The case for cloud computing in genome informatics

With DNA sequencing now getting cheaper more quickly than data storage or computation, the time may have come for genome informatics to migrate to the cloud.     

Cat satellite DNA. Isolation using netropsin with CsCl gradients

The absence of centromeric bands in the karyotype of Felis catus is confirmed. It is also confirmed that no satellite band is visible in CsCl density gradients. However, a satellite is observed both by recentrifuging the fraction of the DNA that bands at high density in CsCl and by using netropsin to enhance the resolution of a CsCl gradient containing total F. catus DNA. The satellite, about 0.5% of total DNA, was isolated by repeated centrifugation in CsCl alone and in CsCl with netropsin. Netropsin was removed and a pure satellite DNA obtained. The reassociation kinetics (C0t1/2 less than 10(-3) M . s) show that the satellite is of the simple sequence type and hence a candidate for centromeric heterochromatin. Its cytological localisation awaits in situ hybridisation experiments.     

Aggregation of tobacco mosaic virus by sodium chondroitin sulfate

The precipitation of tobacco mosaic virus by sodium chondroitin sulfate in an aqueous solution was investigated kinetically by means of turbidimetry. The virus solution became turbid after the addition of chondroitin sulfate. A threshold concentration of chondroitin, 1.33 mg/ml, was required for virus precipitation, irrespective of the virus concentration. The precipitation resulted from a mutual spatial exclusion phenomenon, leading to the separation of the virus as a crystalline phase. The dimension of chondroitin sulfate calculated at the threshold concentration agreed well with that obtained by other methods. The initial slopes and the aggregation half-times of the virus aggregates depended on both chondroitin and virus concentrations and the former increased with the increase in concentration of each. Above the threshold concentration of chondroitin sulfate, tobacco mosaic virus aggregation was a rapid-aggregation process and ended within 100 sec.     

Unraveling the importance of rice fields for waterbird populations in Europe

Rice fields are an alternative habitat for waterbirds and provide food and shelter for many avian species, but there is a lack of information about how the use of rice fields translates into population level effects. The aim of this study was to test the relationship between the use of rice fields by European waterbirds and trends in their populations. We tested this relationship during the autumn migration season and during the breeding season. Based on counts conducted over the last 23 years in natural marshes and areas of rice fields in Doñana (SW Spain), an index of rice field use was constructed for 76 bird species, which was then compared to these species’ European population trends obtained from the literature. A positive relationship was found between waterbird population trends and the use of rice fields during autumn migration season. Our study suggests that changes in the Common Agriculture Policy in Europe leading to reductions in areas of rice cultivation may have important effects on waterbirds. The restoration of former marsh areas and the maintenance of rice cultivation would seem to be more environmentally friendly approaches than the use of these areas to grow alternative crops or solar farms.     

The position of the epistatic S locus in the halothane linkage group in pigs

The linkage of the Phi, Pgd, Po2, S, H and halothane sensitivity loci was followed in a Belgian Landrace family, heterozygous for these systems over 6 generations. Recombination next to the S locus occurred mainly in pigs belonging to this particular family. From this investigation the position of the S locus is proved to be outwith the Phi-Pgd region, next to Phi . Therefore the gene sequence S - Phi - Hal -H- Po2 -Pgd is proposed. Higher recombination rates were observed in the female parental line of the multiheterozygous family when compared to the male parental line. Additional data from animals, unrelated to this strain, confirm the evidence of close linkage of the S system to the nearest marker loci.     

Isoquinoline alkaloids from cell suspension cultures of Fumaria capreolata

Fumaria capreolata was taken into cell suspension culture. The culture yielded a biomass of about 12 g dry weight per liter of medium; the dried cells contained ca. 0.1% of alkaloids. Besides choline, the following ten known isoquinoline alkaloids were isolated from the cell extract in crystalline form: coptisine, dehydrocheilanthifoline; (+)-isoboldine; magnoflorine; N-methylcoclaurine; (+)-reticuline; (–)-pallidine; protopine; sanguinarine; (–)-scoulerine. This is the most diverse isoquinoline alkaloid spectrum thus far published for a cell suspension culture.     

The role of polyamines in animal cell physiology

The ubiquitous distribution of polyamines in nature suggests that they fulfil some fundamental role(s) in living organisms. In animal cells, polyamine content closely parallels changes in the rate of cell proliferation so that the highest content is always observed in rapidly growing cells. The activity of ornithine decarboxylase (which is the first enzyme in the polyamine biosynthetic pathway) has been found to increase significantly in many systems shortly after exposure to hormones. Also, addition of polyamines greatly stimulates cell-free macromolecular synthesis. Observations such as these have suggested that polyamine accumulation stimulates cell growth and is important in the regulation of macromolecular biosynthesis. However, it is also possible to interpret such data as evidence that polyamine accumulation is the result, not the cause, of increased cell growth. This review supports the latter concept and re-examines the significance of the early induction of ornithine decarboxylase activity and of the stimulatory effects of exogenous polyamine on macromolecular synthesis. It is proposed that the polyamines are important only in maintaining cell growth that has already been stimulated by other factors and that their biosynthesis is to a large extent determined by the accumulation of RNA in the cell.     

Indirect assays for deoxyhypusine hydroxylase using dual-label ratio changes and oxidative release of radioactivity

Two procedures for rapid assay of deoxyhypusine hydroxylase activity are described. One of these assays measures changes in the 3H:14C ratio of dual-labeled protein that results from the release of tritium from a specific position in the side chain of the 3H,14C-labeled constituent amino acid deoxyhypusine upon its conversion to [3H,14C]hypusine. The other assay relies upon release of radioactivity from product protein by periodate oxidation of the radiolabeled side chain of component hypusine. The good correspondence of each of these assays with the ion exchange chromatographic method which measures hypusine and deoxyhypusine in acid hydrolysates of protein indicates that each provides a valid means of determining deoxyhypusine hydroxylase activity.