An analysis of simple computational strategies to facilitate the design of functional molecular information processors

BACKGROUND: Biological macromolecules (DNA, RNA and proteins) are capable of processing physical or chemical inputs to generate outputs that parallel conventional Boolean logical operators. However, the design of functional modules that will enable these macromolecules to operate as synthetic molecular computing devices is challenging. RESULTS: Using three simple heuristics, we designed RNA sensors that can mimic the function of a seven-segment display (SSD). Ten independent and orthogonal sensors representing the numerals 0 to 9 are designed and constructed. Each sensor has its own unique oligonucleotide binding site region that is activated uniquely by a specific input. Each operator was subjected to a stringent in silico filtering. Random sensors were selected and functionally validated via ribozyme self cleavage assays that were visualized via electrophoresis. CONCLUSIONS: By utilising simple permutation and randomisation in the sequence design phase, we have developed functional RNA sensors thus demonstrating that even the simplest of computational methods can greatly aid the design phase for constructing functional molecular devices. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-1297-x) contains supplementary material, which is available to authorized users

Enrichment pattern of leachable trace metals in roadside soils of Miri City, Eastern Malaysia

This article presents the results on distribution and enrichment pattern of acid-leachable trace metals (ALTMs) from roadside soil of Miri city, Sarawak, East Malaysia. The city is one of the fastest developing in the Malaysian region with huge petroleum resources. ALTMs Fe, Mn, Cr, Cu, Ni, Co, Pb, Zn and Cd along with organic carbon and carbonates (CaCO3) were analyzed in 37 soil sediments collected from roadside. The enrichment of ALTMs [especially Cu (0.4-13.1 µg g-1), Zn (9.3-70.7 µg g-1), Pb (13.8-99.1 µg g-1)] in the roadside soils indicate that these metals are mainly derived from sources related to traffic exhausts, forest fires and oil refineries. The comparative study and enrichment pattern of elements indicates that Mn, Cu, Zn and Pb are enriched multi-fold than the unpolluted soil and Ni, Pb, Cd in some samples compared to Sediment Quality Guidelines like Lowest Effect Level (LEL) and Effects Range Low (ERL) in the region which is mainly due to the recent industrial developments in the region. © 2014 Springer-Verlag Berlin Heidelberg