Team:WHU-China/Notebook
April
| 2017.04.01 | HP | Communicated with one of the authors of the article "Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation" online to get some latest progress. |
| 2017.04.08 | Attempts in E. coli | Got the Nitratireductor pacificus which contain our gene rdhANP. |
| 2017.04.10 | Attempts in E. coli | Started to culture N. pacificus. |
| 2017.04.11 | Attempts in E. coli | Extracted whole genome of N. pacificus. |
| 2017.04.12 | Attempts in E. coli | Got our gene rdhANP by PCR |
| 2017.04.21 | Attempts in Bacillus subtilis | Amplified rdhANP by colony PCR of N. pacificus |
| 2017.04.25 | Preparation of the protoplast for Bacillus megaterium | Made protoplast of B. megaterium |
| 2017.04.26 | Attempts in B. subtilis | Amplified rdhANP by colony PCR of N. pacificus |
| 2017.04.26 | Preparation of the protoplast for B. megaterium | Prepared prot-medium |
| 2017.04.27 | Attempts in B. subtilis | Agarose gel electrophoresis confirmed that the gene rdhANP is successfully amplified |
| 2017.04.27 | Preparation of the protoplast for B. megaterium | Prepared hyp-medium |
| 2017.04.29 | Attempts in E. coli | Amplified rdhANP by colony PCR of N. pacificus |
| 2017.04.30 | Attempts in E. coli | Cultured the E. coli with plasmid pET28a+ |
May
| 2017.05.01 | Attempts in E. coli | Designed primers for inserting DNA fragment of gene rdhANP into pET28a+ |
| 2017.05.02 | Attempts in E. coli | Got whole gene synthesized rdhANP codon-optimized for B. megaterium |
| 2017.05.03 | Attempts in E. coli | Failed to insert DNA fragment of rdhANP into pET28a+. |
| 2017.05.04 | Preparation of the protoplast for B. megaterium | PEG-6000 arrived. Prepared PEP-G solution |
| 2017.05.05 | HP | Had a meeting with researcher Dongru Qiu, and researcher Feng He to know the regular process of biological methods in sewage treatment. |
| 2017.05.06 | HP | Had a meeting with researcher Dongru Qiu, and researcher Feng He |
| 2017.05.08 | Preparation of the protoplast for B. megaterium | Tested the protoplast through transformation of pET28a+ |
| 2017.05.08 | Attempts in E. coli | Extracted pET28a+ from DH5α |
| 2017.05.12 | Preparation of the protoplast for B. megaterium | Only one clone grew |
| 2017.05.14 | Preparation of the protoplast for B. megaterium | Extracted and verified plasmids, but unfortunately there's no plasmid transformed successfully |
| 2017.05.18 | Preparation of the protoplast for B. megaterium | Change the plasmid for the test |
| 2017.05.20 | Attempts in E. coli | Failed to use Pfu to PCR rdhANP. Used Q5 to PCR but failed again. |
| 2017.05.21 | Attempts in E. coli | Failed to use Pfu to PCR rdhANP |
| 2017.05.21 | HP | Communicated with one of the authors of the article "Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation" online to get some latest progress. |
| 2017.05.23 | Attempts in E. coli | We stop to do the experiment in E. coli , because we don't have any support that RdhANP could express in E. coli . |
June
| 2017.06.02 | HP | Introduced microorganisms and our project to other students in class to popularize the influence of microorganisms and call for help. |
| 2017.06.04 | Construction of plasmid for B. megaterium | PCR xylose promoter linked with RBS and GFP |
| 2017.06.11 | HP | Propagandized iGEM and our project to children in community. Instruct them to make halogenated phenol models and assist them to finish the game based on mechanisms of dehalogenases. |
| 2017.06.12 | Construction of plasmid for B. megaterium | PCR pSB1C3, pUC57, pET28a plasmids excluding their promoters, RBS and coding sequence followed |
| 2017.06.19 | Attempts in B. subtilis | Point mutation of RdhANP-PUC57 |
| 2017.06.20 | Construction of plasmid for B. megaterium | PCR rdhANP |
July
| 2017.07.04 | Brick construction | Cloned rdhANP into PSB1C3 and transformed the construct into DH5α |
| 2017.07.05 | Construction of plasmid for B. megaterium | Constructed plasmid by linking xylose promoter and rdhANP gene and plasmid framework |
| 2017.07.05 | Brick construction | No transformant in treatment and control |
| 2017.07.06 | Brick construction | Cloned rdhANP into PSB1C3 and transformed the construct into DH5α |
| 2017.07.07 | HP | Go to Shenzhen to visit the Chinese National Genebank and iCarbonX and exchange views with a professor of genetic biology in BGI, also the instructor of BGI graduate iGEM team. |
| 2017.07.12 | Brick construction | No transformant in treatment and control |
| 2017.07.16 | Brick construction | Cloned rdhANP into PSB1C3 and transformed the construct into DH5α |
| 2017.07.17 | Brick construction | Cloned rdhANP into PSB1C3 and transformed the construct into DH5α |
| 2017.07.18 | Brick construction | Got transformants in both treatment and control |
| 2017.07.18 | Brick construction | Picked up colony and cultured for 12 hours |
| 2017.07.19 | Brick construction | Sequenced extracted plasmids |
| 2017.07.20 | Brick construction | Biobrick 1 completed and stocked it in glycerol |
| 2017.07.25 | Interlab | Resuspended plasmid from 2017 DNA distribution kit plate 7 |
| 2017.07.25 | Brick construction | Transformation BBa_J61051 into DH5αand cultured overnight |
| 2017.07.26 | Interlab | Transformed DH5α competent cells with 2 µl of resuspension |
| 2017.07.26 | Interlab | Cultured 16h |
| 2017.07.26 | Interlab | Measured OD600 Reference point |
| 2017.07.26 | Interlab | Made FITC fluorescence standard curve |
| 2017.07.26 | Brick construction | Got transformants in both treatment and control |
| 2017.07.26 | Brick construction | Picked up colony and cultured for 12 hours |
| 2017.07.26 | Brick construction | Miniprep plasmid and tested its concentration |
| 2017.07.27 | Interlab | Measured OD600 of the overnight cultures |
| 2017.07.27 | Interlab | Diluted the cultures to a target OD600 of 0.02 |
| 2017.07.27 | Interlab | Incubated the DH5α for 6 hours |
| 2017.07.27 | Interlab | Measured OD and fluorescence of bacteria liquid every other hour |
| 2017.07.27 | Brick construction | Amplified BBa_J61051 by PCR with a truncated prefix and a prolonged suffix including RBS sequence, purified and sequenced |
| 2017.07.28 | Transformation of B. megaterium | Electroporated PMP2444 to B. megaterium at 2100V,2300V and 2500V |
| 2017.07.30 | Brick construction | Overlapping PCR to link Biobrick 1 and terminator |
August
| 2017.08.02 | Brick construction | Overlapping PCR to link RBS and suffix |
| 2017.08.03 | Transformation of B. megaterium | Electroporated PMP2444 to B. megaterium at 1500V,1800V,2100V |
| 2017.08.04 | Brick construction | Overlapping PCR |
| 2017.08.05 | Brick construction | Ligated PCR product into ZT4-simple-blunt vector ,sequenced |
| 2017.08.06 | Brick construction | Glycerol stock positive constructs |
| 2017.08.06 | Brick construction | Ligated DNA fragment to PSB1C3 |
| 2017.08.07 | Brick construction | Overlapping PCR to link prefix |
| 2017.08.07 | Transformation of B. megaterium | Electroporated PMP2444 to B. megaterium at 1200V,1400V 1600V |
| 2017.08.08 | Brick construction | Gel electrophoresis for PCR product |
| 2017.08.09 | Brick construction | Gel extraction and purification |
| 2017.08.09 | Brick construction | Restriction digest |
| 2017.08.10 | Brick construction | Ligation into PSB1C3 vector |
| 2017.08.12 | HP | Hand out questionnaires in New York, Helsinki and Wuhan to know people's knowledge on sewage treatment. |
| 2017.08.15 | Modeling | Set up iGEM mathematical modeling team |
| 2017.08.15 | Brick construction | Got sequencing result One key site is mutated |
| 2017.08.17 | Brick construction | Picked up other colony and sequenced again |
| 2017.08.19 | Brick construction | Get sequencing result One key site is mutated |
| 2017.08.19 | Transformation of B. megaterium | Prepared protoplast of B. megaterium using Protocol 1 and transformed PMP2444 by kit |
| 2017.08.20 | Transformation of B. megaterium | Transformed PMP2444 by PEG-P mediated transportation in Protocol 1 |
| 2017.08.21 | Modeling | First time discussion: determine broad purpose |
| 2017.08.22 | Modeling | Literature review |
| 2017.08.22 | Brick construction | Site-directed mutation by PCR |
| 2017.08.26-28 | Collaboration | Attended the CCiC(Conference of China iGEMers Community) in Fuzhou, China. |
| 2017.08.30 | Brick construction | Gel electrophoresis for PCR product |
September
| 2017.09.01 | Collaboration | Title and abstract uploaded; track selection finalized |
| 2017.09.02 | Brick construction | Gel extraction and purification |
| 2017.09.03 | Brick construction | Sequencing |
| 2017.09.04 | Brick construction | Got sequencing result Right |
| 2017.09.04 | Transformation of B. megaterium | Electroporated pSPAsp-hp to B. megaterium at 2100V,2300V and 2500V |
| 2017.09.05 | HP | Held a meet-and-greet for new students and expand influence of iGEM to prepare for the recruitment next year. |
| 2017.09.07 | Brick construction | Restriction digest |
| 2017.09.08 | Brick construction | Ligation into Psb1c3 vector, Biobrick2 complete |
| 2017.09.08 | Jamboree | Team roster finalized |
| 2017.09.12 | Jamboree | Flying tickets purchased |
| 2017.09.13 | Jamboree | Hotel booked |
| 2017.09.15 | Modeling | Revised the existing modeling to make it applicable for our project |
| 2017.09.15 | Transformation of B. megaterium | Prepared protoplast of B. megaterium and transformed pSPAsp-hp,pHIS1525 and pBE-p43 by Protocol 2 |
| 2017.09.15 | HP | Made panels to educate lab staff about safety in laboratory. |
| 2017.09.16 | Jamboree | Practice session signed up |
| 2017.09.17 | Transformation of B. megaterium | Prepared protoplast of B. megaterium and using Protocol 3 and transformed pSPAsp-hp,pHIS1525 and pBE-p43 by kit |
| 2017.09.19 | Jamboree | Applying for the visa |
| 2017.09.20 | Modeling | Finished modeling revision |
| 2017.09.20 | Brick construction | Found sequences |
| 2017.09.22 | Modeling | Collected modeling raw data by literature review |
| 2017.09.22 | Modeling | Collected modeling raw data by consulting professors |
| 2017.09.23 | HP | Had interviews in the street to know public understanding on sewage treatment. |
| 2017.09.25 | Modeling | Collected modeling raw data by visiting the sewage treatment plant |
| 2017.09.27 | Brick construction | AuGCT company accepted our order for DNA sythesize |
| 2017.09.29 | Collaboration | Submitted interlab data |
| 2017.09.30 | HP | Had a conversation with Wuhan Environmental Protection Bureau and Hubei Environmental Protection Department to get some information about water environment protection situation and pollutants monitoring indicators. |
October
| 2017.10.01 | Modeling | Simulated modeling on MAYLAB |
| 2017.10.01 | Transformation of B. megaterium | Prepared protoplast of B. megaterium and transformed pSPAsp-hp,pHIS1525 by Protocol 2 |
| 2017.10.02 | Collaboration | Safety form part 4 and part 5 completed |
| 2017.10.07 | Modeling | Tested modeling |
| 2017.10.09 | HP | Communicated with one of the sewage treatment plants in Wuhan to know better about biological treatment process and get some data for modeling in our project. |
| 2017.10.11 | Transformation of B. megaterium | Prepared protoplast of B. megaterium using Protocol 4 and transformed pSPAsp-hp,pHIS1525 by electroporation |
| 2017.10.12 | Modeling | Modeling revision |
| 2017.10.12 | Jamboree | Uploaded the banner |
| 2017.10.20 | Collaboration | Parts shipped |
| 2017.10.21 | Brick construction | Our bricks came. |
| 2017.10.27 | Collaboration | Judging form uploaded |
November
| 2017.11.01 | Collaboration | Wiki completed |
