Team:Toronto/Notebook-w01-thu
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Week 1: May 19, 2016
Thursday, 5/19/2016
Final adjustments to the RRF
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Addition to the 5B.1 section with regards to D.Acidovorans and 5B.6 section with chemical burns and hazards from off-gases/by-products.
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Updates on PPE (face shield) and Cryogenics - Gas Law Calculation sheet.
Budget management: pending on access to the account on UofT Medstore.
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In search for previous year receipts - Bohdan searched the lab- receipts were not found.
Research on BACs (Bacteria Artificial Chromosomes):
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Commercially available BACs:
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General research in to protocol design (please see new Protocol)
Explore Delftibactin options:
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In search for potential promoters on the del cluster as a possible route of increasing delftibactin production in D. acidovorans.
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Promoter prediction programs used including Bprom, etc...
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Scanning the potential promoters on the genome of Delftia acidovorans using Benchling.
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Possibility of CRISPR utilization for promoters alternation in NMR collaboration with Dr. Rudraksha Dutta Majumdar (UTSC).
Explore the plasmid design for the sensing project:
- GolB promoter
GolB promoter: cttgaccttccaacactggcaaggtccagactggcaa
- GolS gene: (http://www.genome.jp/dbget-bin/www_bget?stm:STM0354) [465 nucleotides]
atgaacatcggtaaagcagctaaagcatcgaaagtctcggccaaaatgattcgctactat
gaacagattggtctgattcccgcggcaagtcggacggattccggctatcgggcctatacc
caggctgatgttaatcaattgcattttatacgccgcgcgcgcgacctcggtttttcagtt
gctgaaatcagcgacttactgaatctttggaataaccagtcgcggcaaagcgctgacgtc
aaacgcctggcgcagacgcacattgatgaactggacagacgtatccagaacatgcagcac
atggcgcaaaccctcaaagcgctgattcactgctgcgccggcgacgcgctgccagattgc
cccattctgcatacgcttggacaacctgacgatagcgagccggaggcgcgtaccggagcg
gtattgcgacgtcctcgtcgccacggactggcaaagcgtctgtaa
- BioBrick compatible parts must not have the following restriction sites (All these restriction sites belong to the prefix and suffix of the BioBrick assembly standard):
A | B | C | |
1 | Sequence | Type | Enzyme |
2 | gaattc | Illegal | EcoRI |
3 | tctaga | Illegal | XbaI |
4 | actagt | Illegal | SpeI |
5 | ctgcag | Illegal | PstI |
6 | gcggccgc | Avoid | NotI |
Table1
- Proposed blueprint of sensing plasmid (likely missing a UNS before suffix; please confirm)
Agenda for May 20:
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Dr. Radhakrishnan Mahadevan interview from 3-4 pm.
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Remember to print out the Experiment Flow Chart - Facebook group files, Safety Training Certificate & refresher.
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Study the RRF for the interview.
