Cleaning ancient genomes
Geneticists cleaned the Neanderthal
Scientists have found a way to get rid of ancient DNA
from later layers interfering with genetic analysis.Yana Khlyustova, Newspaper.
The problem that geneticists often face when analyzing the DNA of ancient people and animals – contamination – has been solved: scientists have found a method to purify DNA from later contamination and analyzed a sample belonging to a Neanderthal from the Okladnikov cave, determining its place in the genetic tree.
Contamination is a chemical and biological term, contamination of a compound with foreign substances, foreign biological material. The DNA of ancient people and animals can be contaminated both by the microenvironment where the remains of the organism were located, and by the DNA of scientists who worked with the samples found. Such contamination is undoubtedly an obstacle in DNA sequencing (determining the amino acid or nucleotide sequence) – a process that is used to describe the structure of DNA.
A group of researchers from Sweden and Germany led by Pontus Skoglund (Uppsala University), as well as with the cooperation of Russian scientists Mikhail Shunkov and Anatoly Derevyanko (Institute of Archaeology and Ethnography SB RAS) found a method of purification of ancient DNA from external contamination, and also analyzed the DNA of the remains of a Neanderthal from the Okladnikov cave. Svante Paabo, a geneticist who received a complete version of the Neanderthal genome, also took part in the work of scientists.
The full results of the work of geneticists can be found in the journal PNAS (Skoglund et al., Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal; a press release of New method rescues DNA from contaminated Neandertal bones is published on the website of Uppsala University - VM).
The method of determining extraneous layers of DNA is based on the analysis of its natural mutations. Thus, in 30-40% of samples dating back several thousand years, cytosine is converted into thymine, and guanine into adenine. Scientists have developed a system that simulates the processes of natural DNA modification and compares the result with the sample data.
To test the work of the new method, scientists used about 1 million DNA sequences obtained from the remains of an Australian dating back 100 years, from four Neolithic skeletons (found in Scandinavia about 5 thousand years ago), from four Neanderthal skeletons (aged 38 to 70 thousand years) and four modern living people. The system showed the presence of foreign parts of DNA in proportion to the age of the samples. Further, the researchers deliberately polluted the DNA of modern humans with "parts" of Neanderthal DNA – and again the system showed its effectiveness by calculating the "extra" elements.
Thus, at the moment, geneticists have at their disposal a method of purification of ancient DNA from foreign elements, which will have a significant positive impact on DNA research.
This is exactly what the further work of scientists confirmed. The group of Pontus Skoglund studied the DNA of a Neanderthal whose remains were found in the Okladnikov cave (located on the outskirts of the village of Sibiryachikha in the Soloneshensky district of the Altai Territory). Geneticists took 6906 sequences of mitochondrial DNA and analyzed them using a contamination detection system. First of all, by analyzing natural mutations, the system confirmed that the sample really belongs to a Neanderthal, and then revealed 10.2% of the contaminated fragments. To get rid of them, scientists had to reduce the number of sequences studied to 3908, the level of pollution decreased to 1.3%.
The results of DNA sequencing showed that the sequence of mitochondrial genomes of the Neanderthal from the Okladnikov cave does not coincide with the previously described sequences of Neanderthals from Central and Western Europe, but occupies its place in the genetic cluster with them.
The work of Pontus Skoglund's group has unequivocally proved that the creation of a system for separating contamination from DNA will allow geneticists to conduct a more accurate analysis of gene samples of ancient people and animals, which means that it will bring them one step closer to deciphering the secrets embedded in the DNA spiral.
Portal "Eternal youth" http://vechnayamolodost.ru29.01.2014