Identification of Direct Target Genes Using Joint Sequence and Expression Likelihood with Application to DAF-16

A major challenge in the post-genome era is to reconstruct regulatory networks from the biological knowledge accumulated up to date. The development of tools for identifying direct target genes of transcription factors (TFs) is critical to this endeavor. Given a set of microarray experiments, a probabilistic model called TRANSMODIS has been developed which can infer the direct targets of a TF by integrating sequence motif, gene expression and ChIP-chip data. The performance of TRANSMODIS was first validated on a set of transcription factor perturbation experiments (TFPEs) involving Pho4p, a well studied TF in Saccharomyces cerevisiae. TRANSMODIS removed elements of arbitrariness in manual target gene selection process and produced results that concur with one's intuition. TRANSMODIS was further validated on a genome-wide scale by comparing it with two other methods in Saccharomyces cerevisiae. The usefulness of TRANSMODIS was then demonstrated by applying it to the identification of direct targets of DAF-16, a critical TF regulating ageing in Caenorhabditis elegans. We found that 189 genes were tightly regulated by DAF-16. In addition, DAF-16 has differential preference for motifs when acting as an activator or repressor, which awaits experimental verification. TRANSMODIS is computationally efficient and robust, making it a useful probabilistic framework for finding immediate targets

Bactericidal activity of methanol extracts of crabapple mangrove tree (Sonneratia caseolaris Linn.) against multi-drug resistant pathogens

The crabapple mangrove tree, Sonneratia caseolaris Linn. (Family: Sonneratiaceae), is one of the foreshore plants found in estuarine and tidal creek areas and mangrove forests. Bark and fruit extracts from this plant have previously been shown to have an anti-oxidative or cytotoxic effect, whereas flower extracts of this plant exhibited an antimicrobial activity against some bacteria. According to the traditional folklore, it is medicinally used as an astringent and antiseptic. Hence, this investigation was carried out on the extract of the leaves, pneumatophore and different parts of the flower or fruit (stamen, calyx, meat of fruit, persistent calyx of fruit and seeds) for antibacterial activity using the broth microdilution method. The antibacterial activity was evaluated against five antibiotic-sensitive species (three Gram-positive and two Gram-negative bacteria) and six drug-resistant species (Gram-positive i.e. Methicillin-resistant Staphylococcus aureus, Enterococcus faecalis, Enterococcus faecium and Gram-negative i.e. Extended-spectrum beta-lactamase-Escherichia coli, multidrug-resistant-Pseudomonas aeruginosa and Acenetobacter baumannii). The methanol extracts from all tested parts of the crabapple mangrove tree exhibited antibacterial activity against both Gram-positive and Gram-negative bacteria, but was mainly a bactericidal against the Gram-negative bacteria, including the multidrug-resistant strains, when compared with only bacteriostatic on the Gram-positive bacteria. Using Soxhlet apparatus, the extracts obtained by sequential extraction with hexane, dichloromethane and ethyl acetate revealed no discernable antibacterial activity and only slightly, if at all, reduced the antibacterial activity of the subsequently obtained methanol extract. Therefore, the active antibacterial compounds of the crabapple mangrove tree should have a rather polar structure

Disentangling genetic and epigenetic determinants of ultrafast adaptation

A major rationale for the advocacy of epigenetically mediated adaptive responses is that they facilitate faster adaptation to environmental challenges. This motivated us to develop a theoretical–experimental framework for disclosing the presence of such adaptation‐speeding mechanisms in an experimental evolution setting circumventing the need for pursuing costly mutation–accumulation experiments. To this end, we exposed clonal populations of budding yeast to a whole range of stressors. By growth phenotyping, we found that almost complete adaptation to arsenic emerged after a few mitotic cell divisions without involving any phenotypic plasticity. Causative mutations were identified by deep sequencing of the arsenic‐adapted populations and reconstructed for validation. Mutation effects on growth phenotypes, and the associated mutational target sizes were quantified and embedded in data‐driven individual‐based evolutionary population models. We found that the experimentally observed homogeneity of adaptation speed and heterogeneity of molecular solutions could only be accounted for if the mutation rate had been near estimates of the basal mutation rate. The ultrafast adaptation could be fully explained by extensive positive pleiotropy such that all beneficial mutations dramatically enhanced multiple fitness components in concert. As our approach can be exploited across a range of model organisms exposed to a variety of environmental challenges, it may be used for determining the importance of epigenetic adaptation‐speeding mechanisms in general