Notebook
Week 1: Jan 10 – Jan 16
| General | team forming (14.1.2016) |
Week 2: Jan 17 – Jan 23
| General | write motivation letter |
Week 4: Jan 31 – Feb 6
| General | weekly meeting: team forming |
Week 5: Feb 7 – Feb 13
| General | weekly meeting: team forming |
Week 6: Feb 14 – Feb 20
| General | weekly meeting: team forming |
Week 8: Feb 28 – Mar 5
| General | weekly meeting: project brainstorming |
Week 9: Mar 6 – Mar 12
| General | weekly meeting: project brainstorming |
Week 10: Mar 13 – Mar 19
| General | weekly meeting: project brainstorming |
Week 11: Mar 20 – Mar 26
| General | weekly meeting: project brainstorming |
Week 12: Mar 27 – Apr 2
| General | weekly meeting: decide on project |
Week 13: Apr 3 – Apr 9
| HP | Preparations for NBC |
Week 14: Apr 10 – Apr 16
| HP | NBC Wageningen |
| Coding/Wiki | Start with DNA encoder |
Week 15: Apr 17 – Apr 23
| Coding/Wiki | DNA encoder |
Week 16: Apr 24 – Apr 30
| Coding/Wiki | First version of encoder done |
| General lab | starting of setting up the lab |
Week 17: May 1 – May 7
| General lab | setting up the lab |
Week 18: May 8 – May 14
| HP | Preparation for Meeting of Dutch Teams Wageningen |
| Modelling/Coding | Start with MultiAgent System Model |
| Coding/Wiki | DNA encoder |
| General lab | setting up the lab |
| Integration/Lab | plan integration cloning |
Week 19: May 15 – May 21
| HP | Meeting of Dutch Teams - Wageningen |
| Modelling/Coding | Literature MAS |
| Coding/Wiki | DNA encoder |
| General lab | setting up the lab, free license from eLab journal received |
| Integration/Lab | plan integration cloning |
Week 20: May 22 – May 28
| HP | Campus Party Attendance |
| Modelling/Coding | Literature MAS |
| General lab | setting up the lab |
| Integration/Lab | plan integration cloning |
Week 21: May 29 – Jun 4
| HP | Night of Art and Sciences Participation (ScienceLinx) |
| Modelling/Coding | Literature MAS |
| Integration/Lab | plan integration cloning |
Week 22: Jun 5 – Jun 11
| Modelling/Coding | |
| Integration/Lab | plan integration cloning, prepare medium for Bacillus subtilis transformation, |
| Antibiotics/Lab | Preparing sporulation medium |
| RIVM - Safe by Design | First Phone call with RIVM |
Week 23: Jun 12 – Jun 18
| Modelling/Coding | Start MAS Coding |
| General lab | 16.6. first order of lab needs |
| Integration/Lab | plan integration cloning |
| Antibiotics/Lab | Sporulation of B. subtilis 168 |
| RIVM - Safe by Design | Working on proposal Safe by Design |
Week 24: Jun 19 – Jun 25
| Modelling/Coding | Coding |
| Coding/Wiki | Start with wiki |
| Integration/Lab | plan integration cloning |
| Antibiotics/Lab | Testing UV resistance of spores |
| Collaboration Wageningen | skype with Wageningen |
| RIVM - Safe by Design | Working on proposal Safe by Design |
Week 25: Jun 26 – Jul 2
| HP | Research National regulations for Sending |
| Modelling/Coding | Coding |
| Integration/Lab | plan integration cloning |
| RIVM - Safe by Design | Working on proposal Safe by Design |
Week 26: Jul 3 – Jul 9
| HP | Research National Regulations for Sending |
| Modelling/Coding | Genetic Algorithm finished |
| Coding/Wiki | DNA encoder |
| Integration/Lab | plan integration cloning |
| Antibiotics/Lab | Determining optimal plating dilution, MIC of ciprofloxacin |
| RIVM - Safe by Design | First Meeting with RIVM |
Week 27: Jul 10 – Jul 16
| HP | Contact National Cyber Security Center and RIVM for orientation in regulations |
| Modelling/Coding | Coding |
| Coding/Wiki | DNA format finalized |
| General lab | 13.7. first order of the gBlocks |
| Integration/Lab | message and key gBlock order |
| Antibiotics/Lab | Ciprofloxacin MIC and MBC, patterning experiment |
| RIVM - Safe by Design | Working on product of Proposal (booklet) Safe by Design |
Week 28: Jul 17 – Jul 23
| HP | Research International Regulations for Sending/Planning Future Scenearios/Collaboration with iGEM Teams for International Survey |
| Modelling/Coding | Coding |
| General lab | 19.7.clone manager tutorial by Bara, 22.7. half of the gBlocks received, 21.7. competent cells preparation, digestion of linearized plasmid backbones |
| Integration/Lab | message gBlock received -> start of the cloning process |
| Kill switch/Lab | E.coli top10 competent cell preparation, basic layout of kill switches |
| Antibiotics/Lab | Spirofloxacin MIC tests and Photoswitch test |
| RIVM - Safe by Design | Working on product of Proposal (booklet) Safe by Design |
Week 29: Jul 24 – Jul 30
| HP | Release of the Survey to social Media/Planning Future Scnearios |
| Modelling/Coding | First Results Sender |
| General lab | second half of the gBlocks received, preparation of agarose for the gels, amplifying of gBlocks |
| Integration/Lab | cloning procedure of the message into pdr111 (E.coli TOP10) |
| Kill switch/Lab | Primer design, Detailed kill switch layout; nuclease biobrick order |
| Antibiotics/Lab | Spirofloxacin MIC tests |
| Spores/Lab | Test Tonia's and Daniel's protocols |
| RIVM - Safe by Design | Working on product of Proposal (booklet) Safe by Design |
Week 30: Jul 31 – Aug 6
| HP | Interview JanJaap and visit to Groninger Archieven/RADIO PARTICIPATION |
| Modelling/Coding | First Results Criminal |
| Integration/Lab | pDR111+message transformation to Bacillus subtilis trp+, starch test to verify right colonies, samples for sequencing |
| Kill switch/Lab | Cloning - RBS (34), tetR and 2terminator; Cloning repeat - RBS (34) |
| Antibiotics/Lab | Spirofloxacin MIC tests with E. coli |
| Spores/Lab | Test Tonia's and Daniel's protocols |
| RIVM - Safe by Design | Working on product of Proposal (booklet) Safe by Design |
Week 31: Aug 7 – Aug 13
| HP | Planning Future Scenarios/Working on presentation for ScienceLinX Day |
| Modelling/Coding | MAS Paper + Wiki |
| General lab | amplification of gBlocks |
| Integration/Lab | cloning procedure of pDR111+message+sfGFP and pdr111+sfGFP |
| Kill switch/Lab | Cloning - RBS (34) |
| Antibiotics/Lab | Spirofloxacin MIC tests with E. coli |
| Spores/Lab | Daniel's protocol worked best and fastest |
| Collaboration Wageningen | vitamin b12 and guanine stock, recive biobrick |
| RIVM - Safe by Design | Second Phone Call RIVM |
| CRISPR/CAS9 | Starting a new idea (using CRISPR/Cas 9) |
| decoy/sfGFP | cloning plan sfGFP |
Week 32: Aug 14 – Aug 20
| HP | Elaboration of Proposal of Labelling of GMOs |
| Modelling/Coding | Start of Random Mutation Model |
| Integration/Lab | problems with gBlock |
| Kill switch/Lab | Genomic DNA for nuclease; pimer design for nuclease |
| Antibiotics/Lab | Ciprofloxacin-resistant B. sub. by directed evolution |
| Collaboration Wageningen | plan plate reader experiment |
| RIVM - Safe by Design | Working on product of Proposal (booklet) Safe by Design |
| CRISPR/CAS9 | Worked on design plan (e.g. primers, plasmids, labwork) |
| decoy/sfGFP | cloning sfGFP in pDR111/ sequencing validation |
Week 33: Aug 21 – Aug 27
| HP | Planning Future Scenarios/Working on presentation for ScienceLinX Day/Prepairing Lab equipment etc for SienceLinX Day |
| Modelling/Coding | Literature Model 2 |
| Coding/Wiki | Wiki |
| General lab | 22.8. second order of the gBlocks |
| Integration/Lab | problems with gBlock, ordering of the new key sequence as a gBlock |
| Kill switch/Lab | Cloning - RBS (30); nuclease biobrick recieved |
| Antibiotics/Lab | Ciprofloxacin-resistant B. sub. by directed evolution |
| Collaboration Wageningen | microscopy, repeat plate reader experiment |
| RIVM - Safe by Design | Working on product of Proposal (booklet) Safe by Design |
| CRISPR/CAS9 | Worked on design plan (e.g. primers, plasmids, labwork) |
| decoy/sfGFP | integration of sfGFP pDR111 into the genome of B. subtilis |
Week 34: Aug 28 – Sep 3
| HP | ScienceLinX Day/BioART with students/GBB Meeting |
| Modelling/Coding | Coding + Results |
| Coding/Wiki | Wiki |
| General lab | 2.9. second order of lab needs, gBlock received |
| Integration/Lab | key gBlock received -> start of the cloning process, cloning procedure of the key into pdr111 (E.coli TOP10) |
| Kill switch/Lab | Cloning - RBS (30) + nuclease, tetR + RBS (30) + nuclease |
| Antibiotics/Lab | Ciprofloxacin-resistant B. sub. by directed evolution |
| Collaboration Wageningen | repeat plate reader experiment |
| RIVM - Safe by Design | Third Phone Call RIVM |
| CRISPR/CAS9 | Worked on design plan (e.g. primers, plasmids, labwork) |
| decoy/sfGFP | microscopy of B.subtilis+sfGFP |
Week 35: Sep 4 – Sep 10
| HP | Future Scenarios were completed/Meeting with Simone from the university paper |
| Modelling/Coding | More Literature + Autocorrecting Codes |
| Coding/Wiki | Wiki |
| Integration/Lab | transform pDR111+key to Bacillus subtilis, sequence the message obtained from spores, send spores to Wageningen and Eindhoven, time-lapse movie (germination of spores) |
| Kill switch/Lab | Cloning - tetR + RBS (30) + nuclease, tetR + RBS (30) + nuclease + 2terminator |
| Antibiotics/Lab | Ciprofloxacin-resistant B. sub. by directed evolution (experiment 1) |
| RIVM - Safe by Design | Working on product of Proposal (booklet) Safe by Design |
| CRISPR/CAS9 | Worked on design plan (e.g. primers, plasmids, labwork) |
Week 36: Sep 11 – Sep 17
| HP | BBQ/Auction/ New Scientist interview/Shooting Unifocus movie |
| Modelling/Coding | Final Fixes everywhere for Wiki |
| Coding/Wiki | Wiki |
| Kill switch/Lab | Sequencing |
| Antibiotics/Lab | Ciprofloxacin-resistant B. sub. by directed evolution |
| RIVM - Safe by Design | Working on product of Proposal (booklet) Safe by Design |
| CRISPR/CAS9 | Start cloning first steps in lab |
| decoy/sfGFP | plan sfGFP biobrick |
Week 37: Sep 18 – Sep 24
| Coding/Wiki | Wiki |
| Antibiotics/Lab | Ciprofloxacin-resistant B. sub. by directed evolution (experiment 2) |
| RIVM - Safe by Design | RIVM Meeting, Den Haag > Presentation of Product, Safe by Design |
| CRISPR/CAS9 | Start cloning first steps in lab |
Week 38: Sep 25 – Oct 1
| General | Portrait Picture |
| Coding/Wiki | Wiki |
| Integration/Lab | K823023 BioBrick received from iGEM headquarters |
| Kill switch/Lab | Start over clone RBS+nucA in pSB1C3, |
| Antibiotics/Lab | decoy experiment, clone PatpI promoter from gblock in pSB1C3 |
| Collaboration Wageningen | final plate reader experiment |
| CRISPR/CAS9 | The practialside is withdrawn |
| decoy/sfGFP | clone sfGFP in pSB1C3, sequencing |
Week 39: Oct 2 – Oct 8
| HP | Students from High School in NL BioART |
| Coding/Wiki | Wiki chill |
| Integration/Lab | clone key, message in pSB1C3, and K823023 |
| Kill switch/Lab | clone tetR+RBS+nucA in pSB1C3, send RBSnucA for sequencing |
| Antibiotics/Lab | sequence PatpI |
| decoy/sfGFP | decoy experiment FACS, microscopy |
Week 40: Oct 9 – Oct 15
| General | New team photo |
| HP | Publication in the national news (NOS) |
| Coding/Wiki | Wiki cool |
| Integration/Lab | integrate message, key in B. subtili 168, strach test |
| Kill switch/Lab | clone tetR+RBS+nucA+TER2 in pSB1C3, find incorrect suffix in nucA K729004, order primer nucA correct prefix, suffix |
| Antibiotics/Lab | MIC test - E. coli wt vs qnrS1 |
Week 41: Oct 16 – Oct 22
| HP | Interview Dagblad van het Noorden (local newspaper) |
| Coding/Wiki | Wiki freeze! |
| Kill switch/Lab | improve nucA clone it in pSB1C3 with correct prefix and suffix |
| Antibiotics/Lab | MIC tests - B. subtilis 168 (wt) vs (qnrS1) vs (resistant isolate) |
Week 42: Oct 23 – Oct 29
| General | Jamboree! |
