Fast, sensitive discovery of conserved genome-wide motifs

Regulatory sites that control gene expression are essential to the proper functioning of cells, and identifying them is critical for modeling regulatory networks. We have developed Magma (Multiple Aligner of Genomic Multiple Alignments), a software tool for multiple species, multiple gene motif discovery. Magma identifies putative regulatory sites that are conserved across multiple species and occur near multiple genes throughout a reference genome. Magma takes as input multiple alignments that can include gaps. It uses efficient clustering methods that make it about 70 times faster than PhyloNet, a previous program for this task, with slightly greater sensitivity. We ran Magma on all non-coding DNA conserved between Caenorhabditis elegans and five additional species, about 70 Mbp in total, in <4 h. We obtained 2,309 motifs with lengths of 6-20 bp, each occurring at least 10 times throughout the genome, which collectively covered about 566 kbp of the genomes, approximately 0.8% of the input. Predicted sites occurred in all types of non-coding sequence but were especially enriched in the promoter regions. Comparisons to several experimental datasets show that Magma motifs correspond to a variety of known regulatory motifs.     

Autogenous regulatory site on the bacteriophage T4 gene 32 messenger RNA

We have identified the binding site on the bacteriophage T4 gene 32 mRNA responsible for autogenous translational regulation. We demonstrate that this site is largely unstructured and overlaps the initiation codon of gene 32 as previously predicted. Co-operative binding of gene 32 protein to this site specifically blocks the formation of 30 S-tRNA(fMet)-gene 32 mRNA ternary complexes and initiation of translation. The translational operator is bound co-operatively by gene 32 protein and this binding is facilitated by a nucleation site far upstream from the initiation codon. A similar unstructured mRNA lacking this nucleation site is also bound co-operatively, but only at concentrations of gene 32 protein higher than those needed to repress binding of ribosomes to the gene 32 mRNA. Some sequence-specific interactions may also influence this binding. Comparison of the bacteriophage T2, T4 and T6 gene 32 operator sequences leads us to propose that the nucleation site is a pseudoknot.     

Reproductive traits of the freshwater oyster Etheria elliptica (Bivalvia: Etheriidae) in the Pendjari River,Benin: implications for conservation

The African freshwater oyster Etheria elliptica, which is of great economic importance throughout the continent, is facing overharvesting in many fisheries in West Africa. Its reproductive traits (sex ratio, size at sexual maturity, oocyte diameter and fecundity) were studied at four stations located along the Pendjari River, northern Benin, in April 2013. Histological techniques were implemented to identify sex and gonad development stages. Oocyte sizes were measured based on the histological images and mean oocyte diameter was 38 µm. Fecundity, estimated by counting the developing eggs, averaged 106 724 eggs and increased significantly with shell size. The average sex ratio was approximately 1:1. Hermaphrodites were rare. Males reached sexual maturity at 57.6 mm dorsoventral height, earlier than females at 64.7 mm. The majority of the oyster specimens were in ripe-spawning stages, indicating that reproductive activities partly took place towards the end of the dry season. Both mature and immature individuals were subjected to harvesting at all the investigated fishing sites. The mean size of exploited oysters was 60.6 mm, lower than the size of females at maturity. Management strategies must enforce the minimum size of 65 mm required for harvesting, particularly in open access sites where juveniles are mostly harvested.