2009-2014_olga_berillo_scientific researches
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Presentation
Montreal, Canada
INRIA/LIX team AMIB Campus de l'Ecole Polytechnique;
Institute of Problems of Biology and Biotechnology, al-Farabi Kazakh National University;
National Nanotechnology Laboratory of Open Type, al-Farabi Kazakh National University;
Laboratory of Molecular Immunology and Immunobiotechnology,
M.A. Ajtkhozhin Institute of Molecular Biology and Biochemistry
Olga Berillo
PhD, Bioinformatics, Biotechnologist, Scientific Researcheromalaheenee@gmail.com
https://github.com/omalaheenee/mirpy
ca.linkedin.com/in/olgaberillo
Figure 1. Statistics data of in-miRNAs
participated in oncogenesis
Количество статей в PubMedArticles in PubMed NCBI database
Research methods
Computer programs
MiRNAFinder: search for intronic pre-miRNAs in human genome
RNAHybrid, ERNAHybrid, miRTarget: search for miRNA binding sites in mRNAs
GeneNet Builder: visual presentation of gene networkUNAFold: construction of 2D-structures
Developed programs
miRAFinder и GeneAFinder: to get an information about miRNAs and genes TmiRSO и TranslmiRNA: to get a perfect complementary miRNA binding sites and oligopeptides coded by them TmiRUSite и TmiROSite: to get a nucleotide fragments of mRNAs with binding sites and amino acid sequences coded by them.
Objects of researchesNucleotide sequences of 2500 miRNAs and 17500 human genes.
Majority of them participate in development of cancer
Figure 2. Gene net between
host genes and target
genes participated
in esophageal
cancer
Note: Internal circle:
host genes; external circle: target genes
SCP2SCP2miRmiR-1273-1273gg-3-3ppmiRmiR-1273-1273gg--5p5pmiR-1273fmiR-1273fmiR-5095miR-5095
Figure 3: Variability of nucleotides (1) in miR-548j binding sites of orthologous PTPN12 genes and variability of amino
acids (2) in orthologous PTPN12 proteins
1
2
Table 1 – Features of microRNA binding sites in the same places of mRNA
MLLT6 mRNA, 1043 н., CDS
mRNA MLLT6 5' C G G G 3' UGCAGUCUC UCCCU CA ACGUCAGAG AGGGA GU miR-4419a 3' G 5'
mRNA MLLT6 5' C G C 3' UGCAGUCUC UCCCUG AUGUUAGAG AGGGAC miR-4441 3' G A 5'
TLE3 mRNA, 4664 н., 3'UTR
mRNA TLE3 5' A A 3' UUGGGGGGUGGG GAGGGGG GACCCCCCAUCU CUUCUCU miR-6515-3p 3' A 5'
mRNA TLE3 5' U C 3' UUGGGGGG GGGAGAGGGGGA GACCCUCC CCCUCUUCUCCU miR-877-3p 3' U 5'
Figure 4. 3'UTRs with miR-1273 family binding sites
Notes: points are the same nucleotedes, results received by miRTarget and TmiRUSite programs
Figure 5. 3'UTRs with miR-619-5p group binding sites (1 part)
Notes: points are the same nucleotedes, results received by miRTarget and TmiRUSite programs
Figure 6. 3'UTRs with miR-619-5p group binding sites (2 part)
Notes: points are the same nucleotedes, results received by miRTarget and TmiRUSite programs
Figure 7. microRNA binding sites in IKZF3 mRNA at 2D-
structure (fragments of 3’UTR)
Figure 8: conserved
microRNA binding sites in normal and optimised
mRNA sequences of Parvovirus B19
isolates
Note: Yellow color:
binding sites; Red color:
nucleotides of normal mRNA differed from
optimized mRNA;*: conserved mRNAs
of 64 isolates
Figure 9. Definition method of differentiation pathway in the CFC test (morphology)
Thank you for attention
omalaheenee@gmail.comhttps://github.com/omalaheenee/mirpy
ca.linkedin.com/in/olgaberillo
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