Optimized miR-124 reporters uncover differences in miR-124 expression among neuronal populations in vitro.

Introduction: Although intensively studied in the last decades, how microRNAs (miRNAs) are expressed across different cell types in the brain remains largely unknown. Materials: To address this issue, we sought to develop optimized fluorescence reporters that could be expressed in precise cellular subsets and used to accurately quantify miR contents in vivo. Results: Focusing on miR-124, we tested different reporter designs whose efficiency was confirmed in different in vitro settings including cell lines and primary neuronal cultures from different brain structures. Unlike previous reporters, we provide experimental evidence that our optimized designs can faithfully translate miR levels in vitro. Discussion: Tools developed here would enable assessing miRNA expression at the single cell resolution and are expected to significantly contribute to future miRNA research in vivo.

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.