Oryza sativa

31 Mar

Oryza sativa

Ornithine cycle

orthologs genes or proteins found in different spe- cies that are so similar in their nucleotide or amino acid sequences that they are assumed to have origi- nated from a single ancestral gene. The beta globin chain genes in humans and chimpanzees would be trends. examples of orthologs. If one compares the genome of Saccaromyces cerevisiae (q.v.) and Caenorhabditis elegans (q.v.), most orthologs have “core functions.” That is, they generate the proteins used in inter- mediary metabolism, DNA-, RNA-, and protein- metabolism, transport, secretion, and cytoskeletal structures.

In contrast, the genes from C. elegans that function in intercellular signaling and gene reg- ulation are not found in the yeast genome. See Ap- pendix C, 1975, King and Wilson; hemoglobin genes, Hox genes, Pan; contrast with paralogs. orthopteran an organism belonging to the Or- thoptera, an order of the Hemimetabola containing cockroaches, locusts, grasshoppers, and similar in- sects. orthoselection continuous selection on the mem- bers of a lineage over a long time, causing continued evolution in a given direction that may create an im- pression of “momentum” or “inertia” in evolutionary chain genes in humans and chimpanzees would be trends. orthotopic transplantation the transplanation of grafts between identical sites in such a way that the graft maintains its normal orientation.

Oryctolagus cuniculus the rabbit, a mammal com- monly reared in the laboratory and the subject of in- tensive genetic research. An extensive collection of mutations is available influencing a wide variety of morphological and physiological traits. The haploid chromosome number is 22, and about 60 genes have been distributed among 16 linkage groups. See Ap- pendix A, Chordata, Mammalia, Lagomorpha; WHHL rabbit. Oryza sativa rice. Together with wheat, corn, and potatoes, it is one of the world’s four most impor-

Oryzias latipes
tant crops. The haploid chromosome number is 12. The rice genome (389 mbp) is the smallest of the cultivated species. For comparison, Triticum aesti- vum is 16 gbp. See Appendix A, Plantae, Angio- spermae, Monocotyledonae, Graminales; Appendix E, Species Web Sites; Appendix F; helitron. Oryzias latipes the medaka, or killifish, a freshwa- ter fish common to Japan, Korea, and China.

It is easily maintained in the laboratory and was the first fish in which Mendel’s laws were shown to be valid. Y-linked inheritance was first demonstrated in the medaka and the guppy. N = 24; C = 720 mbp. See Appendix A, Chordata, Osteichythes, Neopterygii, Cypriniformes. osmium tetroxide OsO4, a compound often used as a fixative in electron microscopy. osmosis diffusion of a solvent through a semiper- meable membrane separating two solutions of un- equal solute concentrations. The direction of solvent flow tends to equalize the solute concentrations. otu a sex-linked female sterile gene in Drosophila melanogaster that is remarkable because different mutant alleles can produce quite different ovarian pathologies. One class of alleles produces ovarian tu- mors; hence the otu symbol. The tumors are com- posed of hundreds of single cells and clusters of two or three cells joined by ring canals (q.v.).

These ab- normalities preasumably arise from defective fu- somes (q.v.). Another class of mutant alleles is char- acterized by germaria that either lack germ cells or contain germ cells that have undergone only one or two cell divisions.

Mutants belonging to the third class can produce egg chambers, but the transport of nurse cell cytoplasm to the oocyte is inhibited. The nuclei of these abnormal nurse cells contain giant polytene chromosomes, and the largest have 8,000 times the haploid amount of DNA. Studies of the otu gene product have shown that this protein be- longs to a highly conserved superfamily of cysteine proteases, many of which function to break down ubiquitin (q.v.).

See cystocyte divisions, polyfusome, ubiquitin proteasome pathway. Ouchterlony technique a gel-diffusion, antibody- antigen precipitation test that depends on horizontal diffusion from two or more opposite sources. An agar slab is prepared and two or more wells are cut in it. One (A) is filled with an aqueous suspension of antibody molecules, while each of the other wells (B and C in the illustration here) is filled with a dif- ferent antigen preparation. The antigen and anti- body molecules diffuse toward each other and even- tually interact, forming curved precipitation lines. In example I, the antigens in wells B and C are differ- ent. In II, well B contains a single antigen and well C two antigens, one identical to that in B.

See Ap- pendix C, 1948, Ouchterlony. Oudin technique a gel-diffusion, antibody-antigen precipitation test that depends on simple vertical diffusion in one dimension. A gel column is pre- pared containing a homogeneous distribution of an- tibody molecules. Above this is layered an aqueous suspension of antigen molecules. As these diffuse into the gel, a moving zone of antigen-antibody pre- cipitate is formed. If several antigens and antibodies are present, separate zones of interaction will be seen.

See Appendix C, 1946, Oudin. outbreeding the crossing of genetically unrelated plants or animals; crossbreeding. outcross See outbreeding. outgroup a species or higher monophyletic taxon that is examined in the course of a phylogenetic study to determine which of two homologous char- acter states may be inferred to be apomorphic. The most critical outgroup comparison involves the sister group of the taxon under study. Compare with sister group. outlaw gene a gene favored by selection despite its disharmoneous effects on other genes in the same organism. See meiotic drive.

Ouchterlony technique

outron See trans-splicing. ovariectomy the surgical removal of one or both ovaries. ovariole one of several egg tubes constituting the ovary of most insects. ovary the female gonad in animals or the ovule- containing region of the pistil of a flower. overdominance the phenomenon of heterozy- gotes having a more extreme phenotype than either homozygote; monohybrid heterosis. Overdomi- nance generally refers to the situation in which AA′ individuals are more fit than AA or A′A′ indi- viduals. overlapping code a hypothetical genetic code, first proposed by George Gamow, in which any given nucleotide is shared by two adjacent codons. The genetic code used in biological systems was later shown to be nonoverlapping. See overlapping genes for the few exceptions. overlapping genes genes whose nucleotide se- quences overlap to some degree. The overlap may involve regulatory sequences (e.g., tryptophan oper- ator and promoter regions in E. coli) or structural genes (e.g., in bacteriophage phiX174, gene E lies entirely within gene D, but they are translated in dif- ferent reading frames).

See Appendix C, 1976, Bur- rell et al.; bidirectional genes. overlapping inversion a compound chromosomal inversion caused by a second inversion that includes part of a previously inverted segment. overwinding positive supercoiling of DNA, result- ing in further tension in the direction of winding of the two strands of a duplex about each other. ovicide any compound that destroys eggs, espe- cially a compound that destroys insect eggs. oviduct the tube carrying eggs from the ovary to the uterus. ovine referring to members of the sheep family, especially the domestic sheep species Ovis aries. oviparous laying eggs in which the embryo devel- ops outside the mother’s body and eventually hatches. See ovoviviparous, viviparous. oviposition the laying of eggs by a female insect.

ovipositor an organ at the hind end of the ab- domen in female insects, through which eggs are laid. Ovis aries domestic sheep. The blood group ge- netics of this species has been intensively investi- gated. The haploid chromosome number is 27, and about 250 genes have been mapped. The haploid C value is 3.2 × 109 bp of DNA. See Appendix A, Chordata, Mammalia, Artiodactyla; Appendix E; sheep. ovisorption the resorption of oocytes. ovogenesis oogenesis (q.v.). ovotestis the organ of some hermaphroditic ani- mals that functions both as ovary and testis; the go- nad of an animal that undergoes consecutive sexual- ity (q.v.). ovoviviparous bringing forth young that develop from eggs retained within the maternal body, but separated from it by the egg membranes. Many fish, reptiles, molluscs, and insects are ovoviviparous. See oviparous, viviparous. ovulation the release of a ripe egg from the mam- malian ovarian follicle, frequently at the stimulus of a pituitary hormone. ovule the structure found in seed plants which de- velops into a seed after the fertilization of an egg cell within it.

ovum an unfertilized egg cell. oxidation classically defined as the combination of a molecule with oxygen or the removal of hydrogen from it. Since electrons are transferred to the oxidiz- ing reagent, which becomes reduced, oxidation and reduction (q.v.) are always coupled. oxidation-reduction reactions chemical reactions in which electrons are transferred from a reductant to an oxidant; as a consequence of the transfer, the reductant is oxidized and the oxidant is reduced. oxidative phosphorylation the enzymatic phos- phorylation of ADP to ATP, which is coupled to the electron transport chain (q.v.). Thus, respiratory en- ergy is transformed into phosphate-bond energy. See adenosine phosphate, ATP synthase, chemiosmotic theory, mitochondrial proton transport. oxidoreductases enzymes that transfer electrons. Catalase (q.v.) is an oxidoreductase.

oxygen the second most abundant of the biologi- cally important elements. Atomic number 8; atomic weight 15.9994; valence 2−; most common isotope 16O. oxyhemoglobin oxygenated hemoglobin. oxytocin a polypeptide secreted by the hypothala- mus and stored in the neurohypophysis. Oxytocin causes smooth-muscle contraction and may help ter- minate pregnancy. Oxytricha See Stylonichia.

p 1. the smaller arm of a human chromosome. See symbols used in human cytogenetics. 2. a symbol for protein; if followed by a number, that number indi- cates the relative molecular mass of the protein in kilodaltons. See p53. 3. a symbol for plasmid; for ex- ample, pBR322 (q.v.). P 1. probability. 2. phosphorus. 3. phosphate (when combined in an abbreviation such as ADP, ATP). 4. symbol for panmictic index (q.v.). P1 the symbol denoting the immediate parents of the F1 generation. The symbols P2 and P3 are used to designate the grandparental and great-grandparental generations, respectively, if one starts from the F1 and works backward. This genetic symbolism was in- vented by W. Bateson. See Appendix C, 1900, Bateson. 32P a radioactive isotope of phosphorus, widely used to label nucleic acids; it emits a strong beta par- ticle and has a half-life of 14.3 days. 32P was used in the famous Hershey-Chase experiment of 1952.

See Appendix C. Pi inorganic phosphate. p34 (CDC2) a protein of relative molecular mass 34,000, hence the p34 designation. It functions in cell division control, hence the CDC acronym. This protein belongs to the Ser/Thr family of protein ki- nases (q.v.). CDC2 contains 297 amino acids, and phosphorylation at Thr-161 activates it, whereas phosphorylation at Thr-14 or Tyr-15 inactivates it. When combined with cyclin B, it forms the mitosis- promoting factor (MPF) (q.v.). For this reason CDC2 is sometimes called CDK2 (cyclin-dependant kinase-2). CDK2 is responsible for the separation of centrioles, the first step in centrosome duplication. In humans the gene for CDC2 contains 15,688 bases and has been mapped to 10q21.1.

Homologous genes have been found in the mouse, Drosophila, Xenopus, Caenorhabditis, and Schizosaccharomyces. p53 a protein of relative molecular mass 53,000, hence the designation p53. In 1993 Science magazine designated p53 as the “Molecule of the Year,” and it has been referred to as the “cellular gatekeeper for growth and division.” The protein is expressed in most normal tissues and has been highly conserved during evolution. The p53 protein normally plays a role in controlling the entry of cells into the S phase of the cell cycle, in transcriptional regulation, and in the induction of apoptosis (q.v.).

The protein binds to DNA as a tetramer and activates the expression of adjacent genes that inhibit cell proliferation. A mutation in one allele will reduce the concentration of functionally active tetramers. If both alleles are affected, the inhibition will be reduced further. The gene that encodes the p53 protein is symbolized TP53 (q.v.). pachynema See meiosis. pachytene stage See meiosis. packing ratio the ratio of DNA length to the unit length of the fiber containing it. paclitaxel a drug extracted from the bark of the Pacific yew and sold under the tradename Taxol by Bristol-Meyers Squibb. Paclitaxel binds to the tu- bulin of spindles and prevents them from breaking down after the chromosomes have separated. If spindles remain in place, the cell cannot complete cytokinesis.

Taxol is the most broadly effective and commercially successful anticancer drug so far intro- duced. It is used primarily for treatment of cancers of the breast, ovary, and the most common type of lung cancer. See spindle poison. PACs P1 artificial chromosomes (q.v.). paedogenesis a type of precocious sexual matu- rity occurring in the larval stage of some animals. The eggs of paedogenetic females develop partheno- genetically. paedomorphosis an evolutionary phenomenon in which adult descendants resemble the youthful stages of their ancestors; the opposite of “recapitula- tion,” in which the early stages of descendants resemble the adult stages of their ancestors. Paedo- morphosis may be produced either by the accelera- tion of sexual development (progenesis) or by re- tarded somatic development. See heterochrony. Paeonia californica the California peony, a spe- cies with naturally occurring translocation com- plexes.

PAGE polyacrylamide gel electrophoresis. See elec- trophoresis, polyacrylamide gel. pair bonding an intimate and long-lasting associa- tion between male and female animals of the same species, generally facilitating the cooperative rearing of their offspring. paired a recessive lethal mutation on the left arm of chromosome 2 of Drosophila melanogaster. The prd gene belongs to the pair rule class of zygotic seg- mentation mutants (q.v.).

It encodes a protein that contains DNA-binding segments. One, which is composed of amino acids 27 through 154, has been designated the “paired domain.” A homeodomain comprises amino acids 213 through 272. Near the C terminus of the PRD protein is a region rich in histi- dines and prolines. This “PRD repeat” has been found in other Drosophila genes expressed in early embryogenesis. Genes that play an important role in embryogenesis of mice and men encode proteins with paired domains, and therefore these genes have been placed in the paired box (Pax) family. See Ap- pendix C, 1986, Noll et al.; Aniridia, developmental control genes, DNA-binding motifs, eyeless, gene net- working, homeobox, Pax genes, Small eye. pairing synapsis. pairing segments the segments of the X and Y chromosomes which synapse and cross over. The re- maining segments, which do not synapse, are called the differential segments.

pair rule genes See zygotic segmentation mutants. Palearctic designating one of the six biogeographic realms (q.v.) of the globe, including Eurasia except Iran, Afghanistan, the Himalayas, and the Nan-ling Range in China, Africa north of the Sahara, Iceland, Spitzbergen, and the islands north of Siberia. Paleocene the most ancient of the Tertiary ep- ochs. The placental mammals expanded at the ex- pense of the marsupials. Early primates and grasses made their first appearance.

The drifting of conti- nents continued. See geological time divisions. Paleogene a subdivision of the Tertiary period, in- corporating the Oligocene, Eocene, and Paleocene epochs. See geologic time divisions. Paleolithic that phase of human history prior to the cultivation of plants during which tools were manufactured, food was obtained by hunting, fish- ing, or collecting wild nuts and fruits. The Paleo- lithic culture lasted from about 500,000 years ago up to the beginning of the Neolithic stage about 10,000 years ago. paleontology the study of extinct forms of life through their fossils, as opposed to neontology (q.v.). paleospecies the successive species in a phyletic lineage that are given ancestor and descendant status according to the geological strata in which they ap- pear. See anagenesis.

Paleozoic the earliest era of the Phanerozoic eon. Invertebrates flourished during this 320-million year interval. See geologic time divisions. Paley’s watch an argument developed by William Paley (1743-1805) for the existence of God based upon the commonsense notion that a watch is too complicated to have originated by accident; it pre- sents its own evidence of having been purposely de- signed. This argument is commonly applied to living organisms by creationists. palindrome a sequence of deoxyribonucleotide base pairs that reads the same (5′ to 3′) on comple- mentary strands; tandem inverted repeats; example:


Palindromes serve as recognition sites for restriction endonucleases, RNA polymerases, and other en- zymes. In the human Y chromosome (q.v.) some palindromes are as long as 3 mb (q.v.). Gene conver- sions (q.v.) within these palindromes overwrite mu- tations that would lead to male sterility. See cruci- form structure. palynology the study of both living and fossil spores, pollen grains, and other microscopic propa- gules.

Pan the genus containing P. troglodytes, the com- mon chimpanzee, and P. paniscus, the bonobo or pygmy chimpanzee. Pan troglodytes is the living pri- mate genetically closest to man. Pan and Homo di- verged from a common ancestor 5-6 million years ago. The haploid chromosome number for P. troglo- dytes is 24, and about 40 genes have been distributed among 19 linkage groups. See Appendix C, 1967, Sarich and Wilson; 1975, King and Wilson; 1984, Sibley and Alquist; 1988, Kazazian et al.; 2003, An- zai et al.; Appendix E; sequence similarity estimates. Panagrellus redivivus a free-living nematode whose developmental genetics is under study, primarily for comparison with Caenorhabditis elegans (q.v.). It dif- fers from Caenorhabditis in having XX females and XO males. Its cell lineage (q.v.) is known in part.

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