spikelet in grasses, a secondary spike bearing few flowers. spinal bulbar muscular atrophy one of several neurological diseases due to an unstable trinucleotide repeat (q.v.). The X-linked gene involved encodes an androgen receptor, and the trinucleotide repeat is lo- cated in the coding portion of the gene. spindle a collection of microtubules responsible for the movement of eukaryotic chromosomes sub- sequent to their replication. See centromere, centro- some, Fungi, meiosis, microtubule organizing centers (MTOCs), mitosis, spindle pole body. spindle attachment region (also spindle fiber at- tachment, spindle fiber locus) centromere (q.v.). spindle checkpoint a checkpoint (q.v.) that pro- tects the integrity of the genome by initiating a delay in the cell cycle if all the chromosomes are not prop- erly attached to the spindle. See MAD mutations. spindle fiber one of the microtubular filaments of a spindle. spindle poison any compound that binds to cer- tain molecular components of spindles and causes them to malfunction.
A subset of the spindle poi- sons, notably paclitaxel, vinblastine, and vincristine (all of which see), have turned out to be potent anti- cancer drugs. Others like colchicine and podophyllin (both of which see) have been clinical failures. See tu- bulin. spindle pole body in yeast, the organelle that or- ganizes nuclear and cytoplasmic microtubules into a mitotic spindle. The spindle pole body in fungi is the functional equivalent of the centrosome (q.v.) in animals. During mitosis in yeast, the nuclear enve- lope does not break down, and the spindle pole body remains embedded in the nucleus. See tubulin. spineless-aristapedia one of the homeotic muta- tions (q.v.) of Drosophila located at 3-58.5. The dis- tal portions of the antennae are transformed into leg- like structures with claws. The homeotic mutations illustration on page 210 allows a comparison of a normal pair of antennae, each bearing a bristle-like arista (Fig. A) with a mutant antenna which lacks an arista and has distal claws (Fig. B). Mutations of the ssa gene demonstrate that legs and antennae are ho- mologous structures and suggest that antennae of ar- thropods evolved from an anterior pair of legs. See metamerism. spiral cleavage a type of embryonic development seen in invertebrates such as annelids and molluscs. The first and second divisions of the zygote are in vertical planes but at right angles to one another, producing a quartet of blastomeres. The next divi- sions are horizontal, cutting off successive quartets. However, each quartet is slightly displaced from the one above, giving a spiral appearance to the embryo.
The direction of the spiral is genetically determined. spirochete (also spirochaete) bacteria that are nonflagellated, spiral, and move by flexions of the body. See Appendix A, Eubacteria, Spirochaetae; Treponema pallidum. spiroplasmas helical, motile bacteria that resem- ble spirochaetes. Unlike spirochaetes, spiroplasmas lack a cell wall, and they are therefore included in the Aphragmabacteria (see Appendix A). Spiroplas- mas are responsible for certain plant diseases and cause male-specific lethality among the progeny of female Drosophila carrying them. See sex ratio organ- isms. splice junctions segments containing a few nucle- otides that reside at the ends of introns and function in excision and splicing reactions during the process- ing of transcripts from split genes. The sequence at the 5′ end of any intron transcript is called the donor junction and the sequence at the 3′ end the acceptor junction.
U1 RNA (q.v.) contains a segment adjacent to its 5′ cap that exhibits complementarity to the sequences at the donor and acceptor splice junctions of introns. U1 binds to such segments, causing in- trons to loop into a lariat (q.v.) that allows intron excision and exon splicing. See Usn RNAs. spliceosome the intranuclear organelle in which the excision and splicing reactions that remove in- trons from premessenger RNAs occur. See alterna- tive splicing, Cajal body, exon, intron, posttransla- tional processing, RNA splicing, small nuclear RNAs, splice junctions, Usn RNAs. splicing 1. RNA splicing: the removal of introns and the joining of exons from eukaryotic primary RNA transcripts to create mature RNA molecules of the cytoplasm. 2. DNA splicing. See recombinant DNA research. splicing homeostasis a phenomenon in which a maturase (q.v.) helps to catalyze the excision of an intron from its own primary RNA transcript. In so doing, the maturase destroys its own mRNA and thereby limits its own level of activity. split genes genes containing coding regions (ex- ons) that are interrupted by noncoding regions (in- trons). This type of genetic organization is typical of most eukaryotic genes and some animal viral ge- nomes, but introns are not found in prokaryotic or-
ganisms. See Appendix C, 1977, Roberts and Sharp; adenovirus, R-loop mapping. sp. n. new species. SPO 11 a gene which encodes a type 2 topoisom- erase (q.v.) in Saccharomyces cerevisiae. It was iso- lated as a sporulation mutant, hence the spo symbol. No meiotic recombination was observed in the mu- tant, although normal synaptonemal complexes (q.v.) appeared during meiotic prophase. The SPO 11 topoisomerase catalyzes meiosis-specific DNA double-strand breaks. The Drosophila mutant mei- W68 is a homolog of SPO 11. See Appendix C, 1997, Keeney, Giroux, and Kleckner; double-strand break (DSB) formation, recombination nodules (RNs). sponge body a membrane-less, cytoplasmic struc- ture with a sponge-like appearance, found in female germ line cells of Drosophila and thought to function in the assembly and transport of materials required for RNA localization in the oocyte (q.v.). Sponge bodies generally consist of endoplasmic reticulum- like cisternae and vesicles embedded in an electron- dense matrix that is devoid of ribosomes. They con- tain RNA and protein, and are often surrounded by mitochondria. They are first observed during early oogenesis (q.v.) near the nurse cell nuclear mem- brane, change in morphology as development prog- resses, migrate through the ring canals (q.v.), and dissociate toward later oogenesis into smaller parti- cles that are incorporated into the ooplasm (q.v.). Sponge bodies share morphological and functional characteristics with Balbiani bodies and mitochon- drial clouds. See Balbiani body, cytoplasmic localiza- tion, mitochondrial cloud, nurse cells. spontaneous generation the origin of a living sys- tem from nonliving material. See Appendix C, 1668, Redi; 1769, Spallanzani; 1864, Pasteur. spontaneous mutation a naturally occurring mu- tation. spontaneous reaction exergonic reaction (q.v.). sporangium a structure housing asexual spores. spore 1. sexual spores of plants and fungi are hap- loid cells produced by meiosis. 2. asexual spores of fungi are somatic cells that become detached from the parent and can either germinate into new hap- loid individuals or can act as gametes. 3. certain bac- teria respond to adverse growth conditions by enter- ing a spore stage until more favorable growth conditions return. Such spores are metabolically in- ert and exhibit a marked resistance to the lethal ef- fects of heat, drying, freezing, deleterious chemicals, and radiation. spore mother cell a diploid cell that by meiosis gives rise to four haploid spores. sporogenesis the production of spores. sporophyte the spore-producing, 2N individual. In the higher plants the sporophyte is the conspicu- ous plant.
In lower plants like mosses, the gameto- phyte is the dominant and conspicuous generation. See alternation of generations. Sporozoa a class of parasitic protoctists in the phy- lum Apicomplexa that reproduce sexually with an alternation of generations (q.v.). Both haploids and diploids undergo schizogony (q.v.) to produce small infective spores. All species of Plasmodium belong to the Sporozoa. See Appendix A, malaria. sporozoite the stage in the life cycle of the malaria parasite that infects humans. Lance-shaped sporozo- ites reside in the salivary gland of the Anopheles mos- quito and are delivered to the bloodstream of the victim when the mosquito takes a meal. The major surface antigen of the sporozoite is the circumsporo- zoite (CS) protein. In Plasmodium knowlesi, the CS protein contains a 12-amino-acid epitope that is re- peated 12 times. When host antibodies bind to the CS protein, it sloughs off and is renewed.
Thus the CS protein serves as an immune decoy. The nucleo- tide sequence of the gene encoding the entire CS protein has been determined. Unlike most eukaryo- tic genes, it is not interrupted by introns. See Appen- dix C, 1983, Godson et al.; malaria, Plasmodium life cycle. sporulation 1. the generation of a bacterial spore. 2. production of meiospores by fungi and many other eukaryotic organisms. spreading position effect the situation in which a number of genes in the vicinity of a translocation or inversion seem to be simultaneously inactivated. See Appendix C, 1963, Russell. 38,40,45S preribosomal RNAs See preribosomal RNA. src the oncogene of the Rous sarcoma virus (q.v.). The human SRC gene lies at 20 q12-q13, while the Drosophila Src gene is on the third chromosome at 64B. Src genes encode proteins that function as pro- tein tyrosine kinases and are characterized by SH2 and SH3 domains. These are important for intra- and intermolecular interactions that regulate both the catalytic activity of the molecules and their re- cruitment of substrates. SH2 domain is about 100 amino acids long, while SH3 domain is about 50
src tyrosine kinase
amino acids long and is rich in proline. Src PTCs reg- ulate the actin cytoskeleton, and they play a role in the morphogenesis of ring canals (q.v.) during oo- genesis. See actin, c-src, domain, v-src. src tyrosine kinase See pp60v-src. 30S, 40S, 50S, 60S ribosomal subunits See ribo- some. 60S, 70S, 73S, 78S, 80S ribosomes See ribosome, ribosomes of organelles. 4S RNA transfer RNA (tRNA) (q.v.). 7S RNA See signal recognition particle. 5S rRNA a small RNA molecule that is a compo- nent of most ribosomes. The 5S rRNA molecule shown in the illustration is from E. coli. 5S rRNA occurs in the large ribosomal subunit in the cytosol of all prokaryotes and eukaryotes. While the mole- cule stabilizes the structure of the large ribosomal subunit, 5S rRNA does not contribute directly to any of the active sites in the subunit. 5S rRNA oc- curs in the ribosomes of the mitochondria of plants and in the ribosomes of their chloroplasts.
However, the ribosomes of the mitochondria of fungi and ani- mals lack 5S rRNAs. In humans, the 5S rRNA locus is near the telomere of the short arm of chromosome 1. In Drosophila melanogaster, it is on 2R at 56 E-F. See Appendix C, 1963, Rosset and Monier; 1970, Wimber and Steffensen; 1973, Ford and Southern; 1985, Miller, McLachlan, and Klug; Drosophila sali- vary gland chromosomes, ribosomal RNA genes, ribo- some, RNA polymerase, Xenopus. 5.8S rRNA a component of the large ribosomal RNA molecule that is transcribed in the nucleolus. 5.8S rRNA is the structural equivalent of the 5′-ter- minal 160 nucleotides of prokaryotic 23S rRNAs. Thus, in eukaryotes, the 5.8S and 28S coding se- quences are separated by an internal transcribed spacer that is absent from the rDNA unit that is transcribed into the RNA of the large subunit of prokaryotic ribosomes. The 5.8S and 28S molecules are eventually separated by posttranscriptional exci- sion of the spacer. However, these molecules remain associated by intermolecular base pairing interac- tions as the large subunit of the ribosome matures.
See Miller trees, ribosomal RNA genes, ribosome. 16S rRNA the RNA molecule found in the small ribosomal subunits of prokaryotes. This RNA is of- ten abbreviated SSU rRNA (small subunit rRNA). The secondary structure of the 16S rRNA of E. coli is shown on page 423. This 30S subunit also con- tains 20 specific proteins. The folding pattern results from hydrogen bonding of C to G and A to U mole- cules. The nucleotides are numbered starting with 1 at the 5′ end and ending with 1,542 at the 3′ end. Comparison of the nucleotide sequence of 16S rRNAs from widely diverse species has allowed the construction of a “universal tree of life” (q.v.). See Appendix C, 1977, Woese and Fox; 1980, Woese et al.; ribosome, Shine-Dalgarno (S-D) sequence.
16S, 18S, 23S, 28S rRNAs the RNA molecules that reside in the subunits of ribosomes. Prokaryotes have 16S and 23S RNAs in their small and large sub- units, respectively. Eukaryotes have 18S and 28S RNAs in their small and large units, respectively. 5S rRNA genes genes that are transcribed into 5S rRNAs. Such genes occur in tandemly linked clus- ters in all eukaryotes. In Xenopus laevis, 5S rRNA genes account for 0.5% of the entire genome. There are three separate 5S rRNA multigene families. Two of these, the major oocyte and trace oocyte families, are expressed only in oocytes, while a third, somatic 5S rDNA, is expressed in all types of somatic cells. The major oocyte, trace oocyte, and somatic 5S rDNAs are present in 20,000, 1,300, and 400 cop- ies, respectively, per haploid genome. SRY sex-determining region Y, the gene at p11.3 on the Y chromosome that is both required and suf- ficient to initiate testis development in human em- bryos. SRY is an intronless gene that spans 3.8 kb. It encodes a 204 amino acid protein which regulates the transcription of the genes that function in sexual dif- ferentiation by binding to target sequences in their DNAs. XY individuals with loss-of-function muta- tions in the SRY gene are phenotypically female, but with rudimentary ovaries.
See Appendix C, 1987, Page et al.; 2003, Skaletsky et al.; human Y chromosome, selector genes, sex determination, Y chromosome. SSC sister-strand crossover. See sister chromatid ex- change. ssDNA single-stranded DNA. SSU rRNA small subunit rRNA. See 16S rRNA. stabilizing selection normalizing selection (q.v.). stable equilibrium an equilibrium state of alleles at a genetic locus to which the population returns following temporary disturbances of the equilibrium frequencies. For example, a locus with overdomi- nance should form a stable equilibrium as long as selection favoring heterozygotes remains constant. stable isotope a nonradioactive isotope of an ele- 1. the planar alignment of adjacent flat- tish nitrogen bases in a DNA double helix. 2. stack- ing of dye molecules on RNA to yield metachromasy (q.v.).
staggered cuts the result of breaking two strands of duplex DNA at different positions near one an- other, as occurs by action of many restriction endo- nucleases (q.v.). stamen the pollen-bearing organ of the angio- sperm flower. It consists of a filament bearing a ter- minal anther. See flower. standard deviation (s) a measure of the variability in a population of items. The standard deviation of a sample is given by the equation s=√Σ(x−x)2/N−1 where N is the number of items in the sample and Σ(x − x )2 is the sum of the squared deviations of each measurement from the mean (x ).
standard error (SE) a measure of variation of a population of means. SE = s √N − 1 where N = the number of items in the population and s = standard deviation. standard type the most common form of an or- ganism. Stanford-Binet test used to gauge intelligence, it consists of a series of questions and problems grouped for applicability to ages up to 16 years. Some questions require verbal recognition and oth- ers recognition of form and manual skills. The sub- ject’s performance is expressed in terms of his men- tal age. See intelligence quotient. Staphylococcus a genus of spherical, Gram-posi- tive bacteria, belonging to the family Staphylococca- ceae. Of the 19 species identified, only two—S. aureus and S. epidermis—are considered relevant to human health. S. aureus is found predominantly in the nasal passages and S. epidermis on the skin of normal humans. S. aureus has a genome size of 2.80 mbp and an estimated gene number of 2,600. These microbes cause disease or damage tissue when they move away from their normal habitats, particularly in individuals with weakened immune systems.
As a human pathogen, S. aureus produces toxins that can cause a wide array of infections and toxic effects, such as boils, pneumonia, meningitis, urinary tract infections, bone infections, food poisoning, and toxic shock syndrome (q.v.). Pathogenesis by S. epidermis is relatively less understood. Ninety percent of Staphylococcus strains are resistant to penicillin and penicillin-derived antibiotics, presenting a challenge for doctors to treat Staphylococcus-derived ailments. Many genes encoding virulence factors have been characterized, proteins involved in pathogenesis identified, and factors associated with drug resis- tance detected. See Appendix A, Bacteria, Deinocci; Appendix E, Species Web Sites; Gram-staining proce- dure. starch the storage polysaccharide of most plants. It is a polymer made up of α-D-glucose molecules. See formula below. start codon a group of three adjacent ribonucleo- tides (AUG) in an mRNA coding for the methionine in eukaryotes (formylated methionine in bacteria) that initiates polypeptide formation; also called an initiation codon. See genetic code, initiator tRNA. start kinase See cyclins. startpoint in molecular genetics, the base pair on DNA that corresponds to the first nucleotide incor- porated into the primary RNA transcript by RNA polymerase. startsite synonym for startpoint (q.v.). stasigenesis referring to a period during the pale- ontological history of a lineage during which little or no significant evolutionary change occurred. stasipatric speciation speciation resulting from the dispersion of a favorable chromosomal re- arrangement that yields homozygotes that are adap-
tively superior in a particular part of the geographi- cal range of the ancestral species. stasis in evolutionary studies, the persistence of a species over a span of geological time without sig- nificant change. stationary phase a period of little or no growth that follows the exponential growth phase (q.v.) in a culture of microorganisms or in a tissue culture. statistic the value of some quantitative character- istic in a sample from a population. Compare with parameter. statistical errors a “type one” statistical error oc- curs when a purely random fluctuation is taken as evidence for a positive effect. The risk of making a “false positive” error of this sort is symbolized by the Greek letter alpha (α). A type 2 statistical error re- sults when we fail to detect an effect when there is one. The risk of making a “false negative” error of this sort is symbolized by the Greek letter beta (β). Often a false negative error may be extremely costly, and so α is set at a very low value, but this increases the risk of type 2 errors. See confidence limits, null hypothesis method, significance of results. statistics the scientific discipline concerned with the collection, analysis, and presentation of data. The analysis of such data depends on the application of probability theory.
Statistical inference involves the selection of one conclusion from a number of alternatives according to the result of a calculation based on observations. Parametric methods in statis- tical analysis assume that the data follow a defined probability distribution (e.g., a normal, binomial, or Poisson distribution, all of which see), and the results of the calculations are valid only if the data are so distributed. The Student’s t test (q.v.) is an example of a parametric procedure. Nonparametric methods in statistical inference are free from assumptions as to the shape of the underlying probability distribu- tion. The Mann-Whitney rank sum test and the sign test are examples of nonparametric procedures. See analysis of variance, chi-square test, Gaussian curve, null hypothesis, Student’s t test. status quo hormones synonym for allatum hor- mones (q.v.).
steady-state system a system whose components seem unchanging because material is entering and leaving the system at identical rates. stem cells undifferentiated or partially differenti- ated animal or plant cells that can proliferate and are pluripotent (q.v.) or totipotent (q.v.) in nature. Stem cells are generally divided into the following two classes. (1) Embryonic stem cells (ESCs) are un- differentiated cells from the early embryo that can proliferate and are pluripotent or totipotent, i.e., during normal development or upon transfer into an appropriate host or environment, they have the po- tential to differentiate into every adult cell type or to produce a whole animal from a single cell. The term usually refers to stem cells from the mamma- lian embryo. The mammalian zygote (q.v.) and cells produced by early zygotic divisions up to around the blastocyst (q.v.) stage are examples of ESCs. ESCs derived from cultured mouse blastocyst cells differ- entiate into teratocarcinomas when injected into immunodeficient mice, produce pure lines of pluri- potent cells under appropriate experimental condi- tions, and when injected into a host blastocyst, form nearly all the tissues of the chimeric adult animal. (2) Adult tissue stem cells (TSCs) are partially differ- entiated, post-embryonic or postnatal plant or ani- mal cells that have the potential to proliferate, self- renew, and produce one or more types of differenti- ated progeny. Through in vivo (q.v.) and in vitro (q.v.) manipulations, TSCs have been identified in a variety of tissues (e.g., bone marrow, central nervous system, the epidermis, intestinal epithelium, skeletal muscle, the germ line, and shoot and root apical meri- stems), where they serve to replace cells that die, are lost due to injury, or are continually depleted during the life of the organism. TSCs differ from ESCs in that during normal development TSCs are more lim- ited in their in vivo developmental potential, and their cell division gives rise to one daughter cell that acts as a stem cell and another that produces differentiated progeny.
The stem cell state and the developmental capacity of the daughter cells is influenced by signals from the surrounding environment, and TSCs show plasticity in choosing their course of differentiation when their microenvironment is altered. Mutations that affect stem cell fate have been identified in both plants and animals. See chimera, cystocyte divisions, teratocarcinoma. stem structure in molecular biology, the base- paired (unlooped) segment of a single-stranded RNA or DNA hairpin (q.v.). Also known as a stem and loop structure. stereochemical structure the three-dimensional arrangement of the atoms in molecules. stereoisomers molecules that have the same structural formula, but that differ in the spatial ar- rangement of dissimilar groups bonded to a common atom. steric relating to stereochemical structure (q.v.).