Pradeep Kumar Burma
Articles written in Journal of Biosciences
Volume 17 Issue 4 December 1992 pp 395-411
In this article we describe and demonstrate the versatility of a computer program, GENOME MAPPING, that uses interactive graphics and runs on an IRIS workstation. The program helps to visualize as well as analyse global and local patterns of genomic DNA sequences. It was developed keeping in mind the requirements of the human genome sequencing programme, which requires rapid analysis of the data. Using GENOME MAPPING one can discern signature patterns of different kinds of sequences and analyse such patterns for repetitive as well as rare sequence strings. Further, one can visualize the extent of global homology between different genomic sequences. An application of our method to the published yeast mitochondrial genome data shows similar sequence organizations in the entire sequence and in smaller subsequences
Volume 25 Issue 1 March 2000 pp 57-63 Articles
The two-element transposon constructs, utilizing either Ac/Ds or Spm/dSpm, allow random tagging of genes in heterologous model species, but are inadequate for directed tagging of specific alleles of agronomic importance. We propose the use of Ac/Ds in conjunction with Spm/dSpm to develop a four-element system for directed tagging of crop-specific alleles. The four-element based construct would include both Ds and dSpm along with relevant marker genes and would function in two steps. In the first step dSpm(Ds) stocks (a minimum of two) would be crossed to a line containing transposases of Spm and unlinked integrations would be selected from segregating population by the use of a negative selection marker to develop stocks representing integration of dSpm(Ds) at a large number of locations in the genome. Selections would be made for a line in which dSpm(Ds) shows partial or complete linkage to the allele of interest. In the second step selected line would be crossed to a line containing Ac transposase to induce transpositions of Ds element to linked sites thereby exploiting the natural tendency of Ds element to jump to linked sites. Unlinked jumps of dSpm(Ds) and linked jumps of Ds could be monitored by appropriate marker genes. The proposed model would allow tagging of allele of interest in chromosome addition lines and also help in the efficient use of genic male sterility systems for hybrid seed production by tightly marking the fertility restorer gene with a negative selection marker.
Volume 33 Issue 3 September 2008 pp 337-343 Articles
The assessment of activity of promoters has been greatly facilitated by the use of reporter genes. However, the activity as assessed by reporter gene is a reflection of not only promoter strength, but also that of the stability of the mRNA and the protein encoded by the reporter gene. While a stable reporter gene product is an advantage in analysing activities of weak promoters, it becomes a major limitation for understanding temporal expression patterns of a promoter, as the reporter product persists even after the activity of the promoter ceases. In the present study we undertook a comparative analysis of two reporter genes, 𝛽-
Volume 34 Issue 2 June 2009 pp 199-202 Brief communication
Volume 34 Issue 6 December 2009 pp 953-962 Articles
Variations in transgene expression due to position effect and copy number are normalized when analysing and comparing the strengths of different promoters. In such experiments, the promoter to be tested is placed upstream to a reporter gene and a second expression cassette is introduced in a linked fashion in the same transfer DNA (T-DNA). Normalization in the activity of the test promoter is carried out by calculating the ratio of activities of the test and reference promoters. When an appropriate number of independent transgenic events are analysed, normalization facilitates assessment of the relative strengths of the test promoters being compared. In this study, using different modified versions of the Cauliflower Mosaic Virus (CaMV) 35S promoter expressing the reporter gene 𝛽-
Volume 36 Issue 2 June 2011 pp 363-376 Articles
High levels of expression of the
Volume 43 Issue 2 June 2018 pp 351-364 Article
Sirtuins are a family of deacetylases (Class III histone deacetylases) with evolutionarily conserved functions in cellularmetabolism and chromatin regulation. Out of the seven human Sirtuins, the function of Sirt2 is the least understood. Thepurpose of the present study was to investigate the role of Sir2A, a homolog of human Sirt2 in Dictyostelium discoideum(Dd), a lower eukaryote. We created both overexpressing and deletion strains of Ddsir2A to analyse its functions. Weobserved sir2A mRNA expression throughout development and the transcript was present in the prespore/spore region ofmulticellular structures developed. They show a preference towards prestalk/stalk pathway when co-developed with wildtypecells during chimera formation. Deletion strain showed a multi-tipped phenotype, decrease in cell proliferation andinhibition of autophagy. In conclusion, our results show low cAMP levels, reduced cell-adhesion, weak cell migration andimpaired autophagy to be responsible for the phenotype shown by the null cells. This study provides new insights into thefunctions of Ddsir2A.