Swapan K Das

The Indian Genome Variation database (IGVdb): A project overview

Indian population, comprising of more than a billion people, consists of 4693 communities with several thousands of endogamous groups, 325 functioning languages and 25 scripts. To address the questions related to ethnic diversity, migrations, founder populations, predisposition to complex disorders or pharmacogenomics, one needs to understand the diversity and relatedness at the genetic level in such a diverse population. In this backdrop, six constituent laboratories of the Council of Scientific and Industrial Research (CSIR), with funding from the Government of India, initiated a network program on predictive medicine using repeats and single nucleotide polymorphisms. The Indian Genome Variation (IGV) consortium aims to provide data on validated SNPs and repeats, both novel and reported, along with gene duplications, in over a thousand genes, in 15,000 individuals drawn from Indian subpopulations. These genes have been selected on the basis of their relevance as functional and positional candidates in many common diseases including genes relevant to pharmacogenomics. This is the first large-scale comprehensive study of the structure of the Indian population with wide-reaching implications. A comprehensive platform for Indian Genome Variation (IGV) data management, analysis and creation of IGVdb portal has also been developed. The samples are being collected following ethical guidelines of Indian Council of Medical Research (ICMR) and Department of Biotechnology (DBT), India. This paper reveals the structure of the IGV project highlighting its various aspects like genesis, objectives, strategies for selection of genes, identification of the Indian subpopulations, collection of samples and discovery and validation of genetic markers, data analysis and monitoring as well as the project’s data release policy.Indian population, comprising of more than a billion people, consists of 4693 communities with several thousands of endogamous groups, 325 functioning languages and 25 scripts. To address the questions related to ethnic diversity, migrations, founder populations, predisposition to complex disorders or pharmacogenomics, one needs to understand the diversity and relatedness at the genetic level in such a diverse population. In this backdrop, six constituent laboratories of the Council of Scientific and Industrial Research (CSIR), with funding from the Government of India, initiated a network program on predictive medicine using repeats and single nucleotide polymorphisms. The Indian Genome Variation (IGV) consortium aims to provide data on validated SNPs and repeats, both novel and reported, along with gene duplications, in over a thousand genes, in 15,000 individuals drawn from Indian subpopulations. These genes have been selected on the basis of their relevance as functional and positional candidates in many common diseases including genes relevant to pharmacogenomics. This is the first large-scale comprehensive study of the structure of the Indian population with wide-reaching implications. A comprehensive platform for Indian Genome Variation (IGV) data management, analysis and creation of IGVdb portal has also been developed. The samples are being collected following ethical guidelines of Indian Council of Medical Research (ICMR) and Department of Biotechnology (DBT), India. This paper reveals the structure of the IGV project highlighting its various aspects like genesis, objectives, strategies for selection of genes, identification of the Indian subpopulations, collection of samples and discovery and validation of genetic markers, data analysis and monitoring as well as the project’s data release policy.

Effect of pH on the combustion synthesis of nano-crystalline alumina powder

Synthesis of nano-crystalline alumina powder by a chemical pyrophoric reaction using citric acid and ammonia was investigated by varying the pH of the precursor solution, which played an important role in controlling the morphology of the synthesised powder. The flaky morphology obtained at pH=2 could be modified to fine desegregated particulate form by varying the pH of the solution to 10. The sluggish decomposition rate at low pH was found to be responsible for the generation of flaky powders, whereas the rapid decomposition at high pH=10 yielded the fine desegregated powders. The as-prepared powders were amorphous in nature, which yielded the nano-crystalline alumina powder after calcination at elevated temperatures.

Genome-wide analyses of recombination prone regions predict role of DNA structural motif in recombination

HapMap findings reveal surprisingly asymmetric distribution of recombinogenic regions. Short recombinogenic regions (hotspots) are interspersed between large relatively non-recombinogenic regions. This raises the interesting possibility of DNA sequence and/or other cis- elements as determinants of recombination. We hypothesized the involvement of non-canonical sequences that can result in local non-B DNA structures and tested this using the G-quadruplex DNA as a model. G-quadruplex or G4 DNA is a unique form of four-stranded non-B DNA structure that engages certain G-rich sequences, presence of such motifs has been noted within telomeres. In support of this hypothesis, genome-wide computational analyses presented here reveal enrichment of potential G4 (PG4) DNA forming sequences within 25618 human hotspots relative to 9290 coldspots (p<0.0001). Furthermore, co-occurrence of PG4 DNA within several short sequence elements that are associated with recombinogenic regions was found to be significantly more than randomly expected. Interestingly, analyses of more than 50 DNA binding factors revealed that co-occurrence of PG4 DNA with target DNA binding sites of transcription factors c-Rel, NF-kappa B (p50 and p65) and Evi-1 was significantly enriched in recombination-prone regions. These observations support involvement of G4 DNA in recombination, predicting a functional model that is consistent with duplex-strand separation induced by formation of G4 motifs in supercoiled DNA and/or when assisted by other cellular factors.

Tribology of AlSi alloy-graphite composites: triboinduced graphite films and the role of silicon morphology

Abstract AlSi (LM6) alloy and 3 wt.% graphite particle composites were synthesised using a solidification processing technique. The morphology of silicon was altered by sodium modification and heat treatment. Wear tests were conducted under dry and partially liquid lubricated conditions using a pin-on-disc wear test apparatus. Wear surfaces and debris were examined by scanning electron microscopy. Under both dry and partially liquid lubricated conditions, the performance of heat-treated composites was found to be superior to the rest. Wear surfaces of heat-treated composites showed the presence of patchy layers of graphite. The role of silicon morphology in the formation of triboinduced graphite films is explained.

MLC1 gene is associated with schizophrenia and bipolar disorder in Southern India.

BACKGROUND Chromosome 22q13 has shown linkage with schizophrenia (SCZ) and bipolar affective disorder (BPAD). A missense mutation in MLC1 (putative cation-channel gene on 22q13) co-segregating with periodic catatonic schizophrenia has been reported. We have investigated the relationship of MLC1 with SCZ and BPAD in Southern India. METHODS All exons and flanking intronic sequences of MLC1 were screened for novel variations. Case-control (216 BPAD, 193 SCZ, 116 control subjects) and family-based analyses (113 BPAD, 107 SCZ families) were performed to evaluate association of MLC1 with these disorders. RESULTS We found 33 MLC1 sequence variations, including three novel mutations: Val210Ile, Leu308Gln, and Arg328His in six BPAD cases and Val210Ile in one control individual. Minor allele of a common variation, ss16339182 (in approximately 6 Kb Linkage-Disequilibrium [LD]-block) was associated with BPAD in case-control (p = .03) and family-based analyses (transmitted/nontransmitted [T/NT]-44/20; p = .003). Association was observed for rs2235349 and rs2076137 with SCZ and ss16339163 with BPAD in case-control study. Using Block 2 haplotype tagging single nucleotide polymorphisms (htSNPs), GC haplotype revealed association (p = .02) and excess transmission (p = .002) with BPAD. CONCLUSIONS Association of MLC1 with SCZ and BPAD suggests involvement of a common pathway. Rare missense mutations and common variants associated with BPAD favors hypothesis about likely involvement of both rare and common polymorphisms in etiology of this complex disorder.

The significance of the matrix microstructure on the solid lubrication characteristics of graphite in aluminium alloys

Abstract Al alloy 2014-graphite particle composite was synthesized using a solidification processing technique. Wear tests of as-cast and of heat-treated alloys and composites were conducted under dry conditions on a pin-on-disc wear test apparatus. Scanning electron microscopy examination of sliding surfaces did not show the formation of a graphite film. It appeared from the present investigation that graphite particles either were engulfed in the coarse wear debris or might have been pulled off the sliding surfaces because of a poor interfacial bond between aluminium and graphite. However, in (AlSi alloy)-graphite composites in the heat-treated condition, the formation of a graphite film was detected. The present study suggests that the matrix microstructure plays a significant role in the solid lubrication characteristics of graphite in aluminium alloys.

Turbine blade failure in a thermal power plant

The failure of a LP (low pressure) turbine blade of a 220 MW thermal power plant is presented. The blade was made of martensitic stainless steel and the structure was tempered martensite. There was no evidence of degradation of blade material. The fracture took place at the aerofoil region, 113-mm from the root. Throughout the blade surface Si rich phases were detected. Several pits/grooves were found on the edges of the blades and chloride was detected in these pits. These were responsible for the crevice type corrosion. The probable carriers of Cl− were Ca and K, which were found on the blade. The failure mode was intergranular type. Possibly the ultimate failure was due to corrosion-fatigue.

Analysis of failures in boiler tubes due to fireside corrosion in a waste heat recovery boiler

The failures of boiler tubes due to fireside corrosion in a waste heat recovery boiler utilizing the exhaust gas of a gas turbine fired with high-speed diesel has been analyzed. Deposits from the various zones of the boiler were collected and characterized by chemical analysis, scanning electron microscopy and X-ray diffraction. Thermodynamic modeling studies were carried out to study the interaction of the flue gas with the various components of the boiler. The high corrosion propensity and consequent failures in the low temperature sections of the boiler were found to be directly related to the formation of hydrated ferric sulfate in these regions.

Failure of a super heater tube

The failure of two adjacent platen super heater tubes of a thermal power plant has been analysed. One tube fractured with a fish mouth opening and another thinned down considerably. A significant amount of oxide layer was observed in the inner side of the failed tube. In the other tube the inner oxide layer was very small and the tube was thinned down due to fireside corrosion. The unexposed tube from the same lot revealed a ferritic bainitic microstructure. The failed tube also showed a ferrite bainite microstructure but most of the bainitic carbide had transformed to globular form. Considerable carbide precipitation both in grain boundary (GB) and inside grains were observed. A large number of cavities and micro-cracks were observed along the grain boundaries. A similar microstructure was observed on the same tube 10 cm away from the failed region. The micrograph at the fracture location showed a similar microstructure but the grains are very much elongated. The formation of globular oxide on the other tube was compared to that of the failed tube. Due to breakage of oxide scale of the failed tube, the metal surface of the failed tube was exposed to steam at a higher temperature and this accelerated the oxide growth. This led to creep damage of the material. Ultimately, failure occurred due to rapid overheating of the tube material.

Thermal analysis of hydrated calcium aluminates

Differential scanning calorimeter (DSC) has been used to study the dehydration characteristics of hydrated calcium aluminates such as CA, CA2 and C12A7 where C and A stand for CaO and Al2O3 respectively. Dehydration of CAH10 and C2AH8 (whereH=H2O) occur ∼ at 160–180°C and 200–280°C respectively. These two phases are unstable and ultimately get transformed to AH3 and C3AH6. Dehydration of AH3 and C3AH6 occur between 290 and 350°C and overlap at lower scanning rate. The activation energy for dehydration of the stable AH3 and C2AH6 phases has been found to be 107.16 and 35.58 kJ mol−1 respectively. The compressive strength of the hydrated calcium aluminates has been determined. The result shows that in the case of CA, almost 90% of ultimate strength has been attained in 1 day whereas in CA2, ultimate strength has been attained in 14 days and in C12A7 in 1 day. DSC results have been correlated with the rate of strength developments.