Team:AFCM-Egypt/Parts
Parts
List Of Contents
This year AFCM-Egypt team have added to the registry:-
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14 basic parts (13 of which are completely new to the registry)
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3 composite parts
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8 Characterizations of previous parts
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3 Improvements to previous parts
Basic Parts
| BioBrick | Type | Role |
| BBa_K3743000 | Coding | FAS-associated death domain protein (FADD) |
| BBa_K3743001 | RNA | Cobalamin Riboswitch |
| BBa_K3743002 | Coding | MS2 |
| BBa_K3743003 | Protein_Domain | Destabilizing Domain (DD) |
| BBa_K3743005 | Coding | dCas13 |
| BBa_K3743006 | Coding | L7Ae |
| BBa_K3743007 | Coding | L7Ae (dCas13) linked by Gly Ser Linker |
| BBa_K3743008 | Regulatory | ToeHold switch to be fused with x30 degradation motif |
| BBa_K3743009 | Regulatory | 30x degradation motifs |
| BBa_K3743011 | Regulatory | onToehold switch |
| BBa_K3743012 | Regulatory | Small Nuclear Ribonucleoprotein (snRNP) Riboswitch |
| BBa_K3743013 | Coding | BAX mutant (G36E) |
| BBa_K3743014 | Coding | Cas12g |
| BBa_K3743016 | Coding | HBc virus like particles (VLP) |
Composite Parts
| BBa_K3743004 | Coding | MS2 (DD) by fusion |
| BBa_K3743010 | Composite | DegraderToeHold |
| BBa_K3743015 | Composite | L7Ae (Cas12g) linked by Gly Ser Linker |
Characterized Parts
| BioBrick | What we have done |
| BBa_K2365048 | We have characterized & improved this part As shown in BBa_K3743013 by performing mutagenesis prediction of mutational landscape of Bax mutant and testing the effect of these mutations on the evolutionary fitness of the protein after generating multiple sequence alignment of the protein sequence and predict mutational landscapes. |
| BBa_K2100068 | -We made simulations of the dynamics of the used riboswitches which acts as an essential safety switch in our vaccine design. Mathematical modeling is performed using ordinary differential equations (ODEs) and fitted parameters.-We performed mutagenesis prediction of mutational landscape of L7Ae and tested the effect of these mutations on the evolutionary fitness of the protein after generating multiple sequence alignment of the protein sequence and predict mutational landscapes |
| BBa_K2100050 | -We made structural characterization in order to model the structural stability of kink-turns riboswitch-We used mathematical modelling to simulate the dynamics of its use as a riboswitch |
| BBa_K3504000 | We made structural characterization in order to visualize the part & model the structural stability |
| BBa_K3504001 | We made structural characterization in order to visualize the part & model the structural stability |
| BBa_K3504002 | We made structural characterization in order to visualize the part & model the structural stability |
| BBa_K3504003 | We made structural characterization in order to visualize the part & model the structural stability |
| BBa_K1442040 | -by performing mutational landscape of the part to predict the positive fit mutations |
Improved Parts
| BioBrick | What we have done |
| BBa_K2100068 | -We improved this part by adding dcas13 in conjugation with L7Ae protein (that has an inhibitory effect on the transcription by binding to its kink-turn) by Gly Ser linker. The system simply recognizes and binds to mRNA in the cancerous environment which leads to consumption of L7Ae protein. Therefore, not binding to kink-turn to inhibit the inhibitory effect on the transcription which finally leads to stimulation of the transcription in order to increase the yield of the vaccine-We improved this part by adding cas12g by utilizing The Gly Ser linker to conjugate it with the L7Ae protein (which inhibits transcription by binding to its kink-turn). The mechanism simply identifies and attaches to mRNA in the cancerous environment, causing the L7Ae protein to be consumed. As a result of not binding to kink-turn, the inhibitory action on transcription is inhibited, resulting in transcription activation and a rise in vaccine yield. As a result, it is a cell-specific design that binds to PD-L1 mRNA, which plays an immune evasion role in cancerous environments. |
| BBa_K1442040 | -By addition of destabilizing domain to the part making it work as a part of a riboswitch. |
| BBa_K2365048 | -We improved the Assembly compatibility of RFC[21] making it a more suitable option for assembly |
New parts
| BBa_K3743000 | Coding | FAS-associated death domain protein (FADD) |
| BBa_K3743001 | RNA | Cobalamin Riboswitch |
| BBa_K3743002 | Coding | MS2 |
| BBa_K3743003 | Protein_Domain | Destabilizing Domain (DD) |
| BBa_K3743004 | Coding | MS2 (DD) by fusion |
| BBa_K3743005 | Coding | dCas13 |
| BBa_K3743007 | Coding | L7Ae (dCas13) linked by Gly Ser Linker |
| BBa_K3743008 | Regulatory | ToeHold switch to be fused with x30 degradation motif |
| BBa_K3743009 | Regulatory | 30x degradation motifs |
| BBa_K3743011 | Regulatory | onToehold switch |
| BBa_K3743012 | Regulatory | Small Nuclear Ribonucleoprotein (snRNP) Riboswitch |
| BBa_K3743013 | Coding | BAX mutant (G36E) |
| BBa_K3743014 | Coding | Cas12g |
| BBa_K3743016 | Coding | HBc virus like particles (VLP) |
