A generic algorithm for finding restriction sites within DNA sequences

This paper describes a generic algorithm for finding restrictionsites within DNA sequences. The ‘genericity’ ofthe algorithm is made possible through the use of set theory.Basic elements of DNA sequences, i.e. nucleotides (bases), arerepresented in sets, and DNA sequences, whether specific, ambiguousor even protein-coding, are represented as sequences of thosesets. The set intersection operation demonstrates its abilityto perform pattern-matching correctly on various DNA sequences.The performance analysis showed that the degree of complexityof the pattern matching is reduced from exponential to linear.An example is given to show the actual and potential restrictionsites, derived by the generic algorithm, in the DNA sequencetemplate coding for a synthetic calmodulin. Received on October 2, 1990; accepted on December 18, 1990     

Mammalian carbamyl phosphate synthetase (CPS). DNA sequence and evolution of the CPS domain of the Syrian hamster multifunctional protein CAD

Glutamine-dependent carbamoyl-phosphate synthetase (EC 6.3.5.5) catalyzes the first step in de novo pyrimidine biosynthesis. The mammalian enzyme is part of a 240-kDa multifunctional protein which also has the second (aspartate carbamoyltransferase, EC 2.1.3.2), and third (dihydroorotase, EC 3.5.2.3) activities of the pathway. Shigesada et al. (Shigesada, K., Stark, G.R., Maley, J.A., and Davidson, J.N. (1985) Mol. Cell Biol. 175, 1-7) produced a truncated cDNA clone from a Syrian hamster cell line that contained most of the coding region for this protein. We have completed sequencing this clone, known as pCAD142. The cDNA insert contained all of the coding region for the glutaminase (GLN) and carbamyl phosphate synthetase (CPS) domains but lacked a short amino-terminal segment. By comparing the primary structure of the mammalian chimera to monofunctional proteins we have identified the borders of the functional domains. The GLN domain is 21 kDa, close to the size of the functionally similar polypeptide products of the Escherichia coli pabA and hisH genes. The domain has the three regions of homology common to trpG-type glutamine amidotransferases, as well as a fourth region specific to the carbamyl phosphate synthetases. The CPSase domain is similar to other reported CPSases in size (120 kDa), primary structure (37-67% amino acid identity), and homology between its amino and carboxyl halves. Analysis of the nucleotide and amino acid sequence identities among the various carbamyl phosphate synthetases suggests that the gene fusion which joined the GLN and CPS domains was an early event in the evolution of eukaryotic organisms and that the Saccharomyces cerevisiae enzyme consisting of separate subunits arose by defusion from an ancestral multifunctional protein.     

Endurance training amplifies the pulsatile release of growth hormone: effects of training intensity.

The effects of intensity of run training on the pulsatile release of growth hormone (GH) were investigated in 21 eumenorrheic untrained women. The O2 consumption (VO2) at the lactate threshold (LT); fixed blood lactate concentrations (FBLC) of 2.0, 2.5, and 4.0 mM; peak VO2; maximal VO2; body composition; and pulsatile release of GH were measured. Subjects in both the at-lactate threshold (/LT, n = 9) and above-lactate threshold (greater than LT, n = 7) training groups increased VO2 at LT and FBLC of 2.0, 2.5, and 4.0 mM and VO2max after 1 yr of run training. However, the increase observed in the greater than LT group was greater than that in the /LT group (P less than 0.05). No change was observed for the control group (n = 5). No among- or within-group differences were observed for body weight, although trends for reductions in percent body fat (P less than 0.06) and fat weight (P less than 0.15) were observed in the greater than LT group, and both training groups significantly increased fat-free weight (P less than 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)     

The semidian rhythm in flowering response of Pharbitis nil in relation to dark period time measurement and to a circadian rhythm

When seedlings of Pharbitis nil Choisy, cv. Violet, are exposed to a single inductive dark period at 27°C, brief interruptions with red light (R) can be promotive after 2–3 h of darkness but increasingly inhibitory to flowering up to the 8–9th h of darkness. This rhythmic response to R interruptions can be advanced in phase by > 1 h when the preceding light period is interrupted with far-red (FR) 2 h before darkness (FR -2 h) or with FR – 15 h, whereas FR –8 h or FR–22 h retard the rhythm. These shifts in the R interruption rhythm are paralleled by equal shifts in the length of the dark period required for flowering. Brief FR interruptions of darkness displayed a similar rhythm which was also advanced by FR –2 h and retarded by FR –8 h. We conclude therefore that the semidian rhythm in the light, which we have previously described, continues through at least the first 12 h of darkness, is manifested in the R interruption rhythm, and determines the critical night length. A circadian rhythm with a marked effect on flowering was also identified, but several lines of evidence suggest that the circadian and semidian rhythms have independent additive effects on flowering and do not appear to show phase interaction.     

The Sex Ratio of Heterodera glycines at Low Population Densities

The sex ratio of the Arkansas 1 isolate of Heterodera glycines was determined in experiments in which ''Lee'' soybean was inoculated with either one or two larvae. A 3:1 male to female sex ratio was established for this isolate under the test conditions used. No influence of one nematode on the penetration and development to adult of another nematode in the same root was detected in double larval inoculations.     

Spider mites of sugarcane in Australia: a review of grass-feeding Oligonychus Berlese (Acari: Prostigmata: Tetranychidae)

Abstract In many areas of the world, spider mites are significant pests of sugarcane. Australia is currently fortunate in lacking the most destructive species, and usually suffers only sporadic damage. Herein, we provide a key to the genera of spider mites associated with sugarcane, review the most significant genus, Oligonychus Berlese, and provide a key to the species of grass-feeding Oligonychus in the Australasian region. The species O. araneum Davis, O. digitatus Davis, O. grypus Baker and Pritchard, O. orthius Rimando, and O. oryzae (Hirst) are redescribed, while the Australian O. zanclopes sp. n. Beard and Walter from sugarcane and rice, O. turbelli sp. n. Beard and Walter, O. ephamnus sp. n. Beard and Walter and O. festucolus sp. n. Beard and Walter from other grasses, are newly described. Previous records of O. grypus in Australia appear to be misidentifications of what is described here as the new species O. zanclopes .     

Explaining density-dependent regulation in earthworm populations using life-history analysis

At present there is little knowledge about how density regulates population growth rate and to what extent this is determined by life-history patterns. We compared density dependent population consequences in the Nicholsonian sense based on experimental observations and life-history modeling for the earthworms Lumbricus terrestris and Eisenia fetida . Both species differ in their life-histories, L. terrestris being a relatively long-lived species with slow reproduction and occurring at low densities compared to E. fetida which has a more opportunistic strategy with a high reproductive output. E. fetida is able to colonise new habitats rapidly and may occur at relatively high population densities. Density dependency of population growth rate was estimated by incorporating density dependent effects on reproduction and growth using a modified Euler equation. The results point out that E. fetida was not as strongly impacted by density as compared to L. terrestris . Population growth rate in E. fetida was hardly affected at low and moderate density, being reduced only at high level, this compares to L. terrestris where even relatively small density effects resulted in a strong negative effect on population growth rate. Our findings indicate that density-dependent regulation in earthworms can be quantified using life-history analysis. The outcomes are in agreement with empirical field observations for populations (i.e. L. terrestris occurs ar low density, E. fetida at high density). Consideration of the potential importance of Nicholsonian density dependence for field populations of these two species in light of their known biology however produces counterintuitive conclusions. In E. fetida , although density tolerant, rapid population growth may mean this species may be subject to density dependeny regulation. In L. terrestris , although density sensitive, complex behavioural ecology (surface activity, territoriality) may limit of feedback influence on population size.     

Latitudinal variation in population structure of wintering Pacific Black Brant

ABSTRACT.   Latitudinal variation in population structure during the winter has been reported in many migratory birds, but has been documented in few species of waterfowl. Variation in environmental and social conditions at wintering sites can potentially influence the population dynamics of differential migrants. We examined latitudinal variation in sex and age classes of wintering Pacific Black Brant ( Branta bernicla nigricans ). Brant are distributed along a wide latitudinal gradient from Alaska to Mexico during the winter. Accordingly, migration distances for brant using different wintering locations are highly variable and winter settlement patterns are likely associated with a spatially variable food resource. We used resightings of brant banded in southwestern Alaska to examine sex and age ratios of birds wintering at Boundary Bay in British Columbia, and at San Quintin Bay, Ojo de Liebre Lagoon, and San Ignacio Lagoon in Baja California from 1998 to 2000. Sex ratios were similar among wintering locations for adults and were consistent with the mating strategy of geese. The distribution of juveniles varied among wintering areas, with greater proportions of juveniles observed at northern (San Quintin Bay and Ojo de Liebre Lagoon) than at southern (San Ignacio Lagoon) locations in Baja California. We suggest that age-related variation in the winter distribution of Pacific Black Brant is mediated by variation in productivity among individuals at different wintering locations and by social interactions among wintering family groups.     

Hybrid formation within the genus Leishmania?

Leishmanial organisms isolated from a desert rodent (Psammomys obesus) and a feral dog (Canis familiaris) in the Eastern Province of Saudi Arabia were isoenzymically distinct from Leishmania major and L. arabica, organisms usually associated with human and wild animal cutaneous leishmaniasis in this area. Further examination of isoenzyme banding patterns of cloned populations of these organisms, together with karyotyping using orthogonal field alternation gel electrophoresis and the use of highly specific kinetoplast DNA probes, has produced evidence suggesting that these organisms isolated from the dog and the rodent are hybrids of L. major and L. arabica.