Genome laboratory

A brief history of the Laboratory

The Genome Laboratory was organized in 1991. The first laboratory in Kazakhstan for the plant genome and the human genome study. Founder and first head of the laboratory was Academician of the National Academy of Sciences of the Republic of Kazakhstan, Professor, Doctor of biological sciences, Nagima Aitkhozhina. Since 2006 the Genome laboratory is headed by Ismagulova Gulnara Akimzhanovna, Ph.D. in biology. In 2009, the Human genome group separated from the genome laboratory into an independent Laboratory of structural and functional genomics.

Ismagulova Gulnara Akimzhanovna

Ph.D. in biology

Deputy General Director of the M. Aitkhozhin Institute of molecular biology and biochemistry, Head of the genome laboratory

Phone: 7 (727) 293-71-74 (laboratory); +7 (727) 293-52-13

E-mail: g.ismagulova@imbb.org.kz, gulnara_ismagulova@hotmail.com, i_gulnara@mail.ru

Gulnara Ismagulova graduated from the biology faculty of C.M. Kirov Kazakh State University in 1984. She received her Ph.D. degree in 1994 with specialization in biochemistry. Since 2006 till present the Genome laboratory is headed by Gulnara Ismagulova. She has 43 years of work experience in science.

The main directions of research activities

  • Plant genome – structural and functional organization of the genome of cereal crops, expression of genes of the protective response of cereal crops to damage by phytopathogens;
  • Human genome — identifying the features of human genes and their regulatory zones in normal and pathological conditions (localization of mutations, polymorphisms, deletions and insertions), gene diagnostics, identification of risk groups and predisposition to diseases;
  • Paleo- and ethnogenomics – paleogenomic studies of DNA from the biological material of archaeological excavations, ethnogeography and ethnogenomic studies of the populations of Kazakhstan;
  • Genotyping of rare and endangered plants, animals and birds – identification of the genetic diversity of populations of plants, animals, birds listed in the Red Book of Kazakhstan and the World Red Book;
  • Space biology and biotechnologies – revealing the effect of a complex of cosmic factors on some types of higher organisms and developing on their basis ways to protect humans;
  • Functional genomics and genetic engineering of plants;
  • Molecular epidemiology, population and evolutionary genetics of microorganisms.

Research projects

2020-2022

Targeted funding program “Monitoring of domestic varieties of cereal crops for the presence of genes for the synthesis of β-glucan as a functional ingredient of a healthy diet”, scientific supervisor – Ismagulova G.A., Candidate of biological sciences

 2018-2020

АР05136045 “Obtaining new lines of wheat and potatoes based on the use of a complex of innovative approaches of genetic engineering and cell technologies”, scientific supervisor – Skiba Yu.A., Ph.D

2015-2017

3735 / GF4 “Epidemiological monitoring improvement of the brucellosis pathogen circulation in Kazakhstan based on the introduction of innovative technologies for molecular genetic typing of strains of Brucella spp.”, scientific supervisors – Aitkhozhina N.A., Doctor of biological sciences, professor, academician of the National Academy of Sciences of the RK, Skiba Yu.A., Ph.D.

Methods of research

Polymerase chain reaction technologies (RAPD, CAPS, SCAR, PT-PCR), cloning, sequencing, isolation of RNA, DNA and proteins from various objects, gene isolation, creation of genetic constructs, plant transformation, incl. cis-gene, synthesis of oligonucleotides, isolation of plasmid DNA, electrophoresis of nucleic acids and proteins, cultivation of plant cells.

Scientific achievements of the laboratory

Plant genome:

  • Direction “Biologically active substances of plant origin – low molecular weight bioregulators of eukaryotic genome expression”, which has become a priority for Kazakh scientists. New highly effective inhibitors of plant origin for the study of protein, RNA and DNA biosynthesis have been identified: narcein, homoharringtognin, cytisine, caffeine and its analogues, sparteine. The biological properties of amino acid and peptide analogues of colchicine and colchamine have been synthesized and studied.
  • A new mobile element has been described in the genome of Triticum timofeevii, which is directly related to the regulation and transposition mechanisms.
  • A DNA library of Kazakh wheat varieties of genes for the protective response of chitinase 3 classes, 1,3-β-gluconase, oxalate oxidase, Lr10 and Lr21 was created and the features of their structural organization of functionally significant regions were studied for use in practical breeding and genetic engineering of plants.
  • For the first time, the gene of class I chitinase, the 19th family of glycosyl hydrolases ChitSt15, was cloned from wheat of the Kazakh Stepnaya-15 variety. The structural features of the cloned gene were studied using bioinformatics analysis methods and a globular model of the pChitSt15 protein was constructed. The physicochemical and antifungal properties of protein p
  • Molecular-genetic certification of varieties of Kazakhstani selection from the collection of the gene pool department of KazNIIR of the Ministry of Agriculture of the Republic of Kazakhstan was performed in order to identify resistant to brown rust, septoria and yellow leaf spot, varieties-carriers of “null” alleles of waxy-genes and the Gpc-B1

Human genome:

  • The foundations of molecular and population human genetics in Kazakhstan, molecular medicine were laid, allowing to establish the mechanisms of the occurrence of hereditary diseases (atherosclerosis, coronary heart disease, hypertension, multiple sclerosis) and their gene diagnostics, which are of great fundamental and practical importance. DNA polymorphisms were identified, point mutations were localized, and nucleotide substitutions of the apoA, apoB, apoC, pai-1, lpl, and pon 1 genes, angiotensinogen (AT) and angiotensin-converting enzyme (ACE) genes were determined in three populations. Interethnic differences in DNA polymorphism are shown.
  • Studied candidate genes, changes in which lead to the development of neurodegenerative disease – multiple sclerosis, IL-10, IL-13, IL-17, FOXP3, TGF-β.
  • A molecular genetic analysis of the DNA of the mummified remains of people who lived on the territory of the modern Kazakh Altai 2.5 thousand years ago was performed. Comparative analysis of individual sections of the D-loop and polymorphism of the V-region of mitochondrial DNA of the modern population of Kazakhs, ancient people and the world GenBank showed that both modern Kazakhs and their supposed ancestors have Mongoloid and Caucasoid components with a difference in their ratios. The results obtained are important as fundamental knowledge about the features of the genetic structure of the modern Kazakh ethnic group, which allows us to consider issues of intra-ethnic differentiation.

Biotechnology:

  • Molecular biological certification of various populations of the Semirechye frogtooth Ranodon sibiricus, saker falcon Falco cherrug and its hybrids with gyrfalcon and peregrine falcon, golden eagles Aquila chrysaetos, mountain sheep Ovis ammon, horsetail ephedra Ephedra equisetina was performed.
  • The first space biology and biotechnology program in Kazakhstan was developed, implemented in the flights of Kazakhstan’s cosmonauts T. Aubakirov, T. Mussabayev, a number of Russian Federation crews and subsequent experiments on Earth. A program of scientific experiments of Kazakhstan cosmonauts Garysh was developed for performing on the International Space Station board.

Functional genomics and plant genetic engineering:

  • The method of cisgenic transformation of wheat and potatoes has been adapted.
  • For the first time in the Republic of Kazakhstan, the transformation of 2 varieties of common wheat Saratovskaya 29 and Kazakhstanskaya 19 was carried out using the method of cisgenic transfer. 29 lines of common wheat with chitinase and β-1,3-glucanase genes were obtained. The regeneration efficiency for each variety was calculated.
  • As a result of ballistic transformation of potato callus cultures, 56 regenerated plants of Aksor and Nevsky varieties were obtained.
  • A scheme for sample preparation of plant samples has been worked out, which can be used in routine experiments for large-scale screening of plants for resistance to phytopathogens.
  • A procedure for diagnosing Fusarium pollution based on PCR technology has been developed.

Molecular epidemiology, population and evolutionary genetics of microorganisms.

    • Collections of circulating strains of Mycobacterium tuberculosis and their DNA (n>1500) have been created. A system for assigning unique codes for DNA samples, bacterial cultures and initial biological material has been developed. Algorithms for genetic differentiation of Kazakh tuberculosis isolates have been developed, including alternative VNTR typing panels. An information database of genetic profiles of tuberculosis strains has been created. Reagent kits for molecular genetic certification of mycobacterial isolates have been developed and protocols for high-throughput screening in 96- and 384-well formats have been created.
    • The genetic diversity of the Kazakh population of tuberculosis strains was analyzed.
    • A new genetic family of tuberculosis named KAZ-1 has been identified.
    • A genome-wide analysis of Kazakhstani strains of Mycobacterium tuberculosis of various genotypes (Beijing, LAM, NEW-1, KAZ-1) and analysis of deletion polymorphism at the RD181, RD122, RD174, RD-Rio, RD115 loci were carried out.
    • The discovery of a strain of the LAM RD-Rio sublineage in Kazakhstan is described for the first time, while showing its probable introduction to Kazakhstan from the Russian Federation, and not directly from South America or South/Western Europe.
    • With the use of a system based on biological chips TB TEST (BIOCHIP-IMB LLC), a wide range of genetic determinants of drug resistance to first and second line drugs for 400 Kazakhstani strains of tuberculosis of various genotypes was established for the first time, which replenished fundamental knowledge and will serve further practical purposes . The obtained data are consistent with the results of bacteriological tests and Hain GenoType MTBDRplus.
    • Collections of isolates and DNA, as well as databases of genetic profiles of Kazakhstani isolates of Brucella spp were obtained. Based on the results, reagent kits and a standard operating procedure for laboratory molecular genetic differentiation of Brucella strains were developed.
    • Using a panel of 16 loci, manual MLVA genotyping of 428 Brucella isolates was performed and the MLVA 16 method was optimized for genotyping on an automatic capillary analyzer. All obtained data were added to the electronic database of isolate passports.
    • Eight out of 16 MLVA loci were identified as the most informative loci that can be used as a screening panel in the study of the Kazakh population of Brucella and solving a number of epidemiological problems.
  • Based on the results of phylogenetic analysis of both veterinary and human isolates, it was determined that all of them belong to the species Brucellamelitensis and belong to the genetic family East Mediterranean (East Mediterranean type). Analysis of the geographical distribution of these isolates did not show high density and concentration in any place. When comparing the identified genotypes with the current version of the MLVAbank database, it was found that some strains are widespread in a number of regions of Kazakhstan, and are also found in a number of regions in China and Mongolia. Such a significant dissemination of strains of individual genotypes indicates their evolutionary “success” and the presence of advantages over other strains.
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