Friday 25 September 2015

CRISPR WAY TO A BETTER LIFE

<CONTROL-X><CONTROL -V> CRISPR  WAY TO A BETTER LIFE

I am sure all of us are proficient in Cut – Paste / Copy-Paste operations. Most of us have used this route to improve of our output one way or other. My generation was regrettably not able to use these operations for getting better grades but surely we too have used these to embellish our presentations and project reports. At least I have. 

Now just suppose that you could use the same operation for improving your life by getting rid of some bad genes you may have inherited – no fault of yours or your parents though – because they had no control on what they received from their own parents and so on. This may appear as a sci-fi fantasy but the scientists are now confident that they can do so and do so fairly easily. 

In April this year, a team of Chinese researchers created a global uproar when they published a paper describing attempts to edit the genomes of human embryos. Led by Junjiu Huang of Sun Yat-sen University, Guangzhou, they used a new technology called CRISPR / Cas9 to try and edit non-viable, single-cell embryos obtained from fertility clinics.

CRISPR is an acronym for ‘clustered, regularly interspaced, short palindromic repeats’ and Cas9 is an enzyme or a protein which can be guided to specific sites on any gene and can be used to cut one or both the strands of the DNA double helix. It essentially does what we do with our reports, cut out the strings of letters and words and either paste them where we require them or just consign these cut pieces into oblivion. Only in this case, the words and letters CRISPR/Cas9 operates upon are the letters which make up the genetic code, DNA.

A technique using CRISPR/Cas9 has now been developed which can ensure that specific sites on genes can be targeted and the genetic sequence can be modified suitably either by cutting out a few words or patching new ones or adding new ones.   

As you can imagine the implications are tremendous. We now know which genes are responsible for causing as many as three thousand genetic disorders. In theory, if we knew the mutations that give individuals a severe disorder, correcting that genetic defect might now be possible.

A quick backdrop for meaningful understanding of what is involved : Probably all of us are familiar by now with the building blocks of our DNA -  A(Adenine), T(Thiamine), C(Cytosine) and G(Guanine).  Any three of these four building blocks combine to form groups of three called “codons”. There are 64 different codons which can get formed, each of three letters. These codons are “words” which make up a “sentence” which actually represent a “gene”. A gene can be a short sentence or a very long sentence. Any misspelling of one or more words or a repetition or omission of a word can cause malfunction of the gene in question. All of us inherit two copies of any particular gene, one from each parent. Normally even if there is some disorder in one copy of a gene, the other copy takes over and if that one is without any defect, the gene functions normally.

 But there are some diseases where a defective gene controls the functioning irrespective of a “normal” other half being present. One such disease is Huntington’s disease. The gene responsible for this is located on Chromosome 4 of human genome. The gene sequence contains a “word” CAG which is repeated a number of times in a stretch. It could be just 6 times in some individuals, some 30 odd times in others and more than 100 times in a few individuals. If you have up to 35 repeats of CAG in your gene, you will be fine (most of us have 10 to 15 repeats) but if the number exceeds 39 then you are definitely going to get the dreaded disease.

The onset of disease begins with slight deterioration of mental faculties and progresses to jerking of limbs and deep depression, hallucinations and delusions leading to premature death.
The relation between the number of repeats and the age at which the disease sets in is correlated to a remarkable degree. If you have 39 repeats, on an average you will get symptoms by the age of 66; with 40 repeats at 59; with 41 repeats at 54; with 42 repeats at 37; if you have 50 repeats then by the age of 27.    

Apparently no other factor can influence this progressive deterioration. There is no cure or any drug which can even slow the march of this dreaded disease. This is a sort of disease where CRISPR/Cas9 is the only solution. The families in which Huntington’s is common may soon get relief through this technology. It is not clear if patients already affected by onset of this disease can benefit from this treatment but surely the younger patients should be able to get full relief.  

Similar to this, another 5 diseases have been identified which are caused by  mistakes in sequence of CAG in other genes. All are neurological diseases. Hopefully, patients suffering from these can also look forward to relief through this technology. 

This technology can be used for altering genetic structure of any organism, bacteria, plants or animals. This is bound to open up a large number of potential areas of application.
Designing of bacteria which can combat infections and even bacteria for specialized industrial applications should now be possible. 

Botanists will be able to script another green revolution by creating modified plant species which will drastically improve the agricultural output. Disease resistant genes can easily be “cut-pasted” into plants which will yield more output under more stringent climatic conditions which global warming is bound to bestow upon us soon enough. 

A modified strain of (male) mosquitoes has already been developed which will yield predominantly male off-springs; drastically reducing the female mosquito population. In keeping with the conventional wisdom ‘female of the species being deadlier than the male’ it is the female mosquito which feeds on animal blood and is responsible for spreading dengue, malaria and filariasis. One can expect more such initiatives under “gene drive” which will be used to control population of pests. Hopefully the ecology will receive due consideration as this will surely lead to big changes in food-chain which may backfire on us humans.  

Surely no one will have any objections to this technology as long as treating diseases and containment of pests are concerned, but it is doubtful if any one (read governments)  can restrict this technology solely for prevention and cure of diseases. George Orwell stated once ‘Any technology which can be used, will be used’.

With such a powerful tool in hand, research is already afoot to modify genes for a better progeny. Junjiu Huang is just one of the numerous scientists frantically working on such projects. Francis Galton, who happened to be a first cousin of Charles Darwin, had coined a term ‘Eugenics’ to denote the science of improving the stock of human species – like we have done with other species. This had set in motion a strong debate in Britain, Germany and US in the early part of the 19th century. (It will be worth our while to revisit that debate at some other juncture). Luckily the matter did not progress then even after a strong push from Hitler’s Nazi Germany. But with these new easy-to-employ gene-altering tools available to any friendly-neighborhood bio-engineering / genetic–engineering  laboratory, the probability of this technology being kept out of reach of common man is, as mathematicians love to put it, vanishingly small.  

There is every likelihood that both you and me will end up with great grand-kids all looking like either Dev Anand or Madhubala and all with IQ of 160+ to boot. Aldous Huxley must be chuckling in his grave. His ‘brave new world’ would perhaps arrive a few hundred years earlier than he had anticipated.

LazyBee 
25th September 2015

References : Wikipedia, ‘Genome’ By Matt Ridley etc

PS  Just when I was sitting down to do this article, I came across one in Times of India which essentially offered most of the details that I was planning to give. So I had to do some mid-course correction and add some specific examples about how CRISPR is likely to make our lives easier. I am enclosing that article from Subodh Verma of Times of India which will give you more information on the subject matter.  (You can also figure out for yourself where and what I have cut-pasted from his article).
Editing Our Genes

In April this year, a team of Chinese researchers created a global uproar when they published a paper describing attempts to edit the genomes of human embryos. Led by Junjiu Huang of Sun Yat-sen University, Guangzhou, they used a new technology called CRISPR to try and edit 86 non-viable, single-cell embryos obtained from fertility clinics.

They wanted to edit the gene responsible for B-thalassemia, a fatal blood disorder. CRISPR (pronounced like ‘crisper’) has swept through the scientific world in the last few years and is now poised for commercial use. It is thought to be revolutionary because it gives humankind a powerful tool to edit, delete, add, replace, activate or suppress specific genes. Humans can, theoretically, change the genetic basis of various traits — from correcting disease causing mutated genes to genes that determine whether you will have brown eyes or black.

The discovery has led to a dramatic rise in funding for research based on CRISPR and a patent war between various scientific institutions. It has also left scientists sharply divided over whether such a technology can be allowed to pick and choose characteristics of future human generations.

CRISPR is an acronym for ‘clustered, regularly interspaced, short palindromic repeats’. This mouthful of a name was given two decades ago when scientists found a strange thing in bacteria genomes. There were these repeating sequences with no known use. Genetics was still developing and the scientists thought no more of this.

Sometime later it was found that these CRISPR sequences were used by bacteria to ward off predatory viruses. The mechanism was unravelled but again nothing more was thought of it. Then, around 2011, several genetic scientists in the US and Europe hit pay dirt. They found that the CRISPR mechanism could be turned around and manipulated for performing cut-and – paste functions on genomes. And the control was fantastic. You could precisely snip off a bit of DNA from a gene and replace it with another pre-fabricated bit of DNA.

Jennifer Doudna, professor at the University of California, Berkeley, led one of the research groups. She told TOI the technology is a “site-specific DNA ‘scissors’, allowing researchers to cut and then either remove or replace genetic material in a cell or organism.” What this means is: first, a piece of RNA is created for unzipping a DNA strand at the target site; then it is lodged in a protein called Cas9 which is the scissors part of the machinery; this complex unzips and cuts away the specific DNA bit. You can replace it with a totally new DNA bit or a corrected version, as needed.

Another pioneer is Prashant Mali, professor at University of California, San Diego. Born in Rajasthan and educated at IIT-B, John Hopkins and Harvard, Mali explains the intricate working of CRISPR: “The remarkable aspect is that the ability to target a new genomic site simply requires one to alter the sequence on the guide-RNA — this makes the technique really democratic in its  ease of use. This has spurred its widespread adoption by thousands of labs around the world in only a few years.”

After four different groups announced their success with CRISPR in 2013, within eight months various groups used it to cut and change targeted genes in human cells, mice, rats, zebrafish, bacteria, fruit flies, yeast, worms and even crops.

The mechanism is breathtakingly simple and cheap. Doudna says it “can be undertaken in a basic lab environment at remarkably low cost”. Mali confirms that it is “very easy to use and also cost-effective enough that it will be soon be a routine procedure in most biology labs.”
Another pioneer, Feng Zhang of Broad Institute, has founded a company called Editas Medicine for using CRISPR in therapeutics. Its CEO Katrine Bosley said they are working to translate the promise of CRISPR/Cas9 genome editing technology into a new class of medicines to treat serious, genetically driven diseases. “This technology enables precise corrections to errors in DNA, and we are working to apply it to treat a broad range of diseases at the genetic level where patients don’t have good therapeutic options.”

The ethical debate that has erupted around CRISPR is because it can also be used to edit germline cells or pluripotent stem cells. Germline cells are eggs and sperm cells. Any changes in these will naturally be inherited by subsequent generations. Pluripotent stem cells can develop into any kind of tissue, and changes in these would affect large number of cells. Mali says one should venture into this area only after thoroughly understanding “the underlying scientific and ethical implications”. “Using CRISPR-Cas9 to engineer specific traits is still a long way off, but the bioethical implications of the technology are currently being reviewed in many regulatory agencies in the US and elsewhere,” Doudna said.
In other words, the technology is at hand. The question is whether we should use it or not .

Times Of India,
Times & Trends 

Sept 13 2015, Mumbai Edition

Friday 4 September 2015

The Coming Red Revolution - II

The Coming Red Revolution – II

A few years ago, NASA started on a program to develop artificial meat which could be grown “in vitro” on the spaceship itself, with a view to feed astronauts on long flights. A space-ship, as you would realize, has extremely limited resources and needs to conserve and recycle these in order to extend the possible flight time. Probably sometime during this exercise, realization must have dawned that the same considerations apply to Spaceship Earth. After all, essentially we are just a giant spaceship, totally on our own with limited resources and with almost negligible probability of being able to “import” any ingredients that we (may) require except energy from Sun. 

This thinking has been widely accepted now and “sustainability” has become a very important factor of consideration today. The issues which were highlighted in Part-I, regarding livestock farming are receiving a great deal of attention and among other remedies being discussed and probably foremost among them is the production of artificial, laboratory-grown meat.

Almost a century ago, in 1932, Sir Winston Churchill had predicted in an essay about future: “Fifty years hence we shall escape the absurdity of growing a whole chicken in order to eat the breast or wing by growing these parts separately under a suitable medium.” One can infer three things from this statement. One, Sir Winston was an extremely prescient man; two, he was more than a bit optimistic about the time-frame required to achieve such a feat, and three he was not aware of such delicacies as tandoori chicken and tangdi kabab, otherwise he would have surely added chicken legs to chicken wings and breasts in the list of chicken parts to be cultivated.  But overall, his prediction was surely in the right direction.

Worldwide, a number of universities are trying to develop technology for manufacturing artificial meat.  Europe, which must feel the pinch of land shortage more than other developed countries, has taken a lead in this development. Prof. Mark Post of Maastricht University of Netherlands is one of the leading researchers in this space.    

On August 5, 2013, the world's first lab-grown burger was cooked and eaten at a news conference in London. Prof. Mark Post’s team had taken stem cells from a cow and grown them into strips of muscle which they then combined to make a burger. The burger was cooked by chef Richard McGeown of Couch's Great House Restaurant, Cornwall, and tasted by critics and food researchers, who agreed that it does taste like meat though with a slightly different mouthfeel. Overall verdict was “acceptable”. 

Here's how the process works: scientists biopsy stem or satellite muscle cells from a livestock animal, such as a chicken, cow or pig. The cells are then placed in a nutrient-rich medium where they divide and multiply, and are then attached to a scaffolding structure and put in a bioreactor to grow. In order to achieve the texture of natural muscle, the cells need to be physically stretched and flexed, or exercised, regularly. This is done by passing small amounts of current of electricity which mimics electrical signals in the nervous and motor systems of live animals. The end result is a thin layer of muscle tissue that can be harvested and processed into ground beef, chicken or pork, depending on the origin of the cells. The best part is a single set of stem cells can produce hundreds of tones of end-product, thus minimizing the pain to live animals.
Scientists have even coined a term for in-vitro meat, “shmeat” which is derived from “sheet + meat” since the meat formed in-vitro is harvested as thin strips or sheets of meat.

No doubt the technology is far from serving a juicy steak made in-vitro as it requires creation of blood  vessels in the muscle mass and also mechanism for transport of metabolized products etc to give that juicy mouth-feel that a steak has, but scientists are already on their way to make various organs for transplant into human body and incorporation of that technology for in-vitro meat should be within our reach.  

The advantages of “shmeat” over the “classic” meat grown on farms are simply overwhelming. Detailed studies have been conducted to assess the impact of vertical farming.  Today the figures could be treated as “guestimates”. Let’s look at these :

Land : It is claimed that every hectare utilized by ‘vertical farming” (a synonym for “shmeat” production) about 10 - 20 hectares of agricultural land can be freed. Some studies have estimated the land saving to the extent of 98%. Moreover the production need not be confined to land and can be moved to sea. As per one estimate a bio-reactor of half the size of an Olympic swimming pool can feed 20,000 people.

Energy : The vertical farming would cut down the energy requirement for meat production by between 35% - 60%. The energy requirements of bio-reactors can also be met through solar power. Only chicken farmed in a conventional manner may have lower energy consumption than in-vitro meat.

Green House Gases : There would be a major reduction in GHG generated and  moreover it will be feasible to collect methane generated in bio-reactors and use the same for energy generation.

Water : The water consumption in bio-reactors can be controlled and water recycled to a great degree, thus reducing the water requirements to a fraction of conventional requirements and reducing the groundwater contamination drastically.

Health : Livestock farming gives rise to certain diseases like Mad Cow, Avian Flu, Salmonella, Trichomonas, E-Coli and other flesh-borne diseases. All these diseases would cease to be relevant with in-vitro production. Today almost 70% of the antibiotics produced are pumped into livestock, apart from steroids and growth hormones. The pesticides too get introduced in the human food-chain through animal meat.  In-Vitro meat will be totally free of traces of theses.  
In fact, “shmeat” will give us an opportunity to enhance its quality by addition of desirable ingredients such as omega-3 acids apart from controlling the fat content and profile of fatty acids incorporated in it.
So it appears all the factors which we had identified as “negatives” for livestock farming have been cleared as far as “shmeat” / vertical farming is considered.

Now let’s take a look at other factors which make or break a new technology,

1. Economics :  As with any new path-breaking technology the initial cost of production of in-vitro meat is very high but already the fresh estimates claim it that a burger from in-vitro production will cost about $8 which is very encouraging. Researchers are estimating that shortly the cost could come down to as little as $2-2.50 per kg at which point the economics would have conclusively swung the in-vitro way. In Indian context goat meat at Rs 400 per kg may not have many takers if in-vitro meat is available at these prices.

. Regulatory Approvals :  As of now “shmeat” has no clearance from regulatory agencies. It is likely that there are a few hiccups in obtaining the clearances but surely these can be overcome by sheer weight of facts and mandatory testing of products like in the pharma industry. The in-vitro meat can have a much more regulated quality and also meet stringent requirements as far as pollutants are concerned.

3. Consumer Acceptance : This could be the single most important factor as religious sentiments are intricately involved with such a product. Whether the rabbi will consider “shmeat” as “kosher”, or whether church will have any objections, whether maulawis will consider this meat as “halal” or whether “shmeat” from cow’s stem cells will pass muster with Hindu  ideologues in India are questions that need to be worked on. Luckily, there is a large body of population which will not be bothered by these hypothetical considerations. It is these mass of people which will determine the fate of this technological break-through.    
One factor why the acceptance for “shmeat” is likely to be easier is what I term as “moral cowardice” that most non-vegetarians (including this writer) suffer from. We all know that the juicy steak or spicy chicken curry that we are enjoying has come from a once living creature and one way or the other, we are responsible for killing it, but we don’t want to accept that and are always finding ways to justify our actions by comforting ourselves that the slaughter was carried out “painlessly” or that the chicken was anyway destined to be eaten by somebody and that somebody just happens to be you etc. “Shmeat”  will give us a perfect way out and allow our palate full freedom to enjoy steaks and tandoori chicken without feeling guilty. A few of my gourmet friends have often extolled superior qualities of venison over goat or lamb meat but I have always refrained from consuming venison as I consider deer as an endangered species. But I will gladly order an in-vitro venison steak today if it were to be on the menu.

In lighter vein, we may discover that a T Rex tangri kabab or a fried Pterodactyl wing is the most delicious dish in the world and one may have to pre-book a take-away at least a couple of weeks in advance because there was so much demand for the item.         


Today mankind is looking at setting up bases on Moon and Mars. Very clearly there is a need to be at least a two-world civilization to guard against “homegrown” threat of nuclear catastrophe or an external threat like an asteroid strike either of which could obliterate life on the earth before mankind has a chance of taking any steps to survive this 6th extinction. A technology like vertical farming will essentially boost feasibility of maintaining such bases in worlds which may not support conventional agriculture and food grown in laboratories will be the only source of sustenance for early colonists. Therefore, in-vitro meat production and other technologies which can support life in space voyages or on extra-terrestrial colonies need to be perfected at the earliest. This is one Red Revolution that everyone must welcome and support. 

LazyBee aka Shirish Potnis