DNA methylation dynamics during ex vivo differentiation and maturation of human dendritic cells.

Background: Dendritic cells (DCs) are important mediators of innate and adaptive immune responses, but the gene networks governing their lineage differentiation and maturation are poorly understood. To gain insight into the mechanisms that promote human DC differentiation and contribute to the acquisition of their functional phenotypes, we performed genome-wide base-resolution mapping of 5-methylcytosine in purified monocytes and in monocyte-derived immature and mature DCs.

Results: DC development and maturation were associated with a great loss of DNA methylation across many regions, most of which occurs at predicted enhancers and binding sites for known transcription factors affiliated with DC lineage specification and response to immune stimuli.

Reducing experimental variability in variance-based sensitivity analysis of biochemical reaction systems.

Sensitivity analysis is a valuable task for assessing the effects of biological variability on cellular behavior. Available techniques require knowledge of nominal parameter values, which cannot be determined accurately due to experimental uncertainty typical to problems of systems biology. As a consequence, the practical use of existing sensitivity analysis techniques may be seriously hampered by the effects of unpredictable experimental variability.

A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems.

Background: Sensitivity analysis is an indispensable tool for the analysis of complex systems. In a recent paper, we have introduced a thermodynamically consistent variance-based sensitivity analysis approach for studying the robustness and fragility properties of biochemical reaction systems under uncertainty in the standard chemical potentials of the activated complexes of the reactions and the standard chemical potentials of the molecular species. In that approach, key sensitivity indices were estimated by Monte Carlo sampling, which is computationally very demanding and impractical for large biochemical reaction systems.

Probabilistic sensitivity analysis of biochemical reaction systems.

Sensitivity analysis is an indispensable tool for studying the robustness and fragility properties of biochemical reaction systems as well as for designing optimal approaches for selective perturbation and intervention. Deterministic sensitivity analysis techniques, using derivatives of the system response, have been extensively used in the literature. However, these techniques suffer from several drawbacks, which must be carefully considered before using them in problems of systems biology.

[Responses of Agriophyllum squarrosum phenotypic plasticity to the changes of soil nutrient and moisture contents and population density].

This paper studied the phenotypic plasticity of Agriophyllum squarrosum under effects of soil nutrient and moisture contents and population density. The results showed that with the increase of soil nutrient content, the root/shoot ratio of A. squarrosum was decreased from 0.

Hypoxia-inducible factor-1alpha induces the coronary collaterals for coronary artery disease.

Background: Marked variability exists in coronary artery collaterals in patients with ischemic heart disease. Multiple factors are thought to play a role in collateral development; however, the contribution of hypoxia inducible factor-1alpha (HIF-1alpha), which is a transcriptional activator that functions as a master regulator of oxygen homeostasis, is not completely clear. It could play an important role in modulating collateral development.