"Many civilizations originated in the territory of Russia, where they emerged and evolved." An interview with Kharis Mustafin.

— Your laboratory is engaged in a rather unusual field — historical genetics. What prompted you to turn to this area?

— I would also like to start this conversation precisely with historical genetics! There is even a formal reason: our laboratory is celebrating its 10th anniversary.

Exactly 10 years ago, the idea emerged to utilize the technical resources of the Moscow Institute of Physics and Technology (MIPT) and establish a historical genetics laboratory that would allow us to investigate archaeological material for its origins. At that time, the field of paleogenetics was actively developing only in the West. When the idea of creating a laboratory in Russia arose, prominent domestic geneticists claimed that paleogenetic research was impossible in our country. Firstly, there was no technical base even close enough to tackle this task. Secondly, the samples themselves are very complex: harsh climate, aggressive soil — all of this leads to very poor preservation of remains. Everyone insisted that it was practically an unsolvable problem.

And indeed, it was. However, I belong to a somewhat informal community of people interested in history. Among them is Vadim Yakunin, a MIPT graduate, founder, and owner of the pharmaceutical company “Protec.” We often discussed what interesting and useful things could be done by applying scientific methods to domestic archaeology and history. The idea arose to create a laboratory that would solve this seemingly impossible task from the perspective of professional geneticists. And we took the plunge. Just at that time, a genomic center was opened at MIPT.

— Russian classics!

— I already had experience in solving seemingly unsolvable problems. The process of establishing the laboratory turned out to be slow. Initially, we sought someone to lead the laboratory. Initiative can be punishing; I had to take responsibility upon myself. Work began. At first, we interacted with leading specialists in population genetics, who study the genomes of modern humans and determine, among other things, the prehistory of populations. How civilizations originated, advanced, mixed, and developed. This is a vast and extremely interesting topic. But it quickly became clear that we needed to focus on what was virtually uncharted territory in our country: collecting archaeological samples, extracting ancient DNA, reading the information, and working with it.

— But how could this be done if there was no real experience in Russia?

— This is where the technical base at MIPT, in the form of a genomic center, came to our aid. We already had a minimal foundation to begin our work. But the most challenging, key aspect of a paleogenetic laboratory is the conditions under which ancient DNA must be handled. The nuance is that ancient DNA in archaeological samples is found in a severely degraded, destroyed state. These are tiny fragments with very low concentration. Often, the material is more complex than what forensic scientists deal with. Therefore, any contamination of the sample with DNA from modern individuals becomes critical. It is also crucial that even microscopic fragments from other previously studied ancient samples do not enter the archaeological sample being examined. The reliability of the information obtained from the DNA becomes highly questionable if complex and costly protective measures are not implemented. This is a key point.

— What has foreign experience shown?

— There are large laboratories around the world — in Harvard, Leipzig, Jena, and Denmark. The Germans built one of the paleogenetic laboratories in Australia, designing it in such a way that nothing from modern individuals could enter it. It is located 500 meters from the highway, taking into account the wind rose. Any visitor must provide genetic samples so their genome is known.

As a result, we faced a very complex question of creating a laboratory with ultra-clean conditions: airlocks for changing clothes, working in protective suits, and complicated, expensive filter-ventilation systems. We leave DNA everywhere around us. The entire atmosphere is like a broth of particles from various people circulating through the ventilation system. The use of cascade ventilation systems that purify the air is essential. Moreover, after working with an archaeological specimen, everything around must be thoroughly cleaned, because remains from it could contaminate the next sample and distort the information obtained. This is an extremely complex problem. Building such a laboratory is very expensive. It requires either a large state project or significant investments. Our budget did not provide for this, so we had to come up with something unconventional.

— How did you navigate this challenging situation?

— As always, the simplest solution is the most beautiful and correct one. In a standard paleogenetic laboratory, even working with a small sample, sometimes a tooth or a fragment of bone, still takes place in a large room. Moreover, this small fragment must be protected from everything else in that room. We considered it from a different angle: why not protect the artifact being worked on in an isolated small volume? For example, in a glove box that is completely isolated from the surrounding environment? This way, a person can work with the sample without a protective suit, using special gloves connected to the ports of the box.

As always, the simplest solution is the most beautiful and correct one

— With this approach, it's essential to create the right system of glove boxes, so each box fulfills the function of the laboratory room, where sequential processes such as sample preparation, DNA extraction, and others occur. This allows us to create a functional equivalent but without such significant costs.

We developed and created such a chain of boxes — with transition chambers, equipped with powerful ultraviolet lamps that eliminate traces of “parasitic” DNA. The boxes are very convenient to clean because they are small in volume. And most importantly, we resolved the air filtration issues by implementing a radically new solution. Specifically, we do not pass air through a cascade of filters because even the best filters do not provide the level of cleanliness achieved by a special pure nitrogen generator. We extract ultra-pure nitrogen from the atmosphere, effectively separating it from all impurities at the molecular level. We blow the boxes with this nitrogen and work in a virtually neutral environment for all reactions taking place. But the most crucial aspect is that there is no unnecessary organic material from other people or samples in this environment.

This simple solution turned out to be very effective. We immediately began to obtain very good results. It turned out that with this approach, we can extract DNA from samples in a gentle manner. There is no need to burn these samples with powerful ultraviolet light, as our Western colleagues do, which effectively further degrades the DNA due to that radiation.

— Is this what you previously referred to as your innovative method for studying ancient DNA?

— Yes, our technology allows us to avoid traditional “clean” laboratories with expensive filter-ventilation systems that do not fully resolve all the complexities of working with ancient DNA. We obtain DNA concentrations often an order of magnitude higher than those of our Western colleagues from the same samples. We had the opportunity to compare. Essentially, this solution is relatively economical while also being quite effective. But this was the first step in our work.

The second important aspect is gaining access to unique collections of archaeological materials, of which there are many in our country. We have an excellent domestic school of archaeologists and anthropologists. There are enormous collections of archaeological-anthropological material. By establishing cooperation with leading organizations: the Institute of Archaeology of the Russian Academy of Sciences and the Institute of Ethnology and Anthropology of the Russian Academy of Sciences in Moscow, as well as the Institute of the History of Material Culture of the Russian Academy of Sciences in St. Petersburg, we found ourselves in a unique position, gaining access to colossal collections. We also work closely with regional organizations, which has allowed us to encounter significant samples of material. By using our technology, enormous opportunities for in-depth research and obtaining multifaceted results open up.

— How does the process of extracting DNA from such ancient material work?

— First, in glove boxes, we use dental equipment to clean the samples of dust and dirt, as well as traces of contact with other people. Next comes ultrasonic cleaning, where the surface layer is “stripped” at the cellular level. Then, in a special dental mortar, the sample is manually ground, and the crumbs are placed in a ball mill, which grinds them into powder without overheating the materials. Next, the DNA is extracted from the powder in several stages. Then a series of devices quantitatively determine the quality of the DNA, the ratio of long and short fragments, and the concentration. After that, a whole range of methods is employed to read the DNA.

— But ancient DNA is mostly found far from Russia?

— It might be hard for a non-specialist to imagine, but the emergence of many civilizations worldwide is linked to the fact that they originated and developed in the territory that is now our country. For example: where was the wheel invented? Where was the horse domesticated? Where were tools and weapons made from bronze created? This is our Volga-Ural region, the Southern Ural, the steppes of the Black Sea region and the Caspian Sea. It was there, many centuries ago, that cultures emerged that