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CSIR conducts Whole Genome Sequencing of over 1,000 Indians for Biomedical Applications
Oct 25, 2019 (New Delhi)
CSIR conducts Whole Genome Sequencing of over 1,000 Indians for Biomedical Applications
"Programme will lead to predictive and preventive medicine": Dr Harsh Vardhan
The Council of Scientific & Industrial Research (CSIR) has conducted Whole Genome Sequencing of 1,008 Indians from different populations across the country. Announcing details of the IndiGen Genome project, the Union Minister for Science & Technology, Earth Sciences and Health & Family Welfare, Dr Harsh Vardhan said that the whole genome data will be important for building the knowhow, baseline data and indigenous capacity in the emerging area of Precision Medicine. The outcomes of the IndiGen will have applications in a number of areas including predictive and preventive medicine with faster and efficient diagnosis of rare genetic diseases, he added.
The IndiGen initiative was undertaken by CSIR in April 2019, which was implemented by the CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi and CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad. This has enabled benchmarking the scalability of genome sequencing and computational analysis at population scale in a defined timeline. The ability to decode the genetic blueprint of humans through whole genome sequencing will be a major driver for biomedical science.
Dr Harsh Vardhan said that the benefits of this initiative include epidemiology of genetic diseases to enable cost effective genetic tests, carrier screening applications for expectant couples, enabling efficient diagnosis of heritable cancers and pharmacogenetic tests to prevent adverse drug reactions.
On the occasion, Dr Harsh Vardhan unveiled the IndiGenome card and accompanying IndiGen mobile application that enables participants and clinicians to access clinically actionable information in their genomes. He emphasized that it ensures privacy and data security, which is vital for personal genomics to be implemented at scale. Dr Harsh Vardhan elaborated that this is being pilot tested in individuals across India and has evinced interest from several Indian commercial organisations.
The outcomes of the IndiGen will be utilized towards understanding the genetic diversity on a population scale, make available genetic variant frequencies for clinical applications and enable genetic epidemiology of diseases. The whole genome data and knowhow for the analysis of largescale genomic data is expected to enable evidence and aid in the development of technologies for clinical and biomedical applications in India.
Director General, CSIR and Secretary, Department for Scientific & Industrial Research, Dr Shekhar C. Mande said that it is important to ensure that India, with its unparalleled human diversity, is adequately represented in terms of genomic data and develops indigenous capacity to generate, maintain, analyze, utilize and communicate large-scale genome data, in a scalable manner.
CSIR has led human genomic sciences in India and has made major contributions in understanding the "Indian Genome Variation". Pioneering collaborations in genomics has been fostered by CSIR both nationally and internationally. Furthermore, CSIR contributed towards the first personal human genome in India and in understanding ancestral population in India and early migrations that led to what we know today on distinct ethnic groups. CSIR also pioneered the application of genomics in clinical settings in the area of rare genetic diseases in India by means of DNA/Genome based diagnostics and interaction with large number of clinical collaborators.
More information about the CSIR IndiGen Program may be obtained from:
dg@csir.res.in; dgcsir@csir.res.in
director@igib.res.in
director@ccmb.res.in
Source Link : https://pib.gov.in/
Date : 2019-10-28
IGIB finds a protein with better precision in gene-editing
Oct 5, 2019 (New Delhi)
IGIB finds a protein with better precision in gene- editing
The new protein was able to correct sickle cell anaemia mutation in patient-derived stem cells
Researchers at the Delhi-based Institute of Genomics and Integrative Biology (CSIR-IGIB) have discovered a protein variant from a different species of bacteria that can edit the DNA with very high precision. In the tool now commonly used for editing disease-causing mutations in DNA (CRISPR-Cas9), the Cas9 protein behaves like a molecular scissors that cuts the DNA at a specific location and inserts a foreign piece of DNA to correct the mutation that causes the disease.
In addition to binding to the intended target on the DNA, the commonly used Cas9 protein from Strepotococcus pyogenes bacteria (SpCas9) and its engineered derivative tend to potentially bind to DNA at multiple unintended sites thereby leading to unnecessary alterations in the DNA.
The researchers found their new Cas9 protein, which binds and cuts the DNA, was able to correct sickle cell anaemia mutation in patient-derived stem cells. The protein (FnCas9) used by the researchers to edit the DNA is derived from a bacterium - Francisella novicida.
The Cas9 protein is supposed to bind to the DNA only when there is a perfect match between the DNA and the protein, thus reducing the chances of the protein binding at non-target sites on the DNA. But even when three mismatches exist between the protein and the DNA, the currently used SpCas9 protein binds and cleaves the DNA. In contrast, the team led by Debojyoti Chakraborty from IGIB found the new FnCas9 protein showed negligible binding when there exists more than one mismatch in the target DNA. The results were published in the journal Proceedings of the National Academy of Sciences (PNAS).
High specificity
"The high specificity of the new FnCas9 protein arises due to reduced affinity to bind to DNA when there is even a single mismatch. And when there is more than one mismatch, complete absence of binding of the protein to the DNA is seen in many cases," says Dr. Chakraborty.
"If the Cas9 protein remains bound to DNA at mismatched locations for a long time, there is a possibility that it might cut the DNA at these locations. Also, if it remains bound to DNA, the protein might block the transcription (which is the first step in gene expression) at that location. And if Cas9 is bound at multiple unintended sites then the transcription machinery gets stalled and the expression of genes at these locations might be altered," Dr. Chakraborty explains.
In nature, DNA often gets damaged and is routinely repaired through one of the two pathways. In the case of the homology- directed repair (HDR) pathway, which is relatively less error- prone, matching sequences are used to repair the DNA. "The FnCas9 protein was found to increase the HDR repair rate fourfold compared to the widely used SpCas9," says Deepanjan Paul from CSIR-IGIB and one of the first authors of the paper.
Sickle cell anaemia
The researchers tested the precision of binding and cleavage at the desired sites on the DNA using mouse cell lines (embryonic stem cells and brain cells), human kidney cell lines and induced pluripotent stem cells (iPSc). In the case of human iPS cells, the FnCas9 protein was found to bind to the DNA at the specific site, cut and repair the sickle cell anaemia mutation.
"The correction process is the same for any disease-causing mutation and so our FnCas9 protein should theoretically correct any mutation in the DNA. The efficiency might vary, so we must test it for each disorder," says Dr. Chakraborty.
The efficiency of any Cas9 protein delivery as well the ability to correct mutations is generally low in the case of iPS cells. The efficiency of correction is about 1.6%. Though the efficiency to correct mutations is low in iPS cells, the corrected cells can be isolated, multiplied and converted (differentiated) into haematopoietic stem cells. Once differentiated into haematopoietic stem cells, they can be transfused into patients.
"Differentiating iPS cells into haematopoietic stem cells is not trivial. Plenty of experimental work is under way to make it efficient for clinical translation," says Dr. Chakraborty.
Recalling how he started working on FnCas9 protein for genome editing, Dr. Chakraborty recalls that he was looking for a Cas9 protein which can target RNA instead of DNA. There was one study that reported that FnCas9 could potentially target viral RNA. "We were not able to target RNA using FnCas9 proteins. So we started to investigate whether it can target DNA as well since it was not known if FnCas9 can be used for precise gene correction. We found that not only does it target the DNA but does so with very high specificity," he says.
"We are now proceeding for preclinical studies to establish the efficacy of FnCas9 protein for genome-wide binding and targeting using patient-derived cells and mouse models," he says.
Source Link : https://www.thehindu.com
Date : 2019-10-07
Technology awards presented to four labs
Sept 26, 2019 (New Delhi)
Technology awards presented to four labs
President of India Ram Nath Kovind and Minister for Science and Technology, Earth Sciences Dr. Harsh Vardhan on Thursday presented the Technology Awards and other prizes for excellence in science and technology, instituted by the Council of Scientific and Industrial Research (CSIR).
The winners of the CSIR Technology Awards are - Central Drug Research Institute, Lucknow; Central Salt and Marine Chemicals Research Institute, Bhavnagar; Central Institute of Mining and Fuel Research, Dhanbad; and National Aerospace Laboratories, Bengaluru. The awards were instituted in 1990 to foster and encourage multi-disciplinary in-house team efforts and external interaction for technology development, transfer and commercialization.
Prof. Amitabha Chattopadhyay of Centre for Cellular and Molecular Biology, Hyderabad, bagged the G.N.Ramachandran Gold Medal for excellence in biological sciences and technology; Cadila Healthcare Limited and Carborundum Universal Limited got the CSIR Diamond Jubilee Technology Award.
Nine young scientists were presented CSIR Young Scientist Award: Dr Bidyut Purkait of Central Drug Research Institute, Lucknow; Dr Lipi Thukral of Institute of Genomics & Integrative Biology, New Delhi; Dr John Mondal of Indian Institute of Chemical Technology, Hyderabad; Dr Sasidhar B.S. of National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram; Dr Amol Prakash of National Institute of Oceanography, Goa; Dr Bodhisatwa Hazra of Central Institute of Mining and Fuel Research, Dhanbad; Dr Divya Agrawal of Central Scientific Instruments Organisation, Chandigarh; Dr Prabhat Ranjan Prem of Structural Engineering Research Centre, Chennai; and Dr. Shikha of Central Mechanical Engineering Research Institute, Durgapur.
In addition, 17 school children were awarded the CSIR Innovation Award for School Children.
The first prize went to Anmol Rathi and Harsh Agrawal, students of R.K. Sarda Vidya Mandir, Raipur for their innovation on "novel technique for early detection of pancreatic cancer through spermine level in human saliva".
The President also unveiled the first Indigenous High Temperature Fuel Cell System developed by CSIR in partnership with two Indian companies, Reliance Industries Limited and Thermax Ltd, Pune under its flagship program named "New Millennium Indian Technology Leadership Initiative".
The 5 kW system generates power in an environmental-friendly manner using methanol/bio-methane and produces heat and water as bi-products for further use. The cells have been developed based on high temperature proton exchange membrane (HTPEM) technology. They are most suitable for distributed stationary power applications such as for small offices, commercial units and data centres, where highly reliable power is essential with simultaneous requirement for air-conditioning.
This system can also help meet the requirement of efficient, clean and reliable backup power generator for telecom towers, and strategic applications in remote areas. It would replace diesel generating sets and help reduce India's dependence on crude oil.
Three CSIR laboratories were involved in the development : National Chemical Laboratory, Pune; National Physical Laboratory, New Delhi and Central Electrochemical Research Institute, Karaikudi.
The President lauded the accomplishments of CSIR and its technological interventions towards the socio-economic development of the nation. He congratulated all the awardees and urged them to address the challenges facing the country.
Dr Harsh Vardhan expressed pride in CSIR contributions and said that the country has high expectations from CSIR in developing solutions and technologies towards sustainable development in the country. He released a book on on the winners of CSIR's Shanti Swarup Bhatnagar Awards from 1958 to 2018.
Dr Shekhar C Mande, director general of CSIR, in his opening remarks highlighted the need of Science to connect to Society and called upon the scientists and students to excel in pursuit of science.
Source Link : https://www.thehindubusinessline.com/
Date : 2019-09-27
Scientists keen on setting up Cancer Genome Atlas for Indian population
Sept 12, 2019 (Pune)
Scientists keen on setting up Cancer Genome Atlas for Indian population
Scientists are hoping to set up an Indian version of The Cancer Genome Atlas (TCGA), a landmark project in the US which has provided publicly available data sets to help improve diagnostic methods and treatment standards to prevent cancer. While Dr Renu Swarup, secretary, Department of Biotechnology under the Ministry of Science and Technology, said the government was keen on partnering with the initiative, several groups in Pune have come together to push this proposal forward.
"We haven?t had a formal discussion about India partnering in TCGA, but it is a complementary effort. We will be open to discussions on how our existing efforts on cancer genomics can bring in some value to the global initiative," Dr Swarup told The Indian Express.
In a first, the team from TCGA, led by Director Dr Jean Claude Zenklusen, is going to train 60 scientists at a workshop in Pune.
Several translational cancer scientists and onco clinicians from India and abroad will participate in the first TCGA-themed conference and workshop -- Multi-Omics Studies in Cancer -- Learnings from TCGA -- to be held from September 21 to 25 at the Indian Institute of Science Education and Research (IISER). The event is also organised by the Centre for Translational Cancer Research, a joint initiative between Prashanti Cancer Care Mission(PCCM), IISER- Persistent Systems and TCGA, National Institutes of Health, USA.
TCGA, a collaboration between the National Cancer Institute and the National Human Genome Research Institute, has generated comprehensive multi-dimensional maps of the key genomic changes in 33 types of cancer. The TCGA data set has helped the global cancer research community work towards prevention, diagnosis and treatment of the disease.
Dr Santosh Dixit, a senior scientist with the PCCM and convenor of the conference, told The Indian Express that TCGA provided a gold mine of data and changed the face of cancer research. "In the world of biology, TCGA is equivalent to landing on the moon as the molecular analysis of each cancer is significant. Each cancer can be treated differently by knowing the molecular map of that cancer, studying the genes that have gone wrong and providing effective targeted drugs," said Dr Dixit.
While scientists are keen on setting up a similar TCGA for the Indian population, among the key driving forces are Dr L S Shashidhara, a developmental biologist formerly associated with IISER, Dr C B Koppiker, founder of PCCM, and Dr Anand Deshpande, founder and chairman of Persistent Systems, a technology services company.
Dr Deshpande said the project is socially relevant. "We need our own version of the cancer genome atlas. TCGA data is based on the caucasian population. We need to create our own data sets, build upon these initiatives and have our own equivalent of TCGA in India," Dr Deshpande told The Indian Express.
Persistent Systems is the software partner for IISER and PCCM and, according to Dr Deshpande, the software is among the key features of the TCGA initiative.
"We have been trying to get the team from TCGA and convince them to let us use their infrastructure, understand their methods and processes for setting up something similar in the country. They have agreed and while we will learn the same protocol and replicate them here, no biological sample will be sent out of the country. All tests will be done in India," said Dr Deshpande.
Dr Renu Swarup, CSIR director general Dr Shekhar Mande and others will be present during the workshop and participate in the discussion on creating a TCGA-like project in India.
Source Link : https://indianexpress.com
Date : 2019-09-12
New mobile app launched to assist farmers
Aug 2, 2019 (New Delhi)
New mobile app launched to assist farmers
The Ministries of Earth Sciences and Agriculture have launched a mobile application that will provide location, and crop and livestock- specific weather-based agro advisories to farmers in local languages.
To begin with, the service would be available for 150 districts in different parts of the country. It will be extended to rest of the country in a phased manner over the next one year. The Ministries will provide forecast to farmers relating to temperature, rainfall, humidity, and wind speed and direction, which play critical roles in agricultural operations and how to take care of the crops and livestock. The information would be updated twice a week on Tuesdays and Fridays.
The app has been named Meghdoot and can be downloaded from Google Play Store and App Store. The users will have to register their name and location so that they can get area specific information. It has been developed by experts from the India Meteorological Department and Indian Institute of Tropical meteorology and the Indian Council of Agricultural Research.
The app would provide information in the form of images, maps and pictures to help the farmer to have a clearer picture of what is in store. It has been integrated with WhatsApp and Facebook as well to help farmers share information among themselves. It will also be integrated with YouTube in future.
In another related development, IMD has developed new website to disseminate weather and climate information in user-friendly manner. The website has less of technical information and more of important information such as district-wise weather warnings in easy to view and read formats.
The site will also act as a centralized portal to all the meteorological offices in India to update the warnings, bulletins and other data in real-time.Minister for Earth Science, Science and Technology Dr. Harsh Vardhan launched the agro-meteorology advisory application and the new website at a function to mark the Foundation Day of the Ministry of Earth Sciences.
Source Link : https://www.thehindubusinessline.com/
Date : 2019-08-03
GSLV MkIII-M1 Successfully Launches Chandrayaan-2 spacecraft
July 22, 2019 (New Delhi)
GSLV MkIII-M1 Successfully Launches Chandrayaan-2 spacecraft
India's Geosynchronous Satellite Launch Vehicle GSLV MkIII-M1, successfully launched the 3840 kg Chandrayaan-2 spacecraft into an earth orbit today. The spacecraft is now revolving round the earth with a perigee (nearest point to Earth) of 169.7 km and an apogee (farthest point to Earth) of 45,475 km. Today's flight marks the first operational flight of the GSLV Mk III.
After a smooth countdown lasting 20 hours, GSLV MkIII-M1 vehicle majestically lifted off from the Second Launch Pad at the Satish Dhawan Space Centre SHAR (SDSC SHAR), Sriharikota in Andhra Pradesh at the scheduled launch time of 1443 Hrs (2:43 pm) Indian Standard Time (IST) with the ignition of its two S200 solid strap-on motors. All the subsequent flight events occurred as scheduled.
About 16 minutes 14 seconds after lift-off, the vehicle injected Chandrayaan-2 spacecraft into an elliptical earth orbit.Immediately after spacecraft separation from the vehicle, the solar array of the spacecraft automatically got deployed and ISRO Telemetry, Tracking and Command Network (ISTRAC), Bengaluru successfully took control of the spacecraft.
ISRO Chairman Dr K Sivan congratulated the launch vehicle and satellite teams involved in this challenging mission. "Today is a historical day for Space Science and Technology in India. I am extremely happy to announce that GSLV MkIII-M1 successfully injected Chandrayaan-2 into an orbit of 6000 Km more than the intended orbit and is better."
"Today is the beginning of the historical journey of India towards Moon and to land at a place near South Pole to carry out scientific experiments to explore the unexplored. On July 15, 2019 ISRO intelligently observed a technical snag, Team ISRO worked out, fixed and corrected the snag within 24 hours. For the next one and a half day, the required tests were conducted to ensure that corrections made were proper and in right direction. Today ISRO bounced back with flying colours," Dr. Sivan said.
In the coming days, a series of orbit manoeuvres will be carried out using Chandrayaan-2's onboard propulsion system. This will raise the spacecraft orbit in steps and then place it in the Lunar Transfer Trajectory to enable the spacecraft to travel to the vicinity of the Moon.
GSLV Mk III is a three-stage launch vehicle developed by ISRO. The vehicle has two solid strap-ons, a core liquid booster and a cryogenic upper stage. The vehicle is designed to carry 4 ton class of satellites into Geosynchronous Transfer Orbit (GTO) or about 10 tons to Low Earth Orbit (LEO).
Chandrayaan-2 is India's second mission to the moon. It comprises a fully indigenous Orbiter, Lander (Vikram) and Rover (Pragyan). The Rover Pragyan is housed inside Vikram lander.
The mission objective of Chandrayaan-2 is to develop and demonstrate the key technologies for end-to-end lunar mission capability, including soft-landing and roving on the lunar surface. On the science front, this mission aims to further expand our knowledge about the Moon through a detailed study of its topography, mineralogy, surface chemical composition, thermo-physical characteristics and atmosphere leading to a better understanding of the origin and evolution of the Moon.
After leaving earth orbit and on entering Moon's sphere of influence, the on-board propulsion system of Chandrayaan-2 will be fired to slow down the spacecraft. This will enable it to be captured into a preliminary orbit around the Moon. Later, through a set of manoeuvres, the orbit of Chandrayaan-2 around the moon will be circularised at 100 km height from the lunar surface.
Subsequently, the lander will separate from the Orbiter and enters into a 100 km X 30 km orbit around the Moon. Then, it will perform a series of complex braking manoeuvers to soft land in the South polar region of the Moon on September 7, 2019.
Following this, the Rover will roll out from the lander and carry out experiments on the lunar surface for a period of 1 lunar day, which is equal to 14 Earth days. The mission life of the lander is also 1 lunar day. The Orbiter will continue its mission for a duration of one year.The orbiter had a lift-off weight of about 2,369 kg, while the lander and rover weighed 1,477 kg and 26 kg respectively. The rover can travel up to 500 m (half a kilometre) and relies on electric power generated by its solar panel for functioning.
Chandrayaan-2 has several science payloads to facilitate a more detailed understanding of the origin and evolution of the Moon. The Orbiter carries eight payloads, the lander carries three, and the rover carries two. Besides, a passive experiment is included on the lander. The Orbiter payloads will conduct remote-sensing observations from a 100 km orbit while the Lander and Rover payloads will perform in-situ measurements near the landing site.
The ground facilities constitute the third vital element of Chandrayaan-2 mission. They perform the important task of receiving the health information as well as the scientific data from the spacecraft. They also transmit the radio commands to the spacecraft. The Ground Segment of Chandrayaan-2 consists of Indian Deep Space Network, Spacecraft Control Centre and Indian Space Science Data Centre.
Today's successful launch of Chandrayaan-2 is a significant milestone in this challenging mission. A total number of 7500 visitors witnessed the launch live from the Viewer's Gallery at Sriharikota.
Source Link : http://pib.nic.in/
Date : 2019-07-23
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Smart microscopy solution for better diagnostics from CSIR ..
