Protein Sectors: Statistical Coupling Analysis versus Conservation

Statistical coupling analysis (SCA) is a method for analyzing multiple sequence alignments that was used to identify groups of coevolving residues termed “sectors”. The method applies spectral analysis to a matrix obtained by combining correlation information with sequence conservation. It has been asserted that the protein sectors identified by SCA are functionally significant, with different sectors controlling different biochemical properties of the protein. Here we reconsider the available experimental data and note that it involves almost exclusively proteins with a single sector. We show that in this case sequence conservation is the dominating factor in SCA, and can alone be used to make statistically equivalent functional predictions. Therefore, we suggest shifting the experimental focus to proteins for which SCA identifies several sectors. Correlations in protein alignments, which have been shown to be informative in a number of independent studies, would then be less dominated by sequence conservation.     

The structure of DNA as deduced from fiber X-ray crystallography

X-ray diffraction patterns obtained experimentally for fibers, together with their chemical structures, can be analyzed theoretically in terms of an integral equation. The partially unknown electron density function can be solved by iteration. This mathematical technique has been applied with success to study the secondary structures of DNA fibers.     

Expressions of Recombinant Venom Allergen, Antigen 5 of Yellowjacket (Vespula vulgaris) and Paper Wasp (Polistes annularis), in Bacteria or Yeast

Antigen 5 is a major allergen of vespid venom. It has partial sequence identity with proteins from diverse sources. The biologic function of Ag 5 and its related proteins is not known. We are interested in the expression of Ag 5 with the native conformation of the natural protein since its B cell epitopes are mainly of the discontinuous type. When expressed in bacteria, recombinant Ag 5 formed an insoluble intracellular product, and it did not translocate from cytoplasm to periplasm by the addition of a pelB leader sequence to the cloned protein. When expressed in yeast Pichia pastoris, Ag 5 was secreted because the cloned protein contained a yeast α signal leader sequence. Recombinant Ag 5 from yeast was shown to have the native structure of the natural protein and the recombinant Ag 5 from bacteria did not. This was shown by comparison of their solubility, electrophoretic behavior, disulfide bond content, CD spectrum, and binding of IgE antibodies from allergic patients and IgG antibodies from mice immunized with natural Ag 5 or recombinant Ag 5s from yeast or bacteria. These studies were made with Ag 5s from yellowjacket (Vespula vulgaris) and paper wasp (Polistes annularis).     

Weather conditions and voter turnout in Dutch national parliament elections, 1971-2010

While conventional wisdom assumes that inclement weather on election day reduces voter turnout, there is remarkably little evidence available to support truth to such belief. This paper examines the effects of temperature, sunshine duration and rainfall on voter turnout in 13 Dutch national parliament elections held from 1971 to 2010. It merges the election results from over 400 municipalities with election-day weather data drawn from the nearest weather station. We find that the weather parameters indeed affect voter turnout. Election-day rainfall of roughly 25 mm (1 inch) reduces turnout by a rate of one percent, whereas a 10-degree-Celsius increase in temperature correlates with an increase of almost one percent in overall turnout. One hundred percent sunshine corresponds to a one and a half percent greater voter turnout compared to zero sunshine.     

Bradykinin enhances cell migration in human chondrosarcoma cells through BK receptor signaling pathways

Bradykinin (BK) is an inflammatory mediator, and shows elevated levels in regions of severe injury and inflammatory diseases. BK has recently been shown to be involved in carcinogenesis and cancer progression. In this study, we found that BK increased the migration and the expression of α2β1 integrin in human chondrosarcoma cells. We also found that human chondrosarcoma tissues had significantly higher expression of the B1 and B2 receptors comparing to normal cartilage. BK‐mediated migration and integrin up‐regulation was attenuated by B1 and B2 BK receptor siRNA or antagonist. Activations of phospholipase C (PLC), protein kinase Cδ (PKCδ), and NF‐κB pathways after BK treatment was demonstrated, and BK‐induced integrin expression and migration activity was inhibited by the specific inhibitor of PLC, PKCδ, and NF‐κB cascades. Taken together, our results indicated that BK enhances the migration of chondrosarcoma cells by increasing α2β1 integrin expression through the BK receptors/PLC/PKCδ/NF‐κB signal transduction pathway. J. Cell. Biochem. 109: 82–92, 2010. © 2009 Wiley‐Liss, Inc.     

Heart rate and burrowing behavior in the mussel Anodontites trapesialis (Bivalvia: Mycetopodidae) from lotic and lentic sites

Burrowing rate index, diurnal variations in heart rate and heart rate alterations associated with behavioral patterns were studied in Anodontites trapesialis from the Pardo River (PR) and the Galo Bravo Dam (GBD). In both populations the pattern immobile/buried was associated with the lowest (basal) values of heart rate, which increase significantly during burrowing remaining steady in its phases I and II and at the first 10 min of phase III. A decrease in the frequency of digging cycles was significantly correlated with the gradual decrease in heart rate during the phase III of burrowing. Nevertheless, mussels from PR burrow faster than those of GBD and possess higher values of basal heart rate which present a diurnal variation with the higher values occurring during the light phase. Yet, the basal heart rate in mussels from GBD remained stable over the course of 24 h. Also, the increase in heart rate associated with burrowing was higher in mussels from PR and compatible with the highest burrowing index previously detected. Since mussels possess a plastic phenotype it is probable that the cited functional differences are phenotypic adaptations, but we cannot exclude the possibility of these adaptations being genotypic in nature.