Alignment-free prediction of mycobacterial DNA promoters based on pseudo-folding lattice network or star-graph topological indices

The importance of the promoter sequences in the function regulation of several important mycobacterial pathogens creates the necessity to design simple and fast theoretical models that can predict them. This work proposes two DNA promoter QSAR models based on pseudo-folding lattice network (LN) and star-graphs (SG) topological indices. In addition, a comparative study with the previous RNA electrostatic parameters of thermodynamically-driven secondary structure folding representations has been carried out. The best model of this work was obtained with only two LN stochastic electrostatic potentials and it is characterized by accuracy, selectivity and specificity of 90.87%, 82.96% and 92.95%, respectively. In addition, we pointed out the SG result dependence on the DNA sequence codification and we proposed a QSAR model based on codons and only three SG spectral moments.     

Mechanisms of distant enhancer action on DNA and in chromatin

Enhancers and insulators are regulatory DNA sequences that can work over a large distance. Efficient action over a distance clearly requires special mechanisms for facilitating communication between a regulatory region and its target. Studies from our laboratory identified DNA supercoiling as primary factor that mediates efficient enhancer-promoter communication over a distance in prokaryotes through a “DNA slithering” mechanism. These studies allowed rational design and construction of an insulator that can block enhancer action over a distance both in vitro and in vivo. Our most recent studies suggest that eukaryotic chromatin structure can support action over a distance using similar principles, but in a mechanistically distinct way. Published in Russian in Molekulyarnaya Biologiya, 2009, Vol. 43, No. 2, pp. 204–214. The article was translated by the author.     

The role of the DLPFC in inductive reasoning of MCI patients and normal agings: An fMRI study

Previous studies of young people have revealed that the left dorsolateral prefrontal cortex (DLPFC) plays an important role in inductive reasoning. An fMRI experiment was performed in this study to examine whether the left DLPFC was involved in inductive reasoning of MCI patients and normal agings, and whether the activation pattern of this region was different between MCI patients and normal agings. The fMRI results indicated that MCI patients had no difference from normal agings in behavior per-formance (reaction time and accuracy) and the activation pattern of DLPFC. However, the BOLD re-sponse of the DLPFC region for MCI patients was weaker than that for normal agings, and the func-tional connectivity between the bilateral DLPFC regions for MCI patients was significantly higher than for normal agings. Taken together, these results indicated that DLPFC plays an important role in inductive reasoning of agings, and the functional abnormity of DLPFC may be an earlier marker of MCI before structural alterations.     

The automatic discovery of structural principles describing protein fold space

The study of protein structure has been driven largely by the careful inspection of experimental data by human experts. However, the rapid determination of protein structures from structural-genomics projects will make it increasingly difficult to analyse (and determine the principles responsible for) the distribution of proteins in fold space by inspection alone. Here, we demonstrate a machine-learning strategy that automatically determines the structural principles describing 45 folds. The rules learnt were shown to be both statistically significant and meaningful to protein experts. With the increasing emphasis on high-throughput experimental initiatives, machine-learning and other automated methods of analysis will become increasingly important for many biological problems.     

Influence of absorption promoters on pulmonary insulin bioactivity

The purpose of this research was to enhance the bioactivity of insulin by the pulmonary route using a combination of absorption promoters. Aliquots (100 μL) containing 1.0 IU/kg to 7.0 IU/kg doses of porcine insulin solutions with different classes of absorption promoters and combinations of these at 3 concentration levels were instilled intratracheally to the anesthetized rats. Blood concentrations of glucose were measured at specific time points. Out of 3 concentration levels of each of the absorption promoters used, the formulations having the leastconcentration with the maximum percentage of blood glucose reduction were selected for combining absorption promoters, and their pharmacodynamic parameters related to insulin absorption were determined. The pharmacodynamics of porcine insulin following subcutaneous administration of increasing doses were also determined. The relative pulmonary bioactivity of insulin in phosphate buffer pH 7.4 and citrate buffer pH 3.5 was 11.36%±1.27% and 43.20% ±2.48%, respectively, compared to subcutaneous administration. Relative pulmonary bioactivity of 155.60%±5.19% was obtained when oleic acid sodium salt, sodium tauroglycocholate, bestatin, and chymostatin were coadministered in citrate buffer pH 3.5 solution. However, only 61.91%±3.21, 67.09%±3.23%, 67.24%±2.11%, and 69.84%±3.02% were obtained, respectively, upon incorporation of these absorption promoters individually. Absorption promoters in combination have significant potential for increasing the pulmonary bioactivity of insulin. These studies support the argument that pulmonary administration of insulin is a viable alternative to subcutaneous administration for diabetic patients.