mlstdbNet – distributed multi-locus sequence typing (MLST) databases

Background  

Multi-locus sequence typing (MLST) is a method of typing that facilitates the discrimination of microbial isolates by comparing the sequences of housekeeping gene fragments. The mlstdbNet software enables the implementation of distributed web-accessible MLST databases that can be linked widely over the Internet.     

Genetic variation in Echinacea angustifolia along a climatic gradient

BACKGROUNDS AND AIMS: Echinacea angustifolia is a widespread species distributed throughout the Great Plains region of North America. Genetic differentiation among populations was investigated along a 1500 km north-south climatic gradient in North America, a region with no major geographical barriers. The objective of the study was to determine if genetic differentiation of populations could be explained by an isolation-by-distance model or by associations with climatic parameters known to affect plant growth and survival. METHODS: Historical climatic data were used to define the nature of the climatic gradient and AFLP markers were used to establish patterns of population genetic differentiation among ten Echinacea populations collected from North Dakota to Oklahoma. A total of 1290 fragments were scored using six EcoRI/MseI and three PstI/MseI primer combinations. Assessment of the correlation between climatic, genetic and geographic distances was assessed by Mantel and partial Mantel tests. KEY RESULTS: PstI/MseI combinations produced significantly fewer fragments, but a larger percentage was unique compared with EcoRI/MseI markers. Using estimates of F(ST), populations in Oklahoma and southern Kansas were identified as the most divergent from the other populations. Both the neighbour-joining tree and principal co-ordinate analysis clustered the populations in a north-south spatial orientation. About 60% of the genetic variation was found within populations, 20% among populations and the remaining 20% was partitioned among groups that were defined by the topology of the neighbour-joining tree. Significant support was found for the isolation-by-distance model independent of the effects of annual mean precipitation, but not from annual mean temperature and freeze-free days. CONCLUSIONS: Echinacea angustifolia populations exhibit genetic divergence along a north-south climatic gradient. The data support an isolation-by-distance restriction in gene flow that is independent of annual mean precipitation.     

The inhibitory effects of polyoxyethylene detergents on human erythrocyte acetylcholinesterase and Ca2+ + Mg2+ ATPase

The activities of acetylcholinesterase and Ca2+ + Mg2+ ATPase were measured following treatment of human erythrocyte membranes with nonsolubilizing and solubilizing concentrations of Triton X-100. A concentration of 0.1% (v/v) Triton X-100 caused a significant inhibition of both enzymes. The inhibition appears to be caused by perturbations in the membrane induced by Triton X-100 incorporation. No acetylcholinesterase activity and little Ca2+ + Mg2+ ATPase activity were detected in the supernatant at 0.05% Triton X-100 although this same detergent concentration induced changes in the turbidity of the membrane suspension. Also, no inhibition of soluble acetylcholinesterase was observed over the entire detergent concentration range. The inhibition of these enzymes at 0.1% Triton X-100 was present over an eightfold range of membrane protein in the assay indicating an independence of the protein/detergent ratio. The losses in activities of these two enzymes could be prevented by either including phosphatidylserine in the Triton X-100 suspension or using Brij 96 which has the same polyoxyethylene polar head group but an oleyl hydrophobic tail instead of the p-tert-octylphenol group of Triton X-100. The results are discussed in regard to the differential recovery of enzyme activities over the entire detergent concentration range.     

Topological studies on the enzymes catalyzing the biosynthesis of Glc-P- dolichol and the triglucosyl cap of Glc3Man9GlcNAc2-P-P-dolichol in microsomal vesicles from pig brain: use of the processing glucosidases I/II as latency markers

In the current model for Glc3Man9GlcNAc2-P-P-Dol assembly, Man5GlcNAc2- P-P-Dol, Man-P-Dol, and Glc-P-Dol are synthesized on the cytoplasmic face of the ER and diffuse transversely to the lumenal leaflet where the synthesis of the lipid-bound precursor oligosaccharide is completed. To establish the topological sites of Glc-P-Dol synthesis and the lipid-mediated glucosyltransfer reactions involved in Glc3Man9GlcNAc2-P-P-Dol synthesis in ER vesicles from pig brain, the trypsin-sensitivity of Glc-P-Dol synthase activity and the Glc-P- Dol:Glc0-2Man9GlcNAc2-P-P-Dol glucosyltransferases (GlcTases) was examined in sealed microsomal vesicles. Since ER vesicles from brain do not contain glucose 6-phosphate (Glc 6-P) phosphatase activity, the latency of the lumenally oriented, processing glucosidase I/II activities was used to assess the intactness of the vesicle preparations. Comparative enzymatic studies with sealed ER vesicles from brain and kidney, a tissue that contains Glc 6-P phosphatase, demonstrate the reliability of using the processing glucosidase activities as latency markers for topological studies with microsomal vesicles from non-gluconeogenic tissues lacking Glc 6-P phosphatase. The results obtained from the trypsin-sensitivity assays with sealed microsomal vesicles from brain are consistent with a topological model in which Glc-P-Dol is synthesized on the cytoplasmic face of the ER, and subsequently utilized by the three Glc-P-Dol-mediated GlcTases after "flip-flopping" to the lumenal monolayer.      

Mitochondrial gene divergence of Colombian Drosophila pseudoobscura

Isolated populations of drosophila pseudoobscura, separated from North American populations by about 2,400 km, were found in Colombia in 1960. We compared for sequences of the small ribosomal RNA (srRNA) gene on the mitochondria between North American and Colombian D. pseudoobscura in order to clarify the age of the Colombian isolates. The North American populations were not genetically different from each other but were genetically different from the Colombian populations. The Mexican strains represent the area from which the Colombian founders might have come. The estimated net nucleotide divergence between Mexican and Colombian D. pseudoobscura indicates that the Colombian population is not an ancient lineage. Phylogenies using both distance and parsimony methodologies reinforced this conclusion. The Colombian samples group together with both methods but, according to the bootstrap analysis, not significantly. It appears that the populations have not been separated long enough for their DNA sequences to show much divergence.      

Total reconstruction of a two-compartment scrotum by tissue expansion

A case report is presented showing the reconstruction of a two-compartment scrotum out of hair-bearing perineal skin following a severe degloving injury of the scrotum and testicles. We feel that this is an appropriate procedure to be used in patients who have lost the testicles and scrotum traumatically, either one or both testicles, or in the situation where both testicles have been spared. Aesthetically, the result in this patient is superior to skin grafting and should be readily reproducible.     

Location by odour and turn selection as two stages in the spontaneous alternation of rats.

Rats were given two free unrewarded trials per day in different T-mazes, oriented at 90 degrees to each other, and wiped with either Cajuput or Anise, which produced distinctive odours. The rate of spontaneous alternation was 82.8 per cent when the same odour was present on both trials, 62.5 per cent when the odour was changed between trials. This result was taken to support the hypothesis that alternation is a two-stage process, involving location then turn selection, and that odour is one of the stimuli used by the rat in locating itself.