Satyabrata Sahoo

Predicting Gene Expression Level from Relative Codon Usage Bias: An Application to Escherichia coli Genome

We present an expression measure of a gene, devised to predict the level of gene expression from relative codon bias (RCB). There are a number of measures currently in use that quantify codon usage in genes. Based on the hypothesis that gene expressivity and codon composition is strongly correlated, RCB has been defined to provide an intuitively meaningful measure of an extent of the codon preference in a gene. We outline a simple approach to assess the strength of RCB (RCBS) in genes as a guide to their likely expression levels and illustrate this with an analysis of Escherichia coli (E. coli) genome. Our efforts to quantitatively predict gene expression levels in E. coli met with a high level of success. Surprisingly, we observe a strong correlation between RCBS and protein length indicating natural selection in favour of the shorter genes to be expressed at higher level. The agreement of our result with high protein abundances, microarray data and radioactive data demonstrates that the genomic expression profile available in our method can be applied in a meaningful way to the study of cell physiology and also for more detailed studies of particular genes of interest.

Identity elements of archaeal tRNA.

Features unique to a transfer-RNA are recognized by the corresponding tRNA-synthetase. Keeping this in view we isolate the discriminating features of all archaeal tRNA. These are our identity elements. Further, we investigate tRNA-characteristics that delineate the different orders of Archaea.

Energy levels of the Fröhlich polaron in a spherical quantum dot

Abstract The one-phonon variational state is suitably applied to describe the ground state and excited states of the Frohlich polaron bound to a quantum dot. A general analytical expression for the electronic energy spectra and the polaron binding energy for different electronic subband bound states in a quantum dot is presented and discussed with reference to the parameters of a real solid.

Gene expression profile of the cynobacterium synechocystis genome

The expression of functional proteins plays a crucial role in modern biotechnology. The free-living cynobacterium Synechocystis PCC 6803 is an interesting model organism to study oxygenic photosynthesis as well as other metabolic processes. Here we analyze a gene expression profiling methodology, RCBS (the scores of relative codon usage bias) to elucidate expression patterns of genes in the Synechocystis genome. To assess the predictive performance of the methodology, we propose a simple algorithm to calculate the threshold score to identify the highly expressed genes in a genome. Analysis of differential expression of the genes of this genome reveals that most of the genes in photosynthesis and respiration belong to the highly expressed category. The other genes with the higher predicted expression level include ribosomal proteins, translation processing factors and many hypothetical proteins. Only 9.5% genes are identified as highly expressed genes and we observe that highly expressed genes in Synechocystis genome often have strong compositional bias in terms of codon usage. An important application concerns the automatic detection of a set of impact codons and genes that are highly expressed tend to use this narrow set of preferred codons and display high codon bias .We further observe a strong correlation between RCBS and protein length indicating natural selection in favor of shorter genes to be expressed at higher level. The better correlations of RCBS with 2D electrophoresis and microarray data for heat shock proteins compared to the expression measure based on codon usage difference, E(g) and codon adaptive index, CAI indicate that the genomic expression profile available in our method can be applied in a meaningful way to study the mRNA expression patterns, which are by themselves necessary for the quantitative description of the biological states.

tRNA-isoleucine-tryptophan composite gene.

Transfer-RNA genes in archaea often have introns intervening between exon sequences. The structural motif at the boundary between exon and intron is the bulge-helix-bulge. Computational investigations of these boundary structures in Haloarcula marismortui lead us to propose that tRNA-isoleucine and tRNA-tryptophan genes are co-located. Precise in silico identification of the splice-sites on the bulges at the exon-intron boundaries lead us to infer that a single intron-containing composite tRNA-gene can give rise to more than one gene product.

Structural clones of UAG decoding RNA.

Abstract Functions of non-coding RNAs are related in part to their secondary structures. We investigate the uniqueness of the secondary structure of a non-coding RNA (ncRNA) decoding UAG to read pyrrolysine (pyl). Nineteen archaeal methanogens are searched with our tRNA-pyl-tracker, TPYLT, perl-script downloadable from www.gyanxet.com. We observe that aside from the usual pyl-gene-cluster, pyl-carrying Methanosarcinaceae have a good number of conjugate-halves from pyl-tRNA (pylT) gene split at 37/38 spread over their genomes. On insilico ligation, the secondary structures of these pairs clone the clover-leaf of pylT of M. barkeri. Of these nineteen methanogens, four, namely, M. stadtmanae, M. kandleri, M. hungatei, and M. thermautotrophicus, have these pairs at levels at or higher than in the pyl-carrying ones. Screening these we arrive at four pairs, i.e., one from each of these four genomes. On ligation, these are close homologs of pylT gene of M. barkeri. The intervening sequences between the split pairs in these four cases are shown to nearly reproduce the known secondary structures at exon-intron boundaries.

The regular perturbation theory on the stability of the strong-coupling bipolaron

The regular perturbation method for the strong-coupling bipolaron is developed systematically. The ground-state energy of a bipolaron is calculated by the variational method as a function of the Frohlich coupling constants alpha and eta , the ratio of the optic to the static dielectric constant. It is found that the bipolaron is stable in a broad region of eta . The estimated upper bound of eta turns out to be 0.165.

A variational calculation of the stability of the two centre Fröhlich bipolaron

Abstract The formation of a two centre Frohlich bipolaron has been studied in analogy to the formation of a hydrogen molecule. It is shown, by a combination of a unitary transformation and the variational method, that a stable Frohlich bipolaron can exist if the ration of the optic and static dielectric constant satisfies a simple realistic inequality.

A new measure to study phylogenetic relations in the brown algal order Ectocarpales: the "codon impact parameter".

We analyse forty-seven chloroplast genes of the large subunit of RuBisCO, from the algal order Ectocarpales, sourced from GenBank. Codon-usage weighted by the nucleotide base-bias defines our score called the codon-impact-parameter. This score is used to obtain phylogenetic relations amongst the 47 Ectocarpales. We compare our classification with the ones done earlier.

The strong-coupling polaron in reduced dimensionality

Based on the LLP-H approach, a detailed study of the electron confinement in a polar semiconductor heterostructure has been made to derive analytically the ground state energy and the effective mass of the Frohlich polaron in quasi-two-dimensional (Q2D) and quasi-one-dimensional (Q1D) systems.