SRC-dependent signalling regulates actin ruffle formation induced by glycerophosphoinositol 4-phosphate

The glycerophosphoinositols are diffusible phosphoinositide metabolites reported to modulate actin dynamics and tumour cell spreading. In particular, the membrane permeant glycerophosphoinositol 4-phosphate (GroPIns4P) has been shown to act at the level of the small GTPase Rac1, to induce the rapid formation of membrane ruffles. Here, we have investigated the signalling cascade involved in this process, and show that it is initiated by the activation of Src kinase. In NIH3T3 cells, exogenous addition of GroPIns4P induces activation and translocation of Rac1 and its exchange factor TIAM1 to the plasma membrane; in addition, in in-vitro assays, GroPIns4P favours the formation of a protein complex that includes Rac1 and TIAM1. Neither of these processes involves direct actions of GroPIns4P on these proteins. Thus, through the use of specific inhibitors of tyrosine kinases and phospholipase C (and by direct evaluation of kinase activities and inositol 1,4,5-trisphosphate production), we show that GroPIns4P activates Src, and as a consequence, phospholipase Cgamma and Ca(2+)/calmodulin kinase II, the last of which directly phosphorylates TIAM1 and leads to TIAM1/Rac1-dependent ruffle formation.     

The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping.

We developed the SNPlex Genotyping System to address the need for accurate genotyping data, high sample throughput, study design flexibility, and cost efficiency. The system uses oligonucleotide ligation/polymerase chain reaction and capillary electrophoresis to analyze bi-allelic single nucleotide polymorphism genotypes. It is well suited for single nucleotide polymorphism genotyping efforts in which throughput and cost efficiency are essential. The SNPlex Genotyping System offers a high degree of flexibility and scalability, allowing the selection of custom-defined sets of SNPs for medium- to high-throughput genotyping projects. It is therefore suitable for a broad range of study designs. In this article we describe the principle and applications of the SNPlex Genotyping System, as well as a set of single nucleotide polymorphism selection tools and validated assay resources that accelerate the assay design process. We developed the control pool, an oligonucleotide ligation probe set for training and quality-control purposes, which interrogates 48 SNPs simultaneously. We present performance data from this control pool obtained by testing genomic DNA samples from 44 individuals. in addition, we present data from a study that analyzed 521 SNPs in 92 individuals. Combined, both studies show the SNPlex Genotyping system to have a 99.32% overall call rate, 99.95% precision, and 99.84% concordance with genotypes analyzed by TaqMan probe-based assays. The SNPlex Genotyping System is an efficient and reliable tool for a broad range of genotyping applications, supported by applications for study design, data analysis, and data management.     

Biodiversity in South African fynbos and Mediterranean heathland

Abstract. The theory of convergence predicts that, given similar selective regimes, both present and past, unrelated ecological communities will show similar attributes. Mild Pleistocene climate, highly infertile soils, and similar fire regimes explain the remarkable convergence between mediterranean‐type vegetation from South Africa (fynbos) and Australia (kwongan). Heathlands in the Aljibe Mountains, at the western end of the Mediterranean basin, constitute a single vegetation type within the Mediterranean region. We studied the association between endemism and plant life form in a flora from environmentally similar areas of the South African Cape region (fynbos) and the Aljibe Mountains by contingency table analysis. We included two non‐acid, neighbouring areas to the latter region in the analysis as contrasts. We also compared the patterns of variation in three components of biodiversity (species richness, endemism level and taxonomic singularity) of fynbos and Aljibe heathland woody plant communities along similar soil fertility gradients by means of two‐way ANOVAs. At the regional (flora) level, our results show two common features in the biological aspects of endemism between the two regions: (1) edaphic endemism and (2) association of endemism with the shrub growth form. At the community level, we detected strong similarities in the patterns of variation of endemism and taxonomic singularity of woody communities from both regions along an ecological gradient related to soil fertility. We interpret these similarities, both at the regional and community levels, as suggestive of convergence between fynbos and Aljibe heathland.     

Decadal weakening of the wind-induced upwelling reduces the impact of nutrient pollution in the Bay of Málaga (western Mediterranean Sea)

The hypothesis that nitrate versus phosphate regulates the coastal primary production has been assessed at different time scales in the northwest Alboran Sea. Time series of temperature, salinity, nutrients and chlorophyll a obtained at three stations located off Málaga city (the greatest coastal urban core along the Alboran Sea shoreline) from 1992 to 2006 have been analysed. At the decadal scale, temperature increased linearly while salinity decreased. These changes were related to a shift in the wind regime suggesting that coastal upwelling became steadily weaker. In contrast to phosphate, nitrate was positively correlated with salinity at the seasonal scale and decreased linearly from 1992 to 2006. Seasonal and decadal changes in chlorophyll a were correlated with nitrate (and uncorrelated with phosphate). However, non-regular variability in chlorophyll a was correlated with phosphate. Consequently, the results demonstrate that nitrate controls the phytoplankton biomass at the inter-annual scale while both nitrate and phosphate do so at a shorter time scale. The Bay of Málaga receives elevated entries of domestic waste waters that release high loads of phosphate compared to nitrate. Our analysis indicates that the expected impact of this pollution on chlorophyll a at the inter-annual scale is reduced in comparison with the effects of atmospheric forcing.     

Environmental and Animal Characteristics as Factors Associated with American Cutaneous Leishmaniasis in Rural Locations with Presence of Dogs,Brazil

The aim of the study was to investigate the importance of dogs, other domesticated animals and environmental characteristics as risk factors in the epidemiology of American cutaneous leishmaniasis (ACL). A retrospective survey of cases of human ACL in the last ten years and visits to homes in rural locations were carried out in the municipality of Arapongas (southern Brazil) from 2008 to 2010. ACL in humans was significantly associated with a distance of up to 25 meters from the residence to a forest area (OR 5.08; 95% CI: 1.35–21.04), undergrowth area (OR 6.80; 95% CI: 1.69–45.33) and stream (OR 5.87; 95% CI: 1.15–24.59); banana plants near the residence (OR 5.98; 95% CI: 1.49–39.84), absence of ceiling below the roof in the residence (OR 7.30; 95% CI: 1.26–158.1), the dumping of trash in the forest area (OR 26.33; 95% CI: 7.32–93.46) and presence of ACL in dogs in the surrounding area (OR 4.39; 95% CI: 1.37–13.45). In dogs, ACL was associated with a distance of 25 to 50 meters and 51 to 100 meters, respectively, from the residence to a forest area (OR 2.59; 95% CI: 1.08–5.98; OR 3.29; 95% CI: 1.64–6.62), the presence of a stream up to 25 m from the residence (OR 6.23; 95% CI: 2.34–16.54) and banana plants near the residence (OR 0.45; 95% CI: 0.25–0.80). In the locations studied in the municipality of Arapongas (Brazil), the results reveal that canine infection increases the risk of human infection by ACL and the characteristics surrounding the residence increase the risk of infection in both humans and dogs. Thus, integrated environmental management could be a useful measure to avoid contact between humans and phlebotomines.     

Melting studies of short DNA hairpins: Influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability

Spectroscopic and calorimetric melting studies of 28 DNA hairpins were performed. These hairpins form by intramolecular folding of 16 base self‐complementary DNA oligomer sequences. Sequence design dictated that the hairpin structures have a six base pair duplex linked by a four base loop and that the first five base pairs in the stem are the same in every molecule. Only loop sequence and identity of the duplex base pair closing the loop vary for the set of hairpins. For these DNA samples, melting studies were carried out to investigate effects of the variables on hairpin stability. Stability of the 28 oligomers was ascertained from their temperature‐induced melting transitions in buffered 115 mM Na⁺ solvent, monitored by ultraviolet absorbance and differential scanning calorimetry (DSC). Experiments revealed the melting temperatures of these molecules range from 32.4 to 60.5°C and are concentration independent over strand concentrations of 0.5 to 260 μM; thus, as expected for hairpins, the melting transitions are apparently unimolecular. Model independent thermodynamic transition parameters, ΔH_cal, ΔS_cal, and ΔG_cal, were determined from DSC measurements. Model dependent transition parameters, ΔH_vH, ΔS_vH, and ΔG_vH were estimated from a van't Hoff (two‐state) analysis of optical melting transitions. Results of these studies reveal a significant sequence dependence to DNA hairpin stability. Thermodynamic parameters evaluated by either procedure reveal the transition enthalpy, ΔH_cal (ΔH_vH) can differ by as much as 20 kcal/mol depending on sequence. Similarly, values of the transition entropy ΔS_cal (ΔS_vH) can differ by as much as 60 cal/Kmol (eu) for different molecules. Differences in free energies ΔG_cal (ΔG_vH) are as large as 4 kcal/mol for hairpins with different sequences. Comparisons between the model independent calorimetric values and the thermodynamic parameters evaluated assuming a two‐state model reveal that 10 of the 28 hairpins display non‐two‐state melting behavior. The database of sequence‐dependent melting free energies obtained for the hairpins was employed to extract a set of n‐n (nearest‐neighbor) sequence dependent loop parameters that were able to reproduce the input data within error (with only two exceptions). Surprisingly, this suggests that the thermodynamic stability of the DNA hairpins can in large part be reasonably represented in terms of sums of appropriate nearest‐neighbor loop sequence parameters. © 1999 John Wiley & Sons, Inc. Biopoly 50: 425–442, 1999