Assessment of the Effects of Increased Relaxation Dispersion Data on the Extraction of 3-site Exchange Parameters Characterizing the Unfolding of an SH3 Domain

Recently a suite of six CPMG relaxation dispersion experiments has been described for quantifying millisecond time-scale exchange processes in proteins. The methodology has been applied to study the folding reaction of a G48M Fyn SH3 domain mutant that exchanges between the native state, and low populated unfolded and intermediate states. A complex non-linear global optimization protocol allows extraction of the kinetics and thermodynamics of the 3-site exchange process from the experimental data, as well as reconstruction of the amide group chemical shifts of the excited states. We show here, through a series of Monte-Carlo simulations on various synthetic data sets, that the 3-site exchange parameters extracted for this system on the basis of ¹⁵N single-quantum (SQ) dispersion profiles exclusively, recorded at a single temperature, are significantly in error. While a temperature dependent ¹⁵N study improves the robustness of extracted parameters, as does a combined analysis of ¹⁵N and ¹H SQ data sets measured at a single temperature, the best agreement is observed in cases where the full complement of six dispersion profiles per residue is analyzed.     

Compromised root development constrains the establishment potential of native plants in unamended alkaline post-mining substrates

Plant and Soil - In water-limited areas, shrubs influence biological soil crust (biocrust) composition and diversity via soil microenvironment alterations and through modifying biotic interactions...     

Widespread positive selection in the photosynthetic Rubisco enzyme

Background  

Rubisco enzyme catalyzes the first step in net photosynthetic CO₂ assimilation and photorespiratory carbon oxidation and is responsible for almost all carbon fixation on Earth. The large subunit of Rubisco is encoded by the chloroplast rbcL gene, which is widely used for reconstruction of plant phylogenies due to its conservative nature. Plant systematicists have mainly used rbcL paying little attention to its function, and the question whether it evolves under Darwinian selection has received little attention. The purpose of our study was to evaluate how common is positive selection in Rubisco among the phototrophs and where in the Rubisco structure does positive selection occur.     

Noise controlled synchronization in potassium coupled neural models

The paper applies biologically plausible models to investigate how noise input to small ensembles of neurons, coupled via the extracellular potassium concentration, can influence their firing patterns. Using the noise intensity and the volume of the extracellular space as control parameters, we show that potassium induced depolarization underlies the formation of noise-induced patterns such as delayed firing and synchronization. These phenomena are associated with the appearance of new time scales in the distribution of interspike intervals that may be significant for the spatio-temporal oscillations in neuronal ensembles.     

Changes in the biota of Chany Lake along a salinity gradient

Relationships among salinity and diversity, abundance, biomass of major biological components of Chany Lake (western Siberia, Russia) are examined across a salinity gradient. As salinity increased from 0.8 to 6.4 g l⁻¹, the species richness of aquatic vascular plants decreased from 16 to 2 species, of phytoplankton from 98 to 52 species, and of zooplankton from 61 to 16 species, but changes in species diversity of zoobenthos were negligible. Guest Editor: John M. Melack Saline Waters and their Biota     

Sequence-specific ultrasonic cleavage of DNA

We investigated the phenomenon of ultrasonic cleavage of DNA by analyzing a large set of cleavage patterns of DNA restriction fragments using polyacrylamide gel electrophoresis. The cleavage intensity of individual phosphodiester bonds was found to depend on the nucleotide sequence and the position of the bond with respect to the ends of the fragment. The relative intensities of cleavage of the central phosphodiester bond in 16 dinucleotides and 256 tetranucleotides were determined by multivariate statistical analysis. We observed a remarkable enhancement of the mean values of the relative intensities of cleavage (cleavage rates) in phosphodiester bonds following deoxycytidine, which diminished in the row of dinucleotides: d(CpG) > d(CpA) > d(CpT) >> d(CpC). The cleavage rates for all pairs of complementary dinucleotides were significantly different from each other. The effect of flanking nucleotides in tetranucleotides on cleavage rates of all 16 types of central dinucleotides was also statistically significant. The sequence-dependent ultrasonic cleavage rates of dinucleotides are consistent with reported data on the intensity of the conformational motion of their 5′-deoxyribose. As a measure of local conformational dynamics, cleavage rates may be useful for characterizing functional regions of the genome.     

Calcium transients in the model of rapidly induced anoxic tolerance in rat cortical slices: involvement of NMDA receptors

In this study, we investigated the effects of NMDA receptor antagonists on calcium transients induced by a single 2-min preconditioning anoxia (PA) in rat olfactory cortical slices, and on the ability of PA to prevent pathological calcium overload induced by subsequent 10-min test anoxia (TA). Relative changes in the intracellular Ca(2+) concentration (Ca(i)) and in the level of Ca(2+) bound to intracellular hydrophobic domains (Ca(b)) were monitored using fura-2 and chlortetracycline, respectively. Our results confirmed that TA induces prominent long-lasting increases in Ca(i) and Ca(b), reflecting cellular calcium overload. It was found that PA produces moderate increases in both Ca(2+) pools and prevents Ca(2+) overload induced by TA carried out 90 min later. Calcium transients and the protective effects of PA were significantly suppressed in slices treated with NMDA receptor antagonists during and 30 min after PA. These results indicate that moderate activation of the NMDA receptors participates in the mechanism of the PA-induced anoxic tolerance of cortical neurons.