Paralogs

31 Mar

Paralogs

pancreozymin a hormone secreted by the duode- num that causes secretion of pancreatic enzymes. pandemic designating a disease simultaneously ep- idemic in human populations in many parts of the world. panethnic referring to a hereditary disease that is found in a variety of ethnic groups. pangenesis a defunct theory of development, pop- ular in Darwin’s time, proposing that small particles (pangenes) from various parts of the body distill into the gametes, resulting in a blending of parental char- acteristics in their offspring. panhypopituitarism See pituitary dwarfism. panicle See raceme. panmictic index (P) a measure of the relative het- erozygosity. 1−P=F, Wright’s inbreeding coeffi- cient (q.v.). panmictic unit a local population in which mating is completely random.

panmixis random mating, as contrasted with as- sortative mating (q.v.). panoistic ovary See insect ovary types. pantothenic acid a water-soluble vitamin that functions as a subunit of coenzyme A (q.v.). papain a proteolytic enzyme isolated from the la- tex of the papaya plant. paper chromatography See chromatography. Papilio glaucus the swallowtail butterfly, a spe- cies extensively studied in terms of isolating mecha- nisms (q.v.). papillary pattern the pattern of dermal ridges on the fingertips and palms. papilloma a benign cutaneous neoplasm; a wart. See human papilloma virus, Shope papilloma virus. papovavirus a group of animal DNA viruses (in- cluding SV4O and polyoma) responsible for papillo- mas of the rabbit, dog, cattle, horse, and human. parabiotic twins artificial “Siamese twins” pro- duced by joining two animals surgically. Since their blood circulations will eventually anastomose, one can study the transmission of humoral agents from one “twin” to the other.

paracentric inversion an inversion (q.v.) that does not include the centromere. Paracentrotus lividus a common sea urchin ex- tensively used in studies of molecular developmental genetics. See echinoderm. paracrine See autocrine. paracrystalline aggregate a regular linear arrange- ment of stacked molecules. paradigm (pronounced “paradime”) a term with a variety of meanings in the scientific literature. In its weakest sense, it is used as a synonym for model, hypothesis, or theory. It is used most commonly to refer to a known example or incident that serves as a model or provides a pattern for a more general phenomenon.

In a still more restricted sense, para- digm may refer to a ruling model that has replaced all others. Darwin’s theory of evolution by natural selection is an example of such a paradigm. As time passes, the matching of new discoveries with the model may lead to a revision of the paradigm. An example of this would be the transformation of the one gene-one enzyme to the one gene-one polypep- tide paradigm. paraffin section a section of tissue cut by a micro- tome after embedding in a paraffin wax; the classical method of preparing tissues for microscopical study. See Appendix C, 1860, Klebs.

paragenetic referring to a chromosomal change that influences the expression of a gene rather than its structure. See position effect, Lyonization. parallel evolution the occurrence of the same or a similar trend independently evolved in two or more lineages; the lineages are usually, although not nec- essarily, related to one another. paralogs two or more different genes in the same species which are so similar in their nucleotide se- quences that they are assumed to have originated following the duplication of a single ancestral gene. The human alpha and delta hemoglobin chain loci are examples of paralogous genes. The adjective par-

Paramecium

alogous is used when referring to nucleotide se- quence comparisons of repetitive DNAs from a sin- gle species. For example, the rRNA genes from different chromosomes of species A might be homo- geneous in sequence structure and those from spe- cies B might also be homogeneous. These would be paralogous comparisons. However, if rDNAs from species A and B were compared, the data might be more heterogeneous. This would be an orthologous comparison. See orthologs, unequal crossing over. Paramecium a common genus of ciliate protozoa found in stagnant ponds. Common species are P. aurelia, P. caudatum, and P.

bursaria. These are fa- vorite species for the study of nuclear-cytoplasmic interactions. See Appendix C, 1976, Dippell; con- tractile vacuole, universal code theory. Paramecium aurelia a cigar-shaped, heavily cili- ated protoctist, 100-150 micrometers long, living in still or running fresh waters. Paramecium aurelia consists of a group of 14 syngens. Each syngen is ge- netically isolated from every other syngen and is also biochemically unique. However, all syngens are so similar morphologically that they have not been given individual species names. Each syngen has two mating types. Mating types were first discovered in syngen 1.

See Appendix A, Protoctista, Ciliophora; Appendix C, 1937, Sonneborn; 1971, Kung; conju- gation, killer paramecia. parameter the value of some quantitative charac- teristic in an entire population. For example, the mean height of all males 20 years of age or older in a pygmy tribe. Compare with statistic. parametric statistics See statistics. paramutation a phenomenon discovered in corn where one allele influences the expression of an- other allele at the same locus when the two are com- bined in a heterozygote. The first allele is referred to as “paramutagenic,” the second as “paramutable.”

The paramutable allele behaves like an unstable hy- pomorph when the paramutagenic allele is present. paranemic spiral a spiral made up of two parallel threads coiled in opposite directions. The threads can be easily separated without uncoiling. See plec- tonemic spiral, relational coiling. parapatric referring to populations or species that occupy adjacent areas with a narrow zone of overlap within which hybridization commonly occurs. parapatric speciation a mode of gradual specia- tion in which new species arise from populations that maintain genetic contact during the entire pro- cess by a narrow zone of overlap.

Gene flow be- tween the populations is prevented by the rapid evo- lution of pre-mating isolation mechanisms. Also called semigeographic speciation. Compare with allo- patric speciation, alloparapatric speciation, peripatric speciation. paraphyletic 1. in classification, an incomplete clade, i.e., one from which one or more members of a halophyletic group have been omitted. A paraphy- letic group is recognized by the absence of the ho- mologs that define the excluded clades. For exam- ple, group AB in the illustration on p. 323 is paraphyletic because it is defined by the absence of feature 3 (features 1 and 2 are present in group CD as well). 2. in evolution, a monophyletic group that does not include all the groups descended from a single common ancestor. For example, here the AB group is paraphyletic, but group CD is excluded since it is not a direct descendant from common an- cestor 1.

Parascaris equorum a nematode (commonly called the horse thread-worm) studied by early cy- tologists because it exhibited chromatin diminution (q.v.). See Appendix C, 1887, Boveri. parasexuality any process that forms an offspring cell from more than a single parent, bypassing stan- dard meiosis and fertilization. In fungi, for example, diploid nuclei arise from rare fusions of two geneti- cally unlike nuclei in heterokaryons. Somatic cross- ing over occurs, and eventually haploid nuclei show- ing new combinations of genes are formed from the diploids (see Appendix C, 1952, Pontecorvo and Roper).

In viruses, parasexual recombination can oc- cur if genetically different mutant strains multiply in a host cell after it has been infected by viruses of both types (see Visconti-Delbruc¨k hypothesis). In bacteria, there are three phenomena that can lead to parasexual recombination: conjugation, transduc- tion, and transformation (all of which see). Also see sexduction, transfection. parasitemia the presence of parasites at various developmental stages in circulating blood cells of the host. See glucose-6-phosphate dehydrogenase defi- ciency, malaria, merozoite.

Paranemic spiral

Parental imprinting

Paraphyletic 2

parasitic DNA See selfish DNA. parasite theory of sex the proposal by W. D. Hamilton that sexual reproduction has evolved to provide a mechanism to generate the resistance of host species to rapidly multiplying parasites. The ge- netic recombination which accompanies meiosis (q.v.) rapidly produces new combinations of resis- tance factors in the host, and these overcome the susceptibility factors which arise more slowly in the parasites by mutation.

parasitism a symbiotic association that benefits one member (the parasite) but is harmful to the other (the host). parathyroid hormone a hormone that controls calcium and phosphorus balance; it is synthesized by the cells of the parathyroid gland. paratope the site within an immunoglobulin Fab that specifically interacts with an antigenic determi- nant (epitope). Parazoa a subdivision of the animal kingdom con- taining organisms, like sponges, that lack tissues or- ganized into organs, and have an indeterminate shape. See Appendix A. parenchyma 1. plant tissues composed of thin- walled cells that fit loosely together, leaving inter- cellular spaces. 2. a reticulum of cells between the organs of an animal. 3. the cells performing the prin- cipal function of an organ.

parental ditype See tetrad segregation types. parental imprinting the phenomenon whereby the degree to which a gene expresses itself depends upon the parent transmitting it. Huntington disease (q.v.) is an example. Individuals who receive this dominant gene show symptoms during adolescence if it is inherited from their father, but symptoms be- gin during middle age when the gene comes from their mother. The phenomenon of parental imprint- ing may result from differing patterns of DNA methylation (q.v.) which occur during gametogene- sis in the two sexes.

Thus, in oocytes the controlling elements of specific genes might be methylated, but demethylated in spermatocytes. Following fertiliza- tion, the cells of embryos would contain an inactive maternal and an active paternal allele. For such a system to maintain itself generation after generation, it would have to be reversible. Thus, when the off- spring enters gametogenesis, it must demethylate all methylated alleles if it is a male and methylate all demethylated alleles if it is a female. Parental im- printing also occurs in flowering plants. The behav- ior of the R gene in maize provides an example.

The gene controls the color of pigment grains in the aleu- rone (q.v.) of the kernel (q.v.). In the cross rr × RR, the F1 kernels are solid red when RR is the female parent but mottled if RR is the male parent. Extra paternal copies of R do not substitute for maternal R genes. So the maternal copy is preferentially ex- pressed. See Appendix A, 1970, Kermicle; double fer- tilization, H19, Prader-Willi syndrome (PWS), R genes of maize.

Parent-offspring conflict theory
parent-offspring conflict theory the proposal by David Haig that competition between the sexes oc- curred during the evolution of placental mammals. This resulted in a compromise between the robust- ness of the offspring during their period of uterine growth and the health of the mother. In the sperm, genes that increase the cost of the offspring are switched on. Such genes are active in the placenta and cause the embryo to grow rapidly and use up the mother’s resources. In the egg, genes that de- crease the cost of the offspring to the mother are activated. Such genes keep the unlimited growth of the embryo in check, so the mother survives the pregnancy. The genes occur in antagonistic pairs, and parental imprinting (q.v.) controls their func- tioning. See Appendix C, 1992, Haig.

parity the fact of having borne children. A woman of parity 0 has borne no live children although she may have been pregnant one or more times. A woman of parity 1 has given birth only once. How- ever, the number of children produced at this birth may have exceeded one. Parkinsonism a disease first described in 1817 as “shaking palsy” by the London physician James Par- kinson. The disease arises from the death of neurons that synthesize DOPAMINE (q.v.), and these cells reside in a portion of the brain called the substantia nigra. The most common hereditary form of Parkin- sonism is called early-onset, autosomal recessive Par- kinsonism.

It is caused by mutations in a gene now called parkin which resides at 6q25.2-q27. The gene product (PARKIN) is a protein of 465 amino acids which functions as a ubiquitin-conjugating enzyme. This observation suggests that Parkinsonism results from a defect in the system that normally removes potentially toxic proteins that accumulate in dopa- minergic neurons. See proteasome, ubiquitin. paroral cone a protuberance in the oral region of a conjugating ciliate that juts into the body of the partner. The haploid nucleus residing in the paroral cone survives and all others degenerate. See conjuga- tion. pars amorpha See nucleolus. parsimony principle the principle that the sim- plest sufficient hypothesis is to be preferred, even if others are possible. Also called Occam’s razor.

pars intercerebralis that medial region in the in- sect forebrain containing neurosecretory cells. Parthenium argentatum the guayule, a desert plant, reproducing sexually or asexually depending upon its genotype and studied by geneticists accord- ingly. parthenocarpy the natural or artificially induced formation of fruit without seeds because of either (1) lack of pollination, (2) lack of fertilization, or (3) death of the embryo at an early stage of develop- ment. See bananas. parthenogenesis the development of an individ- ual from an egg without fertilization. In most anisog- amous eukaryotes, parthenogenesis is prevented by the inactivation of oocyte centrioles prior to fertil- ization. The centriole, which initiates cytokinesis, is brought in by the fertilizing sperm. See Appendix C, 1845, Dzierzon; arrhenotoky, artificial parthenogen- esis, gynogenesis, heterogony, paedogenesis, sexu- parous, thelytoky. parthenote an organism produced by partheno- genesis (q.v.) and therefore having only genes of ma- ternal origin. partial denaturation an incomplete unwinding of the DNA double helix; GC-rich regions are more resistant to thermal disruption because three hydro- gen bonds form between G and C, whereas only two form between A and T.

See deoxyribonucleic acid. partial diploid See merozygote. partial dominance See incomplete dominance. particle-mediated gene transfer a technique by which selected DNA molecules are quantitatively coated upon gold or tungsten spheres 1-3 micro- meters in diameter and shot into plant or animal tis- sues with sufficient force to penetrate multiple lay- ers of cells. The motive force to accelerate the particles comes from a high-pressure burst of helium gas stored in a tank connected to the gene gun. The targeted animal tissues are generally somatic (skin, liver, and pancreas), and a large number of reporter genes and genes with therapeutic potentials have been expressed in targeted cells.

Gene guns have been used even more effectively in generating trans- genic plants of economic importance. particulate inheritance the Mendelian theory that genetic information is transmitted from one genera- tion to another in the form of discrete units, so that the biological inheritance of offspring is not a solu- tion in which the parental information is blended. P1 artificial chromosomes (PACs) DNA cloning vectors containing regions of the P1 phage (q.v.) ge- nome (q.v.) and capable of accepting large DNA in- serts (i.e., up to 100 kilobases long). In this system, vector DNA and DNA fragments to be cloned are ligated and packaged in vitro into phage particles that can infect Escherichia coli. Once inside the bac-

Pax genes

terium, the packaged DNA is circularized and main- tained as a plasmid (q.v.). A P1 plasmid replicon (q.v.) maintains the DNA at one copy per cell, and a P1 lytic replicon induces amplification of plasmid DNA under appropriate experimental conditions, allowing the isolation of large amounts of DNA for analysis. PACs are useful for cloning large genes, chromosome walking (q.v.), physical mapping, and shotgun sequencing (q.v.) of complex genomes. Compare with bacterial artificial chromosomes (BAC)s, yeast artificial chromosomes (YACs). See bac- teriophage packaging, DNA vector, genomic library, kilobase, physical map, plasmid cloning vector. parturition the act of giving birth to young. Pascal’s pyramid See binomial distribution. PAS procedure periodic acid Schiff procedure (q.v.).

passage number the number of times a culture has been subcultured. passenger in recombinant DNA research, a DNA segment of interest that will be spliced into a DNA vehicle for subsequent cloning. passive equilibrium an unstable equilibrium re- sulting from selective neutrality of alleles at a genetic locus, as occurs in Hardy-Weinberg equilibrium; also called neutral equilibrium. passive immunity the immunity against a given disease produced by injection into a host of serum containing antibodies formed by a donor organism that possesses active immunity to the disease. See ac- tive immunity. Patau syndrome a well-defined set of congenital defects in humans caused by the presence of an ex- tra chromosome 13. Also called trisomy 13 syn- drome or D1 trisomy syndrome.

The median survival time is 3 days and the incidence is 1/10,000 live births. The condition was first described in 1960 by Klaus Patau and four colleagues. See human mitotic chromosomes. patentability of genetically modified organisms the ability to obtain the exclusive legal rights to cre- ate genetically modified organisms. The United States Supreme Court has ruled that a microorgan- ism which was genetically engineered to consume oil slicks can be patented. See Appendix C, 1980, Chak- rabarty. patent period the interval during an infection when the causative agent can be detected. Compare with latent period, prepatent period. paternal effect gene a paternally expressed gene required for normal fertilization and early embry- onic development.

Males homozygous for recessive alleles of such genes produce sperm that cannot sup- port normal development in the embryo, even if the egg is from a female that is homozygous for the wild-type allele, while the reciprocal cross (i.e., wild-type male × homozygous recessive female) pro- duces viable embryos. The genotype of the father thus affects the phenotype of his offsprings. Com- pare with maternal effect gene, zygotic gene. paternal inheritance hereditary traits that are gov- erned by genes or self-reproducing organelles solely contributed to the offspring by the male parent.

For example, in male and female animal embryos the centrioles are derived from a progenitor centriole carried by the fertilizing sperm. Y-linked genes func- tioning in sex determination and spermiogenesis are inherited by males from their fathers. Contrast with maternal inheritance. See Y chromosome. paternal-X inactivation the method of dosage compensation found in marsupials where the pater- nal-X chromosome is inactivated in the somatic cells of females. See random-X inactivation. path coefficient analysis a method invented by Sewall Wright for analyzing quantitatively the trans- mission of genes in regular and irregular breeding systems. pathogenic producing disease or toxic symptoms. pathovar a pathological variant of a bacterial spe- cies; symbolized pv.

For example, the cause of citrus canker is Xanthomonas campestris pv. citri. patroclinous designating an offspring that resem- bles the male more closely than the female parent. The sons of an attached-X female Drosophila are pa- troclinous in terms of their sex-linked genes. See matrocliny. pattern specification the genetically controlled process which specifies the transformation of an ap- parently homogeneous population of cells into sub- populations of cells, each with a specific morphology and temporal behavior. See cell lineage mutations, compartmentalization, floral identity mutations, ge- netic networking, Hox genes, Positional Information Hypotheses, selector genes, zygotic segmentation mutations. Pax genes those genes that contain a Paired box, hence the abbreviation Pax. Pax genes encode a highly conserved family of transcription factors that play key roles in controlling the fates of cells, the

Pax-6 genes

development of patterns, and organogenesis. In Dro- sophila and various species of mammals, Pax genes specify the differentiation of the anterior brain, the cochlea, and the retina. However, Pax genes are also expressed in Trichoplax adhaerans (q.v.), a species which lacks both nervous tissues or sensory organs. See paired, Pax-6 genes. Pax-6 genes a subset of Pax genes (q.v.) that en- code evolutionarily conserved transcription factors essential for eye development in insect and mamma- lian species. In Drosophila, the Pax-6 genes (q.v.) are eyeless (ey) and twin of eyeless (toy); in humans and rodents, the Pax-6 genes are Aniridia (q.v.) and Small eye (q.v.), respectively. P22 bacteriophage See P22 phage. P blood group a human blood group identified by a glycolipid antigen specified by the dominant gene P on the long arm of chromosome 22. The P antigen binds to the fimbriae of certain strains of E. coli.

Therefore, individuals homozygous for null P alleles are less susceptible to infection than P-positive indi- viduals. See fimbria. pBR322 a plasmid cloning vector that grows under relaxed control in E. coli. It contains ampicillin- and tetracycline-resistance genes and several convenient restriction endonuclease recognition sites. See Ap- pendix C, 1979, Sutcliffe. PCR polymerase chain reaction (q.v.).

PDGF platelet-derived growth factor (q.v.). pea See Pisum sativum. Peckhammian mimicry See mimicry. Pecten irradians See Pelecypoda. pectic acid a polymer made up of galacturonic acid subunits. pectin a polysaccharide material within the cell wall and middle lamella. Pectin consists of pectic acid, many of whose COOH groups have been methylated. pedigree a diagram setting forth the ancestral his- tory or genealogical register. Symbols commonly used in such diagrams are illustrated on page 327 in the sample pedigree. Females are symbolized by cir- cles and males by squares. Individuals showing the trait are drawn as solid figures. Offspring are pre- sented beneath the parental symbols in order of birth from left to right.

The arrow points to the pro- positus. The sex of individual II-3 is unknown. II-6 died at an early age and consequently her phenotype relative to the trait in question was unknown. II-7 and II-8 were dizygotic twins, whereas III-1 and III- 2 were identical twins. Other symbols commonly encountered are also shown here. See first-degree relative, second-degree relative. pedigree selection artificial selection of an indi- vidual to participate in mating based upon the mer- its of its parents or more distant ancestors. pedogenesis See paedogenesis. pelargonidin See anthocyanins. Pelargonium zonale the geranium.

Classical stud- ies on the non-Mendelian inheritance of chloroplast mutants were performed on this species. See Appen- dix C, 1909, Correns and Bauer. Pelecypoda the class containing the bivalve mol- luscs. The cytogenetics and quantitative genetics of certain species have been studied because of their economic importance. These include the American oyster (Crassostrea virginica), the clam (Mercenaria mercenaria), the mussel (Mytilus edulis), and the scallop (Pecten jacobeus). P elements transposable elements in Drosophila that are responsible for one type of hybrid dysgene-

Pectic acid

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