Brinjal, interrupted

Fresh controversy surrounds India’s Bt Brinjal after six premier Indian science academies declared it safe and advocated its ‘limited release’ last week. Though they added a corollary that genetically modified crops pose a risk if the science behind them is flawed, that hasn’t done much to douse the rage of the anti-GM lobby in the country.

And most importantly India’s vocal environment minister Jairam Ramesh, who had sought the report from the academies in the first place. Ramesh has lost no time in rubbishing the report on grounds that it lacks ‘scientific rigour’. The report does not have a single citation or reference and there’s no way to know how the authors reached their conclusions, he has been quoted as saying.

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Then came the plagiarism charges — the proverbial last nail. And added discredit when one of the co-authors National Academy of Medical Sciences distanced itself from the report. The academies have, thereafter, taken responsibility of the plagiarism charge and promised a re-examination of the report.

India’s first GM crop faced a roadblock prior to its launch last February on safety issues. And it doesn’t seem like the humble vegetable will have a smooth ride in the country sometime soon. The moratorium continues.

Transgenic cock-a-doodle

First we had the the transgenic mice made using a technique that eliminates the need for hundreds of mice eggs or sacrificing the rodents post-experiment. In short, a deathless technique. Scientists at the National Institute of Immunology at New Delhi made the transgenic animals inserting genes in the testicular germ cells (spermatogonia) of mice through a process called in vivo electroporation or passing mild current for a fraction of a second. The technique would help every biologist generate his own transgenic animals at low cost without the help of specialised labs.

After that we now have the first ‘made in India’ transgenic chicken developed using spermatozoa from male chicken to transfer a green fluorescent protein gene from jellyfish. The protein worked as a marker for the scientists to see if it showed up in the transgenic animals. And it did, with an efficiency of 6%.

The technology is not new (it is already in use in the US, Canada, UK and China). However, developing it in a state poultry body in Hyderabad, Indian scientists have managed to standardise transgenic chicken development at home. That is something to cheer. Also, according to the scientists, transgenic chicken can become a production house for biologically important proteins and peptides for use in medicine. This again is heartening news.

Indian genome

The human genome sequence of an Indian has now been mapped, putting the country in the league of five others — United States, Britain, Canada, China and South Korea — who have demonstrated similar capabilities. This means the 3.1 billion base pairs describing every function of the body of an Indian are now available for further study and as an important diagnostic tool for predictive healthcare.

Devoting over two years on the background work, a team of young scientists from the Indian Institute of Genomics and Integrative Biology (IGIB) in New Delhi mapped the genome sequence of a man in his fifties from Jharkhand. The sequencing revealed his susceptibility to bipolar disorder, collateral cancers, five variations of ulcer and three types of coronary disease.

The project will be followed up with sequencing of various Indian communities — regions, races and castes.

The world’s first human genome sequence was completed in 2003 by the International Human Genome Project with scientists from the US, UK, France, Germany, Japan and China. Resource constraints hindered India’s participation in that project.

IGIB scientists had earlier sequenced the genome of a zebrafish — 1.8 billion base pairs — setting the stage for human genome sequencing.

Earlier in this blog, we had featured the Indian Genome Variation Consortium, a public-private partnership that networks six Council of Scientific and Industrial Research (CSIR) labs and some private software firms, when they completed the genetic mapping of one of the world’s most ethnically diverse populations — Indians — last year.

More sturdy steps for Indian genomic studies!

Gene advantage

Amidst the sorry stories we hear about dwindling (and mostly non-existent) tiger populations across tiger reserves in India, there was something to cheer during the long Independence Day weekend as Indian scientists demonstrated the invaluable genetic diversity of the subcontinent’s big cats.

Samrat Mondol and Uma Ramakrishnan of the National Centre for Biological Sciences, Bangalore, along with K. Ullas Karanth of the Wildlife Conservation Society, New York and Centre for Wildlife Studies, Bangalore urged through their study that conservation efforts “must prioritise regions that harbor more tigers, as well try to capture most of the remaining genetic variation and habitat diversity.” Nature India research highlight.

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Will they grow up to admire these stripes in paintings alone?

Only such prioritisation based on demographic, genetic, and ecological considerations can ensure species recovery and retention of evolutionary flexibility in the face of ongoing global changes, they say.

As widely reported now in the media, thanks to the ever growing concern for the tiger, the trio sampled 73 individual tigers from 28 reserves spread across the Indian subcontinent to find that Indian tigers retain more than half of the extant genetic diversity in the species. Their results suggest that only 1.7% (with an upper limit of 13% and a lower limit of 0.2%) of tigers from historical times remain now.

In an analysis of the study, Oliver A. Ryder of San Diego Zoo’s Institute for Conservation Research in California, USA, says the team’s proposal merits serious consideration, but the realities of providing sufficient habitat for expanding tiger populations should also be calculated into global efforts for tiger conservation.

I spotted a blog post by Anne-Marie Hodge, an undergraduate in biological sciences at Auburn University, Alabama, USA, who raised some rather interesting points on what to make of the genetic diversity issue. I am tempted to quote her from her Nature Network blog here:

“I am increasingly concerned that the public will get the impression that we can claim conservation success merely by preserving genetic diversity. Much has been made of ‘minimum viable populations,’ ‘maximum sustainable yield,’ and the like, with too little regard for the integrity and function of food-webs, and the resulting impacts on not only predators and prey but the ecosystem as a whole. Humans had been doing their best to eradicate large carnivores long before our historical and scientific records began. We would not know how large Indian tiger populations were several centuries ago if analyses like the ones in the current PLoS paper did not allow us to create estimates from molecular evidence. This makes it extremely hard to set appropriate goals for conservation and management plans.

Even if we had a complete tiger genome on hand, it would not do much good if the animals are relegated to zoo cages or small ecotourism resorts. Even if a token number of animals are allowed to roam in the wild, the species would simply be lingering as a present and yet enfeebled shade of its former self, with its role in community interactions and regulation essentially paralysed.

Genetic diversity is still a crucial factor, and the results of this paper are both important and fascinating. This information gives us further clues as to the size and distribution of historic tiger populations, which can lead to further analyses of predator-prey relationships and ecosystem interactions. The news about the remaining genetic diversity is encouraging; inbreeding depression can potentially prevent species from ever recovering from extremely low population numbers, even if their habitat is restored.”

I wonder what Indian conservation experts have to say on the way forward from this important scientific finding. Also, whether this will affect any policy changes in the existing conservation roadmap of the country’s big cats.

Our genes

The Indian Genome Variation Consortium, a public-private partnership that networks six Council of Scientific and Industrial Research (CSIR) labs and some private software firms, has completed genetic mapping of one of the world’s most ethnically diverse populations, the Indians.

With this, the consortium has succeeded in covering the genomic variation in India in terms of population and genomic coverage. The study included 32 large populations, with 10 million or more people in each, and 23 isolated tribal populations, representing a vast ethnic, linguistic and geographical diversity.

The data that the consortium has gathered provides interesting insights into disease susceptibility of these populations and their response to drugs. This will now allow researchers to understand the genetic predisposition of ethnic groups to diseases.

The genetic map will also give pharma companies a headway in predictive medicine and targeted drugs. A great step ahead in Indian genomic studies, indeed!