The neuroprotective effect of Diosgenin in the rat Valproic acid model of autism.

Background And Aim: Autism spectrum disorder (ASD) is a neurodevelopmental disorder with two core behavioral symptoms restricted/repetitive behavior and social-communication deficit. The unknown etiology of ASD makes it difficult to identify potential treatments. Valproic acid (VPA) is an anticonvulsant drug with teratogenic effects during pregnancy in humans and rodents.

Single Mutation in Hammerhead Ribozyme Favors Cleavage Activity with Manganese over Magnesium.

Hammerhead ribozymes are one of the most studied classes of ribozymes so far, from both the structural and biochemical point of views. The activity of most hammerhead ribozymes is cation-dependent. Mg is one of the most abundant divalent cations in the cell and therefore plays a major role in cleavage activity for most hammerhead ribozymes.

Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database.

The discovery of noncoding RNAs (ncRNAs) and their importance for gene regulation led us to develop bioinformatics tools to pursue the discovery of novel ncRNAs. Finding ncRNAs de novo is challenging, first due to the difficulty of retrieving large numbers of sequences for given gene activities, and second due to exponential demands on calculation needed for comparative genomics on a large scale. Recently, several tools for the prediction of conserved RNA secondary structure were developed, but many of them are not designed to uncover new ncRNAs, or are too slow for conducting analyses on a large scale.

Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation.

On the basis of nascent transcript sequencing, it has been postulated but never demonstrated that transcriptional pausing at translation start sites is important for gene regulation. Here we show that the Escherichia coli thiamin pyrophosphate (TPP) thiC riboswitch contains a regulatory pause site in the translation initiation region that acts as a checkpoint for thiC expression. By biochemically probing nascent transcription complexes halted at defined positions, we find a narrow transcriptional window for metabolite binding, in which the downstream boundary is delimited by the checkpoint.

Finding instances of riboswitches and ribozymes by homology search of structured RNA with Infernal.

In the genomics era, computational tools are essential to extract information from sequences and annotate them to allow easy access to genes. Fortunately, many of these tools are now part of standard pipelines. As a consequence, a cornucopia of genomic features is available in multiple databases.