Turning to science to find innovative solutions
For EV Soniya, a scientist with the Rajiv Gandhi Centre for Biotechnology (RGCB) in Thiruvananthapuram, Kerala, science, and especially molecular biology, has been a lifelong passion. Her expertise in the basic tenets of biology has allowed her to expand her research horizons…
Q: What was your main research with black pepper?
There were – and are – a lot of issues with spice cultivation. There are high chances of devastating disease, which can affect our exports. These diseases are common all over Kerala. Because of our tropical climate, the oomycete (reproductive bodies) of fungi can grow very rapidly. This creates a lot of problems. There are many species and subspecies of black pepper across Kerala, but there are no disease-resistant varieties. There is some degree of tolerance, but not resistance. Then comes the yield. In the pepper found in the wild, the yield is typically low. Farmers obviously want high yields. After spending so much time in cultivation, low yields really affect farmer incomes. There was a need for strategies to improve yields. Spices research and agricultural research institutes were developing their own strategies, but again the problem is there is no resistant variety. Being a biotechnology Institute, we started working on genomics and developing strategies to find solutions to this problem.
Q: What strategy did you use to come up with resistant varieties?
We used tissue culture to develop genetically modified pepper using transgenics. At that time, that was the upcoming field. The problem with tissue culture was that the presence of endogenous bacteria [bacteria found inside plant tissue which can potentially cause infections] makes the culturing difficult. Also, some of the tissue was recalcitrant – they were not responding to tissue culture treatments. We had to overcome all these problems. As we moved from tomato to black pepper, we had to spend a lot of time coming up with suitable tissue culture protocols. Then came the gene. Initially, when genetically modified organisms (GMO) were introduced, people were introducing bacterial genes – this also led to some controversies. Others were working to localise a gene that can break down fungal walls and provide protection from fungal disease. We wanted to develop transgenics using genes from resistant varieties. We found certain varieties of black pepper, like Piper colubrinum from Brazil, which is resistant to certain diseases. We wanted to see what resistant genes this species had, that other species lacked. We found that it was mainly a difference in the level of expression of genes.
Q: Over the years of your research on black pepper, have you observed any changes in the field?
One thing I want to stress is that we are not working on pepper in the field – we are working in the lab only. Whenever we wanted to translate our findings in the field, we collaborate with agricultural university, because we always want the expertise from their field. However, I can give you some examples. Karimunda (a popular cultivar in Kerala) is supposed to be a disease-tolerant variety. It is also a wild variety. But, the yield is low, compared to another variety called Panniyur, which gives high-quality seeds and the yield is also high. So, farmers want to use that. One of the main constraints in black pepper production in India is Phytophthora foot rot (‘quick wilt’) caused by an oomycete (plant pathogen) called Phytophthora capsici. Unlike model organisms, there is no rapid elevation in pepper research due to the scarcity of the available genome sequence information. Until now, there is no resistant variety. There are only tolerant varieties. Indian Institute of Spice Research (IISR) has also been developing and distributing new varieties of pepper, including both tolerant and high yielding varieties. Being a biotechnology institute, our prime aim is to pursue basic research. We focus on molecular level. Once product is ready, we tie up with ISSR or Agriculture University to take the products to the field.
Q: Can you talk of your work with bael?
Aegle marmelos (bael in Hindi, vilvam in Tamil and koovalam in Malayalam) is a tree usually found in Shiva temples as the sthala viruksham (temple tree). It is auspicious to use bael during Shivaratri (a Hindu festival dedicated to Shiva). Bael is also used in Ayurvedic preparations – for instance, the preparation dasamularishtam contains bael. I found that this is a wonderful plant. It produces secondary metabolites (specialised chemical compounds) like quinolones that have many anti-microbial and anti-cancer properties. Quinoline alkaloids, found abundantly in the roots of bael possess various biological activities. They are efficient drugs for the treatment of malaria and are considered as potential lead molecules for novel drug designing. For the first time in plants, we characterized a novel enzyme (a type III polyketide synthase) named Quinolone synthase (QNS) involved in quinolone biosynthesis from Bael. We demonstrated the remarkable ability of QNS to catalyze the formation of quinolone. A full-length gene was isolated and expressed in a bacterial system. That protein has to be expressed in bacteria (like Escherichia coli) to make the protein in large amounts. We then went for in vivo and in vitrio assays. For the in vitrio assay, we had had to show that this enzyme is capable of accepting specific substrates to produce the compound. We could show that this particular compound is found at higher levels when you overexpress the quinolone synthase gene. This work was published in the Journal of Biological Chemistry, a prestigious journal in which it is not easy for plant biologists to publish. I was very happy to publish in it.
Q: Can you talk about your work with captive elephants?
This was an offshoot of the DNA fingerprinting lab. Each elephant needed to have a unique genetic identity that should not be found in any other elephant. It was a different experience, with new challenges and again very interesting. With detailed knowledge, there are a lot of things that we can do. We follow the same protocols – marker development, fingerprinting. The main challenge was that we had to find out a particular region that is not repeated. The forest department wanted us to work on captive elephants because of certain issues faced with owners, legal issues. When asked could you do this, my response was, we will do it. We completed the work with great success. We gained a lot of confidence by trying out new projects — we gained the confidence to take up any challenge.
Q: Any other project you found interesting?
I think the elephant project was one of my most interesting. I don’t think anyone in India has tried such a project. The application of this fingerprinting to multiple research questions, anything at all actually, is interesting. There are cases sometimes that the Kerala government or police department asks us to work on. We get a lot of paternity cases. We also work on wildlife forensics – for instance, cases of animal poaching. We get samples through the court and we have to identify whether it is from a wild animal or other animals. We have been getting a lot of poaching cases.
Q: They send an animal part and the lab has to find out what animal it is?
Not just the animal part! It can even be a dish made out of a wild animal – it can be deer, for example. It can be the animal in any form! Initially, I was a bit reluctant to accept the responsibility of the DNA fingerprinting facility. I was comfortable just doing my research. The facility takes up a lot of time and I lose the research time. But later, I understood: if I am working continuously, service to society is also important. I can be a part of the process.