From DNA test to postmortem report, this Hyderabad lab plays CSI for animals

  • Ayesha Minhaz
  • Updated: Aug 15, 2016 18:46 IST
(Representative image) An 18-year-old elephant died after being captured and kept at the Varagaliar Elephant Camp at Tamil Nadu. (Ankush Saikia/HT File Photo)

When Madukkarai Maharaj, an 18-year-old elephant, died after being captured and kept at the Varagaliar Elephant Camp at Tamil Nadu Annamalai on June 21, 2016, tributes poured in from conservationists, who claimed that the animal had never caused much trouble to humans.

The tusker was captured by the forest department for allegedly entering human habitation and damaging crops for over three years. Maharaj received a heart-rending farewell, and his death stoked the debate again whether the animal would have survived if he hadn’t been captured. Luckily, this time, there was actual evidence to settle the argument.

The postmortem reports attributed the elephant’s death to multiple fractures. But how did the fractures take place? Did the attempt to capture him cause his death? Wildlife forensic scientists are working to answer these questions. Even the question of whether or not he was stressed was determined with the help of wildlife forensics. And playing animal CSI, determining the ‘unknown’ from the known, was India’s Centre for Cellular and Molecular Biology – the Laboratory for the Conservation of Endangered Species (CCMB, LaCONES) located in Hyderabad.

“In such cases, one can take a look at the cortisol hormones found in faecal matter and determine the level of stress the animal was undergoing. It would definitely have helped more to analyse the stress level when the animal was alive so that it could have survived. Once it has died, we can only generate a report and leave it at that,” Dr Karthikeyan Vasudevan, senior principal scientist at CCMB-LaCONES, said.

The CCMB-LaCONES project is a biotechnology lab working towards conservation of endangered wildlife species of the country. From providing technological support in the field of wildlife forensics to disease diagnostics, the lab has been efficiently supporting conservation of India’s wildlife since 2000. The lab has investigated over 1,330 cases of wildlife-related crimes. From the Wildlife Crime Control Bureau to the customs department to the forest department, everyone looks for support of the CCMB-LaCONES for solving cases of suspicious animal deaths, illegal trafficking, poaching and other such wildlife crimes.

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For instance, in cases where protected wildlife has been killed and cooked, the poachers may protest innocence by saying that it is not an endangered species.

One of the earliest cases solved by the lab was of an Indian Peafowl killing in Mahabubnagar, Andhra Pradesh. Suspecting that a wildlife crime had occurred, the district forest officer asked for samples of cooked meat, remnants of offal, and a wooden block that was used for chopping the bird to be seized. Attempts were made by the poachers to mislead the investigation by providing samples of cooked and raw chicken. But DNA samples retrieved from the wooden block showed that peafowl had, indeed, been slaughtered, proving the forest department’s case.

In 2000, Saki, a 13-month old Royal Bengal tigress in Nehru Zoological Park, was brutally killed and skinned. When a suspect in possession of tiger skin and claws was arrested, the biological samples were analysed to see if they matched with that of Saki’s. It did. To put the nail in the poacher’s coffin, samples of Saki’s biological parents and siblings were also analysed.

The CCMB-LaCONES project is a biotechnology lab working towards conservation of endangered wildlife species. (Picture courtesy: Official website CCMB-LaCONES)

In the tragic case of Madukkarai Maharaj, an entire carcass was available to retrieve samples for the forensic tests, but the job is often done just as efficiently with tiny samples, scientists from CCMB-LACONES said. Even a scrap from a utensil in which meat was cooked is enough to determine the species of the animal.

“Hair, blood, tusks, meat, remains from the mouth, fecal samples, an axe with which the animal was slaughtered, a rope which was used to bind the animal and so on — the tiniest of biological components can be a sample enough for our Universal Primer technology to isolate the DNA and determine the species,” Dr Rakesh K Mishra, director of CCMB, said.

Sometimes it may be too late to prevent animal killings or trafficking, but forensic evidence can be crucial in nabbing criminals and preventing further crimes. Even a finished product like an artefact made out of an elephant’s tusk or a leather purse that isn’t chemically processed can serve as a sample for forensic scientists. For instance, a couple of years ago, the flying squad of the forest department in Kerala’s Kannur division retrieved three polythene packets containing dry crystals from a hotel room. They were dried snake venom samples, later found to be of the Indian Cobra. On the basis of the report, a case was booked against the accused.

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On another occasion, the deputy conservator of forests, Bannerghatta National Park, seized a sample of ‘snake wine’ from a bar in Bengaluru. Snake wine is an alcoholic beverage produced by infusing whole snakes in rice wine or grain alcohol. It’s primarily consumed in China, Vietnam and southeast Asia. The denatured venom is believed to be good for virility and stop hair loss by snake-wine lovers. When the lab did a DNA sequencing, they were able to establish that the wine actually contained an Indo-Chinese spitting cobra.

But it isn’t only the government that uses the lab’s services: it also accepts private requests. If one wants to get a sample of meat from a restaurant analysed to ascertain the species, the lab will provide the report for a fee. “We do offer services to the private sector too. But, this is done after carefully assessing whether it might lead to misuse of the reports generated by us,” Mishra said. This is to ensure that it isn’t a poacher ring that’s trying to use the services of the lab. “Even in the cases of wildlife crime, we don’t get involved in the trial of the cases to ensure that there is no conflict of interest of any kind,” he added. This is to ensure that no lobbying impacts their final report on the matter.

The lab invented and patented a technology called Universal Primer back in 2001 to identify biological samples. “Once a sample is received, the DNA is isolated from the tissues. The DNA is then amplified so that there is a sufficient amount to conduct the various tests. The DNA sequence is then analysed and compared with the available database. It is a fairly simple technology and even high-school students isolate DNA during the workshops we conduct for schools.” Mishra explained.

The lab’s patented technology can be used to fetch minute information, like what kind of food an animal has eaten, but it does have some limitations. It is largely helpful to monitor terrestrial animals. Collecting faecal or tissue samples of birds and aquatic animals isn’t so easy.

Although the Universal Primer technology is primarily used in wildlife forensics, it serves a multitude of purpose, including monitoring migration, distribution of population and census of endangered species. Mishra recalls a case they helped solve around a decade ago. An Indian Air Force base was facing bird-collisions frequently, and the fighter planes would often have blood droplets or remains of birds stuck to them. However, there was no sign of bird habitation inside the base.

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The lab came to the rescue. First, they retrieved the samples of the bird remains and identified them as that of ‘house swifts’. There were no birds in the base but the collisions happened just outside. This helped the Indian Air Force solve a long-standing mystery, and they sought technical support for similar cases of collisions with bats, Rock Pigeons and Black Kites. The solution usually involved chopping of fruit-bearing trees or having radars put up to identify rare birds.

“Most often it is wildlife crime cases for which the forest department reaches out to the CCMB lab. However, there are at times conservation efforts taken up in collaboration by multiple government organisations. One such effort was the breeding of mouse deer in Nehru Zoological Park of Hyderabad,” B Lakshman, the forest range officer of Mannanur region, said. An endangered species, this animal had disappeared from the Mannanur Forest region couple of years ago. The Central Zoo Authority of India and CCMB-LaCONES worked in collaboration in this project for the conservation of Mouse Deer. And in April this year, an enclosure was sanctioned to relocate the Mouse Deer, which were bred in Hyderabad, Lakshman said.

CCMB wants to develop a way to tag endangered animals using the Universal Primer technique. (Official website: CCMB-LaCONES)

CCMB also regularly monitors the outbreak of diseases in several species of monkeys. The tedious job demands that field assistants go around collecting faecal samples of monkeys near human habitation. The samples need to be preserved and can’t be contaminated. “There are days when a field assistant waits near a tree for a monkey to expel some body waste. That’s no easy job. There are other ways to do the same job, but we do this because we don’t need to sedate an animal or capture it or control it, because that’s what conservation is all about,” Mishra, the lab’s director, said.

It needs highly dedicated and motivated individuals to be able to work in wildlife forensics, senior scientists point out. It’s long hours on all counts, and for the field staff, it can be weeks at a stretch in the forests. There are times when the staff of CCMB-LaCONES has to wait for a year just to collect a sample.

“Sadly, the brightest minds [in India] don’t come to science,” Mishra said. Apart from the difficulty that the job — technological expertise included — entails, there are external factors that may ruin weeks of efforts to generate a report. “Poorly preserved samples is one such factor,” a principal scientist with CCMB-LaCONES said.

“Very often, we receive tissues preserved in formaldehyde [from forest officials and/or the judiciary]. It is such a commonly available compound. Nothing can be retrieved from those samples and the report can’t be generated. Many cases are not booked, and when it is booked, the lack of proper preservation ruins everything. At least 30% of the cases we receive fail to yield DNA for the same reason,” Vasudevan said. Only when the samples are correctly preserved can the lab begin its slow process. It takes anywhere between four days to six weeks to generate a report.

“Most often, the delay in generating a report is because of non-technical issues like non-payment of charges by the government agencies. It might look like an absurd reason, but it is a part of the procedure. All we can do is send mails and wait for replies,” Vasudevan added.

Apart from wildlife conservation, the lab plans to extend the usage of the Universal Primer technique to plants, to make it easier to classify them. Once accomplished, this will have quite an important role to play in nutrition-related plant products, they opine.

“If a firm claims that a product has plant products of a specific species, we will soon be able to tell you if it genuine or garbage. Estimating food quality will become easier. This will take a while because it is easier to use the technique for animals,” Dr Mishra explained. This can help detect food adulteration, or verify the composition of herbal products and so on.

Another idea is to develop a way to tag endangered animals using this technology, which could for instance help curb poaching to a large degree by knowing the extent of the area an animal travels in and improving its security provisions.

“One can use machines [like GPS-enabled tracking collars] to follow animals in real-time, but it is not a sensible approach. It requires interfering with their habitat or even catching them,” Dr Mishra pointed out.

A view of the Centre for Cellular and Molecular Biology – the Laboratory for the Conservation of Endangered Species (CCMB, LaCONES) located in Hyderabad. (Picture courtesy: Official website)

All the tests are done at the lab located in Hyderabad, and the job isn’t outsourced to anyone else. “In forensics, the quality of the report determines how the case goes. We don’t let anyone touch the samples,” Mishra said.

A recent development has, however, raised a few concerns. Dr Mishra said that in June, the cabinet gave the nod for the signing of anMoU between India and the US to bring their wildlife forensics expertise into the country and to improve cooperation.

However, scientists at CCMB state that the lab is more than self-sufficient on all fronts. “I have no bias towards technology, but we are concerned about both the interests of the nation and of the lab. Since CCMB is one of the constituent national laboratories of the Council of Scientific and Industrial Research (CSIR) India, we have sent a letter to them about the same. We have been assured that our interests will be protected,” Mishra said.

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Way back in 2006, Therion International, which a Fish and Wildlife Conservation, Forensics laboratory located in New York used the Universal Primer technology in a case which was called the Florida Fish Scandal — sale of cheap seafood as exotic varieties. India has 14 patents in nine countries, and the technology has been used and appreciated internationally, including in the United States.

“India is an undoubted leader in this field. In fact, we can provide help to the other countries more efficiently,” Mishra said. While the lab doesn’t seem thrilled by the MoU, they are looking forward to a new bill related to wildlife conservation which will be tabled in the next session of Parliament. “It is a more comprehensive bill, which deals with DNA-related uses and misuse. We are doing fine in terms of laws related to conservation. There is scope and this bill will fill the gaps,” Mishra informed.

The work done by CCMB-LaCONES largely goes unnoticed unless a wildlife crime is widely reported and the help of the lab is sought. In 2014, the lab submitted research that the elephants used in processions are highly stressed, for instance. “It is a sad state. We need to be connected to the public because they are our employers. CCMB has plans to make the lab more accessible to the public using social media platforms,” Mishra said.

In September every year, the CCMB campus is thrown open to the public. At least 5,000 people visit the lab and get acquainted with the work done there. Taking time off from their hectic schedules, the scientists conduct workshops for schools on a regular basis wherein high school students conduct experiments along with a team from the lab. When students see things firsthand, such as how the heart of a fish beats, they learn better, say the scientists.

“Research papers in professional journals are a necessity, but for us to stay motivated, we need to be in touch with the young and curious minds,” Mishra said. “We need them more than they need us.”

For now, the lab is working for an elephant that needs their version of justice. In a couple of weeks, CCMB-LaCONES will release its verdict on the tragic events that led to the death of Madukkarai Maharaj.

(This story has been published in arrangement with GRIST Media)

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