Laboratory of systems biology

The Laboratory of systems biology conducts the researches in the sphere of the problems of data integration of transcriptional, proteomic and metabolic activity of the genome of biological objects. In the research projects carried out in the sphere of post-genomic biology and medicine, not only information about the complete DNA sequence of the studied object is used, but also the persistence of the genome is studied, its micro- and macroheterogeneity is described as well as cause-and-effect relationships that occur in case of the DNA instability on the level of matrix RNA and proteins.

A key condition of the systems biology projects is a creation of a technological complex of methods, the so-called technological platform, which will allow to carry out researches at four levels of the cell organization, i.e. to define the stability parameters of the genome of the studied object (full genome sequencing), to determine the level of gene transcription (transcription profile), to measure the proteins expression and their post-translational modification (proteomic profile), as well as to register the flows of metabolites.

The Laboratory was founded in 2013 as a part of the MIPT Life Sciences Center for the research of omix human data for the needs of medicine, biotechnological industry, knowledge generation in the field of life sciences, and for the search of new drug compounds.

Laboratory Services

  • High-efficiency sequencing
  • Sanger sequencing, fragment analysis, DNA fingerprinting
  • Full-transcriptome expression analysis, full-genome polymorphism analysis with the help of the biochip analysis system
  • Digital analysis of the distribution of molecular protein masses, lengths of DNA and RNA fragments, flow cytometry with the use of the microfluidic electrophoresis system
  • Preparative DNA amplification, qualitative and quantitative analysis of DNA and RNA
  • Identification of DNA, RNA and proteins concentration

Personnel

Vadim Markovich Govorun — the Head of the Laboratory, Doctor of Biological Sciences, Professor and the Correspondent Member of the Russian Academy of Medical Sciences.

Elena Sergeyevna Kostryukova — the Deputy Head of the Laboratory, senior research scientist, Candidate of Biological Sciences

Dmitry Glebovich Alekseev — the Deputy Head of the Laboratory, senior research scientist, Candidate of Biological Sciences

Igor Aleksandrovich Fesenko — senior research scientist, Candidate of Biological Sciences

Current Projects

The study of the M.gallisepticum proteome in the stress conditions and the study of Hu-protein activity in Ecoli bacteria.

Fig. Mass tryptic gidrolizatat chromatogram of a complete proteome of E.coli.bacteria

  1. TIC
  2. MS1 spectrum in the given period of time.
  3. MS2 spectrum of one of the components.

Fig. Mass chromatogram for the directed quantitative analysis by MRM method.

Fig. Mass tryptic gidrolizatat chromatogram of a complete proteome of E.coli. bacteria
Up: TIC. In the middle: the diagram of the mass distribution in gradient time for MS1 spectra.
Down: The distribution of the mass-time components selected for MS2 analysis. .

Conferences

  1. International Human Microbiome Congress (IHMC) ' 2013 (Китай, Hangzhou 2013) Tyakht A.V., Popenko A.S., Zelenin A.S., Kovarsky B.A., Alexeev D.G., Karpova I.Y., Larin A.K., Solopova G.G., Dzhandarova D.T., Roumiantsev S.A., Kostryukova E.S. Temporal evolution of gut microbiota during chemotherapy in acute leukemia pediatric patients
  2. FEBS (Saint-Petersburg, 2013) Yuri Kosinsky, Kirill Peskov, Anna Popenko, Aleksаndr Tyakht,, Dmitry Alexeev. Modeling of short-chain fatty acids metabolism in human gut: reconstruction of possible relations between microbiota composition and type 2 diabetes status.

Publications

  1. D.D. Kharlampieva, V.A. Manuvera, O.V. Podgorny, S.I. Kovalchuk, O.V. Pobeguts, I.A. Altukhov, D.G. Alexeev, V.N. Lazarev, V.M. Govorun, Purification and characterisation of recombinant Bacteroides fragilis toxin-2, Biochimie 95 (2013) 2123-2131
  2. E.N. Ilina, E.A. Shitikov, L.N. Ikryannikova, D.G. Alekseev, D.E. Kamashev, M.V. Malakhova, T.V. Parfenova, M.V. Afanas’ev, D.S. Ischenko, N.A. Bazaleev, T.G. Smirnova, E.E. Larionova, L.N. Chernousova, A.V. Beletsky. Comparative Genomic Analysis of Mycobacterium tuberculosis Drug Resistant Strains from Russia. PLoS ONE, 2013, 8(2): e56577. doi:10.1371/journal.pone.0056577
  3. Elena N Ilina, Maya V Malakhova, Ivan N Bodoev, Nina Y Oparina, Alla V Filimonova, Vadim M Govorun. Mutation in ribosomal protein S5 leads to spectinomycin resistance in Neisseria gonorrhoeae. Frontiers in microbiology. 01/2013; 4:186.
  4. Gorbachev Y Alexey, Fisunov Y Gleb, Izraelson Mark, Evsyutina V Darya, Mazin V Pavel, Alexeev G Dmitry, Pobeguts V Olga, Gorshkova N Tatyana, Kovalchuk I Sergey, Kamashev E Dmitry, Govorun M Vadim, DNA repair in Mycoplasma gallisepticum, BMC Genomics.2013, 14:726.
  5. Tyakht AV, Kostryukova ES, Popenko AS, Belenikin MS, Pavlenko AS, Larin AK, Karpova IY, Selezneva OV, Semashko TA, Ospanova EA, Babenko VV, Maev IV, Cheremushkin SV, Kucheryavy YA, Shcherbakov PL, Grinevich VB, Efimov OI, Sas EI, Abdulkhakov RA, Abdulkhakov SA, Lyalyukova EA, Livzan EA, Vlassov VV, Sagdeev RZ, Tsukanov VV, Osipenko MF, Kozlova IV, Tkachev AV, Sergienko VI, Alexeev DG., Govorun V.M., Novel human gut microbiota compositions found across urban and rural populations of Russia. Nature communications, 2013 Sep 16;4:2469.
  6. Shitikov, E. A., Bespyatykh, J. A., Ischenko, D. S., Alexeev, D. G., Karpova, I. Y., Kostryukova, E. S., ... & Govorun, V. M. (2014). Unusual Large-Scale Chromosomal Rearrangements in Mycobacterium tuberculosis Beijing B0/W148 Cluster Isolates. PloS one, 9(1), e84971.
  7. Ponomarenko, E. A., Kopylov, A. T., Lisitsa, A. V., Radko, S. P., Kiseleva, Y. Y., Kurbatov, L. K., ... & Archakov, A. I. (2013). Chromosome 18 Transcriptoproteome of Liver Tissue and HepG2 Cells and Targeted Proteome Mapping in Depleted Plasma: Update 2013. Journal of proteome research, 13(1), 183-190.

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