Deciphering the cross-talking of human competitive endogenous RNAs in K562 chronic myelogenous leukemia cell line.

Chronic myelogenous leukemia (CML) is a myeloproliferative disorder characterized by increased proliferation or abnormal accumulation of granulocytic cell line without the depletion of their capacity to differentiate. A reciprocal chromosomal translocation proceeding to the 'Philadelphia chromosome', involving the ABL proto-oncogene and BCR gene residing on Chromosome 9 and 22 respectively, is observed to be attributed to CML pathogenesis. Recent studies have been unraveling the crucial role of genomic 'dark matter' or the non-coding repertoire in cancer initiation and progression. The intricate cross-talk between competitive endogenous RNAs (ceRNAs) provides a scaffold to systematically functionalize the miRNA response element harboring non-coding RNAs and incorporate them with the protein-coding RNA dimension in complex ceRNA networks. This network of coding and non-coding transcriptome linked by shared miRNAs evidently offers a platform to elucidate the complex regulatory interactions at the post-transcriptional level in human cancers. In this context, analyzing CML, from the perspective of the ceRNA hypothesis, surely craves intensive attention and a comprehensive discussion. Here, we performed RNA-seq data analysis to retrieve Lymphoblastoid and CML coding as well as non-coding repertoire and constructed a ceRNA network for the CML cell line, considering the non-cancer lymphoblastoid cell line as the control. We investigated if any alteration exists in the ceRNA landscape of the transcripts which are exhibiting differential expression across the two cell lines and observed that the major ceRNA regulators vary in cancer network when compared with the Lymphoblastoid network. The top ranked significant functional modules in the ceRNA network display cancer associated attributes and reveal putative regulators in CML pathogenesis.

Genomic adaptation of prokaryotic organisms at high temperature.

One of the central issues of evolutionary genomics is to find out the adaptive strategies of microorganisms to stabilize nucleic acid molecules under high temperature. Thermal adaptation hypothesis gives a link between G+C content and growth temperature if there is a considerable variation of guanine and cytosine content between species. However, there has been a long-standing debate regarding the correlations between genomic GC content and optimal growth temperature (Topt). We urged that adaptation to growth at high temperature requires a coordinated set of evolutionary changes affecting: (i) nucleic acid thermostability and (ii) stability of codon-anticodon interactions. Moreover, in Bacillaceae family we have demonstrated that a higher genomic GC level do not have any role in stabilizing mRNA secondary structure at high growth temperature. Comparative analysis between homologous sequences of thermophilic Thermus thermophilus and mesophilic Deinococcus radiodurans suggests that increased levels of GC contents in the coding sequence corresponding to strand structure of Thermus thermophilus genes have stabilizing effect on the mRNA secondary structure, whereas increased levels of GC contents in coding sequences corresponding to aperiodic structure have destabilizing effect on the mRNA secondary structure. In this perspective, a critical review of thermal adaptation hypothesis is further advocated.

Neutron reactions in accreting neutron stars: a new pathway to efficient crust heating.

In our calculation of neutron star crust heating we include several key new model features. In earlier work electron capture (EC) only allowed neutron emission from the daughter ground state; here we calculate, in a deformed quasi-random-phase approximation (QRPA) model, EC decay rates to all states in the daughter that are allowed by Gamow-Teller selection rules and energetics. The subsequent branching ratios between the 1n,...,xn channels and the competing gamma decay are calculated in a Hauser-Feshbach model. In our multicomponent plasma model a single (EC, xn) reaction step can produce several neutron-deficient nuclei, each of which can further decay by (EC, xn). Hence, the neutron emission occurs more continuously with increasing depth as compared to that in a one-component plasma model.

Studies on synonymous codon and amino acid usage biases in the broad-host range bacteriophage KVP40.

In this study, the relative synonymous codon and amino acid usage biases of the broad-host range phage, KVP40, were investigated in an attempt to understand the structure and function of its proteins/protein-coding genes, as well as the role of its tRNAs. Synonymous codons in KVP40 were determined to be ATrich at the third codon positions, and their variations are dictated principally by both mutational bias and translational selection. Further analysis revealed that the RSCU of KVP40 is distinct from that of its Vibrio hosts, V. cholerae and V. parahaemolyticus. Interestingly, the expression of the putative highly expressed genes of KVP40 appear to be preferentially influenced by the abundant host tRNA species, whereas the tRNAs expressed by KVP40 may be required for the efficient synthesis of all its proteins in a diverse array of hosts. The data generated in this study also revealed that KVP40 proteins are rich in low molecular weight amino acid residues, and that these variations are influenced primarily by hydropathy, mean molecular weight, aromaticity, and cysteine content.

Compositional correlations in canine genome reflects similarity with human genes.

The base compositional correlations that hold among various coding and noncoding regions of the canine genome have been analysed. The distribution pattern of genes, on the basis of GC(3) composition, shows a wide range similar to that observed in human. However the occurrence of maximum number of genes was observed in the range of 65-75% of GC(3) composition. The correlation between the coding DNA sequences of canine with the different noncoding regions (introns and flanking regions) is found to be significant and in many cases the degree of correlation show similarity to human genome. We found that these correlations are not limited to the GC content alone, but is holding at the level of the frequency of individual bases as well. The present study suggests that canines ideally belong to the predicted 'general mammalian pattern' of genome composition along with human beings.

Synonymous codon usage analysis of the mycobacteriophage Bxz1 and its plating bacteria M. smegmatis: identification of highly and lowly expressed genes of Bxz1 and the possible function of its tRNA species.

The extent of codon usage in the protein coding genes of the mycobacteriophage, Bxz1, and its plating bacteria, M. smegmatis, were determined, and it was observed that the codons ending with either G and / or C were predominant in both the organisms. Multivariate statistical analysis showed that in both organisms, the genes were separated along the first major explanatory axis according to their expression levels and their genomic GC content at the synonymous third positions of the codons. The second major explanatory axis differentiates the genes according to their genome type. A comparison of the relative synonymous codon usage between 20 highly- and 20 lowly expressed genes from Bxz1 identified 21 codons, which are statistically over represented in the former group of genes. Further analysis found that the Bxz1- specific tRNA species could recognize 13 out of the 21 over represented synonymous codons, which incorporated 13 amino acid residues preferentially into the highly expressed proteins of Bxz1. In contrast, seven amino acid residues were preferentially incorporated into the lowly expressed proteins by 10 other tRNA species of Bxz1. This analysis predicts for the first time that the Bxz1-specific tRNA species modulates the optimal expression of its proteins during development.