Is there an association between oral submucous fibrosis and ABO blood grouping?

BACKGROUND: Oral submucous fibrosis (OSMF) is one of the most common premalignant conditions in Indian subcontinent due to the traditional use of Areca nut and its various preparations. The genetic predisposition has also been reported in its etiopathogenesis. The rate of malignant transformation is between 7% to 14%. AIM: To evaluate whether ABO blood group is related to OSMF risk. SUBJECTS AND METHODS: It was a cross-sectional hospital-based study. A convenient sample of 164 study subjects constituted the cases and 180 subjects constituted the comparison group. STATISTICAL ANALYSIS USED: The results were analyzed using chi-square test and odds ratio. RESULTS: The chi-square analysis could not establish any significant relationship between OSMF and ABO blood group. But, when the strength of the association was measured using odds ratio, subjects with blood group A had 1.181 times higher risk of developing OSMF in comparison to other groups. CONCLUSION: The subjects with blood group A were at higher risk of developing OSMF in comparison to others. By performing blood group determination using a routine method at outreach programs, the susceptible individuals can be identified and counselled to quit the habit, thereby avoiding potential complications.

A comparison of oral hygiene status and dental caries experience among institutionalized visually impaired and hearing impaired children of age between 7 and 17 years in central India.

AIM: The aim of this study is to compare the oral hygiene status and dental caries experience among institutionalized visually impaired and hearing impaired children of age between 7 and 17 years in Bhopal city of Madhya Pradesh located in Central India. MATERIALS AND METHODS: A total of 95 hearing impaired and 48 visually impaired children of age between 7 and 17 years were recruited from special care institutions (one institution of hearing impaired and two institutions of visually impaired) in Bhopal city. Information related to different study variables was obtained from both groups. Oral hygiene index simplified (OHI[S]), decayed,extracted, filled teeth (deft and DECAYED, MISSING, FILLED TETTH (DMFT)) indices were used to record the oral hygiene status and dental caries experience. RESULTS: Mean OHI(S) score for hearing impaired was 1.15 ± 0.72 while it was 1.51 ± 0.93 for visually impaired children (P < 0.05). Mean DMFT score was 1.4 ± 1.95 and 0.94 ± 1.45 among hearing impaired and visually impaired respectively. The hearing impaired had a mean deft score of 0.47 ± 1.01 and in visually impaired it was 0.19 ± 0.79 and the difference was statistically significant (P < 0.05). CONCLUSION: Oral hygiene status of hearing impaired children was better than visually impaired and the difference was statistically significant. There was no significant difference between both groups with respect to DMFT. The hearing impaired children had significantly higher deft than visually impaired.

Development of a molecular linkage map of pearl millet integrating DArT and SSR markers.

Pearl millet is an important component of food security in the semi-arid tropics and is assuming greater importance in the context of changing climate and increasing demand for highly nutritious food and feed. Molecular tools have been developed and applied for pearl millet on a limited scale. However, the existing tool kit needs to be strengthened further for its routine use in applied breeding programs. Here, we report enrichment of the pearl millet molecular linkage map by exploiting low-cost and high-throughput Diversity Arrays Technology (DArT) markers. Genomic representation from 95 diverse genotypes was used to develop a DArT array with circa 7,000 clones following PstI/BanII complexity reduction. This array was used to genotype a set of 24 diverse pearl millet inbreds and 574 polymorphic DArT markers were identified. The genetic relationships among the inbred lines as revealed by DArT genotyping were in complete agreement with the available pedigree data. Further, a mapping population of 140 F(7) Recombinant Inbred Lines (RILs) from cross H 77/833-2 × PRLT 2/89-33 was genotyped and an improved linkage map was constructed by integrating DArT and SSR marker data. This map contains 321 loci (258 DArTs and 63 SSRs) and spans 1148 cM with an average adjacent-marker interval length of 3.7 cM. The length of individual linkage groups (LGs) ranged from 78 cM (LG 3) to 370 cM (LG 2). This better-saturated map provides improved genome coverage and will be useful for genetic analyses of important quantitative traits. This DArT platform will also permit cost-effective background selection in marker-assisted backcrossing programs as well as facilitate comparative genomics and genome organization studies once DNA sequences of polymorphic DArT clones are available.

An integrated pipeline of open source software adapted for multi-CPU architectures: use in the large-scale identification of single nucleotide polymorphisms.

The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets. We report here a pipeline of open source software extended to run on multiple CPU architectures that can be used to mine large EST datasets for SNPs and identify restriction sites for assaying the SNPs so that cost-effective CAPS assays can be developed for SNP genotyping in genetics and breeding applications. At the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the pipeline has been implemented to run on a Paracel high-performance system consisting of four dual AMD Opteron processors running Linux with MPICH. The pipeline can be accessed through user-friendly web interfaces at http://hpc.icrisat.cgiar.org/PBSWeb and is available on request for academic use. We have validated the developed pipeline by mining chickpea ESTs for interspecies SNPs, development of CAPS assays for SNP genotyping, and confirmation of restriction digestion pattern at the sequence level.

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.

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.

Indomethacin therapy and chronic hemodialysis during pregnancy. A case report.

Numerous complications can prevent the successful outcome of a pregnancy conceived while a woman is undergoing chronic hemodialysis. Among the difficulties encountered, premature labor and polyhydramnios are common. In such a patient indomethacin was used to treat those problems, with the subsequent delivery of a healthy infant.