Genomics and Bioinformatics

Head: Dr. biol. Natalia Paramonova
Email: natalia.paramonova@lu.lv
Research Interest
The research interests are focused on plant, animal and human genomics and bioinformatics including basic and applied research:

• Development of the molecular marker systems such as microsatellites (MSs), SNP-markers (single nucleotide polymorphisms) and genome mobile elements (transposons and retrotransposons) in cereals, mainly barley and farm animals (cows and others);
• Evaluation of the genetic diversity in wild and cultivated barley and farm animal populations based on molecular marker genotyping and haplotype analysis;
• Application of marker assisted selection (MAS) in barley and farm animals breeding programs;
• New polymorphism detection in candidate genes for the economically important traits in barley and cow based on genomic DNA sequencing;
• Identification and characterization of the genomic sites involved in nuclear rearrangements during barley plant development;
• Association study on candidate-gene polymorphisms, cardiovascular, autoimmune and metabolic disorders in humans.

 Recent References: GERMINI, D., TSFASMAN, T., ZAKHAROVA, V.V., SJAKSTE, N., LIPINSKI, M. and VASSETZKY, Y., 2017. A Comparison of Techniques to Evaluate the Effectiveness of Genome Editing. Trends in biotechnology, . PRESS GERMINI, D., BOU SAADA, Y., TSFASMAN, T., OSINA, 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 and Clinical Development, 5, pp. 43-50. 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.  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.

Staff
Permanent scientific staff
Natalia Paramonova	Dr. Biol., leading researcher
Kristine Osina	Master of Biology, PhD student, researcher
Kristine Dokane	Master of Biology, PhD candidate, researcher

 Equipment The laboratory has a full set of equipment for studies in genomics and molecular genetics including DNA amplification, genotyping, cloning and gene expression analysis. International activities: 2011. – 2013.                 Taiwan – Latvia – Lithuania cooperation project “Proteasomal gene alleles as risk factors for bronchial asthma in Latvian, Lithuanian and Taiwanese populations” 2010.– 2011.                 OSMOSE Latvia-France (CNRS unit UMR-8126) cooperation „Functional significance of the repeats in 14q13.2 and 4q35 regions predisposed to human pathologies”. 2007.– 2008.                 NordPlus Neighbour Nordic-Baltic network cooperation “Genomics for all: bringing new tools to breeders”.  Pacipitation in national reseach programms 2013.–2015. ESF 2013/0043/1DP/1.1.1.2.0/13/APIA/VIAA/002.projekts „Jaunas starpnozaru grupas izveide efektīvu diabētiskas neiropātijas ārstēšanas līdzekļu meklējumiem” 2011.–2013.    ERAF 2010/0315/2DP/2.1.1.1.0/10/APIA/VIAA/026project „Autoimūno slimību agrīnās diagnostikas metodes izstrāde”. 2014.-2017.  VPP 2014/VPP 2014-2017, 7. program. – (AgroBioRes), Project VP29.3. “Vietējas izcelsmes slaucamo govju un cūku saimnieciski nozīmīgo pazīmju ģenētiskā izpēte kvalitatīvu pārtikas produktu ražošanai un dabīgas izcelsmes barības sastāvdaļu izstrāde un pārbaude (LOPKOPĪBA)” 2014-2017.   VPP 2014/VPP2014-2017, Biomedicine, Project „DNS reparācijas fermentu molekulārģenētiskā un farmakoloģiska izpēte saistība ar metabolām slimībām”. Patents: 1.“1,4-Dihidropiridīna atvasinājums DNS pārrāvumu novēršanai cukura diabēta apstākļos”
List of authors: Evita Rostoka,  Jeļizaveta Sokolovska, Nikolajs Sjakste, Tatjana Sjakste, Kristīne Ošiņa. (Numb. 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” List of authors: Tatjana Sjakste, Natalia Paramonova, Nikolajs Sjakste
(European Patent Office, 80298 Minhene, Germany; numb: 13192748.5- 1404; numb.of ref: LAP 2/2456)
status: on examination