Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

Background: Regulation of gene expression in Plasmodium falciparum (Pf) remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found. Results: The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf. Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. Four motifs – the 'G-rich', the 'C-rich', the 'TGTG' and the 'CACA' motifs – were identified, and zero to all four of these occur in the 13 sets of upstream regions. The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. For functional groups expressed in each transition, the motifs tended to be similar. Upstream motifs in some functional groups showed 'positional conservation' by occurring at similar positions relative to the translational start site (TLS); this increases their significance as regulatory motifs. In the ribonucleotide synthesis, mitochondrial, proteasome and organellar translation machinery genes, G-rich, C-rich, CACA and TGTG motifs, respectively, occur with striking positional conservation. In the organellar translation machinery group, G-rich motifs occur close to the TLS. The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action. Conclusion: The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

A new Fuzzy-LOGIC based Model for Chlorophyll-a in Pulicat Lagoon, India

Coastal lagoons are complex ecosystems exhibiting a high degree of non-linearity in the distribution and exchange of nutrients dissolved in the water column due to their spatio-temporal characteristics. This factor has a direct influence on the concentrations of chlorophyll-a, an indicator of the primary productivity in the water bodies as lakes and lagoons. Moreover the seasonal variability in the characteristics of large-scale basins further contributes to the uncertainties in the data on the physico-chemical and biological characteristics of the lagoons. Considering the above, modelling the distributions of the nutrients with respect to the chlorophyll-concentrations, hence requires an effective approach which will appropriately account for the non-linearity of the ecosystem as well as the uncertainties in the available data. In the present investigation, fuzzy logic was used to develop a new model of the primary production for Pulicat lagoon, Southeast coast of India. Multiple regression analysis revealed that the concentrations of chlorophyll-a in the lagoon was highly influenced by the dissolved concentrations of nitrate, nitrites and phosphorous to different extents over different seasons and years. A high degree of agreement was obtained between the actual field values and those predicted by the new fuzzy model (d = 0.881 to 0.788) for the years 2005 and 2006, illustrating the efficiency of the model in predicting the values of chlorophyll-a in the lagoon.