Simulating the aggregation of DNA oligonucleotides

In this work we have studied, by means of Molecular Dynamics simulations, the process of denaturation and self-assembly of short oligonucleotides. Supramolecular ordering of DNA short strands is a promising field which is constantly enriched with new findings. Examples are provided by micellar and fibrils formations and due to the selectivity of DNA bindings, "intelligent" devices have been developed to perform simple logic operations. It is worth to notice that computer simulations of these DNA nanosystems would complement experiments with detailed insight into processes involved in self-assembly. In order to obtain an accurate description of the interactions involved in the complex structure of DNA we used oxDNA, a coarse-grained model developed by Ouldridge. We simulated the melting transition of 4, 6, and 8 base pair sequences. Sequence and length dependence were analyzed, specifically we compared thermodynamic parameters DeltaH, DeltaS and the melting temperature with literature results. Moreover, we have attempted to reproduce liquid crystal ordering of the ultrashort sequence GCCG at relatively high saline concentration, until now only experimentally observed in Bellini's works. We found that our simple model successfully reproduces the experimental phase sequence (isotropic, nematic, columnar) at T= 5 °C as a function of oligonucleotide concentration, and we fully characterized the microscopic structure of the three phases.

Polyhydroxyalkanoates production from salted food waste using mixed microbial cultures.

Plastic is an essential asset for the modern lifestyle, given its superiority as a material from the points of view of cost, processability and functional properties. However, plastic-related environmental pollution has become nowadays a very significant problem that can no longer be overlooked. For this reason, in recent decades, the research for new materials that could replace fossil fuel-based plastics has been focused on biopolymers with similar physicochemical properties to fossil fuel-based plastics, such as Polyhydroxyalkanoates (PHA). PHAs are a family of biodegradable polyesters synthesized by many microorganisms as carbon and energy reserves. PHA appears as a good candidate to substitute conventional petroleum-based plastics since it has similar properties, but with the advantage of being biobased and biodegradable, and has a wide range of applications (e.g., packaging). However, the PHA production cost is almost four times higher (€5/kg) than conventional plastic manufacturing. The PHA production by mixed microbial cultures (MMC) allows to reduce production costs as it does not require aseptic conditions and it enables the use of inexpensive by-products or waste streams as these cultures are more amenable to deal with complex feedstocks. Saline wastewaters (WWs), generated by several industries such as seafood, leather and dairy, are often rich in organic compounds and, due to a strong salt inhibition, the biological treatments are inefficient, and their disposal is expensive. These saline WWs are a potential feedstock for PHA production, as they are an inexpensive raw material. Moreover, saline WWs could allow the utilization of seawater in the process as dilution and cleaning agent, further decreasing the operational costs and the environmental burden of the process. The main goal of the current project is to assess and optimize the PHA production from a mixture of food waste and brine wastewater from the fishery industry by MMC.