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     

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.     

Chondroitin sulphate at the endothelial lumen of pig aorta: Assay by radiolabelling and by X-ray microanalysis

Trypsin-releasable glycosaminoglycans from the luminal surface of intact pig aorta were measured following metabolic labelling with³⁵S]sulphate. Chondroitin sulphate was found to be present at a surface density equal to that already established for heparan sulphate (5×10¹¹ chains per cm²). This result was confirmed by X-ray microanalysis of the luminal sulphur content before and after treatment with specific glycosaminoglycan-degrading enzymes. This result implies that approximately half of the luminal surface is occupied by sulphated glycosaminoglycans.     

Evaluation of active versus passive uptake of metabolites by Rhizobium japonicum bacteroids.

Rhizobium japonicum bacteroids were isolated anaerobically from soybean [Glycine max (L.) Merr] nodules. The bacteroids, which were capable of acetylene reduction and respiration, were used to study the uptake of metabolites by a method which permits correction for nonspecific adsorption of metabolites and estimation of total cell volume. These determinations permit active uptake to be assessed from metabolite accumulation against a concentration gradient. Succinate, malate, alpha-ketoglutarate, and glutamate were absorbed via an active mechanism. Plots of 1/V versus 1/[S] for succinate and malate indicated the presence of two uptake components: a saturable and presumably active or carrier-mediated component and a nonsaturable and presumably passive component. The uptake of glucose, malonate, D-pinitol, myo-inositol, and glucose 6-phosphate was slow and not active.     

Natural immunity to murine gonococcal bacteremia: roles of complement, leucocytes, and sex

The roles of the serum bactericidal system, inflammatory cells, and sex in resisting gonococcal infection were studied in a murine model of gonococcal bacteremia. The role of serum killing in defense was investigated with complement component 5 deficient (C5-deficient) (B1O.D2/OSN) and normal (B1O.D2/NSN) mice. No significant differences were found between LD50's with either murine serum-sensitive or serum-resistant gonococci in those two mouse strains. However, in vitro experiments revealed a heat-stable factor in mouse serum which killed gonococci. Thus it appeared that the C5-deficient mouse is not a good model for the study of the role of C-mediated killing in resistance to gonococcal infection. Mice with Chediak-Higashi disease were used to study the role of phagocytes and natural killer cells. The difference in LD50's between affected mice (C57B1/6J beige J) and controls (C57B1/6J) was significant. The CBA/N mice, which have a B-cell maturation defect, were no more resistant to infection than control mice, which was taken as further evidence that B cells were less important than other leucocytes in innate immunity to gonococcal infection. Finally, male mice were significantly more resistant than female mice to gonococcal bacteremia. Thus, in this study the two most important determinants of resistance to gonococcal infection were inflammatory cells and sex.     

The relationship between sister-chromatid exchange and perturbations in DNA replication in mutant EM9 and normal CHO cells

The majority of the high (12-fold elevated) baseline sister-chromatid exchanges (SCEs) that occur in the CHO mutant line EM9 appear to be a consequence of incorporated BrdUrd, and they arise during replication of DNA containing BrdUrd in a template strand. In normal CHO cells the alkaline elution patterns of DNA newly replicated on a BrdUrd-containing template are significantly altered compared with those seen during the replication on an unsubstituted template. The nascent DNA synthesized on such an altered template is delayed in reaching mature size, possibly because replication forks are temporarily blocked at sites occurring randomly along the template. Transient blockage of replication forks may be a prerequisite for SCE. The delay in replication on BrdUrd-substituted templates was greater in EM9 cells than in parental AA8 cells and was also greater in AA8 cells treated with benzamide, an inhibitor of poly(ADPR) polymerase, than in untreated AA8 cells. Under these conditions, treatment with benzamide also produced a 7-fold increase in SCEs in AA8. An EM9-derived revertant line that has a low baseline SCE frequency showed less delay in replication on BrdUrd-substituted templates than did EM9. However, under conditions where the template strand contained CldUrd, which was shown to produce 4-fold more SCEs than BrdUrd in AA8 cells, the replication delay in AA8 was not any greater in the CldUrd-substituted cells. Thus, other factors besides the delay appear to be involved in the production of SCEs by the template lesions resulting from incorporation of the halogen-substituted pyrimidine molecules.     

Metabolism of C-labeled photosynthate and distribution of enzymes of glucose metabolism in soybean nodules

The metabolism of translocated photosynthate by soybean (Glycine max L. Merr.) nodules was investigated by ¹⁴CO₂-labeling studies and analysis of nodule enzymes. Plants were exposed to ¹⁴CO₂ for 30 minutes, followed by ¹²CO₂ for up to 5 hours. The largest amount of radioactivity in nodules was recovered in neutral sugars at all sampling times. The organic acid fraction of the cytosol was labeled rapidly. Although cyclitols and malonate were found in high concentrations in the nodules, they accumulated less than 10% of the radioactivity in the neutral and acidic fractions, respectively. Phosphate esters were found to contain very low levels of total label, which prohibited analysis of the radioactivity in individual compounds. The whole nodule-labeling patterns suggested the utilization of photosynthate for the generation of organic acids (principally malate) and amino acids (principally glutamate).

The radioactivity in bacteroids as a percentage of total nodule label increased slightly with time, while the percentage in the cytosol fraction declined. The labeling patterns for the cytosol were essentially the same as whole nodule-labeling patterns, and they suggest a degradation of carbohydrates for the production of organic acids and amino acids. When it was found that most of the radioactivity in bacteroids was in sugars, the enzymes of glucose metabolism were surveyed. Bacteroids from nodules formed by Rhizobium japonicum strain 110 or strain 138 lacked activity for phosphofructokinase and NADP-dependent 6-phosphogluconate dehydrogenase, key enzymes of glycolysis and the oxidative pentose-phosphate pathways. Enzymes of the glycolytic and pentose phosphate pathways were found in the cytosol fraction.

In three experiments, bacteroids contained about 10 to 30% of the total radioactivity in nodules 2 to 5 hours after pulse-labeling of plants, and 60 to 65% of the radioactivity in bacteroids was in the neutral sugar fraction at all sampling times. This strongly suggests some absorption and metabolism of sugars by bacteroids in spite of the lack of key enzymes. Bacteroids did possess enzymes for the formation of hexose phosphates from glucose or fructose. Radioactivity in α,α-trehalose in bacteroids increased until, after 5 hours, trehalose was a major labeled compound in bacteroids. Thus, trehalose synthesis may be a major fate of sugars entering bacteroids.

     

Preparation and some properties of stable and carbon-14 and tritium-labeled short-chain aliphatic hydroxamic acids

A simple and safe procedure has been described for the preparation of short-chain aliphatic hydroxamic acids in quantities as large as 1 mole and as small as 0.01 mole. The procedure is equally suitable for the preparation of isotopically labeled hydroxamates, as has been demonstrated in the case of 1-¹⁴C-acetohydroxamic acid and ³H-acetohydroxamic acid. Some physical and chemical characteristics, including infrared spectra of formo-, aceto-, propiono-, and isobutyro-hydroxamic acids prepared by this method have been described.