Flexibility of short-strand RNA in aqueous solution as revealed by molecular dynamics simulation:are A′-RNA and A-RNA distinct conformational structures?

We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A'-RNA forms in the presence of counterions and explicit water. Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA namely major groove width, inclination and the number of base pairs in a helical twist over a 30 ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A'-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors). © CSIRO 2009.

Nanopatterned UV curable hydrogels for biomedical applications

With an increasing use of emerging patterning technologies such as UV-NIL in biotechnological applications there is at the same time a raising demand for new material for such applications. Here we present a PEG based precursor mixed with a photoinitiator to make it UV sensitive as a new material aimed at biotechnological applications. Using HSQ patterned quartz stamps we observed excellent pattern replication indicating good flow properties of the resist. We were able to obtain imprints with <20 nm residual layer. The PEG based resist has hydrogel properties and it swelling in water was observed by AFM.

Transglutaminase overexpression sensitizes neuronal cell lines to apoptosis by increasing mitochondrial membrane potential and cellular oxidative stress

'Tissue' transglutaminase (tTG) selectively accumulates in cells undergoing apoptosis both in vivo and in vitro. Considering the central role played by mitochondria in apoptosis, we investigated the relationships existing amongst tTG expression, apoptosis and mitochondrial function. To this aim we studied the mechanisms of apoptosis in a neuronal cell line (SK-N-BE (2)) in which the tTG-expression was driven by a constitutive promoter. Furthermore, a tet-off inducible promoter was also used in 3T3 fibroblastic cells used as control. Both cell lines, when expressing tTG, appeared 'sensitized' to apoptosis. Strikingly, we found major differences in the morphological features of mitochondria among cell lines in the absence of apoptotic stimuli. In addition, these ultrastructural characteristics were associated with specific functional features: (i) constitutively hyperpolarized mitochondria and (ii) increased reactive oxygen intermediates production. Importantly, after mitochondrial-mediated apoptosis by staurosporine, a rapid loss of mitochondrial membrane potential was found in tTG cells only. Taken together, these results seem to suggest that, via hyperpolarization, tTG might act as a 'sensitizer' towards apoptotic stimuli specifically targeted to mitochondria. These results could also be of pathogenetic relevance for those diseases that are characterized by increased tTG and apoptotic rate together with impaired mitochondrial function, e.g. in some neurodegenerative disease.

Optimisation of two-stage raman converter based on phosphosilicate core fibre:Modelling and experiment

Parameter optimization of a two-stage Raman fibre converters (RFC) based on phosphosilicate core fiber was presented. The optimal operational regime was determined and tolerance of the converter against variations of laser parameters was analyzed. Converter was pumped by ytterbium-doped double-clad fibre laser with a maximum output power of 3.8W at 1061 nm. A phosphosilicate-core RFC with enhanced performance was fabricated using the results of numerical modelling.

Technical efficiency and human capital in the retail sector

The performance of the British retail sectors in terms of productivity growth is not brilliant. This paper focuses on a specific component of productivity growth (technical efficiency) and tests the extent to which its variance across the sector can be explained by the differences in the educational attainment of the pool of workers to which retail firms have access. The empirical analysis is carried out on a sample of 1061 retail firms from the Annual Respondents Database, 1997-2005. The results confirm that the county-level differences of the stock of human capital can explain the technical efficiency differentials across the sector. © 2011 Taylor and Francis Group, LLC.