DNA pattern recognition using canonical correlation algorithm.

We performed canonical correlation analysis as an unsupervised statistical tool to describe related views of the same semantic object for identifying patterns. A pattern recognition technique based on canonical correlation analysis (CCA) was proposed for finding required genetic code in the DNA sequence. Two related but different objects were considered: one was a particular pattern, and other was test DNA sequence. CCA found correlations between two observations of the same semantic pattern and test sequence. It is concluded that the relationship possesses maximum value in the position where the pattern exists. As a case study, the potential of CCA was demonstrated on the sequence found from HIV-1 preferred integration sites. The subsequences on the left and right flanking from the integration site were considered as the two views, and statistically significant relationships were established between these two views to elucidate the viral preference as an important factor for the correlation.

Stem cells in the light of evolution.

All organisms depend on stem cells for their survival. As a result, stem cells may be a prerequisite for the evolution of specific characteristics in organisms that include regeneration, multicellularity and coloniality. Stem cells have attracted the attention of biologists and medical scientists for a long time. These provide materials for regenerative medicine. We review in this paper, the link between modern stem cell research and early studies in ancient organisms. It also outlines details on stem cells in the light of evolution with an emphasis on their regeneration potential, coloniality and multicellularity. The information provided might be of use to molecular biologists, medical scientists and developmental biologists who are engaged in integrated research involving the stem cells.

Effect of caffeine, norfloxacin and nimesulide on heartbeat and VEGF expression of zebrafish larvae.

The use of pharmaceuticals during pregnancy may causes abnormalities to the embryo. Sometime the drug also effect to the new born if the drug transferred through lactation. We have used zebrafish model to see the effect of some pharmaceuticals on embryos and larvae. Three drugs, caffeine, norfloxacin and nimesulide, were used for this study to see the effect mainly the hatching rate of eggs, heart beat rate and the vascular endothelial growth factor (VEGF) expression of the larvae. VEGF is an important signaling protein that involved generating the new blood vessels during embryonic development. We have used 10, 20, 50, 100 Ag ml-1 concentrations of all the drugs to see the effect. No significant mortality or malformations were observed in zebrafish embryos. Hatching was stared from 60 hr. In control group, 91% hatching rate was observed. Lowest hatching rate was observed using highest concentration of norfloxacin (100 Ag ml-1) and nimesulide (100 Ag ml-1) i.e. 55 and 56% respectively. In control group, 110 to 115 heart beat rate was counted per minute. Significantly higher heart beat was observed in caffeine treated group which is 125 to140 min-1. Lower heart beat was noted in nimesulide treated group which is 100 min-1. We have tried to observe the possible effect of VEGF of the larvae by these three drugs. Expression of VEGF was very low in caffeine treated group. Almost no VGF expression was observe in 100 Ag ml-1 caffeine treated group. These studies suggest that there is a possibility that high dosage of caffeine can harm the unborn baby or new born babies, if the mothers use caffeine.

Mechanisms and roles of the RNA-based gene silencing

RNA silencing is a remarkable type of gene regulation. This process has been found to occur in many different organisms such as plants (co-suppression), fungi (quelling), and animals (RNA interference; RNAi). Double-stranded RNA (dsRNA) is a potent trigger in RNA silencing mechanisms operating in a wide range of organisms. This mechanism recognizes dsRNA and processes them into small 21-25nt RNAs (smRNAs). Small RNAs can guide post-transcriptional degradation of complementary messenger RNAs and in plants, transcriptional gene silencing is occurred by methylation of homologous DNA sequences. In plants, it serves as an antiviral defense, and many plant viruses encode suppressors of silencing such as helper component-proteinase of potyviruses (HC-Pro) and the p25 protein encoded by potato virus X (PVX). HC-Pro acts by preventing accumulation of smRNAs that provide specificity determinant for homologous RNA degradation, but p25 viral protein acts by targeting the mobile silencing signal. The encouraging view is that RNA silencing is part of a sophisticated network of interconnected pathways for cellular defense and development and that it may become a powerful tool to manipulate gene expression experimentally.

Overexpression for commercial production of recombinant human insulin as A-chain and B-chain fusion protein in Escherichia coli through genetically engineered plasmids.

The construction of expression vectors encoding either the human insulin A- or B-chains fused to a synthetic peptide and the temperature-induced expression of the recombinant genes in Escherichia coli are reported. Using this two-chain approach we also describe the separate isolation of the insulin A- and B-chains from inclusion bodies and their subsequent assembly into native human insulin. The expression yields about 600 mg of the insulin B-chain per litre of culture. Under similar conditions the expression yield of the insulin A-chain corresponds to approximately 500 mg per litre of culture. This is the highest yield from shake flask experiments.