A species goes extinct when there are none of its kind left. In other words, extinction is about small numbers, so how does big data help us study extinction? Luckily for us, each individual of a species carries with it signatures of its past, information on how connected/ isolated it is today, and other information on what may predict its future, in its genome. The last fifteen years have witnessed a major change in how we can read genomes, and information from genomes of individuals and species can help better plan their conservation.
All life on Earth harbours genetic material. Often called the blueprint of life, this genetic material could be DNA or RNA. We all know what DNA is, but another way to think of DNA is as data. All mammals, for example harbour between 2 to 3.5 billion bits of data in every one of their cells. The entire string of DNA data is called the whole genome. Recent changes in technology allow us to read whole genomes. We read short 151 letter long information bits many, many times, and piece together the whole genome by comparing it to a known reference. This helps us figure out where each of these 151 letter long pieces go in the 3 billion letter long word. Once we have read each position on an average of 10 or 20 times, we can be confident about it. If each genome is sequenced even ten times and only ten individuals are sampled, for mammals each dataset would consist of 200 to 350 billion bits of data!
Over time, the genome changes because of mutation, or spelling errors that creep in. Such spelling errors create variation, or differences between individual genomes in a population (a set of animals or plants). Similarly, large populations with many individuals will hold a variety of spellings or high genetic variation. Since DNA is the genetic blueprint, changes in the environment can also get reflected in these DNA spellings, with individuals with certain words in their genome surviving better than others under certain conditions. Changes in population size often changes the variety of letters observed at a specific location in the genome, or variation at a specific genomic position. Migration or movement of animals into a population adds new letters and variation. Taking all these together, the history of a population can be understood by comparing the DNA sequences of individuals. The challenge lies in the fact that every population faces all of these effects: changes in population size, environmental selection, migration and mutation, all at once, and it is difficult to separate the effects of different factors. Here, the big data comes to the rescue.
Genomic data has allowed us to understand how a population has been affected by changes in climate, and whether it has the necessary genomic variation to survive in the face of ongoing climate change. Or how specific human activities have impacted a population in the past. We can understand more about the origins of a population. How susceptible is a population to certain infections? Or whether the individuals in a population are related to each other. Some of these large datasets have helped identify if certain populations are identical and should be managed together or separately. All of these questions help in the management and conservation of a population.
We have worked on such big genomic datasets for tigers, and our research has helped us identify which populations of tigers have high genomic variation and are more connected to other populations. We have identified populations that are small and have low genomic variation, but also seem to have mis-spelled or badly spelled words, or a propensity of ‘bad’ mutations. We have identified unknown relationships between individuals within populations and have suggested strategies that could allow these isolated populations to recover their genomic variation. It has been amazing to peek into animals lives through these big data approaches, and we hope these types of genomic dataset will contribute to understanding how biodiversity can continue to survive on this Earth.
Uma Ramakrishnan is fascinated by unravelling the mysteries of nature using DNA as tool. Along with her lab colleagues, she has spent the last fifteen years studying endangered species in India.She hopes such understanding will contribute to their conservation. Uma is a professor at the National Centre for Biological Sciences.
Dr. Anubhab Khan is a wildlife genomics expert. He has researching genetics of small isolated populations for past several years and has created and analyzed large scale genome sequencing data of tigers, elephants and small cats among others. He keen about population genetics, wildlife conservation and genome sequencing technologies. He is passionate about ending technology disparity in the world by either making advanced technologies and expertise available or by developing techniques that are affordable and accessible to all.
This series is an initiative by the Nature Conservation Foundation (NCF), under their programme ‘Nature Communications’ to encourage nature content in all Indian languages. To know more about birds and nature, Join The Flock.
Neuralink Expected to Begin Human Trials in Six Months, Elon Musk Says
Elon Musk said on Wednesday a wireless device developed by his brain chip company Neuralink is expected to begin human clinical trials in six months.
The company is developing brain chip interfaces that it says could enable disabled patients to move and communicate again. Based in the San Francisco Bay Area and Austin, Texas, Neuralink has in recent years been conducting tests on animals as it seeks US regulatory approval to begin clinical trials in people.
“We want to be extremely careful and certain that it will work well before putting a device into a human but we’ve submitted I think most of our paperwork to the FDA and probably in about six months we should be able to upload Neuralink in a human,” Musk said during a much-awaited public update on the device.
The event was originally planned for October 31 but Musk postponed it just days before without giving a reason.
Neuralink’s last public presentation, more than a year ago, involved a monkey with a brain chip that played a computer game by thinking alone.
Musk is known for lofty goals such as colonizing Mars and saving humanity. His ambitions for Neuralink, which he launched in 2016, are of the same grand scale. He wants to develop a chip that would allow the brain to control complex electronic devices and eventually allow people with paralysis to regain motor function and treat brain diseases such as Parkinson’s, dementia and Alzheimer’s. He also talks about melding the brain with artificial intelligence.
Neuralink, however, is running behind schedule. Musk said in a 2019 presentation he was aiming to receive regulatory approval by the end of 2020. He then said at a conference in late 2021 that he hoped to start human trials this year.
Neuralink has repeatedly missed internal deadlines to gain US Food and Drug Administration (FDA) approval to start human trials, current and former employees have said. Musk approached competitor Synchron earlier this year about a potential investment after he expressed frustration to Neuralink employees about their slow progress, Reuters reported in August.
Synchron crossed a major milestone in July by implanting its device in a patient in the United States for the first time. It received US regulatory clearance for human trials in 2021 and has completed studies in four people in Australia.
© Thomson Reuters 2022
NASA’s Orion Spacecraft Enters Lunar Orbit a Week After Artemis I Launch
NASA’s Orion spacecraft was placed in lunar orbit Friday, officials said, as the much-delayed Moon mission proceeded successfully.
A little over a week after the spacecraft blasted off from Florida bound for the Moon, flight controllers “successfully performed a burn to insert Orion into a distant retrograde orbit,” the US space agency said on its website.
The spacecraft is to take astronauts to the Moon in the coming years — the first to set foot on its surface since the last Apollo mission in 1972.
This first test flight, without a crew on board, aims to ensure that the vehicle is safe.
“The orbit is distant in that Orion will fly about 40,000 miles above the Moon,” NASA said.
While in lunar orbit, flight controllers will monitor key systems and perform checkouts while in the environment of deep space, the agency said.
It will take Orion about a week to complete half an orbit around the Moon. It will then exit the orbit for the return journey home, according to NASA.
On Saturday, the ship is expected to go up to 40,000 miles beyond the Moon, a record for a habitable capsule. The current record is held by the Apollo 13 spacecraft at 248,655 miles (400,171 km) from Earth.
It will then begin the journey back to Earth, with a landing in the Pacific Ocean scheduled for December 11, after just over 25 days of flight.
The success of this mission will determine the future of the Artemis 2 mission, which will take astronauts around the Moon without landing, then Artemis 3, which will finally mark the return of humans to the lunar surface.
Those missions are scheduled to take place in 2024 and 2025, respectively.
ISRO’s RH200 Sounding Rocket Registers 200th Consecutive Successful Launch
ISRO on Wednesday announced that RH200, the versatile sounding rocket of the Indian space agency, has registered its 200th consecutive successful launch from the shores of Thumba, Thiruvananthapuram. The Indian Space Research Organisation (ISRO) has termed it a “historic moment”. It was witnessed by former President Ram Nath Kovind and ISRO chairman S Somanath, among others.
The successful flight of RH200 took off from the Thumba Equatorial Rocket Launching Station (TERLS).
“Indian sounding rockets are used as privileged tools for the scientific community for carrying out experiments on meteorology, astronomy and similar branches of space physics,” an ISRO statement said.
Campaigns such as Equatorial ElectroJet (EEJ), Leonid Meteor Shower (LMS), Indian Middle Atmosphere Programme (IMAP), Monsoon Experiment (MONEX), Middle Atmosphere Dynamics (MIDAS), and Sooryagrahan-2010 have been conducted using the sounding rocket platform for scientific exploration of the Earth’s atmosphere, it said.
The Rohini Sounding Rocket (RSR) series have been the forerunners for ISRO’s heavier and more complex launch vehicles, with a continued usage even today for atmospheric and meteorological studies, the national space agency headquartered here said.
“The 200th consecutive successful flight stands testimony to the commitment of Indian rocket scientists towards unmatched reliability demonstrated over the years,” it said.
Meanwhile, ISRO is all set to launch PSLV-C54/ EOS-06 mission with Oceansat-3 and eight nano satellites, including one from Bhutan, from the Sriharikota spaceport on November 26. The launch is scheduled at 11.56am on Saturday, the national space agency said on Sunday.
Last week, ISRO announced that the payload capability of India’s heaviest LVM3 rocket has been enhanced by up to 450kg with a successful engine test. According to the Indian Space Research Organisation, the CE20 cryogenic engine indigenously developed for Launch Vehicle Mark 3 (LVM3) was subjected to a successful hot test at an uprated thrust level of 21.8 tonnes for the first time on November 9, according to the country’s national space agency.
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