the woolly monkey (q.v.). This oncogenic virus carries the v-sis oncogene, which encodes a transforming protein p28sis. Nucleotide sequences related to v-sis have been located on human chromosome 22 at a site subsequently called c-sis. See Appendix C, 1983, Doolittle et al.; platelet-derived growth factor, proto- oncogene, Rous sarcoma virus. simian virus any of a group of viruses that attack nonhuman primates. simian virus 40 a DNA virus that readily infects cultured primate cells. SV40 is lytic in monkey cells, but temperate in mouse cells, causing occasional neoplastic transformations. The virus replicates in the nuclei of host cells and may become stably inte- grated into the host genome.
The virus genome con- sists of a circular DNA molecule containing 5,227 base pairs. The complete nucleotide sequence for this virus has been determined, and it contains both conventional genes, overlapping genes, and split genes. See Appendix C, 1971, Dana and Nathans; 1978, Reddy et al.; Appendix F; enhancer, oncogenic virus, transformation. simple-sequence DNA satellite DNA (q.v.). simplex See autotetraploidy. Sinanthropus pekinensis a group of extinct homi- nids, originally found near Beijing (formerly spelled Peking), China, but no longer considered a distinct species; now included in the species Homo erectus. SINEs See repetitious DNA. single-copy plasmids plasmids maintained in bacterial cells in a ratio of one plasmid for each host chromosome. single-event curve a dose-response curve in radio- biology which gives a linear relation when the log of survival is plotted against radiation dose.
See multi- ple-event curve, target theory. single-nucleotide polymorphisms (SNPs) small variations in DNA sequence in which at any given position a single nucleotide (q.v.) is replaced by one of the other three nucleotides. Those SNPs (pro- nounced “snips”) found in protein-coding regions are designated cSNPs. Most of the genetic variation in man is thought to be in the form of SNPs, and the human genome (q.v.) contains at least 10 million of them, or one at every 300 base pair interval. Human SNPs tend to be inherited stably as haplotype blocks and can serve as useful landmarks when scanning the genome for specific mutations. The SNPs known to date, together with their exact locations in the hu- man genome, are catalogued in a public database called dbSNP. See Appendix E, Individual Databases; haplotype, sequence similarity estimates. single-strand assimilation the process whereby a single strand of DNA displaces its homologous strand in a duplex, forming a D loop (q.v.). The re- action is mediated by RecA protein (q.v.) and is in- volved in recombination and heteroduplex forma- tion. single-stranded DNA binding protein in E. coli, a tetrameric protein of 74,000 daltons that binds to the single-stranded DNA generated when a helicase (q.v.) opens the double helix.
This stabilizes the sin- gle-stranded molecule and prevents reannealing or the formation of intrastrand hydrogen bonds. Com- pare with helix-destabilizing proteins. See replisome. single-strand exchange pairing of one strand of duplex DNA with a complementary strand in an- other DNA molecule, displacing its homolog in the other duplex. See 5-bromodeoxyuridine. sire the male parent in animal breeding. Compare with dam. siRNAs small interfering RNAs (q.v.). sister chromatid cohesion cohesion between the two chromatids formed from each chromosome dur- ing the S phase of the cell cycle (q.v.). The evolu- tionarily conserved multiprotein complex cohesin (q.v.) is the primary effector of sister chromatid co- hesion in all eukaryotes. This cohesion ensures that
sister chromatid exchange
the two chromatids attach to microtubules with op- posite orientations, which is a precondition for each being drawn subsequently toward the opposite pole of the dividing cell. See chromatid, microtubules, sep- arase. sister chromatid exchange the exchange of DNA sequences between sister chromatids due to break- age at apparently homologous sites followed, after switching partners, by reunion of the broken ends. See crossing over. sister chromatids identical nucleoprotein mole- cules joined by a centromere. See chromatid. sister group a species or higher monophyletic taxon that is hypothesized to be the closest genea- logical relative of a given taxon. Sister taxa are de- rived from an ancestral species not shared by any other taxon.
Graphically, sister groups appear on a cladogram (q.v.) as lineages that arise as branches from a single divergence node. Compare with out- group. site the position occupied by a mutation within a cistron. site-specified mutagenesis a technique that in- troduces nucleotide alterations of known composi- tion and location into a gene under study.
See oligo- nucleotide directed mutagenesis. site-specific recombinase an enzyme which brings together two short stretches of similar DNA sequences and catalyzes a reciprocal exchange be- tween them, called site-specific recombination (q.v.). Sequence comparisons have identified two major families of site-specific recombinases, the integrase family and the resolvase family, which differ from one another in protein sequence and structure, and in the mechanism of recombination. The integrase family is named after the lambda bacteriophage in- tegrase (q.v.), and members of this family are found in bacteriophage, bacteria, and yeast. Integrases from the human immunodeficiency virus (HIV) and avian sarcoma virus (ASV) have been widely stud- ied.
The resolvase family is named after the recom- binase encoded by the Tn3 and γσ transposons, which is involved in resolution of a cointegrate structure (q.v.). Members of this family are found in prokaryotes. See FLP/FRT recombination. site-specific recombination a type of recombina- tion catalyzed by a site-specific recombinase (q.v.), in which there is exchange of genetic material be- tween two short, defined DNA segments containing only a small region of homology. This process in- volves breakage and reformation of specific phos- phodiester bonds within the DNA targets, and does not require DNA synthesis or energy from a nucleo- tide cofactor. Recombination between inverted re- peats results in inversion of a DNA segment, be- tween repeat sequences on two DNA molecules in their cointegration, and between repeats on one DNA molecule in the excision of a DNA segment.
The integration of lambda phage into the bacterial genome and its excision, and FLP/FRT recombina- tion (q.v.), are examples of processes involving site- specific recombination. Compare with homologous recombination. skeletal DNA hypothesis a concept developed to explain the observation that over 90% of the ge- nomes of most eukaryotes are made up of noncoding DNAs. According to Cavalier-Smith, this “second- ary” DNA functions as a skeleton that increases the volume of the nucleus and so gives the coding genes more space in which to operate. The skeletal DNA determines the size of the nucleus, and this in turn controls cell volume, which is optimized by selec- tion. See Appendix C, 1999, Beaton and Cavalier- Smith; cryptomonads, C value paradox, junk DNA, selfish DNA. SLC 24A5 a gene at 15q21.1 in humans that en- codes a protein which functions as a cation ex- changer in melanosomes.
The gene exists in two al- lelic forms varying at one codon. The ancestral form (A) is present in most African populations, while the derived form (a) is present in most Europeans. AA individuals are dark skinned, aa are light skinned, and Aa are intermediate. This polymorphism ac- counts for most of the skin pigmentation differences between human races. See Appendix C, 2005, Lama- son et al.; melanin, melanocytes. sleeping sickness the common name for African human trypanosomiasis, a disease which is caused by infection with the parasite Trypanosoma brucei and which affects populations in sub-Saharan Africa, as well as in South America and Asia.
Human infection results from the bite of a tsetse fly infected with the parasite. The disease is characterized by fever in the early stages, followed by heart, kidney, and neuro- logical impairment, and eventually, death. Also called African sleeping sickness. See Appendix C, 2005, Berriman et al.; Glossina, Trypanosoma. sliding filament model a theoretical mechanism that explains muscle contraction by the making and breaking of cross bridges between adjacent thick (myosin) and thin (actin) filaments. A similar model is postulated to explain the lengthening of the mi- crotubules of the spindle apparatus, whereby separa-