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Biotechnology & Genomics R&D in Pakistan

Complete gene mapping of a Pakistani citizen by Human Genome Project in Karachi has put the country on a very short list of nations which have accomplished this scientific feat. To assess the state of genomics and biotechnology in Pakistan, let's take a look at what is happening in the country in this field:

1. Researchers at the Panjwani Center for Molecular Medicine and Drug Research (PCMD) in Karachi collaborated with Beijing Genomics Institute (BGI) to complete gene mapping of Dr. Ata-ur-Rahman, according to SciDev. Dr. Rehman, President of Pakistan Academy of Sciences, volunteered himself for the project.

2. More than two hundred life sciences departments are engaged in genomics and biotechnology research at various Pakistani universities, according to a report in The News.

3. Pakistan has been a Science Watch rising star for several years for research papers in multiple fields, particularly in biological sciences. Publications by Pakistani research teams have increased four-folds in the last decade, and the majority of publications from major universities are in life sciences.

4. Pakistan began producing biotechnology based pharmaceuticals in 2009. The first of these plants was set up by Ferozesons in Lahore to produce interferon for treatment of hepatitis, according to Nature magazine.

5. Pakistan has significant research efforts in seed and livestock development at various agriculture universities, institutes and departments. Pakistani researchers and scientists are currently collaborating in life sciences with their counterparts in the US and China. A number of crops like cotton, rice, wheat, corn, potato, ground nut are being developed locally or with the collaboration of Chinese and US seed companies.

6. Post-doctoral research on biotechnology and related agricultural issues is being funded under a Young Scientists Program, as part of the USDA-funded sustainable endowment to support the Agricultural Linkages Program at the Pakistan Agricultural Research Council (PARC). An MOU for $7.5 million has been signed under the Pakistan-U.S. Science and Technology Program between Pakistan’s Higher Education Commission (HEC) and the Ministry of Science and Technology and the U.S Agricultural Research Service (ARS) for scientific collaboration and capacity building of scientists.

7. National Biosafety Committee has allowed stacked gene (Cry 1A and Cry 2Ab) in cotton developed by Center of Excellence in Molecular Biology (CEMB), Lahore. Several other stacked gene products are in the pipe line and will be put for approval soon.

8. Pakistan is building the capacity of its young scientists in the legislative, regulatory, and policy areas related to agricultural biotechnology, biosafety and nanotechnology. A small project has been funded in Agricultural Nanobiotechnology related to the use of nanoparticles for plant genetic engineering utilizing a Bio-Rad biolistic gene gun at National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad.

While the universities have stepped up their research programs in life sciences as a result of the higher education reforms undertaken in the last decade, it's still a major challenge to translate the academic work into tangible benefits in terms of improved human health and higher crop and livestock yields in the country.

Part of the challenge stems from the need for regulatory framework for introducing biotech products and technology for humans, plants and animals. To make progress on this front, Pakistan has ratified the Cartagena Protocol of Biosafety (CPB) with a framework for handling GMO’s. The proposed regulatory guidelines are built upon on a three-tier system composed of the National Biosafety Committee (NBC); a Technical Advisory Committee (TAC); and Institutional Biosafety Committees (IBC), according to USADA GAIN report on Pakistan.

In the regulatory framework, the Secretary of the Ministry of Environment heads the NBC, and is responsible for oversight of all laboratory work and field trials, as well as authorizing the commercial release of GM products. The three monitoring and implementing bodies administer enforcement of the National Biosafety Guidelines. The IBC may make recommendations to the NBC regarding the awarding of exemptions for laboratory and fieldwork related to products of bioengineering. These recommendations may be accepted, and formal approval granted, if sufficient information and grounds exist to consider the risk as being minimal or non-existent. After permission for deregulation is granted by the NBC, approval can still be withdrawn provided sufficient technical data and other evidence later becomes available that warrants a review. The other important ministry dealing with production and release of GM crop is Ministry of Food and Agriculture (MINFA). The ministry developed several Standard Operating Procedures (SOP’s) for handling of cases of import/approval/release of GM crops; however, all these have yet to be promulgated.

Genomics and biotechnology have great potential to fight diseases and help improve human lives and increase productivity. So far, the benefits of these advances have accrued mostly to the rich countries because they are driven by market incentives. The time has now come for Pakistan to take advantage of such technological advances. Take crop yields as an example. Wheat is the staple of Pakistan and planted on the largest acreage. It contributes about three percent to the GDP. The national average yield is about 2.7 tons per hectare, far below the average in European countries such as France, Germany and the United Kingdom where they are above seven tons per hectare, according to recent Op Ed by Dr. Ata-ur-Rehman.

There is significant opposition to the use of GM seeds in South Asia today. In his book The Rational Optimist, author Matt Ridley recalls that there was similar resistance in 1960s to Nobel Laureate Norman Borlaug's Mexican dwarf wheat. Ridley writes about how Borlaug's efforts helped spark the Green Revolution in India and Pakistan. Ridley argues that it was Borlaug's work with his new seeds and chemical fertilizer that disproved Paul Ehrlich's claim in his book The Population Bomb that India would never feed itself.

Pakistani farmers have already begun planting biotech cotton since 2011. With 2.6 million hectares of Bt cotton planted in 2011, Pakistan ranks 8th in terms of the area for biotech crops in the world, according to International Service for the Acquisition of Agri-Biotech Applications (ISAAA) report. US ranks number 1, Brazil 2, Argentina 3, India 4, Canada 5, China 6, Paraguay 7 and Pakistan 8. South Africa 9 and Uruguay 10 round out the top 10. Pakistan has had a bumper crop of cotton in 2011-2012 mainly because of the planting of Bt seeds.

While extra caution is absolutely warranted before introducing genetically modified organisms in the environment, an irrational fear of the unknown would be unacceptable in a country like Pakistan with its dwindling water resources and a growing young population that needs to be fed, clothed, educated and nurtured. Clearly, the technology can help cure diseases and lead to development of new drought-resistant seed varieties producing high crop yields.

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Tags: Biotechnology, Genomics, Pakistan

Comment by Riaz Haq on March 8, 2012 at 10:30am

Here's a Dawn report on new supercomputer at NUST:

This supercomputer can perform parallel computation at a peak speed of 132 Teraflops i.e. 132 Trillion Operations per second.

It is equipped with multicore processors and graphics co-processors with inter-processor communication speed of 40 Gbps.

Besides its extensive utilization in the computation-intensive research projects in the areas of Fluid Dynamics and Biosciences, this massively parallel facility can also be utilized to handle huge data processing applications of social sciences such as Flood and Weather Forecasting, Oil and Gas Exploration, energy efficient building designs and transportation management at national-level.

The chief guest in his address appreciated the efforts of the entire team associated with the project and encouraged all institutions to come forward and benefit from this massive computational facility acquired by NUST.

He also assured full support by HEC in this regard.

Rector NUST Engr. Muhammad in his welcome address shared his strategic vision and thoughts. He specifically mentioned that acquisition of this supercomputing facility would be a source of inspiration for our valued PhD scholars abroad to return to Pakistan.

This will have an impetus on the collaborative research between universities and other research organizations in country and abroad. Dr Imran Akhtar, the key note speaker, gave a highly motivating and thought provoking talk on the occasion. He encouraged the young researchers to come forward and exploit the facility at its maximum by using their domain knowledge and expertise in computational science in solving the national challenges in the areas of engineering, bio-informatics, political science, psychology and social sciences.

http://www.dawn.com/2012/03/08/nust-unveils-pakistans-fastest-super...

Comment by Riaz Haq on March 8, 2012 at 6:43pm

Details of latest supercomputer at NUST in Pakistan by HPC Wire:

Following India’s announcement of installing that country’s fastest supercomputer, news out of Islamabad reports that Pakistan has just unveiled its speediest super as well.

The system will reside at the Research Center for Modeling and Simulation (RCMS), which was acquired by Pakistan’s National University of Sciences and Technology (NUST) through a grant provided by the country’s Ministry of Science and technology. An inauguration event was held where RCMS Principal, Sikandar Hayat noted that the new system is the fastest GPU-based parallel computer in the country.

The system, known as ScREC, is named after the university’s supercomputing research and education center. The cluster consists of 66 nodes equipped with a total of 30,992 cores. The NUST site breaks down the components as follows: 32 dual-socket quad-core nodes, 32 NVIDIA GPUs, a QDR InfiniBand interconnect, and 26.1 TB of storage. Specifics on the CPU or GPU parts were not provided.

While Linpack performance has not been posted, the system runs at a peak of 132 teraflops. Given that most GPU-accelerated TOP500 systems only achieve about a 50 percent Linpack yield of peak performance (depending upon the CPU-GPU ratio and interconnect), the system should deliver at least 60 Linpack teraflops. That would place the system in the current list, giving Pakistan a slot in the TOP500. Unfortunately the rankings are a moving target, and the June update may well exclude sub-60-teraflop machines. The slowest supercomputer on the current TOP500 is at 51 teraflops.

ScREC will be used to assist NUST with research in the areas of computational biology, computational fluid dynamics, image processing, cryptography, medical imaging, geosciences, computational finance, and climate modeling. Specifically, RCMS is currently developing a direct simulation Monte Carlo (DSMC) method for subsonic nanoscale gas flows. Other projects include external flow analysis of heavy vehicles to reduce fuel consumption, and numerical investigation on performance and stability of axial compressors used in aircraft engines and gas turbines.

In a welcome address, Rector Nust Engr Muhammad Asghar said, “This will give an impetus for collaborative research between universities and other research organizations within the country and abroad.” and explained that the new facility will inspire scholars studying abroad to return to Pakistan.

Takeaway

Pakistan’s investment in terascale computing exhibits a willingness to promote scientific research – a forward-leaning strategy for a developing nation on the cusp of becoming industrialized. Unlike India’s HPC plans, Pakistan is not attempting to join the ‘supercomputing elite’ here, but rather to promote science collaborations, while creating an incentive for Pakistani researchers and engineers who work abroad to return to the country.

http://www.hpcwire.com/hpcwire/2012-03-07/pakistan_deploys_132-tera...

Comment by Riaz Haq on March 8, 2012 at 10:01pm

Here's an interesting NY Times story on computing for genomics:

In Silicon Valley, the line between computing and biology has begun to blur in a way that could have enormous consequences for human longevity.

“Genomes are now being sequenced incredibly cheaply,” said Russ B. Altman, who is a founder of Personalis, a start-up based in Palo Alto, Calif., that is developing software to interpret genomes. “On the discovery and science side we will be able to do clinical trials. We’ll be able to check the entire genome.”

Recently, on the company’s Web site, Dr. Reid predicted that the cost of gene sequencing could eventually be as low as that of a blood test: “I believe that the impact on the medical community of whole human genome sequencing at a cost comparable to a comprehensive blood test will be profound, and it will raise a host of public policy issues (privacy, security, disclosure, reimbursement, interpretation, counseling, etc.), all important topics for future discussions,” he wrote.
-------------
In 2011, Complete Genomics became one of the market leaders. This year, it has produced more than 3,000 sequences at a cost of about $5,000 each. Dr. Banyai’s higher capacity second generation system is now being installed and will begin production during the first half of this year. A third generation design has been completed.

What initially set Complete Genomics apart from the field was its strategy of offering gene sequencing as a service, rather than selling a machine to laboratories. More recently, Illumina, one of its crucial competitors, has also begun offering sequencing as a service, in addition to selling its machines.

“Our competitors have to supply kits that can be executed by a graduate student rolling out of bed with a hangover,” said Dr. Reid. “We don’t live with that standard, and that can be tremendously liberating. Ours can be horrifically complex as long as it can be executed by a robot.”

The company also began with the business intent of sequencing only the human genome, rather than those of other species, too — a strategy that was heresy in 2005, when the founders set out to raise money. At that time, only two human genomes had been sequenced. However, Complete Genomics founders argue that focusing just on the human genome has given them a leg up.

“You make a whole bunch of decisions that don’t work well for corn or bacteria, but they work very well for humans,” Dr. Reid said.

http://www.nytimes.com/2012/03/08/technology/cost-of-gene-sequencin...

Comment by Riaz Haq on March 15, 2012 at 4:32pm

The number of research papers published by Pakistani scientists in peer-reviewed international science journals has grown from 1,174 in 2000 (rank 54) to 6987 in 2010 (rank 43), according to SCImago Journal & Country Rank (SCR).

Comment by Riaz Haq on March 26, 2012 at 6:26pm

Here's a description of a genomics project at the Center for Non-commuicable Diseases to collect and analyze data for 2500 Pakistanis in Lahore, Pakistan:

The 1000 Genomes Project is the first large scale project that aims to sequence the genomes of 2500 people of different global ethnicities, to provide a comprehensive resource on human genetic variation. The goal of the 1000 Genomes Project is to find most genetic variants that have frequencies of at least 1% in the populations studied. Such information will be useful for a range of genetic investigations specifically including genome-wide association studies and mutation screens for various monogenic disorders.

To sequence a person's genome, many copies of the DNA are broken into short pieces and each piece is sequenced. The many copies of DNA mean that the DNA pieces are more-or-less randomly distributed across the genome. The pieces are then aligned to the reference sequence and joined together. The Project currently plans to sequence each sample to about 4X coverage; at this depth sequencing cannot provide the complete genotype of each sample, but should allow the detection of most variants with frequencies as low as 1%. Combining the data from 2500 samples should allow highly accurate estimation (imputation) of the variants and genotypes for each sample that were not seen directly by the light sequencing. As with other major human genome reference projects, data from the 1000 Genomes Project will be made available quickly to the worldwide scientific community through freely accessible public databases.

The Center for Non-Communicable Diseases is the local coordinating center to collect DNA samples from 150 Pakistani individuals (50 families). These samples have been collected from Lahore, Punjab. These Pakistani Punjabi samples are the first South Asian samples that have been collected from South Asia; and will provide a useful resource to conduct informative imputations for genome-wide association studies. These samples will be genotyped for whole-genome and exome sequencing and transformed to develop lymphoblastoid cell lines for various functional experiments.

http://cncdpk.com/index.php?Itemid=504

Comment by Riaz Haq on March 26, 2012 at 6:28pm

Here's a APP report on use of genomics in medicine in Pakistan:

Karachi—Medical scientists and researchers stressed the importance of Human Genetics as a subject of vital importance for the progress and betterment of mankind at a three day workshop on Bioinformatics jointly organized by SIUT and COMSTECH.

Clinicians and young researchers, from different parts of the country and from Islamic world, working in the field of life sciences were introduced to the use of internet resources to analyze the vast amount of genetic data being produced by laboratories worldwide during the program that concluded at Sindh Instittue of Urology and Transplant (SIUT) on Saturday.

Hands on training was provided to them as how to use web based bioinformatics tools and resources in order to analyze the enormous amount of genetic data produced through DNA sequences.

Dr. Qasim Ayub and Luca Pagani, globally known for their contributions to the genetic analyses on human populations at the famous Wellcome Trust Sanger Institute, in Cambridgeshire, United Kingdom, supervised the deliberations of the workshop.

Characterizing genetic modifications that have enabled modern humans to adapt to their changing environment like those whose ancestors moved out of Africa, greatly help in understanding of the origin and migrations of human populations.

This is of particular relevance for Pakistan because it has been at the cross roads of human migrations for thousands of years, said the experts conducting the workshop.

Dr Qasim Mehdi from SIUT, a leading scientist in the field and the main coordinator of the workshop said that this was an opportune time for conducting such a workshop as thousands of human genomes, including hundreds of Pakistani individuals, are being completely sequenced by an international team of collaborators involved in the ‘1000 Genomes Project’ at the Sanger Institute.

“The ongoing genetic revolution is poised to improve the traditional medical practice,” he said. The paradigm is changing from ‘diagnose and treat’ to ‘predict and prevent’ he commented.

Speakers on the occasion were of unanimous opinion that the development will bring immense benefit to mankind and will enable treatments tailored to the individual and improve our understanding of previously untreatable diseases such as kidney disorders, diabetes, heart diseases and cancer.

http://pakobserver.net/detailnews.asp?id=146881

Comment by Riaz Haq on April 14, 2012 at 9:43am

Here's a News report on US assistance for higher education & research in Pakistan:

Dr. Rajiv Shah, Administrator of the US Agency for International Development (USAID) signed a Memorandum of Understanding (MoU) with Dr. Javaid Laghari, Chairman of the Higher Education Commission (HEC) to create three Centers for Advanced Studies at Pakistani universities.

With US support, these centers will promote the development of Pakistan's water, energy, and agriculture sectors through applied research, training for specialists, university linkages, and the contributions towards policy formulation, said in a press statement issued by US Embassy here on Friday.

"US-Pakistan cooperation in higher education spans more than six decades. This new program presents a new milestone in our joint efforts to strengthen Pakistan's university system to support the growth of the country's economy," said Dr. Rajiv Shah at the signing ceremony.

The Centers for Advanced Studies is a five-year $127 million program sponsored by USAID. The Center for Advanced Studies in Agriculture and Food Security will be established with US support at the University of Agriculture in Faisalabad, Punjab.

The Center for Advanced Studies in Water will be created at the Mehran University of Engineering and Technology in Jamshoro. Meanwhile, the National University of Science and Technology (NUST) in Islamabad will open the Center for Advanced Studies in Energy.

A satellite center for energy will be established at the University of Engineering and Technology in Peshawar.

A key component of the Center for Advanced Studies Program is linking Pakistani universities to universities in the United States.

These linkages will help engender, support, and fund joint applied research, student and faculty exchanges, pedagogical improvement, and development of new courses according to the needs of industry. It is expected that other universities will use these centers as a model for future growth and improvements.

The signing ceremony for the launch of the Centers for Advanced Studies Program was attended by the Vice Chancellors from the four participating universities, representatives from the Higher Education Commission, members of the Ministry of Science and Technology, other officials, and students.

http://www.thenews.com.pk/article-44233-USAID,-HEC-sign-MoU-for-adv...

Comment by Riaz Haq on May 4, 2012 at 7:38pm

Here's Pak Observer on canola hybrid seeds developed in Pakistan:

Islamabad—Pakistan can earn Rupees 200 billion by producing canola crop. This was stated by Dr. Akbar Shah, Director, Oil seed Programme at the National Agricultural research Centre (NARC), while addressing the farmers invited to attend Mela, organized by Oil Seed Programme of the NARC for introduction of Canola Hybrid crop here at NARC. The Mela was attended by Framers and other stake holders and scientists.

It is to be noted that Canola oil is the healthiest of all commonly used edible oils. It is lowest in saturated fat, high in cholesterol-lowering mono-unsaturated fat and the best source of omega-3 fats of all popular oils. Canola oil has distinct health benefits than many other vegetable edible oils. It is fast emerging as healthiest oils in tandem with olive oil.

Dr. Akbar said that Pakistan is spending huge amount on import of edible oil. So to reduce the import bill PARC scientists introduced the new Canola Hybrid variety to farmers, he added. He informed that Pakistan’s annual edible oil requirement is 2 million tones. Keeping in view the importance of this crop NARC has developed Canola Hybrid for increasing the oilseed production to make the country self sufficient in edible oil. He said that farmers can earn Rs.40, 000 to 50,000 from one acre by producing canola crop.

Dr. Akbar said that Canola is an important crop for enhancing edible oil production. Farmers can benefit to enhance their income by cultivating Canola crop which not only help to meet the country’s requirement but also help to cut down the edible oil import, he added.

http://pakobserver.net/detailnews.asp?id=153678

Comment by Riaz Haq on May 7, 2012 at 5:27pm

Here's a Dawn report on decline in nanotech research in Pakistan: Nanotechnology research in Pakistan, which had shown a trend of higher publication numbers over the last decade, has suffered from the country’s present financial crisis, a study said.

In 2008 the government did not extend the term of the National Commission for Nanoscience and Technology, initially set up in 2003 for three years and later extended for two more years.

The study, published online on 29 March in Scientometrics, said research publications in the field had grown from seven in 2000 to an impressive 542 papers in 2011, registering a 29 per cent annual growth rate.

This is higher than the average annual growth rate of 23 per cent registered globally, said Rizwan Sarwar Bajwa, research associate at the Preston Institute of Nanoscience and Technology in Islamabad who, together with his colleague Khwaja Yaldram, had carried out the study.

Much of the contribution came from 13 universities while only two state-owned research and development institutions in the country participated in nanoscience and nanotechnology research.

The study attributed the spurt in research and publications to heavy government spending on manpower training and procuring the latest equipment for laboratories working in the field.

“Unfortunately, the present financial crunch faced by the country could have a negative impact on the progress achieved so far,” the study concluded.

“The publication shows that despite availability of funding, the research and development institutes contributed very little in the field of nanoscience and nanotechnology,” Bajwa, lead author of the study.

If developing countries such as Pakistan do not engage in basic research in nanoscience, they will end up as consumers of hi-tech products from other countries, he said.

Pervez Hoodbhoy, professor of physics at Quaid-e-Azam University, Islamabad, observed that higher publication numbers are not a true indicator of progress in a field.

“A better indicator is citations. But, if self-citations are removed the numbers will collapse,” Hoodbhoy said.

“Another metric of progress could be the creation of nanodevices and their commercial production. In the absence of such steps, it is not clear what is being achieved by the mass production of papers,” added Hoodbhoy.

Bajwa attributed the country’s few patents in the field to a dearth of funds for research, due to which many scientists confine themselves to teaching.

http://dawn.com/2012/05/07/funds-crunch-hits-pakistans-surge-in-nan...

Comment by Riaz Haq on May 27, 2012 at 11:19am

In a recent book "Abundance", author Peter Diamandis argues that that advanced science is becoming much more accessible to a wider number of people through movements such as the world-wide DIY movement spurred by better low-cost tools and technologies for things such as "bio-hacking" and development of artificial intelligence. It's no longer an exclusive preserve of a few elite scientists in multi-million dollar labs.

http://books.google.com/books?id=lCifxlN8ZIoC&printsec=frontcov...

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