Comparison of carbon-stock changes,eddycovariance carbon fluxes and model estimates in coastal Douglas-fir stands in British Columbia

Background: The global network of eddy-covariance(EC) flux-towers has improved the understanding of the terrestrial carbon(C) cycle, however, the network has a relatively limited spatial extent compared to forest inventory data and plots. Developing methods to use inventory-based and EC flux measurements together with modeling approaches is necessary evaluate forest C dynamics across broad spatial extents.Methods: Changes in C stock change(ΔC) were computed based on repeated measurements of forest inventory plots and compared with separate measurements of cumulative net ecosystem productivity(ΣNEP) over four years(2003 – 2006) for Douglas-fir(Pseudotsuga menziesii var menziesii) dominated regeneration(HDF00), juvenile(HDF88and HDF90) and near-rotation(DF49) aged stands(6, 18, 20, 57 years old in 2006, respectively) in coastal British Columbia. ΔC was determined from forest inventory plot data alone, and in a hybrid approach using inventory data along with litter fall data and published decay equations to determine the change in detrital pools. These ΔC-based estimates were then compared with ΣNEP measured at an eddy-covariance flux-tower(EC-flux) and modelled by the Carbon Budget Model- Canadian Forest Sector(CBM-CFS3) using historic forest inventory and forest disturbance data.Footprint analysis was used with remote sensing, soils and topography data to evaluate how well the inventory plots represented the range of stand conditions within the area of the flux-tower footprint and to spatially scale the plot data to the area of the EC-flux and model based estimates.Results: The closest convergence among methods was for the juvenile stands while the largest divergences were for the regenerating clearcut, followed by the near-rotation stand. At the regenerating clearcut, footprint weighting of CBM-CFS3 ΣNEP increased convergence with EC flux ΣNEP, but not for ΔC. While spatial scaling and footprint weighting did not increase convergence for ΔC, they did provide confidence that the sample plots represented site conditions as measured by the EC tower.Conclusions: Methods to use inventory and EC flux measurements together with modeling approaches are necessary to understand forest C dynamics across broad spatial extents. Each approach has advantages and limitations that need to be considered for investigations at varying spatial and temporal scales.     

Jackknife resampling for precision measurement of direct gene flow estimates

Gene flow from outside pollen sources reduces the expected genetic gain of seed orchards, and has been quantified by genotyping seed samples from crop years to determine the proportion of seed sired by outside sources. Random bulk seed sampling and microsatellite genotyping allows for fast, unbiased identification of orchard contamination rates. Bulk seed sampling has been employed in multiple studies of seed orchard gene flow, but a method of determining precision of gene flow estimates from this sampling method has yet to be described. In this study, we used jackknife resampling to generate random samples of migrant and within-population genotypes obtained from an empirical sample of Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) genotypes of five microsatellite loci. We generated samples of 50, 100, 150, 200, and 250 genotyped individuals from a sample of 400 seeds, with genotypes corresponding to low (6%), moderate (14%), or high (56%) pollen contamination levels. The mean gene flow estimate and confidence interval were calculated for each sample size and gene flow scenario to determine the precision of gene flow estimates obtained from each sample size in each contaminant gene flow scenario. Genotyping 150 individuals was sufficient to produce gene flow estimates with calculated confidence interval values below ± 1%, indicating that 150 genotyped individuals were sufficient for precise gene flow estimation in this population. This resampling method will enable precise and unbiased estimation of gene flow into seed orchards for future monitoring of gene flow, to allow better management of seed orchard genetic resources.     

Combinatorial ShcA docking interactions support diversity in tissue morphogenesis

Changes in protein-protein interactions may allow polypeptides to perform unexpected regulatory functions. Mammalian ShcA docking proteins have amino-terminal phosphotyrosine (pTyr) binding (PTB) and carboxyl-terminal Src homology 2 (SH2) domains, which recognize specific pTyr sites on activated receptors, and a central region with two phosphorylated tyrosine-X-asparagine (pYXN) motifs (where X represents any amino acid) that each bind the growth factor receptor-bound protein 2 (Grb2) adaptor. Phylogenetic analysis indicates that ShcA may signal through both pYXN-dependent and -independent pathways. We show that, in mice, cardiomyocyte-expressed ShcA directs mid-gestational heart development by a PTB-dependent mechanism that does not require the pYXN motifs. In contrast, the pYXN motifs are required with PTB and SH2 domains in the same ShcA molecule for the formation of muscle spindles, skeletal muscle sensory organs that regulate motor behavior. Thus, combinatorial differences in ShcA docking interactions may yield multiple signaling mechanisms to support diversity in tissue morphogenesis.     

High-throughput identification of catalytic redox-active cysteine residues

Cysteine (Cys) residues often play critical roles in proteins; however, identification of their specific functions has been limited to case-by-case experimental approaches. We developed a procedure for high-throughput identification of catalytic redox-active Cys in proteins by searching for sporadic selenocysteine-Cys pairs in sequence databases. This method is independent of protein family, structure, and taxon. We used it to selectively detect the majority of known proteins with redox-active Cys and to make additional predictions, one of which was verified. Rapid accumulation of sequence information from genomic and metagenomic projects should allow detection of many additional oxidoreductase families as well as identification of redox-active Cys in these proteins.     

A mutation in the TRPC6 cation channel causes familial focal segmental glomerulosclerosis

Focal and segmental glomerulosclerosis (FSGS) is a kidney disorder of unknown etiology, and up to 20% of patients on dialysis have been diagnosed with it. Here we show that a large family with hereditary FSGS carries a missense mutation in the TRPC6 gene on chromosome 11q, encoding the ion-channel protein transient receptor potential cation channel 6 (TRPC6). The proline-to-glutamine substitution at position 112, which occurs in a highly conserved region of the protein, enhances TRPC6-mediated calcium signals in response to agonists such as angiotensin II and appears to alter the intracellular distribution of TRPC6 protein. Previous work has emphasized the importance of cytoskeletal and structural proteins in proteinuric kidney diseases. Our findings suggest an alternative mechanism for the pathogenesis of glomerular disease.     

The optical resonances in carbon nanotubes arise from excitons

Optical transitions in carbon nanotubes are of central importance for nanotube characterization. They also provide insight into the nature of excited states in these one-dimensional systems. Recent work suggests that light absorption produces strongly correlated electron-hole states in the form of excitons. However, it has been difficult to rule out a simpler model in which resonances arise from the van Hove singularities associated with the one-dimensional band [corrected] structure of the nanotubes. Here, two-photon excitation spectroscopy bolsters the exciton picture. We found binding energies of approximately 400 millielectron volts for semiconducting single-walled nanotubes with 0.8-nanometer diameters. The results demonstrate the dominant role of many-body interactions in the excited-state properties of one-dimensional systems.     

Robust, tunable biological oscillations from interlinked positive and negative feedback loops

A simple negative feedback loop of interacting genes or proteins has the potential to generate sustained oscillations. However, many biological oscillators also have a positive feedback loop, raising the question of what advantages the extra loop imparts. Through computational studies, we show that it is generally difficult to adjust a negative feedback oscillator's frequency without compromising its amplitude, whereas with positive-plus-negative feedback, one can achieve a widely tunable frequency and near-constant amplitude. This tunability makes the latter design suitable for biological rhythms like heartbeats and cell cycles that need to provide a constant output over a range of frequencies. Positive-plus-negative oscillators also appear to be more robust and easier to evolve, rationalizing why they are found in contexts where an adjustable frequency is unimportant.     

Molecular mechanism for switching of P. falciparum invasion pathways into human erythrocytes

The malaria parasite, Plasmodium falciparum, exploits multiple ligand-receptor interactions, called invasion pathways, to invade the host erythrocyte. Strains of P. falciparum vary in their dependency on sialated red cell receptors for invasion. We show that switching from sialic acid-dependent to -independent invasion is reversible and depends on parasite ligand use. Expression of P. falciparum reticulocyte-binding like homolog 4 (PfRh4) correlates with sialic acid-independent invasion, and PfRh4 is essential for switching invasion pathways. Differential activation of PfRh4 represents a previously unknown mechanism to switch invasion pathways and provides P. falciparum with exquisite adaptability in the face of erythrocyte receptor polymorphisms and host immune responses.