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.     

Electrophoretic evaluation of the taxonomic status of two species of sea anemone

Puerto Rican populations of two species of sea anemones (Bunodosoma cavernata and B. granulifera) which had previously been considered one were assayed electrophoretically for enzymes encoded by 12 loci. The two species shared no common allozymes at 6 of the 12 loci. Genetic distance and identity values based on these allozymes were computed for the Puerto Rican populations and for B. cavernata from Florida and B. granulifera from Panama. The Puerto Rican populations of both species had much higher genetic identities for their geographically distant conspecifics than for each other. These results indicate that the two species are reproductively isolated and should be considered as separate valid species. Average heterozygosities are presented which are the first published for coelenterate species.     

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.     

Content of red blood-cell sialic acid in BW 35 blood donors. Relation to magnesium concentration and pyruvate kinase activity

Previous studies have shown that the concentration of red blood cell (RBC) magnesium is significantly lower in subjects carrying an HLA-BW 35 antigen (p less than 0.001) than in non-carriers. As this finding might be related to modifications of the RBC membrane sialoglycoconjugates, RBC sialic acid was comparatively determined in BW 35+ and BW 35- subjects. Pyruvate-kinase activity mean RBC volume, and reticulocyte count have also been determined in order to estimate whether some significant variations in the level of these age markers could be detected between the HLA BW 35+ and BW 35- subjects. A significant negative correlation between sialic acid and RBC magnesium concentrations was observed for the whole population tested (n 57, p less than 0.005), 61% of the BW 35+ and only 25% of the BW 35- individuals having sialic acid values above, and magnesium values below the overall mean (p less than 0.01). The variance of mean RBC volume was also larger for the BW 35+ group. Other determinations did not show any significant variations, suggesting that the results are not related to RBC age.     

Effects of EEG of the osmotic opening of the blood-brain barrier in rats

EEG activity was recorded in rats submitted to osmotic opening of the BBB by intracarotid mannitol infusion.This procedure produced an immediate short-lasting depression of the EEG and a tardive paroxysmal EEG activity. Both these phenomena were more relevant on the ipsilateral hemisphere. In some instances a tonico-clonic seizure was recorded.Pre-treatment with diazepam abolished the occurrence of the tardive EEG and behavioral modifications.In accord with previous findings, focal seizure activity is likely to be responsible for the metabolic abnormalities associated with osmotic opening of the BBB. This preparation therefore produces in the brain unphysiological states in respect to local metabolism and electrical function.     

Contribution to catalysis and stability of the five cysteines in Escherichia coli aspartate aminotransferase. Preparation and properties of a cysteine-free enzyme.

The five cysteines, at positions 82, 191, 192, 270, and 401, of Escherichia coli aspartate aminotransferase (AATase) were, individually and in some combinations, converted to alanine by site-directed mutagenesis (C82A, C191A, C192A, C270A, C401A). Cys-191, which is conserved in all AATase isozymes, was mutated to serine as well (C191S). A quintuple mutant, with all cysteines converted to alanines (Quint), was also constructed. The effects of these single and multiple mutations were examined by steady-state kinetics and urea denaturation. The thermal stabilities of Quint and of the wild-type enzyme (WT) were determined by differential scanning calorimetry. The mutants had kcat values up to 50% greater than that of WT and KMAsp and KM alpha-KG values up to 1.5- and 3.3-fold higher than that of WT. The mutants C82A and C191A exhibit nearly the same CM in urea denaturation experiments as WT, while the other single mutants and Quint are less stable, with CM differences of up to 0.7 M urea. Quint is also less thermostable than WT, with a delta TM of 3.3-4.4 degrees C. Thus the five cysteine replacements yield small, but significant, changes in catalytic and denaturation parameters, but none of the cysteines was found to be essential. The changes manifested in the mutation of the conserved Cys-191 to alanine are no greater than those observed with the four nonconserved cysteines. We consider the evolutionary implications of these findings.