Team:Siberia/Education
ASBS modules:
LABx1 (Isolation of plasmid DNA and transformation of bacterial cells)
Our students independently isolated plasmid DNA which carried the gene for the fluorescent protein GFP from bacteria of the DH5 alpha strain. This strain is useful in that it is good for the production of plasmid DNA since it contains a mutation in the endA1 gene, which blocks the synthesis of an endonuclease. The students then chemically transformed the isolated DNA into another bacterial strain, BL21 (DE3), which is used by researchers to produce a protein product. After transformation, bacteria were plated on Petri dishes and incubated at 37C until the next day.
BIOINFx1 (Modelling 3D protein structures) - Nikita Ivasenko
Students were introduced to the modelling of 3D protein structures. The lecturer told the students about the features of the AlphaFold program and helped them model their own proteins by changing the properties of the protein of interest.
LABx2 (IMAC method)
Our students worked on chromatographic purification of a fluorescent recombinant protein and its accumulation on a polyacrylamide gel by electrophoresis. Immobilized metal affinity chromatography (IMAC) is a widely used method to purify proteins that contain a hexahistidine tag. The sorbent contains functional groups of nitrilotriacetic acid, which chelate to the cations Cu2 +, Ni2 +, Co2 +, and Zn2 +. The charged sorbent specifically binds proteins via the polyhistidine tag. This approach allows us to obtain a sufficiently pure protein in one chromatography experiment.
BIOINFx2 (Biological applications of Python) - Aleksandr Bobrovskikh
During the second bioinformatics module, students listened to basic theory on Python programming and learned how to write code in Jupyter Notebook and Spyder. The lecturer then explained the specifics of Python application for biological tasks. Students learnt how to generate random sequences of a given length from letters of genetic code - A, T, G, C - using the NumPy library and also how to write the result in a FASTA file. At the end of the lecture, the students were presented with various biological problems, such as how to calculate the GC-composition in 100 random sequences, each 60 bp long.
LABx3 (DNA sequence analysis: PCR and restriction)
In the final laboratory module, students analysed the products of a gene-editing system. An experiment on editing the EGFP gene by the CRISPR / Cas9 method was carried out at the Laboratory of Genomic and Protein Engineering of the ICBFM SB RAS. As a result, Petri dishes with colonies containing plasmids with gene fragments of the original and mutant EGFP were obtained, which were offered to students for analysis. Through the use of PCR and restriction analysis, students were able to determine the efficiency of the gene-editing system by identifying how many colonies contain the mutant EGFP gene and which ones contain the normal gene. Thus, the students were introduced to the TA cloning method.
BIOINFx3 (Ugene) - Dmitrii Sukhomlinov
In the last bioinformatics module, students were introduced to the interface of the Ugene program and learned how to use some of its basic functions. With some guidance from their lecturer, students found unique sites of the restriction endonucleases NcoI and BamHI in the pET-28 plasmid, cut the EGFP gene at these sites from another plasmid and then inserted it into the pET-28 plasmid vector. Thus, students learned how to simulate in vitro processes using the Ugene software.
Lectures for students:
*Corresponding Members of the Russian Academy of Sciences
Training for educators:
Genetics and Molecular Biology in:
Business exhibits
Design and branding
Anna’s logo and Danil’s graphic design use elements uniquely associated with our town and incorporates a biological aspect to reflect the subject of the school - synthetic biology. We plan to make the ASBS an annual event, so much effort was put into creating a simple and immediately identifiable logo and design aesthetic.
SIBIRIA