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20/4
- First team meet up
- Introduction of team members
25/4
- Discussion on DNA structure and replication, Chargaff’s rule, primers and enzymes
27/4
- Discussion on plasmids, digestion, ligation, transformation and 3A assembly
- Brainstorming on this year’s project - square wave generator
28/4
- Discussion on reference papers of repressilator, synchronous oscillations,
robustness etc.
29/4
- Discussion on Gel electrophoresis and blue-white screening
april
To read...
P+E
Differential equations of rate of change of ES and P discussed with equations of conservation
of mass for the same.
Graphical analysis of ES/E0 vs S/S0 with discussion on quasi steady state.
Graphical discussion on Concentration vs Time of the reaction.
5. Michaelis menten equation
6. Discussion on Degradation Tag and how it works in a bacterium where translation and
transcription happen in the same compartment and there are no stop codons.
7. Discussion on Cancer Cell about how it was thought to find a cure of cancer using
these logic gates with inputs as miRNA(regulate genes) and output as apoptosis.
8. Example of virus that can be used as vectors for human cells. e.g. Vaccinia virus
18/05
Discussion on ways to generate different signal responses in bacterial gene regulatory
circuits
22/05
Discussion on :-
1) Chemotactic response in bacteria
2) Temporal and spatial response in chemotaxis
3) Mechanism of chemotaxis in bacteria flagellum
4) Electrical model of chemotaxis
5) Adaptation time of chemotaxis
6) Finding electrical analogue of the biological system by varying frequency of the electrical circuit
made
7) Finding optimal frequency
8) Biological Robustness and causes of it in a biological system
9) System controls, bistability, modularity, buffering, bow-tie framework, decoupling
10) Robustness in signal transduction pathways and insect's segmental development
11) Robustness trade-offs
24/05
Discussion on :-
1) Design principles of biochemical oscillators
2) Time delay's relevance in oscillation
3) Introduction of time delay with Intermediates
4) Limit cycles, conservative cycles and circadian rhythms
5) Time delay by positive feedback
6) Different classes of feedback
7) Linear and hyperbolic response
8) Goldbeter Kosher Function
9) Sniffers
10) Toggle Switch
11) Mutual inhibition and mutual activation
26/05
Discussion on :-
1) A brief review of Sniffers, Buzzers and Toggle switch
2) Negative feedback oscillations
3) Positive feedback oscillations
4) Neutral feedback oscillations
5) Sub-critical and Super-critical hop bit
6) Study of mitosis
27/05
Prepared lab supplies like LA, LB etc. to be used in the lab
29/05
1) Preparation of LuxI and PLux double digest using restriction enzymes EcoRI and PstI
2) Preparation of buffer and electrophoresis gel
3) Loading ladder, control and digest in the wells in gel
4) Electrophoresis and subsequent observation of gel to ensure digestion of plasmids
31/05
Discussion on:-
1) Plasmid isolation
2) Lysis solutions and their composition
3) Function of each component in the solutions
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