Parts contribution
Basic parts
Our team has added 11 new Basic Parts to the Registry. Three proteins for multiplex detection of vaccinia viruses: L1, A27, and A33, were also lacking in the Registry as parts. They were added to the Registry as well as 1st and 4 sushi ectodomains of B5R, where mutagenesis Cys-140 modified to Ser amino acid. Along with sequences, two reverse and one forward primer for two ectodomains of B5R were added. Future iGEM teams can find sequences of two different aptamers for detecting protein L1, which can substitute monoclonal antibodies for other detection systems.
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Code |
Description |
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1 |
B5R (all 4 sushi domains) |
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2 |
B5R 1st sushi |
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3 |
DNA aptamer for L1 protein |
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4 |
DNA aptamer for L1 protein (2) |
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5 |
L1 protein encoding sequence |
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6 |
A33 protein encoding sequence |
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7 |
A27 protein encoding sequence |
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8 |
Forward B5R sequence primer |
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9 |
Reverse primer for B5 protein (all 4 sushi domains) |
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10 |
Reverse primer B5R sequnce (only 1st sushi) |
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11 |
Codon optimized B5R (all 4 sushi domains) |
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12 |
B5R sequence with altered Cys140 to Ser |
Figure 1: 4 sushi ectodomain of B5R
Figure 2: 1st sushi ectodomain of B5R
3D structures of B5R in alpha fold
There were no available 3D structures of B5R protein before. Our team was the first to make folded protein structures of B5R in the alpha fold (Fig. 1,2). You can download PDB files of both 1st and 4 sushi ectodomains of B5R protein from the GitHub library via the link https://gitlab.igem.org/2022/software-tools/nu-kazakhstan
Contribution to parts from Distribution kit
Resuspension of plasmids p1E and p5A from the iGEM distribution kit were transformed into Dh5α E. coli cells. However, as shown in figures 3 and 4, the transformation was unsuccessful for both plasmids.
p1E = BBa_B0025 (double terminator)
p5A = BBa_E0020 (fluorescent SIAM)
Figure 3: p1E, psB1A2, for Dh5α cells on agar plate with ampicillin
Figure 4: p5A, psB1A2, for DH5α on agar plate with ampicillin
Software contribution
Analysis of data from optical fibre sensors
We created software called Viraless with a convenient interface to analyse experimental data from a fibre-optic sensor. The general limitation of such data analysis is the necessity to adapt each time you enter a new reading. Other iGEM teams that will be investigating optical fibres as detection systems can analyse their inputs using our software, which makes this process automated.
dnaTurner: a useful tool in predicting 3D-structure of single-stranded DNAs
A conventional way to predict 3D structures of single-stranded DNA molecules involves a laborious process of manually changing the PDB files of RNA molecules. We made dnaTurner - software to automate this process. Other iGEM teams (and anyone) can use it in case they want to predict 3D structures of single-stranded DNA molecules.
Informational contribution
Guide for using Making Aptamers Without Selex (MAWS)
MAWS is an aptamer designing tool which uses a fragment-based algorithm to create an aptamer sequence against target molecules by the progressive selection of appropriate bases using an entropic criterion. Here you can find a step-by-step guide written by our team on how to use MAWS.
Guide for organising summer camp
We believe sharing experience and getting relevant knowledge and guidance from other iGEM teams are equally important. It is possible to go beyond the project and discover new development chances by creating such co-guiding opportunities. In the frames of our sharing experience activities, we have created a guidebook for offline Summer Camp. This guidebook provides instructions for organising a successful science summer camp. It is intended for those who will also hold a similar event.
Tactile 3D Models of cells for accessible education for all
3D printable models of animal and plant cells were designed and printed. These 3D models of cells have annotations in the Braille system, allowing people with visual impairments to understand the structure of the cell organelles and their location in animal and plant cells. Each cell is accompanied by a description sheet that contains the appropriate number of organelle with its name. This could improve science communication and increase the inclusivity level for future iGEM teams. You can find files for 3D printing and their annotations below.
These models were demonstrated at our Bioart exhibition, which in turn was the first event combining biology and art in Central Asia. If you want to know more details about organising such an event, follow the link below.
Figure 5:3D model of plant cell.
Figure 6:3D model of animal cell.
Figure 7:Photo of tactile 3D Models from Bioart exhibition