Mutations in WDR62, encoding a centrosomal and nuclear protein, in Indian primary microcephaly families with cortical malformations

Primary microcephaly is an autosomal recessive disorder characterized by smaller than normal brain size and mental retardation. It is genetically heterogeneous with seven loci: MCPH1-MCPH7. We have previously reported genetic analysis of 35 families, including the identification of the MCPH7 gene STIL. Of the 35 families, three families showed linkage to the MCPH2 locus. Recent whole-exome sequencing studies have shown that the WDR62 gene, located in the MCPH2 candidate region, is mutated in patients with severe brain malformations. We therefore sequenced the WDR62 gene in our MCPH2 families and identified two novel homozygous protein truncating mutations in two families. Affected individuals in the two families had pachygyria, microlissencephaly, band heterotopias, gyral thickening, and dysplastic cortex. Using immunofluorescence study, we showed that, as with other MCPH proteins, WDR62 localizes to centrosomes in A549, HepG2, and HaCaT cells. In addition, WDR62 was also localized to nucleoli. Bioinformatics analysis predicted two overlapping nuclear localization signals and multiple WD-40 repeats in WDR62. Two other groups have also recently identified WDR62 mutations in MCPH2 families. Our results therefore add further evidence that WDR62 is the MCPH2 gene. The present findings will be helpful in genetic diagnosis of patients linked to the MCPH2 locus.

Carnatic music analysis: Shadja, swara identification and rAga verification in AlApana using stochastic models

We analyze the AlApana of a Carnatic music piece without the prior knowledge of the singer or the rAga. AlApana is ameans to communicate to the audience, the flavor or the bhAva of the rAga through the permitted notes and its phrases. The input to our analysis is a recording of the vocal AlApana along with the accompanying instrument. The AdhAra shadja(base note) of the singer for that AlApana is estimated through a stochastic model of note frequencies. Based on the shadja, we identify the notes (swaras) used in the AlApana using a semi-continuous GMM. Using the probabilities of each note interval, we recognize swaras of the AlApana. For sampurNa rAgas, we can identify the possible rAga, based on the swaras. We have been able to achieve correct shadja identification, which is crucial to all further steps, in 88.8% of 55 AlApanas. Among them (48 AlApanas of 7 rAgas), we get 91.5% correct swara identification and 62.13% correct R (rAga) accuracy.

Bold strategies for Indian science

When an Indian prime minister publicly admits that India has fallen behind China, it is news. Manmohan Singh's statement last January at the Indian Science Congress in Bhubaneswar that this is so with respect to scientific research, and that “India's relative position in the world of science has been declining”, has rung alarm bells. Singh was not springing anything new on Indian scientists; many of us will admit that things are not well1. Recognizing the problem is the first step towards reversing this slide.

Climate change and crop yields in the Indian Cardamom Hills, 1978-2007 CE

In this study we analyzed climate and crop yields data from Indian cardamom hills for the period 1978-2007 to investigate whether there were significant changes in weather elements, and if such changes have had significant impact on the production of spices and plantation crops. Spatial and temporal variations in air temperatures (maximum and minimum), rainfall and relative humidity are evident across stations. The mean air temperature increased significantly during the last 30 years; the greatest increase and the largest significant upward trend was observed in the daily temperature. The highest increase in minimum temperature was registered for June (0.37A degrees C/18 years) at the Myladumpara station. December and January showed greater warming across the stations. Rainfall during the main monsoon months (June-September) showed a downward trend. Relative humidity showed increasing and decreasing trends, respectively, at the cardamom and tea growing tracts. The warming trend coupled with frequent wet and dry spells during the summer is likely to have a favorable effect on insect pests and disease causing organisms thereby pesticide consumption can go up both during excess rainfall and drought years. The incidence of many minor pest insects and disease pathogens has increased in the recent years of our study along with warming. Significant and slight increases in the yield of small cardamom (Elettaria cardamomum M.) and coffee (Coffea arabica), respectively, were noticed in the recent years.; however the improvement of yield in tea (Thea sinensis) and black pepper (Piper nigrum L.) has not been seen in our analysis.

Multi-scale interactions and predictability of the Indian summer monsoon

Following the seminal work of Charney and Shukla (198 1), the tropical climate is recognised to be more predictable than extra tropical climate as it is largely forced by 'external' slowly varying forcing and less sensitive to initial conditions. However, the Indian summer monsoon is an exception within the tropics where 'internal' low frequency (LF) oscillations seem to make significant contribution to its interannual variability (IAV) and makes it sensitive to initial conditions. Quantitative estimate of contribution of 'internal' dynamics to IAV of Indian monsoon is made using long experiments with an atmospheric general circulation model (AGCM) and through analysis of long daily observations. Both AGCM experiments and observations indicate that more than 50% of IAV of the monsoon is contributed by 'internal' dynamics making the predictable signal (external component) burried in unpredictable noise (internal component) of comparable amplitude. Better understanding of the nature of the 'internal' LF variability is crucial for any improvement in predicition of seasonal mean monsoon. Nature of 'internal' LF variability of the monsoon and mechanism responsible for it are investigated and shown that vigorous monsoon intraseasonal oscillations (ISO's) with time scale between 10-70 days are primarily responsible for generating the 'internal' IAV. The monsoon ISO's do this through scale interactions with synoptic disturbances (1-7 day time scale) on one hand and the annual cycle on the other. The spatial structure of the monsoon ISO's is similar to that of the seasonal mean. It is shown that frequency of occurance of strong (weak) phases of the ISO is different in different seasons giving rise to stronger (weaker) than normal monsoon. Change in the large scale circulation during strong (weak) phases of the ISO make it favourable (inhibiting) for cyclogenesis and gives rise to space time clustering of synoptic activity. This process leads to enhanced (reduced) rainfall in seasons of higher frequency of occurence strong (weak) phases of monsoon ISO.