Arrival at IIB at 9 AMInteractions with the team and our mentorsToured the department and the lab.Team divided into two groups for an activity to design a device which will save the egg ifdropped from two storey building.Sketch our life on charts and then present it.Received goodie bags.Met our PI Dr. Faisal. Delivered an inspiring and motivational lecture.Discussed “Fundamentals of Synthetic Biology”Social Media 101 Lecture with Mr. Jawad.Team divided into three groups and tasked to make a video using the tips and apps discussedduring the lecture.
Lecture on “Tips and Guidelines about iGEM” by Co PI Mr. Adnan Niazi.Division of labor amongst the team regarding all the aspects and sections of the wiki and beyond.Presentation of each group about their respective idea.3 ideas selected via voting which will be going to the next round.Lit sky lanterns at the end of the day.Final pitches attended by Dr. Faisal.Selected “Bio-reporter Fish” as our project idea for iGEM 2017.Work meet at McDonalds to discuss about the project and its details.First day in the lab.Welcomed by Dr. Faisal. Delivered a lecture on lab safety, the traditions and most importantlythe lab honor code.Lab Safety Training started.Sarah, our mentor, explained all the basic procedures performed in the lab.Team divided into two, each performing Miniprep for practice.Received our DNA Distribution Kit along with a lot of cool goodies.Team investigated and searched for all the parts required for the project and also its alternativesto prepare a catalogue.Learnt about Gel Electrophoresis and performed it.Performed Classic Miniprep in groups of 3.Skype with Team Sweden.
Meeting with Dr. Faisal about Human Practices and Outreach.Discussed about the recently attended Makers Fest event at Lahore. Afterwards discussedabout the deliverables required for medals.Division of labor called by Dr. Faisal in order to work more efficiently.Each group prepared a plan for their respective work in form of “Objectives, Activities andOutcomes”.Skype session:1. Team Uppsala. They invited us to join them at their webinar.Performed MiniPrep using NEB Monarch Kit Method.Met with Mr. Syed Mahmood Nasir, Inspector General Forestry of Pakistan. Acknowledged ourefforts and also offered his support.Announcement of KP Summer Camp in the following week.Different teams will travel to different cities for their outreach sessions.Preparation for Summer Camp over the weekend.
Optimized the protocol for Restriction Digest.Discussions:1. Current progress in lab2. Team wiki3. Awards page on wiki4. Requirements for Gold Medal5. Blogs & What IfsFormulated plans for our Human Practices and what things would we target.Talked to a few food chains regarding our Human Practices plan.Meeting with our PI Dr. Faisal today.Following are things we should look for:1. Interlab study2. New functional biobrick3. Meaningful collaboration4. Is the project safe, responsible, and good?5. Input from modeling6. Optimize new parts7. Does it work?Performed:1. Transformation2. Competent Cell Prep3. Antibiotic plates for selectionQuiz about general lab work and problemsDiaries were submitted for checkingReceived a Case Study: Elon Musk
Lecture with Dr. Sohail on “History of Molecular Biology”Worked on different ideas for our final project.Lab diaries received today.Omar Zeb, a team member gave lecture on Microfluidics.Skype sessions:1. Team San Diego2. Team Mexico3. Team PasteurBrainstorming on ideas.Team interviews and photo sessions with Mr. JawadTeam meeting regarding outreach and human practices.Extensive research about the project and its applications.Discussion with Dr. Faisal regarding our ideas.Three-minute pitches in front of Dr. Faisal and a chief guest from San Francisco, USA.Met with Dr. Nadhman.
Performed:1. Gel Electrophoresis2. Restriction Digest3. PCRDiscussed plans and ideas for unique Human Practices activities.Discussed ideas about our official logo.Interaction with a team of medical students from RMC, discussing about SynBio and its impactand role in the field of health and medicine.Skype:1. Team Pittsburg2. Team PostdamFour members of the team went to Lahore to attend Makers Fest event.Rest of the team prepared for outreach session at a local school in Peshawar.First local outreach session for iGEM Peshawar 2017 at Peshawar Model School, Dalazak Road.Presentation regarding SynBio followed by DIY DNA Extraction using Kitchen Protocol.Reading and discussion on biosafety.Quiz related to our respective perspective on different aspects of our own selves and life.12 duties in the lab distributed amongst the team.
KP Summer Camp week.Team travelled 6 divisions in KP in 4 groups.Combined we visited a total of 11 schools and travelled almost 2075 km, reaching out to 1280+people in these 5 days.Activities:1. SynBio presentation2. Do It Yourself (DIY) DNA Extraction3. Interviews4. Ideas Challenge
Looked for parts in kit plates1. Part A: RBS + CDS + T (codes yellow color)2. Part B: Promoter with repressor ArsRPerformed PCR of following things:1. PCR ofa. Cadmium promoterb. Arsenic promoter and composite partc. Ligated products using prefix F suffix Rd. dNTPs to check contaminatione. Colony PCR2. Media prep for competent cells, Miniprep, broth for culture of Ars cells3. Gel Electrophoresis4. Sub-culturing for BioArts5. R.Da. Ars Promoterb. CDSc. Plasmid6. Competent Cell Prep7. Ligationsa. Parts with plasmid in varying concentrations8. AutoclaveHad a lecture with Dr. Sohail on expression systems and reporters.Discussed notebook design for wiki1. Road timeline (ushma)2. Coral reef design (Dawood)Samples of RD were run on gel. All results were positive.Prepared transformations for inter-lab study.Cells then plated on petri platesTransformations for inter lab were checked. We got positive results as well.Results of competent cells after 17 hours were observed.Results of PCR not satisfactory, now moving forward with broth miniprep and then RD.Troubleshooting of ligation carried out
Performed1. Digestion of miniprep of Arsenic device.2. Gel Electrophoresis of R.D products.3. Prepared samples for interlab study.4. Prepared Master Mix for PCRMeeting with Dr. Faisal regarding interlab study and human practices.Logo designs discussed by the team.Two members of the team went to NUST, Islamabad to complete Interlab study.Meeting with Dr. Faisal, discussed about the informative booklet plan and the what if campaign.
Performed:1. Transformation was done using the same protocol but a few minute changes:a. 10 ul DNAse fresh water in plate for resuspensionb. DNA sample 1.0 ul instead of 0.5 ulc. 300 ul SOC media instead of 400 ul.2. Ligations3. Miniprep4. Gel Electrophoresis5. Restriction Digesta. Hg deviceb. Cd Promoterc. YFPd. D.D of RFPAll plates showed positive results.Gel Electrophoresis to check results.Work on Sponsorship Proposal also started.Received package from Team in Taiwan for testing their device.Study about mercury chloride salt solution preparation to test our Hg device.
Performed:1. Ligations:a. Hg promoter and YFPi. With plasmidii. Without plasmid
2. PCR:a. Hg-Hg ligated productb. Colony PCRi. RFP 2
3. Media preparation for salt testing4. Salt solution preparationChecked OD of broths with different ppm salts.Gel Electrophoresis
Tasks specified to three members in the lab by Dr. Faisal.1. Arsenic device working ppm literature2. Cd device basic part ligation3. IDDP TheoryPerformed:1. PCRa. 1N (RBS) with pSB1C32. Restriction Digesta. S.D of pCadA and RBSb. D.D of pSB1C3c. D.D of 7G (pCadA) and 1N (RBS)3. Ligationa. 7G (pCadA) with 1N (RBS)
Gel ElectrophoresisiGEM Peshawar 2017 Survey is online.Talk session at Rehman Medical College (RMC) on Synbio and applications in health andmedicine.
Performed:1. Competent cell preparation2. Ligationa. 10O + 6Pb. 10O + 6P*c. 10O + 7Jd. 10O + 7J*e. IDT parts (merR, Lilac CDS, PnsrB) with pSB1C33. TransformationsFish Farm visit to discuss about our integrated human practicesPart submission DONE!
Performed:1. Antibiotic media preparation2. Gel Electrophoresis3. R.D of pSB1C3Prepared antibiotic mediaMeeting with Dr. Faisal regarding:1. Questionnaire designed to analyze people’s response towards SynBio products2. What Ifs campaign3. Updates about current progress and future line of action regarding project4. Need to read some articles
Performed:1. R.Da. Cd deviceb. RFPc. 3Gd. RFP 22. PCR3. Ligations:a. RFPb. 3O + YFPc. RFP 2 + pSB1C3d. Cd deviceGel Electrophoresis
Performed:1. Restriction Digestionsa. P2 ligation deviceb. 1O (Hg device)c. YFPd. RFP 2 Miniprepe. 3F (terminator)2. Ligationsa. 1O + YFP + pSB1C3b. 1O + YFP3. PCRa. 1O + YFPi. With Taqii. With Q5b. RFP 2i. With Taqii. With Q5
Gel ElectrophoresisMeeting with Dr. Faisal about the deliverables, what if cards and general survey.Redistribution of tasks amongst the available team members.
Report to Dr. Faisal on content for wiki.Performed:1. Restriction Digesta. D.D of composite part 6P (RBS + YFP + TT)b. D.D of 10O and 6Pc. D.D of 7G (pCadA), 6P and 7J2. PCRa. 7G (pCadA)b. Ligation productsi. 10O + 6P + pSB1C3ii. 10O + 7J + pSB1C3
3. Ligationa. 10O + 6Pb. 10O + 7Jc. 10O + 6P + pSB1C3d. 10O + 7J + pSB1C34. TransformationsProve IDDP Theory by checking O.D every 30 minutes. RFP 2 expresses color first.Gel ElectrophoresisDiscussions1. IDDP Theorya. Graphsb. Tables2. Part Improvement3. Project Improvement4. Protocols page for wiki.