Prof Ramin Golestanian

Abstract:

Biological cilia pump the surrounding fluid by asymmetric beating that is driven by dynein motors between sliding microtubule doublets. The complexity of biological cilia raises the question about minimal systems that can re-create similar patterns of motion. One such system consists of a pair of microtubules that are clamped at the proximal end. They interact through dynein motors that cover one of the filaments and pull against the other one. Here, we study theoretically the static shapes and the active dynamics of such a system. Using the theory of elastica, we analyse the shapes of two filaments of different lengths with clamped ends. Starting from equal lengths, we observe a transition similar to Euler buckling leading to a planar shape. When further increasing the length ratio, the system assumes a non-planar shape with spontaneously broken chiral symmetry after a secondary bifurcation and then transitions to planar again. The predicted curves agree with experimentally observed shapes of microtubule pairs. The dynamical system can have a stable fixed point, with either bent or straight filaments, or limit cycle oscillations. The latter match many properties of ciliary motility, demonstrating that a two-filament system can serve as a minimal actively beating model.

Abstract:

Background

Little is known about cytochrome P450 3A4 (CYP3A4) DNA methylation and transcription alterations in gastric cancer.

Objective

In this paper, we initially aimed to address the effect of diazinon pesticide on DNA methylation and transcription changes of the CYP3A4 gene in a human gastric cell line. In the next step, we studied the methylation differences of CpG sites within the upstream regulatory regions of the CYP3A4 gene among human gastric cancerous and healthy tissues.

Methods

For the in vitro assay, the methylation changes of the C/EBP response element and transcript level of the CYP3A4 gene were studied following treatment of the AGS cell line with various concentrations of diazinon pesticide. In the next phase, the methylation percentages of 24 CpG sites within or around the upstream regulatory elements, including near promoter, C/EBP binding site, XREM, and CLEM4, in 11 specimens of human gastric cancer tissue were compared to their adjacent healthy tissues.

Results

Treatment with 10 μM Diazinon significantly increased the CYP3A4 gene transcription by approximately 27-fold, which was correlated with the hypermethylation of 3 CpGs in C/EBP binding sites, including -5998, -5731 and -5725 (p<0.001 for all comparisons). Results of bisulfite sequencing revealed that the CpG sites which are located in -1521 (p=0.003), -1569 (p=0.027), -10813 (p=0.003), -10851 (p=0.001) and -10895 (p=0.0) bp from transcription start site, were significantly hypermethylated in cancerous tissues comparing to their healthy cohort.

Conclusion

Hypermethylation of CLEM4 and a region near the core promoter may have a significant association with gastric cancer incidence.

Abstract:

Micrometer-sized objects are widely known to exhibit chemically driven motility in systems away from equilibrium. Experimental observation of reaction-induced motility or enhancement in diffusivity at the much shorter length scale of small molecules is, however, still a matter of debate. Here, we investigate the molecular diffusivity of reactants, catalyst, and product of a model reaction, the copper-catalyzed azide-alkyne cycloaddition click reaction, and develop new NMR diffusion approaches that allow the probing of reaction-induced diffusion enhancement in nanosized molecular systems with higher accuracy than the state of the art. Following two different approaches that enable the accounting of time-dependent concentration changes during NMR experiments, we closely monitored the diffusion coefficient of reaction components during the reaction. The reaction components showed distinct changes in the diffusivity: while the two reactants underwent a time-dependent decrease in their diffusivity, the diffusion coefficient of the product gradually increased and the catalyst showed only slight diffusion enhancement within the range expected for reaction-induced sample heating. The decrease in diffusion coefficient of the alkyne, one of the two reactants of click reaction, was not reproduced during its copper coordination when the second reactant, azide, was absent. Our results do not support the catalysis-induced diffusion enhancement of the components of the click reaction and, instead, point to the role of a relatively large intermediate species within the reaction cycle with diffusivity lower than that of both the reactants and product molecule.