Academic CentreLaboratory of Genomics and bioinformations
Address: Jelgavas street 1, LV-1004 Riga
Phone: +371 28303631
E-mail: natalia.paramonova @lu.lv
Head of Laboratory: Dr. biol. Natalia Paramonova
Staff
Laboratory staff consists of six members, five of which are Doctors of Biology and Medicine.
Natalia Paramonova | Dr. biol., leading researcher |
Nikolajs Sjakste | Dr. habil. biol., leading researcher |
Ilva Trapiņa | Dr.med., researcher |
Kristīne Dišlere | Dr. biol., researcher |
Samanta Pļaviņa | scientific assistant |
Elīna Ļeonova | Dr. biol., researcher |
Research directions
Research area includes human and animal genomics and bioinformatics, and it combines theoretical and applied research:
- association studies for candidate gene polymorphisms linked with human cardiovascular, autoimmune and metabolic diseases.
- development of molecular marker system: microsatellites (MS), single nucleotide polymorphism (SNP) markers, and mobile elements in genome (transposons and retrotransposons) of farm animals (cows and others);
- evaluation of genetic diversity in farm animals using genotyping of molecular markers and haplotype analysis;
- application of marker assisted selection (MAS) in livestock breeding programs;
- detection of new polymorphisms in candidate genes of economically important livestock traits using genomic DNA sequencing;
Equipment
The laboratory is equipped in accordance with modern requirements for molecular genetics research, including DNA genotyping, cloning and gene expression analysis.
Participation in the provision of studies
Laboratory scientists supervise UL students' coursework, as well as bachelor's and master's theses.
Projects
2020–2022 - Taiwan-Lithuania-Latvia cooperation project "Comparative study of vitamin D and its receptor gene polymorphisms in Lithuanian, Latvian and Taiwanese children and adults with atopic dermatitis and asthma".
2017–2020 - European Regional Development Agency project: "Detection of proteasome-related genetic, epigenetic and clinical markers of multiple sclerosis".
2016–2020 - University of Latvia research project: "Biomedicine, pharmacy" subproject: "Proteasome gene structure, expression and pharmacogenomics research".
2016–2018 - ERA NET RUS program project: "Evaluating a new post-replication modification of polymerase Poly (ADP-ribose) polymerase and its impact on anticancer therapy".
2014–2017 - National Research Program VPP-14-2-6 "Biomedicine" un VPP-2014-5-4 "EKOSOC-LV"
VPP 2014/VPP2014-2017, 7. program - Agricultural resources for sustainable production of quality and healthy food in Latvia (AgroBioRes), Subproject VP29.3. Genetic research of economically important traits of dairy cows and pigs of local origin for the production of quality food and development and testing of feed materials of natural origin (LIVESTOCK).
VPP 2014/VPP2014-2017, BIOMEDICINA, Subproject "Molecular genetic and pharmacological research of DNA repair enzymes in relation to metabolic diseases".
2013.– 2015. ESF 2013/0043/1DP/1.1.1.2.0/13/APIA/VIAA/002. project "Creation of a new interdisciplinary group in search of effective treatments for diabetic neuropathy"
2011. – 2013. ERAF 2010/0315/2DP/2.1.1.1.0/10/APIA/VIAA/026project „ Development of an early diagnostic method for autoimmune diseases ”
2011. – 2013. Taiwan – Latvia – Lithuania cooperation project “Proteasomal gene alleles as risk factors for bronchial asthma in Latvian, Lithuanian and Taiwanese populations”
2010.– 2011. Latvian and French (CNRS department UMR-8126) project OSMOSE „Functional significance of the repeats in 14q13.2 and 4q35 regions predisposed to human pathologies”
2007.– 2008. Nord Plus Neighbor Nordic-Baltic network cooperation project “Genomics for all:bringing new tools to breeders”
N. PARAMONOVA, J. KALNINA, K.DOKANE, K. DISLERE, I. TAPINA, T. SJAKSTE, N. SJAKSTE. Genetic variations in the PSMA6 and PSMC6 proteasome genes are associated with multiple sclerosis risk and response to interferon beta therapy in Latvians. Int J Mol Med. (2020), https://www.spandidos-publications.com/ijmm. Submitted, under review.
ZALIZKO P, STEFANOVICS J, SOKOLOVSKA J, PARAMONOVA N, KLAVINA E, ERTS R, ROVITE V, KLOVINS J, PUKITIS A, Therapeutic Advances in GastroenterologyThiopurine S-methyltransferase genetic polymorphisms in adult patients with inflammatory bowel diseases in the Latvian population. Ther Adv Gastroenterol 2020;Vol. 13: 1–8 DOI: 10.1177/ 1756284820937426.
N. PARAMONOVA, I.TRAPINA, K. DOKANE, J. KALNINA, T.SJAKSTE, N. SJAKSTE. An Intergenic rs9275596 Polymorphism on Chr. 6p21 Is Associated with Multiple Sclerosis in Latvians. Medicina 2020;Vol. 56, N 4, 154, p.1-11. DOI: 10.3390/medicina56040154.
SOKOLOVSKA, J., DEKANTE, A.,BAUMANE, L., PAHIRKO, L., DIŠLERE, K., ROVITE, PIRAGS, V., SJAKSTE N.Nitric oxide metabolism is impaired by type 1 diabetes and diabetic nephropathy, Biomedical Reports, V12. Issue 5; doi.org/10.3892/br.2020.1288 , Pages: 251-258
SJAKSTE T, LEONOVA E, PETROVS R, TRAPINA I, RÖDER MS, SJAKSTE N. Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences. PeerJ. 2020;8:e8569. Published 2020 Feb 18. doi:10.7717/peerj.8569
BORISOVS, V., ĻEONOVA, E., BAUMANE, L. KALNIŅA, J., MJAGKOVA, N., SJAKSTE, N. 2019. Blood levels of nitric oxide and DNA breaks assayed in whole blood and isolated peripheral blood mononucleated cells in patients with multiple sclerosis. Mutation Research - Genetic Toxicology and Environmental Mutagenesis, Volume 843, 90-94.
LEONOVA, E., OŠIŅA, K DUBURS, G, BISENIEKS, E., GERMINI, D. VASSETZKY, Y., SJAKSTE, N. Metal ions modify DNA-protecting and mutagen-scavenging capacities of the AV-153 1,4-dihydropyridine. Mutation Research - Genetic Toxicology and Environmental Mutagenesis. Volume 845,403077
SJAKSTE, T., ĻEONOVA, E., PETROVS, R., RÖDER, M.S., & SJAKSTE, N. (2019). Guanine-quadruplex-enriched sequences in the tight DNA-protein complexes of barley seedlings. Biopolym. Cell. 35(3):234-234
KAPPOS, L., BAR-OR, A., CREE, B.A.C., (…….), KALNINA, J., (………..), ZIEMAN, U.,ZIEMSSEN, T. 2018. Siponimod versus placebo in secondary progressive multiple sclerosis (EXPAND): a double-blind, randomised, phase 3 study. The Lancet. 391 (10127), 1263-1273
GERMINI, D., TSFASMAN, T., ZAKHAROVA, V.V., SJAKSTE, N, LIPINSKI, M., VASSETZKY, Y.A 2018 Comparison of Techniques to Evaluate the Effectiveness of Genome Editing. Trends in Biotechnology 36(2), pp. 147-159
LEONOVA, E., ROSTOKA, E., SAUVAIGO, S., BAUMANE, L., SELGA, T., SJAKSTE, N. 2018. Study of interaction of antimutagenic 1, 4-dihydropyridine AV-153-Na with DNA-damaging molecules and its impact on DNA repair activity. PeerJ, 6, e4609.
LEONOVA, E., ROSTOKA, E., BAUMANE, L., BORISOVS, V., SMELOVS, E., BISENIEKS, I., BRŪVERE, I., BISENIEKS, E., DUBURS, G., SJAKSTE, N. 2018. DNA-binding studies of a series of novel water-soluble derivatives of 1, 4-dihydropyridine. Biopolymers and Cell, 34(2), 127-141.
OŠIŅA, K., LEONOVA, E., ISAJEVS, S., BAUMANE, L., ROSTOKA, E., SJAKSTE, T., BISENIEKS, E., DUBURS, G., VIGANTE, B. and SJAKSTE, N., 2017. Modifications of expression of genes and proteins involved in DNA repair and nitric oxide metabolism by carbatonides [disodium-2,6-dimethyl-1,4-dihydropyridine- 3,5-bis(carbonyloxyacetate) derivatives] in intact and diabetic rats. Arhiv za Higijenu Rada i Toksikologiju, 68(3), pp. 212-227.
GERMINI, D., SAADA, Y. B., TSFASMAN, T., OŠIŅA, K., ROBIN, C., LOMOV, N., RUBTSOV, M., SJAKSTE, N., LIPINSKI, M.and VASSETZKY, Y., 2017. A One-Step PCR-Based Assay to Evaluate the Efficiency and Precision of Genomic DNA-Editing Tools. Molecular Therapy-Methods & ClinicalDevelopment, 5, 43-50.
SJAKSTE, N., 2017. Experimental and human population studies of DNA lesions in healthy individuals. Biopolymers and Cell, 33(1), pp. 24–33.
DOKĀNE, K., MEGRE, D., LAZDĀNE, M. and KONDRATOVIČS, U., 2017. Influence of the Calcarisporium arbuscula Preuss on in vitro growth and ex vitro adventitious rooting of two elepidote rhododendron cultivars. Propagation of Ornamental Plants, 17(2):39-47.
GERMINI, D., SAADA, Y.B., OŠIŅA, K., TSFASMAN, T., ROBIN, C., SJAKSTE, N., LIPINSKI, M. and VASSETZKY, Y., 2016. A one-step PCR-based assay to evaluate efficiency and precision of genomic DNA-editing tools. Molecular Therapy - Methods & Clinical Development. 2016. PRESS
LEONOVA, E., SOKOLOVSKA, J., BOUCHER, J.-., ISAJEVS, S., ROSTOKA, E., BAUMANE, L., SJAKSTE, T. and SJAKSTE, N., 2016. New 1,4-Dihydropyridines Down-regulate Nitric Oxide in Animals with Streptozotocin-induced Diabetes Mellitus and Protect Deoxyribonucleic Acid against Peroxynitrite Action. Basic and Clinical Pharmacology and Toxicology,119(1), pp. 19-31.
OŠIŅA, K., ROSTOKA, E., ISAJEVS, S., SOKOLOVSKA, J., SJAKSTE, T. and SJAKSTE, N., 2016. Effects of an Antimutagenic 1,4-Dihydropyridine AV-153 on Expression of Nitric Oxide Synthases and DNA Repair-related Enzymes and Genes in Kidneys of Rats with a Streptozotocin Model of Diabetes Mellitus. Basic and Clinical Pharmacology and Toxicology, .PRESS
SJAKSTE, T., KALNINA, J., PARAMONOVA, N., NIKITINA-ZAKE, L. and SJAKSTE, N., 2016. Disease-Specific and Common HLA and Non-HLA Genetic Markers in Susceptibility to Rheumatoid Arthritis, Type 1 Diabetes Mellitus and Multiple Sclerosis. Journal of Molecular and Genetic Medicine, 2016.
RAZIN, S.V., IAROVAIA, O.V, SJAKSTE, N., Sjakste, T., Bagdoniene, L., Rynditch, A.V., Eivazova, E.R., Lipinski, M., Vassetzky, Y.S. 2016. Chromatin domains and regulation of transcription. J Mol Biol. IN PRESS.
OŠIŅA, K., ROSTOKA, E., SOKOLOVSKA, J., PARAMONOVA, N., BISENIEKS, E., DUBURS, G., SJAKSTE, N. and SJAKSTE, T., 2016. 1,4-Dihydropyridine derivatives without Ca2+-antagonist activity up-regulate Psma6 mRNA expression in kidneys of intact and diabetic rats. Cell biochemistry and function, 34(1), pp. 3-6
PARAMONOVA, N., WU, L.S.S., RUMBA-ROZENFELDE, I., WANG, J., SJAKSTE, N. and SJAKSTE, T., 2014. Genetic variants in the PSMA6, PSMC6 and PSMA3 genes associated with childhood asthma in Latvian and taiwanese populations. Biopolymers and Cell, 30(5), pp. 377-387.
SJAKSTE, T., PARAMONOVA, N., RUMBA-ROZENFELDE, I., TRAPINA, I., SUGOKA, O. and SJAKSTE, N., 2014. Juvenile idiopathic arthritis subtype- and sex-specific associations with genetic variants in the PSMA6/PSMC6/PSMA3 gene cluster. Pediatrics and Neonatology, 55(5), pp. 393-403.
ZEMECKIENE, Z., SITKAUSKIENE, B., GASIUNIENE, E., PARAMONOVA, N., TAMASAUSKIENE, L., VITKAUSKIENE, A., SJAKSTE, T. and SAKALAUSKAS, R., 2015. Evaluation of proteasomal gene polymorphisms in Lithuanian patients with asthma. Journal of Asthma, 52(5), pp. 447-452.
SOKOLOVSKA, J., ISAJEVS, S., ROSTOKA, E., SJAKSTE, T.,TRAPIŅA, I., OŠIŅA, K., PARAMONOVA, N. and SJAKSTE, N., 2015. Changes in glucose transporter expression and nitric oxide production are associated with liver injury in diabetes. Cell biochemistry and function, 33(6), pp. 366-374.
SJAKSTE, T., PARAMONOVA, N., WU, L.S., ZEMECKIENE, Z., SITKAUSKIENE, B., SAKALAUSKAS, R., WANG, J.-. and SJAKSTE, N., 2014. PSMA6 (rs2277460, rs1048990), PSMC6 (rs2295826, rs2295827) and PSMA3 (rs2348071) genetic diversity in Latvians, Lithuanians and Taiwanese. Meta Gene, 2(1), pp. 283-298.
KUPCA, S., SJAKSTE, T., PARAMONOVA, N,. SUGOKA, O., RINKUZA, I., TRAPINA, I., DAUGULE, I., SIPOLS, A.J., and RUMBA-ROZENFELDE, I., 2013. Association of obesity with proteasomal gene polymorphisms in children. J Obes. 2013;2013:638154. doi: 10.1155/2013/638154. Epub 2013 Dec 21. PubMed PMID: 24455213; PubMed Central PMCID: PMC3880696.
ZEMECKIENE, Z., VITKAUSKIENE, A., SJAKSTE, T., SITKAUSKIENE, B. and SAKALAUSKAS, R., 2013. Proteasomes and proteasomal gene polymorphism in association with inflammation and various diseases. Medicina (Kaunas), 49(5), pp 207-213. PubMed PMID: 24247915.
SJAKSTE, T., PARAMONOVA, N. and SJAKSTE, N., 2013. Functional significance of microsatellite markers. Medicina-lithuania 49(12) pp. 505-509
WU, LS., SJAKSTE, T., SAKALAUSKAS, R., SITKAUSKIENE, B., PARAMONOVA, N. ,GASIUNIENE, E., JAN, RL. and WANG, JY., 2012. The burden of allergic asthma in children: a landscape comparison based on data from Lithuanian, Latvian, and Taiwanese populations. Pediatr Neonatol, 53(5), pp 276-282.
SJAKSTE, N., BIELSKIENE, K., BAGDONIENE, L., LABEIKYTE, D., GUTCAITS, A., VASSETZKY, Y. and SJAKSTE, T., 2012. Tightly bound to DNA proteins: possible universal substrates for intranuclear processes. Gene, 492(1), pp 54-64.
SOKOLOVSKA, J., ISAJEVS, S., SUGOKA, O., SHAPIROVA, J., LAUBERTE, L., ISAJEVA, D., ROSTOKA, E., SJAKSTE, T., KALVINSH, I. and SJAKSTE, N., 2012. Comparison of the Effects of Glibenclamide on Metabolic Parameters, GLUT1 Expression, and Liver Injury in Rats With Severe and Mild Streptozotocin-Induced Diabetes Mellitus. Medicin, 29(1), pp 55-63
SJAKSTE, T., PARAMONOVA, N., GRISLIS, Z., TRAPINA, I. and KAIRISA, D., 2011. Analysis of the single-nucleotide polymorphism in the 5'UTR and part of intron I of the sheep MSTN gene. DNA Cell Biol., 30(7), pp 433-44. Epub 2011 Feb 16. PubMed PMID: 21323579
SOKOLOVSKA, J., ISAJEVS, S., SUGOKA, O., SHARIPOVA, J., LAUBERTE, L., SVIRINA, D., ROSTOKA, E., SJAKSTE, T., KALVINSH, I. and SJAKSTE, N. (2011) Correction of glycaemia and GLUT1 level by mildronate in rat streptozotocin diabetes mellitus model. Cell Biochem Funct., 29(1), pp 55-63. PMID: 21264891
KALENDAR, R., FLAVELL, A.J., ELLIS, T.H., SJAKSTE, T. and MOISY, C., 2011. Schulman AH.Analysis of plant diversity with retrotransposon-based molecular markers. Heredity,106(4), pp 520-530. PubMed PMID: 20683483; Central PMCID: PMC3183911.PMID:22001404.
SJAKSTE, N., BAGDONIENE, L., GUTCAITS, A., LABEIKYTE, D., BIELSKIENE, K., TRAPINA, I., MUIZNIEKS, I., VASSETZKY, Y. and SJAKSTE, T., 2010. Proteins tightly bound to DNA: New data and old problems. Biochemistry (Moscow), 75(10), pp. 1240-1251.
SJAKSTE, T., TRAPINA, I., RUMBA-ROZENFELDE, I., LUNIN, R., SUGOKA, O. and SJAKSTE, N., 2010. Identification of a novel candidate locus for juvenile idiopathic arthritis at 14q13.2 in the Latvian population by association analysis with microsatellite markers. DNA and cell biology, 29(9), pp. 543-551.
SOKOLOVSKA, J., ISAJEVS, S., SUGOKA, O., SHARIPOVA, J., LAUBERTE, L., SVIRINA, D., ROSTOKA, E., SJAKSTE, T., KALVINSH, I. and SJAKSTE, N., 2010. Influence of metformin on GLUT1 gene and protein expression in rat streptozotocin diabetes mellitus model. Archives of Physiology and Biochemistry, 116(3), pp. 137-145.
BELICKA, I., BLEIDERE, M., LEGZDINA, L., SUGOKA, O., SAMAVSKA, L. and SJAKSTE, T. 2010. Allelic diversity of the beta-amylase gene Bmy1 in Latvian barley breeding lines. Acta Biol. Univ. Daugavp., 10(1), 17 - 22.
1"1,4-Dihydropyridine derivative for the prevention of DNA disruption in diabetic conditions". List of authors: Evita Rostoka, Jeļizaveta Sokolovska, Nikolajs Sjakste, Tatjana Sjakste, Kristīne Ošiņa. (Nr. P-15-89; OSI-2015-007).
2.“A method and a kit suitable for determining that a human subject has or is at risk of developing type 1 diabetes mellitus” A List of authors: Tatjana Sjakste, Natalia Paramonova, Nikolajs Sjakste (European Patent Office, 80298 Minhene, Vācija; nr: 13192748.5-1404; ref. nr. LAP 2/2456) Status: expertise.