Biomedical subjects

B Jayashree

Publications and source records attributed to B Jayashree.

5 recordsLinked to original sources

PubMed2006

Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping.

BACKGROUND: With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow. RESULTS: A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics. CONCLUSION: A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from http://www.icrisat.org/gt-bt/lims/lims.asp.

Algorithms↗

PubMed2005

Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus.

BACKGROUND: Chickpea is a major crop in many drier regions of the world where it is an important protein-rich food and an increasingly valuable traded commodity. The wild annual Cicer species are known to possess unique sources of resistance to pests and diseases, and tolerance to environmental stresses. However, there has been limited utilization of these wild species by chickpea breeding programs due to interspecific crossing barriers and deleterious linkage drag. Molecular genetic diversity analysis may help predict which accessions are most likely to produce fertile progeny when crossed with chickpea cultivars. While, trait-markers may provide an effective tool for breaking linkage drag. Although SSR markers are the assay of choice for marker-assisted selection of specific traits in conventional breeding populations, they may not provide reliable estimates of interspecific diversity, and may lose selective power in backcross programs based on interspecific introgressions. Thus, we have pursued the development of gene-based markers to resolve these problems and to provide candidate gene markers for QTL mapping of important agronomic traits. RESULTS: An EST library was constructed after subtractive suppressive hybridization (SSH) of root tissue from two very closely related chickpea genotypes (Cicer arietinum). A total of 106 EST-based markers were designed from 477 sequences with functional annotations and these were tested on C. arietinum. Forty-four EST markers were polymorphic when screened across nine Cicer species (including the cultigen). Parsimony and PCoA analysis of the resultant EST-marker dataset indicated that most accessions cluster in accordance with the previously defined classification of primary (C. arietinum, C. echinospermum and C. reticulatum), secondary (C. pinnatifidum, C. bijugum and C. judaicum), and tertiary (C. yamashitae, C. chrossanicum and C. cuneatum) gene-pools. A large proportion of EST alleles (45%) were only present in one or two of the accessions tested whilst the others were represented in up to twelve of the accessions tested. CONCLUSION: Gene-based markers have proven to be effective tools for diversity analysis in Cicer and EST diversity analysis may be useful in identifying promising candidates for interspecific hybridization programs. The EST markers generated in this study have detected high levels of polymorphism amongst both common and rare alleles. This suggests that they would be useful for allele-mining of germplasm collections for identification of candidate accessions in the search for new sources of resistance to pests / diseases, and tolerance to abiotic stresses.

Biomarkers↗

PubMed2001

Mechanism of protection against radiation-induced DNA damage in plasmid pBR322 by caffeine.

PURPOSE: Caffeine (1,3,7-trimethyl xanthine), a dietary component, has been shown to have widely varying effects on DNA damage induced by UV and ionizing radiation, depending upon pre- or post-irradiation administration and its concentration. Caffeine administered post-UV irradiation is known to inhibit enzymatic repair of DNA lesions, leading to potentiation of damage, whereas its presence before or during irradiation elicits protection in a wide range of test systems: bacteria, cultured human cells, plant seeds and mouse. The purpose of this study is to test whether caffeine present during gamma-irradiation of plasmid DNA, a system devoid of replication and repair, could elicit protection by scavenging free radicals. MATERIALS AND METHODS: Plasmid pBR322 DNA was exposed to gamma-radiation in the presence or absence of caffeine at a dose-rate of 1.20 Gy min(-1) and damage measured as single-strand breaks. To understand the mechanisms of the observed protection, especially under oxic conditions, reaction of caffeine with superoxide radical (O(2)(-)), hydrogen peroxide (H(2)O(2)) and the deoxyribose peroxyl radical (ROO(*)) were studied. RESULTS: Irradiation of pBR322 was observed to induce a dose-dependent increase in single-strand breaks. Caffeine itself did not induce strand breaks but reduced radiation-induced strand breaks at micromolar to millimolar concentrations. Caffeine has been shown to react with the radiation-derived oxidants. The reaction rate constants observed were 7.5x10(1) M(-1) s(-1) with O(2)(-) 1.05x10(8) M(-1) s(-1) with ROO(*) and 8.8x10(1) M(-1) s(-1) with H(2)O(2). CONCLUSIONS: Caffeine effectively protects DNA against ionizing radiation in a system devoid of repair and replication machinery. Thus, DNA protection shown by caffeine is possibly due to the scavenging of radiation-derived primary as well as secondary reactive oxygen species, and this physicochemical protective pathway possibly pre-empts any subsequent inhibitory effect of caffeine on the enzymatic repair of DNA.

Caffeine↗

PubMed2000

Differential modification by caffeine of oxygen-dependent and independent effects of gamma-irradiation on rat liver mitochondria.

PURPOSE: Following the demonstration that caffeine effectively competes with oxygen for electrons and also scavenges hydroxyl radicals and singlet oxygen, the differential modification of oxygen-dependent and independent effects of gamma-radiation by caffeine in membranes was examined, using rat liver mitochondria as a model system. MATERIALS AND METHODS: Mitochondria were isolated from the livers of Wistar rats and exposed to gamma-radiation in the dose range of 45-600 Gy (dose rate 15 Gy/min) in the presence or absence of caffeine. To examine the 'oxygen effect', post-irradiation incubation was carried out in the presence of oxygen or nitrogen in buffers saturated with the respective gases. Membrane damage was examined as lipid peroxidation (assessed as formation of thiobarbituric acid-reactive substances (TBARS), lipid hydroperoxides (LOOH) and conjugated dienes (CD), protein oxidation, depletion of protein thiols, superoxide dismutase or glutathione. RESULTS: Lipid peroxidation increased as a function of radiation dose, from 45 to 600 Gv. Post-irradiation incubation of mitochondria under nitrogen decreased the response, while incubation under oxygen saturation enhanced it significantly. The presence of caffeine during radiation exposure inhibited lipid peroxidation significantly as a function of concentration, in the range of 5 microM to 4 mM. The inhibition was highest with 4 mM of caffeine. Under oxic conditions, inhibition at 1 mM was significantly more than under anoxia. Anoxia was either ineffective or marginally increased peroxidation in the presence of caffeine. A similar observation was obtained when membrane damage was assessed as protein oxidation. Radiation-induced depletion of protein thiols was greatly enhanced by oxygen saturation and this was completely prevented by caffeine. This compound also protected against the radiation-induced loss of the antioxidant glutathione and the enzyme superoxide dismutase. CONCLUSIONS: The results suggest that caffeine effectively protected membranes against the oxic component of damage but may not do so for the anoxic component.

Animals↗

PubMed1998

Characterization of mouse fibroblast (NIH3T3) and fibrosarcoma cell lines (WEHI-164 and MFS 8) using PMRS.

Proton magnetic resonance Spectroscopy (PMRS) has been used to study the differences between immortalized fibroblasts and fibrosarcoma cells of different grade. One and two dimensional purged correlation spectroscopy (PCOSY) have been used to assess intact viable fibroblast and fibrosarcoma cells, and differences in the triglyceride, cellular metabolite, and cell surface fucosylation patterns between the three cell lines have been observed. The clinical implication of this study is the potential use of PMRS as an adjunct to conventional histopathology.

3T3 Cells↗