Biojournal of Science & Technology

Number 2, 2015

11
A multi-objective evolutionary approach to reconstruct gene regulatory network using recurrent neural network model

Authors: Sumon Ahmed, Md. Nurul Ahad Tawhid, Kazi Sakib, Md. Mustafizur Rahman

Abstract

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With the advent of various data assaying techniques, gene expression time series data have become a useful resource to investigate the complex interactions occurring amongst the transcription factors and genes. While a number of methodologies have been developed to describe Gene Regulatory Network (GRN), the presence of high noise in gene expression data have made the estimation of non-linear interactions among the genes an ill-posed one. In this work, a multi-objective evolutionary strategy has been proposed to efficiently reconstruct the skeletal structure of the biomolecular network using the Recurrent Neural Network (RNN) formalism. Moreover, this work presents a second criterion for model evaluation to exploit the sparse and scale free nature of GRN. This evaluation criterion systematically adapts the max-min in-degrees to effectively narrow down the search space, which reduces the computation time significantly and improves the model accuracy. The two well-known performance measures applied to the experimental studies on synthetic network with expression data having different noise-levels. The experimental results clearly demonstrate the suitability of the proposed method in capturing gene interactions correctly with high precision even with noisy time-series data. The experiments carried out on analyzing well-known real expression data set of the SOS DNA repair system in Escherichia coli show a significant improvement in reconstructing the network of key regulatory genes.

13
Identification of the positively selected genes governing host-pathogen arm race in Vibrio sp. through comparative genomics approach

Authors: Atai Rabby, Sajib Chakraborty*, Atiqur Rahman, Shamma Shakila Rahman, Shahjalal Soad, Kaniz Fatima Chanda, Rajib Chakravorty.

Abstract

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Bacterial evolution is due to the adaptive nature of the core bacterial genomes that plays critical role in diversification, fitness and adaptation of the species to different environment and host. Since Vibrio cholerae represents an appropriate model organism for studying the interplay of environment and host driven factors shaping the microbial genome structure and function, the current study aims to identify genes that are under these strong forces in V. cholerae. Here, we employed a comparative genomics approach to identify genes that are under positive selection in ten strains of Vibrio sp. including four pathogenic V. cholerae strains. From the available genome sequence data, a total of 422 orthologous genes were identified by reciprocal BLAST best-hit method, recombination breakpoint frequency analysis and tree comparison method. These 422 genes, representing the core genome of Vibrio sp., constituted the dataset to be analyzed for evolutionary selections. The analysis of natural selection, based on Maximum Likelihood method on synonymous and non-synonymous substitution rate, confirms the hypothesis that the bacterial core genomes are mostly under purifying selection with a few positively selected regions. However, our finding also reveals that positively selected sites in the Vibrio genome occur in a wide range of different genes encompassing diverse functional pathways including cell surface proteins (e.g. outer membrane-specific lipoprotein transporter/assembly proteins etc.), cell motility proteins (e.g. flagellar motor switch proteins, flagellar hook and assembly proteins), nutrient acquisition (e.g. amino acid, carbohydrate and phosphate ABC transporters), DNA repair and transcription related proteins. Interestingly, these positively selected gene products are directly involved with host-pathogen interactions and fitness in gastrointestinal environment. Therefore, the collective evidences of these positively selected genes spanning several pathways raise the possibility of their involvement in evolutionary arms races with other bacteria, phages, and/or the host immune system. This finding points to the natural selections which is the responsible factor for the diversification of Vibrio genus.