Showing papers by "Sudip Kundu published in 2014"

Genome Wide Expression Profiling during Spinal Cord Regeneration Identifies Comprehensive Cellular Responses in Zebrafish

Abstract: Background Among the vertebrates, teleost and urodele amphibians are capable of regenerating their central nervous system. We have used zebrafish as a model to study spinal cord injury and regeneration. Relatively little is known about the molecular mechanisms underlying spinal cord regeneration and information based on high density oligonucleotide microarray was not available. We have used a high density microarray to profile the temporal transcriptome dynamics during the entire phenomenon.

Metabolic trade-offs between biomass synthesis and photosynthate export at different light intensities in a genome-scale metabolic model of rice.

Abstract: Previously we have used a genome scale model of rice metabolism to describe how metabolism reconfigures at different light intensities in an expanding leaf of rice. Although this established that the metabolism of the leaf was adequately represented, in the model, the scenario was not that of the typical function of the leaf --- to provide material for the rest of the plant. Here we extend our analysis to explore the transition to a source leaf as export of photosynthate increases at the expense of making leaf biomass precursors, again as a function of light intensity. In particular we investigate whether, when the leaf is making a smaller range of compounds for export to the phloem, the same changes occur in the interactions between mitochondrial and chloroplast metabolism as seen in biomass synthesis for growth when light intensity increases. Our results show that the same changes occur qualitatively, though there are slight quantitative differences reflecting differences in the energy and redox requirements for the different metabolic outputs.

Sequence and 3D structure based analysis of TNT degrading proteins in Arabidopsis thaliana.

Abstract: TNT, accidentally released at several manufacturing sites, contaminates ground water and soil It has a toxic effect to algae and invertebrate, and chronic exposure to TNT also causes harmful effects to human On the other hand, many plants including Arabidopsis thaliana have the ability to metabolize TNT either completely or at least to a reduced less toxic form In A thaliana, the enzyme UDP glucosyltransferase (UDPGT) can further conjugate the reduced forms 2-HADNT and 4-HADNT (2-hydroxylamino-4, 6- dinitrotoluene and 4-hydroxylamino-2, 6- dinitrotoluene) of TNT Based on the experimental analysis, existing literature and phylogenetic analysis, it is evident that among 107 UDPGT proteins only six are involved in the TNT degrading process A total of 13 UDPGT proteins including five of these TNT degrading proteins fall within the same group of phylogeny Thus, these 13 UDPGT proteins have been classified into two groups, TNT-degrading and TNT-non-degrading proteins To understand the differences in TNT-degrading capacities; using homology modeling we first predicted two structures, taking one representative sequence from both the groups Next, we performed molecular docking of the modeled structure and TNT reduced form 2-hydroxylamino-4, 6- dinitrotoluene (2-HADNT) We observed that while the Trp residue located within the active site region of the TNT- degrading protein showed π-Cation interaction; such type of interaction was absent in TNT-non-degrading protein, as the respective Trp residue lay outside of the pocket in this case We observed the conservation of this π-Cation interaction during MD simulation of TNT-degrading protein Thus, the position and the orientation of the active site residue Trp could explain the presence and absence of TNT-degrading capacity of the UDPGT proteins

Estimating malaria parasitaemia in images of thin smear of human blood

Abstract: Digital image processing techniques are being explored for accurate and timely diagnosis of malaria, a serious parasitic infection of humans. A key decision factor in the diagnosis is the degree of infection, also called parasitaemia. This paper presents an efficient method for estimating parasitaemia using the digital images of thin blood smears that has been stained with Gimsa or equivalent stain. The method utilizes the 4-connected set properties of digital images to identify the various regions existing within the image. Properties of the different identified regions, such as centroids, major and minor axis, etc., are used to arrive at the number of RBCs (good and infected) present in the image. The method addresses the issues of partially visible RBCs, as well as that of overlapped RBCs. It also addresses image imperfections, caused by dust on the slide, etc.

No3CoGP: non-conserved and conserved coexpressed gene pairs.

Abstract: Background Analyzing the microarray data of different conditions, one can identify the conserved and condition-specific genes and gene modules, and thus can infer the underlying cellular activities. All the available tools based on Bioconductor and R packages differ in how they extract differential coexpression and at what level they study. There is a need for a user-friendly, flexible tool which can start analysis using raw or preprocessed microarray data and can report different levels of useful information.