Biophysical stratification of the Amazon basin

In field measurement programmes, stratified sampling can optimize sampling efficiency, but stratification is often undertaken subjectively, and is frequently based on a priori classification schemes such as those used for vegetation maps. In order to avoid the problems associated with a priori subjective schemes, we explore here an objective procedure, Regression Tree Analysis (RTA). RTA has previously been used in local-scale studies, but here we apply it to a very large study domain, namely the entire humid tropical zone of South America. The aim of the study was to develop an optimal sampling design in preparation for the Large Scale Biosphere-Atmosphere Experiment in Amazonia (LBA). Co-registered spatially continuous fields of rainfall, temperature, photosynthetically active radiation (PAR), the normalized difference index (NDVI), an index of surface moisture, and other independent variables were used to predict three dependent variables, annual net radiation (Rn), latent heat (LE) and net primary production (NPP). Rather than simply dividing the study area based on differing levels of the three dependent variables, empirical models were developed using RTA to indicate how the relationships between these and possible forcing variables vary across the study area. For each variable long-term seasonal indices such as annual average, monthly minimum and amplitude were used to exclude effects of temporal phase differences between the hemispheres. The resulting hierarchical models revealed variations in the interdependence of the forcing variables throughout the study area and therefore provided a basis for a stratified sampling and identifying the most important variables to be collected in LBA for the Amazon basin as a whole as well as optimizing the sampling scheme for scaling up findings from the field scale to larger areas.     

Strong poison revisited

Selenium in the form of selenocysteine plays an essential role in a number of proteins, but its role in non-enzymatic biochemistry is also important. In this short review we discuss the interactions between inorganic selenium, arsenic and mercury under physiological conditions, especially in the presence of glutathione. This chemistry is obviously important in making the arsenic and mercury unavailable for more toxic interactions, but in the process it suggests that a side-effect of chronic arsenic and/or mercury exposure is likely to be functional selenium deficiency.     

Staphylococcus aureus protein A activates TACE through EGFR-dependent signaling

Among the many adhesins and toxins expressed by Staphylococcus aureus, protein A is an exceptionally complex virulence factor, known to interact with multiple eukaryotic targets, particularly those with immunological functions. Protein A acts as a ligand that can mimic TNF-alpha to activate TNFR1 and subsequent proinflammatory signaling. It also stimulates the cleavage of TNFR1 from the surface of epithelial cells and macrophages, which serves to limit TNF-alpha signaling. We characterized the signaling pathway responsible for TNFR1 shedding and identified protein A mutants which could activate TNFR1-dependent signaling, but were unable to activate TACE, the TNFR1 sheddase. Activation of TACE was dependent upon a discrete interaction between the previously defined IgG-binding domain of protein A and the epidermal growth factor receptor (EGFR), which in turn induced TACE phosphorylation through a c-Src-erk1/2-mediated cascade. This novel interaction was independent of the autocrine activation of EGFR and protein A-induced TGF-alpha was neither required nor sufficient to activate TNFR1 shedding. Thus, staphylococci exploit the ubiquitous and multifunctional EGFR to regulate the availability of TNFR1 on mucosal and immune cells.     

Consequences of hoxb1 duplication in teleost fish

Vertebrate evolution is characterized by gene and genome duplication events. There is strong evidence that a whole-genome duplication occurred in the lineage leading to the teleost fishes. We have focused on the teleost hoxb1 duplicate genes as a paradigm to investigate the consequences of gene duplication. Previous analysis of the duplicated zebrafish hoxb1 genes suggested they have subfunctionalized. The combined expression pattern of the two zebrafish hoxb1 genes recapitulates the expression pattern of the single Hoxb1 gene of tetrapods, possibly due to degenerative changes in complementary cis-regulatory elements of the duplicates. Here we have tested the hypothesis that all teleost duplicates had a similar fate post duplication, by examining hoxb1 genes in medaka and striped bass. Consistent with this theory, we found that the ancestral Hoxb1 expression pattern is subdivided between duplicate genes in a largely similar fashion in zebrafish, medaka, and striped bass. Further, our analysis of hoxb1 genes reveals that sequence changes in cis-regulatory regions may underlie subfunctionalization in all teleosts, although the specific changes vary between species. It was previously shown that zebrafish hoxb1 duplicates have also evolved different functional capacities. We used misexpression to compare the functions of hoxb1 duplicates from zebrafish, medaka and striped bass. Unexpectedly, we found that some biochemical properties, which were paralog specific in zebrafish, are conserved in both duplicates of other species. This work suggests that the fate of duplicate genes varies across the teleost group.     

Intrinsic site‐selectivity of ubiquitin dimer formation

The post‐translational modification of proteins with ubiquitin can take on many forms, including the decoration of substrates with polymeric ubiquitin chains. These chains are linked through one of the seven lysine residues in ubiquitin, with the potential to form a panoply of linkage combinations as the chain length increases. The ensuing structural diversity of modifications serves a variety of signaling functions. Still, some linkages are present at a much higher level than others in cellulo. Although ubiquitination is an enzyme‐catalyzed process, the large disparity of abundancies led us to the hypothesis that some linkages might be intrinsically faster to form than others, perhaps directing the course of enzyme evolution. Herein, we assess the kinetics of ubiquitin dimer formation in an enzyme‐free system by measuring the rate constants for thiol–disulfide interchange between appropriate ubiquitin variants. Remarkably, we find that the kinetically expedient linkages correlate with those that are most abundant in cellulo. As the abundant linkages also appear to function more broadly in cellulo, this correlation suggests that the more accessible chains were selected for global roles.