Siddhartha Sankar Satapathy

TREEPSI: tree based energy efficient protocol for sensor information

Limited battery powers of sensor nodes demand routing protocol for sensor network that consume minimum possible amount of energy and hence give longer life to the system. In a sensor network, sensor nodes are the potential source of information and they need to send their sensed/collected information to a remote base station (BS)/Sink. Generally, it needs a fixed amount of energy to receive one bit of information and an additional amount of energy to transmit the same. This additional amount depends on the transmission range. So, if all nodes transmit directly to the BS, then they will quickly deplete their energy. Therefore, a multi-hop routing protocol is needed to give longer life of the network. LEACH (aW. Heinzelman et al., 2000) (aW. Heinzelman et al., 2000) is an elegant energy efficient protocol where clusters are formed to fuse data before transmission to base station. By randomizing the cluster heads chosen to transmit to the base station, LEACH achieves a factor of 8 improvements over direct transmission, as measured in terms of nodes longevity. PEGASIS (aS. Lindsey and C. Raghavendra, 2001, 2002) is a chain based protocol that is an improvement over LEACH. In PEGASIS, each node communicates only with a close neighbor and takes turns in transmitting to the base station, thus reducing the amount of energy spent per round. It performs better than LEACH by about 100 - 300% for different network sizes and topologies. In this paper, we propose TREEPSI (tree based energy efficient protocol for sensor information) which gives up to 30% better performance (in terms of energy efficiency) than PEGASIS

Transfer RNA Gene Numbers may not be Completely Responsible for the Codon Usage Bias in Asparagine, Isoleucine, Phenylalanine, and Tyrosine in the High Expression Genes in Bacteria

It is generally believed that the effect of translational selection on codon usage bias is related to the number of transfer RNA genes in bacteria, which is more with respect to the high expression genes than the whole genome. Keeping this in the background, we analyzed codon usage bias with respect to asparagine, isoleucine, phenylalanine, and tyrosine amino acids. Analysis was done in seventeen bacteria with the available gene expression data and information about the tRNA gene number. In most of the bacteria, it was observed that codon usage bias and tRNA gene number were not in agreement, which was unexpected. We extended the study further to 199 bacteria, limiting to the codon usage bias in the two highly expressed genes rpoB and rpoC which encode the RNA polymerase subunits β and β′, respectively. In concordance with the result in the high expression genes, codon usage bias in rpoB and rpoC genes was also found to not be in agreement with tRNA gene number in many of these bacteria. Our study indicates that tRNA gene numbers may not be the sole determining factor for translational selection of codon usage bias in bacterial genomes.It is generally believed that the effect of translational selection on codon usage bias is related to the number of transfer RNA genes in bacteria, which is more with respect to the high expression genes than the whole genome. Keeping this in the background, we analyzed codon usage bias with respect to asparagine, isoleucine, phenylalanine, and tyrosine amino acids. Analysis was done in seventeen bacteria with the available gene expression data and information about the tRNA gene number. In most of the bacteria, it was observed that codon usage bias and tRNA gene number were not in agreement, which was unexpected. We extended the study further to 199 bacteria, limiting to the codon usage bias in the two highly expressed genes rpoB and rpoC which encode the RNA polymerase subunits β and β′, respectively. In concordance with the result in the high expression genes, codon usage bias in rpoB and rpoC genes was also found to not be in agreement with tRNA gene number in many of these bacteria. Our study indicates that tRNA gene numbers may not be the sole determining factor for translational selection of codon usage bias in bacterial genomes.

Selection on GGU and CGU codons in the high expression genes in bacteria.

The fourfold degenerate site (FDS) in coding sequences is important for studying the effect of any selection pressure on codon usage bias (CUB) because nucleotide substitution per se is not under any such pressure at the site due to the unaltered amino acid sequence in a protein. We estimated the frequency variation of nucleotides at the FDS across the eight family boxes (FBs) defined as Um(g), the unevenness measure of a gene g. The study was made in 545 species of bacteria. In many bacteria, the Um(g) correlated strongly with Nc′—a measure of the CUB. Analysis of the strongly correlated bacteria revealed that the U-ending codons (GGU, CGU) were preferred to the G-ending codons (GGG, CGG) in Gly and Arg FBs even in the genomes with G+C % higher than 65.0. Further evidence suggested that these codons can be used as a good indicator of selection pressure on CUB in genomes with higher G+C %.

Cotranslational protein folding reveals the selective use of synonymous codons along the coding sequence of a low expression gene.

Due to the degeneracy in the genetic code, many amino acids are encoded by more than one codon, called synonymous codons. The usage of synonymous codons in a coding sequence is not random, a phenomenon known as codon usage bias (CUB) that occurs in all genomes. It is believed that synonymous codons are not equivalent with respect to their coding efficiency during translation. This phenomenon has been demonstrated by the difference between the high expression genes (HEG) and low expression genes (LEG) within a genome with respect to the compositional abundance values of different synonymous codons (Ermolaeva 2001; Hershberg and Petrov 2008; Plotkin and Kudla 2011). Optimal codons, whose frequency is higher in HEGs than in LEGs or whole genome, are believed to be translated more rapidly and accurately than the other synonymous codons or nonoptimal codons (Sharp et al. 2005; Ran and Higgs 2010; Satapathy et al. 2014). As greater numbers of proteins are synthesized by the HEGs (Ghaemmaghami et al. 2003; dos Reis et al. 2003; Ishihama et al. 2008; Hiraoka et al. 2009), selection pressure on the coding sequence of these genes is believed to be higher for efficient translation to occur. Therefore, synonymous codons that are more efficient in translation are found in higher frequency in these genes in comparison to the LEGs (Satapathy et al. 2012). Thus, the translational selection pressure is considered to be the major determining factor for CUB in HEGs. In contrast, translational selection pressure is believed to be weaker in LEGs as a fewer number of protein molecules are synthesized by these genes. Therefore, CUB in LEGs are predominantly determined by mutation pressures such as genomeG+C composition (Muto and Osawa 1987; Palidwor et al. 2010) and strand

Higher tRNA diversity in thermophilic bacteria: A possible adaptation to growth at high temperature

We have done a comparative study of tRNA diversity and total tRNA genes among different strains of bacteria with respect to the optimum growth temperature of the cells. Our observation suggests that higher tRNA diversity usually occurs in thermophiles in comparison to non-thermophiles. Among psychrophiles total tRNA was observed to be more than two-fold higher than in the non-psychrophiles. Though tRNA diversity and total tRNA have recently been shown to be affected by an organisms genomic GC% and growth rate, this work is the first report on growth temperature affecting these features in bacteria. This work extends the list of molecular features undergoing adaptation due to growth temperature and supports the view that growth temperature acts as a selecting factor at the molecular level during evolution.

Codon degeneracy and amino acid abundance influence the measures of codon usage bias: improved Nc (N̂c) and ENCprime (N̂′c) measures

Effective number of codons ( N^c ) and its variant N^′c (effective number of codons prime) are the two widely used methods for measuring unequal usage of synonymous codons in coding sequences, known as the codon usage bias (CUB). The mathematical formula used in calculating N^c and N^′c values is giving inappropriate measures of CUB in case of low abundance of amino acids. In addition, the magnitude of error also varies according to codon degeneracy. In this study, a modified formula for N^c and N^′c has been developed to measure the CUB more accurately. Online implementations of the modified formula are available in the web portal at http://agnigarh.tezu.ernet.in/~ssankar/cub.php.

Comparative analysis of codon usage bias in Crenarchaea and Euryarchaea genome reveals differential preference of synonymous codons to encode highly expressed ribosomal and RNA polymerase proteins

The present study was undertaken to investigate the pattern of optimal codon usage in Archaea. Comparative analysis was executed to understand the pattern of codon usage bias between the high expression genes (HEG) and the whole genomes in two Archaeal phyla, Crenarchaea and Euryarchaea. The G + C% of the HEG was found to be less in comparison to the genome G + C% in Crenarchaea, whereas reverse was the case in Euryarchaea. The preponderance of U/A ending codons that code for HEG in Crenarchaea was in sharp contrast to the C/G ended ones in Euryarchaea. The analysis revealed prevalence of U-ending codons even within the WWY (nucleotide ambiguity code) families in Crenarchaea vis-à-vis Euryarchaea, bacteria and Eukarya. No plausible interpretation of the observed disparity could be made either in the context of tRNA gene composition or genome G + C%. The results in this study attested that the preferential biasness for codons in HEG of Crenarchaea might be different from Euryarchaea. The main highlights are (i) varied CUB in the HEG and in the whole genomes in Euryarchaea and Crenarchaea. (ii) Crenarchaea was found to have some unusual optimal codons (OCs) compared to other organisms. (iii) G + C% (and GC3) of the HEG were different from the genome G + C% in the two phyla. (iv) Genome G + C% and tRNA gene number failed to explain CUB in Crenarchaea. (v) Translational selection is possibly responsible for A + T rich OCs in Crenarchaea.

Discrepancy among the synonymous codons with respect to their selection as optimal codon in bacteria

The different triplets encoding the same amino acid, termed as synonymous codons, are not equally abundant in a genome. Factors such as G + C% and tRNA are known to influence their abundance in a genome. However, the order of the nucleotide in each codon per se might also be another factor impacting on its abundance values. Of the synonymous codons for specific amino acids, some are preferentially used in the high expression genes that are referred to as the ‘optimal codons’ (OCs). In this study, we compared OCs of the 18 amino acids in 221 species of bacteria. It is observed that there is amino acid specific influence for the selection of OCs. There is also influence of phylogeny in the choice of OCs for some amino acids such as Glu, Gln, Lys and Leu. The phenomenon of codon bias is also supported by the comparative studies of the abundance values of the synonymous codons with same G + C. It is likely that the order of the nucleotides in the triplet codon is also perhaps involved in the phenomenon of codon usage bias in organisms.

Constraint on di-nucleotides by codon usage bias in bacterial genomes.

It has been reported earlier that the relative di-nucleotide frequency (RDF) in different parts of a genome is similar while the frequency is variable among different genomes. So RDF is termed as genome signature in bacteria. It is not known if the constancy in RDF is governed by genome wide mutational bias or by selection. Here we did comparative analysis of RDF between the inter-genic and the coding sequences in seventeen bacterial genomes, whose gene expression data was available. The constraint on di-nucleotides was found to be higher in the coding sequences than that in the inter-genic regions and the constraint at the 2nd codon position was more than that in the 3rd position within a genome. Further analysis revealed that the constraint on di-nucleotides at the 2nd codon position is greater in the high expression genes (HEG) than that in the whole genomes as well as in the low expression genes (LEG). We analyzed RDF at the 2nd and the 3rd codon positions in simulated coding sequences that were computationally generated by keeping the codon usage bias (CUB) according to genome G+C composition and the sequence of amino acids unaltered. In the simulated coding sequences, the constraint observed was significantly low and no significant difference was observed between the HEG and the LEG in terms of di-nucleotide constraint. This indicated that the greater constraint on di-nucleotides in the HEG was due to the stronger selection on CUB in these genes in comparison to the LEG within a genome. Further, we did comparative analyses of the RDF in the HEG rpoB and rpoC of 199 bacteria, which revealed a common pattern of constraints on di-nucleotides at the 2nd codon position across these bacteria. To validate the role of CUB on di-nucleotide constraint, we analyzed RDF at the 2nd and the 3rd codon positions in simulated rpoB/rpoC sequences. The analysis revealed that selection on CUB is an important attribute for the constraint on di-nucleotides at these positions in bacterial genomes. We believe that this study has come with major findings of the role of CUB on di-nucleotide constraint in bacterial genomes.

A symmetric key based secured data gathering protocol for WSN

Wireless sensor network (WSN) is usually used in civil and military applications for gathering data from the surrounding environment. As WSN is a self configured network and mostly works in an unattended wireless environment, there is a lot of scope for the adversaries to tamper the sensed data as well as may try to alter the underlying working principle of the network. Several factors like, physical exposure of the sensor nodes to the adversaries, the ad-hoc network infrastructure etc. makes WSN more prone to security threats. Providing security solution to the WSN is again a difficult task due to inherent constraints associated with the sensor nodes like, limited processing power, smaller memory and fixed battery power. Security solutions based on public key cryptography are not usually recommended for WSN because of comparatively more computational cost. In this paper we have analyzed different security threats associated with the energy efficient data gathering protocol HCEPSN and proposed a symmetric key based security solution to it.