ScienceHub # 03: Synthetic Microbiology

    Continuing to go to laboratories and watch how domestic scientists are going into the future, we looked at the microbiologist, genetics, Konstantin Severinov, and he told us about what are the most active currents in biology, which scientists will soon need in this area, and what kind of tasks they will decide.


    Synthetic Microbiology. To the history of the issue


    Since the topic of the conversation, indicated in the title of the post, sounds like synthetic microbiology, we will start with it. There are many ways to define this science, it is important that in it all professions and fields of knowledge are intertwined, as it was in click chemistry . But here it’s not even a matter of interdisciplinarity, but that physicists and mathematicians can now bring much more to biology than “wet” biologists. What do they want: to answer the question of how the work of genes in the cell is controlled. To do this, they began to simulate the processes occurring in the genes artificially.

    Another area of ​​microbiology is that you can synthetically create a DNA molecule yourself, and then place it in a cell in which there is no genetic information. So a new cell will appear, which is programmed in the same way as its creator, in this case a scientist.

    Konstantin Severinov: “Synthetic microbiology emerged when a certain number of physicists and mathematicians, from old memory, decided to take up microbiology. Whenever a crisis begins in physics or mathematics - they have nothing more to look for - either to prove Fermat's theorem or the Higgs boson, they go to biology and start doing something there. It's good. And the result of this kind of activity was that physicists wondered how exactly the work of genes in the cell is controlled. Biologists also dealt with this, but physicists approached this from the other side, they began to model these processes, use various methods up to differential equations to look at the process of how genes work in a cell. It turned out that in a number of cases it is possible, depending on a number of conditions that they themselves control, to change the spectrum of genes, working in the cell, biologically active substances that the cell produces and so on. This is part of synthetic biology. Another synthetic biology of a very high technological level is the science that Craig Venter continues to develop - a person who sequenced the human genome, himself. And this science is this: if we can determine the genome, that is, the totality of the sequences of the entire gene of the body, and this is DNA, then no one bothers us in principle to create such a DNA molecule synthetically by ourselves. It will be very long, but we made it ourselves. ” who sequenced the genome of man, himself. And this science is this: if we can determine the genome, that is, the totality of the sequences of the entire gene of the body, and this is DNA, then no one bothers us in principle to create such a DNA molecule synthetically by ourselves. It will be very long, but we made it ourselves. ” who sequenced the genome of man, himself. And this science is this: if we can determine the genome, that is, the totality of the sequences of the entire gene of the body, and this is DNA, then no one bothers us in principle to create such a DNA molecule synthetically by ourselves. It will be very long, but we made it ourselves. ”



    When the human genome was completely determined in the early 2000s, and we were able to read all three billion "letters" of which it consists, a new area arose - bioinformatics. It is designed to store and analyze the information that geneticists were able to get. And now, when there is a lot of data, we need serious technical support. We must at least understand how and where to store all this data, what technologies are needed for this. And bioinformatics should analyze, identify some interesting sequences that can be experimentally worked on later. This is one of the most promising areas now in biology.

    What for?


    The fact is that synthetic microbiology is an ideal example of the science of the future, therefore, so far there are only projects, and it is impossible to feel the results of scientists. But in what areas it is applicable. This applies, for example, to biofuels. If we still stop pumping hydrocarbons from the earth, then bacteria will have to produce them, which will be created by scientists specifically for this. They can do this on a large scale and much cheaper.

    KS: “An article was published in the October issue of Nature magazine, where it was shown that the usual E. coli, the bacterium of which lives in our intestines, was made a factory for the production of oil, or rather, not oil, but oil degradation products, which can be used as petrol. And this was due to the fact that using various analysis methods, sets of enzymes were developed that can build an aliphatic chain, aliphatic substances - this is what oil consists of, of a certain length from simple precursors, such as carbon dioxide, ammonium and so on , and it turned out that E. coli, in which such genes are introduced, does indeed produce hydrocarbons. From here until the time when the corresponding hydrocarbons appear at the gas station, there is still a long way to go, but the first steps will certainly impress at least venture investors. ”



    The second important point at which the huge forces of biologists are now thrown is the creation of new antibiotics. If this problem is not resolved in the near future, then humanity can return to the situation of the 19th century, when people were dying from the diseases that we now seem to be able to treat, such as tuberculosis and cholera. Now bacteria are emerging that are resistant to the forms of antibiotics that scientists have created. That is, the situation is obtained, according to Darwin's theory, because in hospitals where antibiotics are used a lot, a selection of bacteria resistant to antibiotics has taken place. And now they live and breed there, and antibiotics do not act on them. Accordingly, in the future it may happen that we come to the hospital, pick up a bacterium that is empty by modern standards, and die.

    KS: “But now with the development of genomics, an understanding has arisen that the number of bacteria in the world is huge, and the number of bacteria that we can cultivate, that is, grow in a cup, is very small, that is, 99.9% of all bacteria are dark matter - we cannot cultivate them, therefore we cannot feel them and excrete pharmacological substances. But the development of these methods for determining genomic sequences that allow us to make a gene work in a model organism, rather than in its natural environment, suddenly reveals a range of possibilities in terms of the achievement of new genes and complexes encoding new antibiotics. Bioinformatic predictions must be made, genes that can give something interesting should be highlighted, and then someone should appear who will make these genes work. ”



    Scientists of a new type


    The education that biologists receive in modern universities is not enough now to solve these problems. “Wet” biologists dealing with test tubes and experiments will be a thing of the past, as future specialists should be able to analyze the data obtained. Moreover, now in the USA and Europe there are companies that outsource doing all this “wet” work. This is not so expensive and is much more effective than the situation when scientists in the laboratory do the same. That is, there is a specialist who comes up with a concept on the basis of the existing database, and to check it, he orders the company to prepare some genes, strains or organisms, thanks to which he then checks his predictions.

    Ideally, of course, the scientist of the future should combine the skills of both a microbiologist and bioinformatics, but most likely there will be no firms taking orders soon, but there will be robotic stations that perform all the necessary procedures. That is, the number of scientists in the modern sense who can and do something with their hands will fall, and people who can think, put forward concepts and theories based on data obtained by robots will be in demand.

    Where do such people come from. Now you can only retrain existing specialists, but the question arises of who to retrain. Konstantin believes that it’s not biologists, but mathematicians who can correctly pose the biological question and create the scheme of the experiment, but do not deal with the experiment itself. He believes that mathematics is easier to teach experimental biology than a biologist to learn to understand data that is not related to transfusion of fluid and or the study of a microbe.


    KS: “Apparently, part of the workforce could be engaged in computer analysis. This is similar to the Borges Library of Babel - a huge number of texts - it is so large that it contains all the texts that existed, exist and will exist, but they cannot be found. And we find ourselves in a similar situation, because the machines that sequenced the genomes do this every day. Right now millions of genetic texts are in some kind of database. They contain information about all living things. There is, for example, information on how to defeat cancer - the only question is how to find it, how to organize it, what to look at, and what questions to ask. But how capacious this is in terms of the number of people I can’t imagine. Bioinformatics is a sought-after profession, and a molecular biologist is smaller. It turns out

    Those who are too lazy to read can watch a video with Konstantin Severinov here.

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