Bioinformatics in Russia: wanted the best way…
Russian science facing a new threat
Professor Pavel Pevsner told "Polit.<url>", that he and his colleagues from the St. Petersburg Academic University have developed a method for decoding the genomes of bacteria known as the "dark matter of life". However, the new rules for financing mega-grants may lead to the fact that young bioinformatics with their knowledge and developments will leave Russia.
DiscoveriesScientists from St. Petersburg Academic University have developed a method for decoding (sequencing) the genomes of bacteria, which are known as the "dark matter of life".
This is what scientists call most of the thousands of bacterial species that previously defied modern methods of decoding genomes, while producing unknown antibiotics or living in the human body. "This part of life on Earth, which has always been a mystery, has now become accessible to scientists," said project leader Pavel Pevsner, professor at the University of California (San Diego, USA).
Traditional methods of reading genomes require at least a million cells, which must first be grown in the laboratory. However, 99% of bacteria do not want to grow in the laboratory and remain invisible to modern science. Pevsner and his team demonstrated how to read genomes from a single cell. This result allows us to study microbes that play an important role in our lives, because 10% of our weight is made up of bacteria. Some can greatly complicate our lives, while others work around the clock to help us digest food. Still others, as recently shown, even manipulate us by forcing us to eat more than we need. Unfortunately, if we do not know the lion's share of the bacteria living in us, it is very difficult to understand how this complex world inside us functions. The new method allows you to read the genomes of all these players, both bad and good.
Sequencing of individual cells is one of the fastest growing and most important areas of modern genomics. In the fall of 2011, Pevsner's group, in collaboration with Roger Lasken, a pioneer in single cell sequencing, developed the E+V-SC program, which for the first time made it possible to analyze the genomes of individual cells, and published it in the journal Nature Biotechnology. A new algorithm developed by Russian scientists (also led by Pevsner) in record time and recently published in the Journal of Computational Biology has improved the American E+V-SC by an order of magnitude. The algorithm was named SPAdes (Saint Petersburg Assembler) and it has every chance to become the first Russian brand in biotechnology – an area where Russian science has never shone.
Currently, researchers from the Academic University of the Russian Academy of Sciences are using SPAdes to sequence the "dark matter of life" and human pathogens. Recall that Pevsner became one of the winners of the first megagrant competition. Thanks to megagrant and Rector of the Academic University Zhores Alferov, Laboratories of Algorithmic Biology and the first master's program in this field in Russia appeared in St. Petersburg.
Pevsner managed to assemble a team of talented young mathematicians and programmers who at first knew nothing about genome sequencing. All of them were trained in bioinformatics schools and two months later began to develop SPAdes. "Assembling DNA fragments is a task very similar to assembling a puzzle of a billion pieces. It is considered one of the most difficult problems of bioinformatics. The development of a new assembler can take years from a professional bioinformatics laboratory. The fact that the guys from Russia without a bioinformatic background coped with it so quickly in six months is wonderful," Pavel Pevsner commented on the work of colleagues to the portal. Phys.org .
Plans and threatsAre you and your colleagues planning to switch from reading bacterial "dark matter of life" to reading equally mysterious cancer cells?
Reading individual cancer cells is one of the hottest trends in modern genomics.
Modern technology requires at least a million cells to read the cancer genome. This means that cancer remains invisible to modern sequencing machines until it has accumulated the first million cancer cells, and this is often too late. That's why the initial stages of cancer (up to the first million cells) remain a secret behind seven locks, and the United States and China invest huge efforts in reading individual cells in order to open these locks. Both experimental and equally important computational aspects of this problem.
How does your St. Petersburg laboratory plan to participate in this race? Russia has now unexpectedly become a bioinformatic leader in one of the fastest developing areas of genomics, and I am proud that very young guys from my laboratory are successfully competing (and cooperating!) in this field.
with leading genomic centers. We have come close to creating, perhaps, the first global brand in genomic bioinformatics, developed in Russia.
However, answering your question about how we plan to continue participating in this race, I'm afraid that in no way, since, apparently, my (and many others) megagrant laboratory will close soon. And as has happened many times before, the ideas originally developed in Russia will be finally implemented and commercialized in the West. Due to the unclear prospects for the continuation of mega-grants, some guys from my team are already starting to pack their bags. Frankly, I will be happy to take them as students and postdocs to the University of California.
Why do you have such gloomy forecasts about the future of megagrants? They are not gloomy, but realistic.
Megagrants undoubtedly represented a very timely and useful experiment in Russian science. 2 years ago, when I arrived, there was not a single expert on algorithms for reading genomes in Russia. But without such experts, there can be no serious genomics and personal medicine in Russia. Of course, there are bioinformatic stars like Mikhail Gelfand in Russia, but they can be counted on the fingers of one hand and many key areas in this rapidly developing discipline (such as algorithmic biology, which is engaged in the assembly of genomes) are simply absent in Russia. I am very glad that in less than 2 years a world-class team in this field has appeared in Russia. However, megagrants, having started well, I'm afraid, will end up with a goal in their own goal. I wouldn't be surprised if some successful mega-grant labs close down and just move West in 2013.
The fact is that the financing of mega-grants worked for only 2 years. In no country in the world are serious scientific projects of this scale planned for such a short period – usually it is 5 years. Peter the Great understood this well when he gave the first Russian mega-grants (as much as 1,000 gold rubles a year!). And as a result, the great Leonard Euler came to Russia for 30 years.
But the Russian government does not seem to understand this. What is even more unexpected, according to the new rules, mega-grants can be continued only if co-financed in an equal amount by the university where the laboratory was organized within the framework of the mega-grant. This is another purely Russian invention – there is no such thing in any country in the world. Even in the USA, a country of rich universities, especially compared to Russian universities, which often eke out a miserable existence. If I went to my rector in California and asked for a million dollars for funding, he would think I was crazy – it's just not a function of universities. I can still imagine that such huge universities as MSU will be able to scrape together co-financing by hook or by crook, but my laboratory is located in a small elite university that is 100 times smaller than MSU.
It seems that you don't have a very flattering opinion about the new rules of megagrants and about the Ministry of Education and Science in general? I actually have a high opinion of both the current and the past minister – I like their initiatives on mega-grants and on the new map of Russian science.
But I saw how good initiatives in Russia collide with the administrative reality when people in my laboratory did not receive a salary for six months and when it took them a year to buy the first computers.
What do you suggest? According to the Hamburg account, Russian science has shrunk to the level of one decent American university in such key areas as biology and computer science - two disciplines that are setting the fashion in Silicon Valley today.
For example, my university in the USA is significantly ahead of "Russia as a whole" in these disciplines in terms of the number of star scientists. Therefore, every world-class Russian laboratory is now worth its weight in gold.
Last year I proposed a project to create a Russian National University (RNU) aimed at preserving such laboratories. It seems that the roadmap of Russian science currently being developed pursues the same goal, and I sincerely wish it success. I really don't understand why it takes six months to create such a map – in my disciplines (biology and computer science) – I could draw such a map in a couple of hours. And I'm afraid that while the Ministry is working on this map, the leading Russian teams created by mega-grants will simply move to the West, or even to the East. After all, in China and Singapore, the financing of scientific projects is much more stable than in Russia. It is also not necessary to count on Russian business yet, since few Russian businessmen understand the financial prospects in genomics and personal medicine.
Portal "Eternal youth" http://vechnayamolodost.ru06.09.2012