Tuesday, December 8, 2020

Pakistani Scientists Publishing CRISPR Gene Editing Work in International Journals

CRISPR CAS9 is the latest revolutionary gene editing technology to take the world by a storm. Pakistan is among a select group of nations where scientists are publishing their work on CRISPR in international journals. In fact, Brazil, China, India, Iran and Pakistan are the only developing nations listed among the countries where scientists published CRISPR research in 2018. The rest of the list is made up of highly developed countries of North America, Europe and East Asia. A quick Google search revealed several CRISP papers authored by Pakistani scientists. 

CRISPR Gene Editing Papers Published in 2018. Source: Science Magazine


What is CRISPR/CAS? 

CRISPR CAS9 (clustered regularly interspaced short palindromic repeats- CRISPR associated protein 9) technology was developed by Dr. Jennifer Doudna of UC Berkeley. She has recently won the Nobel Prize in Chemistry for 2020 for her discovery.  This gene editing technology has been adapted from the natural defense mechanisms of bacteria which use CRISPR-derived RNA and various CAS proteins, including CAS9, to foil attacks by viruses and other foreign bodies. They do so primarily by cutting up and destroying the DNA of a foreign invader. When some of these chopped up components are selectively transferred into other, more complex, organisms, the manipulation of genes, or "gene editing" is enabled. 

Pakistan is among a select group of nations where scientists are publishing their work on it. In fact, Brazil, China, India, Iran and Pakistan are the only developing nations listed among the countries where scientists published CRISPR research in 2018. The rest of the list is made up of countries from North America, Europe and East Asia. A quick Google search revealed several CRISP papers authored by Pakistani scientists. 

Potential Applications:

CRISPR-CAS9 technology is raising serious fears about humans manipulating the genetic code, and those manipulations get passed on from one generation to the next. Such genetic changes could lead to antibiotic resistance or other mutations that spread into the human population and become very difficult to control. 

On the other hand, the technology could have a range of major positive impacts from treatment for serious human diseases such as cancer and designing new plant varieties to increase food production. 

There is obviously a need to regulate the use of this technology to prevent the worst consequences of its misuse. 

Stanford University


Stanford's Top 2% Scientists List:

Stanford University has ranked 243 Pakistani scientists among the world's top 2% scientists for 2019.  Among them are 81 Pakistani professors who are recognized in the lifetime research work list of 160,000 scientists. The list of the top 2% of the world's scientists has been created by experts from Stanford University based on data from Elsevier’s Scopus, the abstract and citation database. It covers 22 scientific fields and 176 subfields and provides standardized information on citations, h-index, co-authorship-adjusted hm-index, citations to papers in different authorship positions, and a composite indicator.    




Pakistani Professors on Stanford List


Highly Cited Researchers (HCR):


Last year, Clarivate Analytics listed 6 Pakistani and 10 Indian researchers in its list of the world's 4000 most highly cited researchers (HCR).  It included 12 Iranians and no Bangladeshis and no Sri Lankans. This Highly Cited Researchers list included 17 Nobel Laureates. It represented more than 60 nations, but more than 80% of them were from the 10 nations and 70% from the first five – a remarkable concentration of top talent. Here are the top 10 nations in order:  United States, United Kingdom, China, Germany, Australia, Netherlands, Canada, France, Switzerland and Spain.

Most Highly Cited Pakistani Scientists. Source: Clarivate Analytics



The United States led among HCRs with 2,639 scientists followed by the United Kingdom's 546 and China's 482.  Top three institutions producing world's most highly cited researchers were: Harvard University (186), National Institutes of Health (148) and Stanford University (100).  Chinese Academy of Sciences ranks 4th with 99 highly cited researchers.

CRISPR-related papers published in 2018. Source: Science Magazine


Research Output Growth: 

Pakistan is one of the world's top two countries where the research output rose the fastest in 2018, according to Nature Magazine. The publication reports that the "global production of scientific papers hit an all-time high this year...with emerging economies rising fastest".

Countries With Biggest Rises in Research Output. Source: Nature



Pakistan ranked first or second depending  on whether one accepts the text or the graphic (above) published by Nature.  The text says Egypt had 21% growth while the graph shows Pakistan with 21% growth. Here's an excerpt of the text: "Emerging economies showed some of the largest increases in research output in 2018, according to estimates from the publishing-services company Clarivate Analytics. Egypt and Pakistan topped the list in percentage terms, with rises of 21% and 15.9%, respectively. ...China’s publications rose by about 15%, and India, Brazil, Mexico and Iran all saw their output grow by more than 8% compared with 2017".

Scientific Output:

Pakistan's quality-adjusted scientific output (Weighted Functional Count) as reported in Nature Index has doubled from 18.03 in 2013 to 37.28 in 2017. Pakistan's global ranking has improved from 53 in 2013 to 40 in 2017. In the same period, India's WFC has increased from 850.97 in 2013 to 935.44 in 2017. India's global ranking has improved from 13 in 2013 to 11 in 2017.

Top 10 Pakistan Institutions in Scientific Output. Source: Nature Index

Pakistan's Global Ranking:

Pakistan ranks 40 among 161 countries for quality adjusted scientific output for year 2017 as reported by Nature Index 2018.  Pakistan ranks 40 with quality-adjusted scientific output of 37.28. India ranks 11 with 935. Malaysia ranks 61 with 6.73 and Indonesia ranks 63 with 6.41. Bangladesh ranks 100 with 0.81. Sri Lanka ranks 84 with 1.36. US leads with almost 15,800, followed by China's 7,500, Germany 3,800, UK 3,100 and Japan 2,700.

Nature Index:

The Nature Index is a database of author affiliation information collated from research articles published in an independently selected group of 82 high-quality science journals. The database is compiled by Nature Research. The Nature Index provides a close to real-time proxy of high-quality research output and collaboration at the institutional, national and regional level.

The Nature Index includes primary research articles published in a group of high-quality science journals. The journals included in the Nature Index are selected by a panel of active scientists, independently of Nature Research. The selection process reflects researchers’ perceptions of journal quality, rather than using quantitative measures such as Impact Factor. It is intended that the list of journals amounts to a reasonably consensual upper echelon of journals in the natural sciences and includes both multidisciplinary journals and some of the most highly selective journals within the main disciplines of the natural sciences. The journals included in the Nature Index represent less than 1% of the journals covering natural sciences in the Web of Science (Clarivate Analytics) but account for close to 30% of total citations to natural science journals.

Pakistan vs BRICS:

In a report titled "Pakistan: Another BRIC in the Wall", author Lulian Herciu says that Pakistan’s scientific productivity has quadrupled, from approximately 2,000 articles per year in 2006 to more than 9,000 articles in 2015. During this time, the number of Highly Cited Papers featuring Pakistan-based authors increased tenfold, from 9 articles in 2006 to 98 in 2015.

Top Asian Universities:

British ranking agency Quacquarelli Symonds (QS) has recently ranked 23 Pakistani universities among the top 500 Asian universities for 2019, up from 16 in 2018.  Other South Asian universities figuring in the QS top universities report are 75 from India, 6 from Bangladesh and 4 from Sri Lanka.

In terms of the number of universities ranking in Asia's top 500, Pakistan with its 23 universities ranks second in South Asia and 7th among 17 Asian nations topped by China with 112, Japan 89, India 75, South Korea 57, Taiwan 36, Malaysia 26, Pakistan 23, Indonesia 22, Thailand 19, Philippines 8, Hong Kong 7, Vietnam 7, Bangladesh 6, Sri Lanka 4, Singapore 3, Macao 2 and Brunei 2.

Summary:

Pakistan is among a select group of nations where scientists are publishing their work in international journals. In fact, Brazil, China, India, Iran and Pakistan are the only developing nations listed among the countries where scientists published CRISPR research in 2018. The rest of the list is made up of countries from North America, Europe and East Asia. A quick Google search revealed several CRISP papers authored by Pakistani scientists.  Stanford University has ranked 243 Pakistani scientists among the world's top 2% scientists for 2019.  Among them are 81 Pakistani professors who are recognized in the lifetime research work list of 160,000 scientists. Last year Clarivate Analytics listed 6 Pakistani and 10 Indian researchers in its list of the world's 4000 most highly cited researchers (HCR). There were 12 Iranians and no Bangladeshis and no Sri Lankans on it.  Pakistan is among the world's top two countries where the research output rose the fastest in 2018. Pakistan's quality-adjusted scientific output (WFC) as reported in Nature Index has doubled from 18.03 in 2013 to 37.28 in 2017. 
Related Links:

Haq's Musings

South Asia Investor Review

Pakistani-American is Top US Expert in Quantum Computing

AI Research at NED University Funded By Silicon Valley NEDians

Pakistan Hi-Tech Exports Exceed A Billion US Dollars in 2018 

Pakistan Becomes CERN Member

Pakistani Scientists at CERN

Rising College Enrollment in Pakistan

Pakistani Universities Listed Among Asia's Top 500 Jump From 16 to 23 in One Year

Genomics and Biotech Research in Pakistan

Human Capital Growth in Pakistan

Educational Attainment in Pakistan

Pakistan Human Development in Musharraf Years

Robotics Growth in Pakistan 

Riaz Haq's Youtube Channel

5 comments:

Riaz Haq said...

Very excited that two
@maxplanckpress
scientists are among the 2021 #LeibnizPreis recipients: our Vice President Asifa Akthar, MPI of Immunobiology & Epigenetics
@AsifaAkhtar1

@mpi_ie
& Volker Springel, MPI for Astrophysics. Congratulations!Partying faceGrinning facehttps://bit.ly/2VY5AX4
@dfg_public

https://twitter.com/maxplanckpress/status/1337056859400900611?s=20

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Pakistan-born scientist to receive prestigious Leibniz Prize

https://www.brecorder.com/news/40040190/pakistan-born-scientist-to-receive-prestigious-leibniz-prizes

Leibniz Prizes, most important research award in Germany for outstanding work from all scientific areas will be awarded on March 15 next year in a virtual ceremony.
The Gottfried Wilhelm Leibniz Prize has been awarded annually by the DFG since 1986.

Pakistan-born scientist Asifa Akhtar among 10 others will receive prestigious Leibniz Prizes next year, the committee announced on Thursday.

Leibniz Prizes, most important research award in Germany for outstanding work from all scientific areas will be awarded on March 15 next year in a virtual ceremony.

Asifa Akhtar is the vice president of The Max Planck Society. It is Germany’s most successful research organisation. Since its establishment in 1948, no fewer than 18 Nobel laureates have emerged from the ranks of its scientists, putting it on a par with the best and most prestigious research institutions worldwide.

Born in Karachi, she obtained her doctorate at the Imperial Cancer Research Fund in London, UK, in 1997. She then moved to Germany, where she was a Postdoctoral fellow at the European Molecular Biology Laboratory (EMBL) in Heidelberg and the Adolf-Butenandt-Institute in Munich from 1998 to 2001.

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Pakistan-born scientist becomes first woman to head section at renowned body

https://www.dawn.com/news/1569093

Pakistan-born scientist ​​​​​​​​Asifa Akhtar has become the first international female vice president of the biology and medicine section at Germany’s prestigious Max Planck Society.

The Max Planck Society is Germany’s most successful research organisation. Since its establishment in 1948, no fewer than 18 Nobel laureates have emerged from the ranks of its scientists, putting it on a par with the best and most prestigious research institutions worldwide.

Riaz Haq said...

Research breakthrough: Humans are not the first to repurpose CRISPR

https://www.sciencedaily.com/releases/2020/03/200324131820.htm

In recent years, the development of CRISPR technologies and gene-editing scissors in particular have taken the world by storm. Indeed, scientists have learned how to harness these clever natural systems in the biotech and pharmaceutical industries, among other areas.

New research from the University of Copenhagen shows that we are not the first to find a way to exploit the benefits of the CRISPR technique. Apparently, primitive bacterial parasites have been doing so for millions of years.

The researchers studied the least described and most enigmatic of the six CRISPR-Cas systems found in nature -- Type IV CRISPR-Cas. Here, they uncovered characteristics that differ entirely from those in other systems.

Redefining CRISPR

"Until recently, CRISPR-Cas was believed to be a defense system used by bacteria to protect themselves against invading parasites such as viruses, much like our very own immune system protects us. However, it appears that CRISPR is a tool that can be used for different purposes by diverse biological entities," according to 28-year-old Rafael Pinilla-Redondo, a PhD at UCPH's Department of Biology who led the research.

One of these biological entities are plasmids -- small DNA molecules that often behave like parasites and, like viruses, require a host bacterium to survive.

"Here we found evidence that certain plasmids use type IV CRISPR-Cas systems to fight other plasmids competing over the same bacterial host. This is remarkable because, in doing so, plasmids have managed to turn the system around. Instead of protecting bacteria from their parasites, CRISPR is exploited to perform another task," says Pinilla-Redondo, adding:

"This is similar to how some birds compete for the best nesting site in a tree, or how hermit crabs fight for ownership of a shell."

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FACTS:

In nature, CRISPR-Cas are adaptive immune systems used by bacteria to cut the DNA of invading genetic parasites.
There are six types of naturally occurring CRISPR-Cas systems. The new research shows that Type IV CRISPR-Cas -- unlike the other known CRISPR-Cas types -- is not found in the genome of bacteria, but in the genetic material of plasmids. Plasmids are parasitic genetic elements that require a host bacterium to survive.
Among other things, the researchers identified several new subtypes and variants of the Type IV CRISPR-Cas system.
Several recent articles from other researchers also suggest that different types of so-called mobile genetic elements (a group of genetic entities to which plasmids belong) use CRISPR-Cas components to perform tasks other than protecting bacteria from viruses.

Riaz Haq said...

The groundbreaking research that brought Doudna and Charpentier to the top of the world has the potential to control future pandemics, whether it's overcoming the next viral plague through better detection and treatment or developing people with better disease resistance programmed into their cells. Their patented gene-editing technology, which stands for CRISPR-Cas9, allows DNA fragments to be selectively cut and edited as if there were so many seams to lift or waistbands to loosen. The method is based on the defense mechanisms that bacteria have developed in the fight against viruses by their ancestors.

Doudna and Charpentier, one American and the other French, are the sixth and seventh women to have won the Nobel Prize in chemistry in more than 100 years of history. (Marie Curie was the first in 1911, followed by her daughter Irene in 1935). Doudna and Charpentier's names were clearly linked in 2015 when they jointly won the $ 3M Life Sciences Innovation Award and in 2018 when they received the coveted Kavli Prize in Norway. Although they never belonged to the same research institution, they have worked successfully with each other and with many colleagues from different countries based on common interests, camaraderie, and skills.

Summary, A.S. SUMMARY OF THE CODE BREAKER BY WALTER ISAACSON (pp. 7-8). Kindle Edition.

Riaz Haq said...

CRISPR Cas System: an efficient tool for cancer modelling
November 2020
Journal of the Pakistan Medical Association
DOI: 10.47391/JPMA.801


https://www.researchgate.net/publication/345830261_CRISPR_Cas_System_an_efficient_tool_for_cancer_modelling



The Clustered Regularly Interspaced Short Palindromic Repeats-Cas-9 (CRISPR-Cas9) system has been a revolutionising tool in the field of molecular genetics, which provides a versatile range of editing potentials. Researchers can produce breaks or alter genomes with ease using the system. Cancer is one of the multi-gene diseases whose genes need to be studied in detail. The CRISPR-Cas9 technology may also provide a promising potential in the field of cancer genetics. The current narrative review comprised 50 research articles which were keenly analysed and the applications and outcomes of CRISPR-Cas9 system in cancer genetics were comprehensively and critically discussed. It was concluded that application of the system had great potential to help understand cancer biology of various types and could be used for its genetic modelling. However, much work is still needed to be done to apply the technology for understanding the mechanism of cancers and to help in the designing of appropriate therapies.



Riaz Haq said...

Obama Advisers Say CRISPR is a Bioterror Threat

https://scipol.duke.edu/news/obama-advisers-say-crispr-bioterror-threat

MIT Technology Review – Scientific advisers to President Obama warn that the U.S. urgently needs a new biodefense strategy and should regularly brief President-elect Donald Trump on the dangers posed by new technologies like CRISPR, gene therapy, and synthetic DNA, which they say could be coƶpted by terrorists.

In a letter to the president, the President’s Council of Advisors on Science and Technology (PCAST) urges the creation of a new entity charged with developing a national biodefense strategy within six months. Such a strategy was developed in 2009, but it's carried out by several government agencies in an uncoƶrdinated approach, says Piers Millet, a bioterror expert at the Wilson Center in Washington, D.C.

The council is also urging the president to ask Congress to establish a $2 billion fund to respond to public health emergencies that could be caused by new biotechnologies.

For the past two decades, the government has focused its biodefense efforts on a list of known pathogens—such as anthrax, smallpox and Ebola—declared by the Department of Health and Human Services and Department of Agriculture to have the “potential to pose a severe threat to public health and safety.” Government-funded research on these pathogens receives special scrutiny, and the National Institutes of Health limits researchers from conducting experiments that could make certain germs, like influenza, more dangerous.

But PCAST members say the recent “exponential” growth of biotechnology has rendered this approach outdated. A new strategy, they say, “must prepare not only for known biological agents, but also for a much wider array of novel and ever-changing biological threats that may be impossible to fully anticipate.”

Specifically, the council argues that synthetic DNA, gene therapy, and genome editing technologies like CRISPR open up new possibilities for intentional misuse, such as modifying a virus or bacteria to make it resistant to drugs. Synthetic DNA refers to artificial DNA that can be created in a lab, while gene therapy and gene editing are methods to alter the DNA inside living cells. And advances in genomic sequencing are allowing scientists to quickly and cheaply generate the entire readout of an organism’s DNA—information that could potentially be used by terrorists to create a bioweapon.

“If you can get access to the sequence data, that’s really all you need,” says Todd Kuiken, senior research scholar with the Genetic Engineering and Society Center at North Carolina State University.

It will be nearly impossible to monitor all such experiments, Kuiken says. But a better national surveillance system that includes detailed information about a germ’s DNA, as is suggested in the letter, could tell government officials whether pathogens involved in disease outbreaks have been engineered or modified.

The council members also propose investing in the development of new antibiotic and antiviral drugs against both natural and manmade threats, and setting aside $250 million annually to stockpile vaccines.

But while Kuiken says he sees the letter as a step in the right direction, it only addresses traditional biological threats, like viruses and other pathogens. He says it doesn’t do enough to consider more exotic biological attacks, like an insect that has been genetically modified to wipe out the country’s supply of a staple crop.