Occurrence of Horizontal Gene Transfer of PIB-type ATPase Genes among Bacteria Isolated from the Uranium Rich Deposit of Domiasiat in North East India

Uranium (U) tolerant aerobic heterotrophs were isolated from the subsurface soils of one of the pre-mined U-rich deposits at Domiasiat located in the north-eastern part of India. On screening of genomic DNA from 62 isolates exhibiting superior U and heavy metal tolerance, 32 isolates were found to be positive for P_IB-type ATPase genes. Phylogenetic incongruence and anomalous DNA base compositions revealed the acquisition of P_IB-type ATPase genes by six isolates through horizontal gene transfer (HGT). Three of these instances of HGT appeared to have occurred at inter-phylum level and the other three instances indicated to have taken place at intra-phylum level. This study provides an insight into one of the possible survival strategies that bacteria might employ to adapt to environments rich in uranium and heavy metals.     

Induction of spherule formation in Physarum polycephalum by polyols

A method has been developed for inducing spherule formation (spherulation) in the myxomycete Physarum polycephalum by transferring the culture to synthetic medium containing 0.5 m mannitol or other polyols. This morphogenetic process occurred within 12 to 35 hr after the inducer was added. The mature spherules existed as distinct morphogenetic units, in contrast to the clusters of spherules formed during starvation. Ninety per cent of the spherules germinated by 24 hr in synthetic medium. The changes in the synthesis of ribonucleic acid (RNA), deoxyribonucleic acid (DNA), and protein during plasmodial growth, spherulation, and germination of spherules are described. When spherule formation was completed, RNA, protein, and DNA decreased, compared with the values at the beginning of the conversion. The incorporation of (3)H-uridine into trichloroacetic acid-insoluble material was different in each of these periods, and this incorporation was sensitive to actinomycin D. The amount of glycogen increased during growth, whereas it decreased during spherulation. (14)C-glucose could be taken up by the cells in the presence of the inducer, and mannitol could not replace glucose as a source of energy. The mode of action of mannitol and its mechanism of induction are discussed.     

Handling class imbalance problem in miRNA dataset associated with cancer

MiRNAs are small (~22nt long) non-coding RNA sequences; binds to the complementarity target sites in 3'' Untranslated Region (UTR) of mRNA sequences but not restricted to other mRNA regions viz., 5'' UTR and Coding sequences (CDS). Complementarity binding of miRNA to mRNA target sites either results in complete degradation of the mRNA itself or it may regulate the mRNA as an oncogene or as a tumor suppressor gene. However, the exact mechanism involved in identifying a miRNA to be associated with cancer is still unclear. Further, with the outburst in the number of miRNAs sequences recorded every year in miRBase, the gap is still widening mainly due to the laborious and economically unfavorable experimental procedures associated with the functional annotation. Motivated by the fact, we constructed a two-step support vector machine-based predictive model - miRSEQ and miRINT. However, the major pitfall during the construction of the model is the class imbalance problem. Hence, in order to overcome class imbalance problem, in the present study we empirically compare the effectiveness of two different methods viz., Synthetic Minority Oversampling Technique (SMOTE) and cost-senstive learning method. Performance measures were evaluated in terms of Precision and Recall. Based on our result, it was observed that for miRNA dataset with high class imbalance utilized for predicting association of cancer, cost-sensitive method outperformed the oversampling method.     

Identification of UDP-linked murein precursors as contaminants in recombinant proteins of low molecular weight.

The A(280)/A(260) ratio of a purified protein is frequently used as an indication of the purity of the preparation with respect to nucleic acids. We show here that for low-molecular-weight recombinant proteins purified from Escherichia coli, a low A(280)/A(260) ratio can also result from contamination with UDP-linked murein precursors derived from bacterial cell wall metabolism. Although these precursors are small molecules of molecular weight 1000-1200, they comigrate in gel filtration with recombinant human FKBP (MW 11,820). This gel filtration behavior, which is distinct from that of unmodified mononucleotides, does not reflect binding interactions with FKBP, but is an intrinsic property of these precursors. Therefore, these molecules would be expected to copurify with other low-molecular-weight proteins, especially in the abbreviated purification protocols made possible by freeze-thaw release of recombinant proteins from E. coli (Johnson, B. H., and Hecht, M. H. (1994) BioTechnology 12, 1357-1360). Several alternative strategies are discussed for integrating these findings into the design of improved purification procedures for low-molecular-weight recombinant proteins.