Notebook

8 May: Exams get over and we discusses ideas with Anantha ma'am(Instructor). One interesting study could be lignocellulosic mass conversion to other useful and economically high valued products.
8-10 May: We do and extensive literature survey for this project and Acinetobacter baylyi ADP1 seems to be good candidates.
14 May: We finalise to work on lignin conversion to biofuels using Acinetobacter baylyi ADP1. We choose this organisms over other because, it is non pathogenic and has amazing capabilities of degrading aromatic compounds like caffeate, vaillate, etc. Above all, it is naturally competent and Guhan sir's lab have expertise in working with this organism.
15 May: We finalize to work on lignin conversion to biofuels using Acinetobacter baylyi ADP1. We choose this organisms over other because, it is non pathogenic and has amazing capabilities of degrading aromatic compounds like caffeate, vaillate, etc. Above all, it is naturally competant and Guhan sir's lab have expertise in working with this organism.
16 May: Acinetobacter baylyi has 6 copies of transposonal elemets which were remove in 2017 and a new strain of this organism was engineered called ADP-!Sx (Suárez GA, Renda BA, Dasgupta A, Barrick JE. Reduced Mutation Rate and Increased Transformability of Transposon-Free Acinetobacter baylyi ADP1-ISx. Kivisaar M, ed. Applied and Environmental Microbiology. 2017;83(17):e01025-17. doi:10.1128/AEM.01025-17.) We request barrick to send us the engineered strain.
18 May: We plan to compile all literature and decide for direction of the project. Vanillin production seems to be potential candidate but experiments fail.
22 May: We realise that we need a proper toolkit and well established methods to work with A. baylyi. So we plan our project to take it into direction of Expanding the toolbox of A. baylyi ADP1.
23 May: We finalise upon the things we want to try out: Codon optimized Reporters and promoter. If time permits then terminator. 25 May: Anantha ma'am asks sagar to place order of CO GFP and mCherry for now to GenScript Meanwhile we do a lit survey for various approahes for promoter design.
29 May: GenScript gets back to us with a reply that there is no reliable codon usage table available. They send us link of kasuza website which has a codon table based on 2 coding regions.
30 May: We knew that coding region annotation was present on NCBI website. we discussed this problem with KD and idea of CUTE was born.
31 May: Workplan was made to start working on Promoter Design, Codon usage table on A. baylyi and Codon optimization. We fixed upon using pBAV1K vector as it is known to work in A. baylyi and sagar had preliminary results for it KD, burhan sathvik were assigned on Codon table of A. baylyi
Richa, Burhan, Sathvik get on Promoter design.

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Team:IIT-Madras/Notebook

Notebook