Determining the electronic structure and chemical potentials of molecules in solution

A simulation scheme is proposed for determining the excess chemical potential of a substance in solution. First, a Monte Carlo simulation is performed with classical models for solute and solvent molecules. A representative sample of these configurations is then used in a hybrid quantum/classical (QM/MM) calculation, where the solute is treated quantum-mechanically, and the average electronic structure is used to construct an improved classical model. This procedure is iterated to self-consistency in the classical model, which in practice is attained in one or two steps, depending on the quality of the initial guess. The excess free energy of the molecule within the QM/MM approach is determined relative to the classical model using thermodynamic perturbation theory with a cumulant expansion. The procedure provides a method of constructing classical point charge models appropriate for the solution and gives a measure of the importance of solvent fluctuations.

Solvation effects on equilibria: Triazoles and N-methyl piperidinol

We have performed calculations of the solvation effects on a number of equilibrium constants in water using a recently proposed hybrid quantum classical scheme in which the liquid environment is modelled using classical solvent molecules and the solute electronic structure is computed using modern quantum chemical methods. The liquid phase space is sampled from a fully classical simulation. We find that solvation effects on both triazole tautomeric equilibrium constants and piperidinol conformational equilibrium constants can be interpreted in terms of subtle differences in the local environment which can be seen in probability densities and radial distribution functions. Lower level calculations were performed for comparison and we conclude that the solvation thermodynamics can be predicted from a good classical model of solvent and solute molecules, but the implicit models that we tried are less successful.

Semi-formal Models to Support Program Development: Autonomic Management within Component Based Parallel and Distributed Programming

Functional and non-functional concerns require different programming effort, different techniques and different methodologies when attempting to program efficient parallel/distributed applications. In this work we present a "programmer oriented" methodology based on formal tools that permits reasoning about parallel/distributed program development and refinement. The proposed methodology is semi-formal in that it does not require the exploitation of highly formal tools and techniques, while providing a palatable and effective support to programmers developing parallel/distributed applications, in particular when handling non-functional concerns.

DNA methyltransferase expression in the mouse germ line during periods of de novo methylation

DNA methyltransferase (DNMT) 3A and DNMT3B are both active de novo DNA methyltransferases required for development, whereas DNMT3L, which has no demonstrable methyltransferase activity, is required for methylation of imprinted genes in the oocyte. We show here that different mechanisms are used to restrict access by these proteins to their targets during germ cell development. Transcriptional control of the Dnmt3l promoter guarantees that message is low or absent except during periods of de novo activity. Use of an alternative promoter at the Dnmt3a locus produces the shorter Dnmt3a2 transcript in the germ line and postimplantation embryo only, whereas alternative splicing of the Dnmt3b transcript ensures that Dnmt3b1 is absent in the male prospermatogonia. Control of subcellular protein localization is a common theme for DNMT3A and DNMT3B, as proteins were seen in the nucleus only when methylation was occurring. These mechanisms converge to ensure that the only time that functional products from each locus are present in the germ cell nuclei is around embryonic day 17.5 in males and after birth in the growing oocytes in females.

Direct reprogramming of adult cells: avoiding the pluripotent state

The procedure of using mature, fully differentiated cells and inducing them toward other cell types while bypassing an intermediate pluripotent state is termed direct reprogramming. Avoiding the pluripotent stage during cellular conversions can be achieved either through ectopic expression of lineage-specific factors (transdifferentiation) or a direct reprogramming process that involves partial reprogramming toward the pluripotent stage. Latest advances in the field seek to alleviate concerns that include teratoma formation or retroviral usage when it comes to delivering reprogramming factors to cells. They also seek to improve efficacy and efficiency of cellular conversion, both in vitro and in vivo. The final products of this reprogramming approach could be then directly implemented in regenerative and personalized medicine.

MicroRNA-199b modulates vascular cell fate during iPS cell differentiation by targeting the notch ligand jagged1 and enhancing VEGF signaling

Aims: Recent ability to derive endothelial cells (ECs) from induced pluripotent stem (iPS) cells holds a great therapeutic potential for personalised medicine and stem cell therapy. We aimed that better understanding of the complex molecular signals that are evoked during iPS cell differentiation towards ECs may allow specific targeting of their activities to enhance cell differentiation and promote tissue regeneration.

Methods and Results: In this study we have generated mouse iPS cells from fibroblasts using established protocol. When iPS cells were cultivated on type IV mouse collagen-coated dishes in differentiation medium, cell differentiation toward vascular lineages were observed. To study the molecular mechanisms of iPS cell differentiation, we found that miR-199b is involved in EC differentiation. A step-wise increase in expression of miR-199 was detected during EC differentiation. Notably, miR-199b targeted the Notch ligand JAG1, resulting in VEGF transcriptional activation and secretion through the transcription factor STAT3. Upon shRNA-mediated knockdown of the Notch ligand JAG1, the regulatory effect of miR-199b was ablated and there was robust induction of STAT3 and VEGF during EC differentiation. Knockdown of JAG1 also inhibited miR-199b-mediated inhibition of iPS cell differentiation towards SMCs. Using the in vitro tube formation assay and implanted Matrigel plugs, in vivo, miR-199b also regulated VEGF expression and angiogenesis.

Conclusions: This study indicates a novel role for miR-199b as a regulator of the phenotypic switch during vascular cell differentiation derived from iPS cells by regulating critical signaling angiogenic responses.