Team:Peshawar/Notebook

iGEM Peshawar

Notebook

Click on each week to expand read about them!

Arrival at IIB at 9 AM
Interactions with the team and our mentors
Toured the department and the lab.
Team divided into two groups for an activity to design a device which will save the egg if
dropped 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 discussed
during 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 importantly
the 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 alternatives
to 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 discussed
about 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 and
Outcomes”.
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 our
efforts 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 lab
2. Team wiki
3. Awards page on wiki
4. Requirements for Gold Medal
5. Blogs & What Ifs
Formulated 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 study
2. New functional biobrick
3. Meaningful collaboration
4. Is the project safe, responsible, and good?
5. Input from modeling
6. Optimize new parts
7. Does it work?
Performed:
1. Transformation
2. Competent Cell Prep
3. Antibiotic plates for selection
Quiz about general lab work and problems
Diaries were submitted for checking
Received 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 Diego
2. Team Mexico
3. Team Pasteur
Brainstorming on ideas.
Team interviews and photo sessions with Mr. Jawad
Team 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 Electrophoresis
2. Restriction Digest
3. PCR
Discussed 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 impact
and role in the field of health and medicine.
Skype:
1. Team Pittsburg
2. Team Postdam
Four 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 presentation
2. Do It Yourself (DIY) DNA Extraction
3. Interviews
4. Ideas Challenge

Looked for parts in kit plates
1. Part A: RBS + CDS + T (codes yellow color)
2. Part B: Promoter with repressor ArsR
Performed PCR of following things:
1. PCR of
a. Cadmium promoter
b. Arsenic promoter and composite part
c. Ligated products using prefix F suffix R
d. dNTPs to check contamination
e. Colony PCR
2. Media prep for competent cells, Miniprep, broth for culture of Ars cells
3. Gel Electrophoresis
4. Sub-culturing for BioArts
5. R.D
a. Ars Promoter
b. CDS
c. Plasmid
6. Competent Cell Prep
7. Ligations
a. Parts with plasmid in varying concentrations
8. Autoclave
Had a lecture with Dr. Sohail on expression systems and reporters.
Discussed notebook design for wiki
1. 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 plates
Transformations 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

Performed
1. Digestion of miniprep of Arsenic device.
2. Gel Electrophoresis of R.D products.
3. Prepared samples for interlab study.
4. Prepared Master Mix for PCR
Meeting 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 resuspension
b. DNA sample 1.0 ul instead of 0.5 ul
c. 300 ul SOC media instead of 400 ul.
2. Ligations
3. Miniprep
4. Gel Electrophoresis
5. Restriction Digest
a. Hg device
b. Cd Promoter
c. YFP
d. D.D of RFP
All 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 YFP
i. With plasmid
ii. Without plasmid

2. PCR:
a. Hg-Hg ligated product
b. Colony PCR
i. RFP 2

3. Media preparation for salt testing
4. Salt solution preparation
Checked 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 literature
2. Cd device basic part ligation
3. IDDP Theory
Performed:
1. PCR
a. 1N (RBS) with pSB1C3
2. Restriction Digest
a. S.D of pCadA and RBS
b. D.D of pSB1C3
c. D.D of 7G (pCadA) and 1N (RBS)
3. Ligation
a. 7G (pCadA) with 1N (RBS)

Gel Electrophoresis
iGEM Peshawar 2017 Survey is online.
Talk session at Rehman Medical College (RMC) on Synbio and applications in health and
medicine.

Performed:
1. Competent cell preparation
2. Ligation
a. 10O + 6P
b. 10O + 6P*
c. 10O + 7J
d. 10O + 7J*
e. IDT parts (merR, Lilac CDS, PnsrB) with pSB1C3
3. Transformations
Fish Farm visit to discuss about our integrated human practices
Part submission DONE!

Performed:
1. Antibiotic media preparation
2. Gel Electrophoresis
3. R.D of pSB1C3Prepared antibiotic media
Meeting with Dr. Faisal regarding:
1. Questionnaire designed to analyze people’s response towards SynBio products
2. What Ifs campaign
3. Updates about current progress and future line of action regarding project
4. Need to read some articles

Performed:
1. R.D
a. Cd device
b. RFP
c. 3G
d. RFP 2
2. PCR
3. Ligations:
a. RFP
b. 3O + YFP
c. RFP 2 + pSB1C3
d. Cd device
Gel Electrophoresis

Performed:
1. Restriction Digestions
a. P2 ligation device
b. 1O (Hg device)
c. YFP
d. RFP 2 Miniprep
e. 3F (terminator)
2. Ligations
a. 1O + YFP + pSB1C3
b. 1O + YFP
3. PCR
a. 1O + YFP
i. With Taq
ii. With Q5
b. RFP 2
i. With Taq
ii. With Q5

Gel Electrophoresis
Meeting 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 Digest
a. D.D of composite part 6P (RBS + YFP + TT)
b. D.D of 10O and 6P
c. D.D of 7G (pCadA), 6P and 7J
2. PCR
a. 7G (pCadA)
b. Ligation products
i. 10O + 6P + pSB1C3
ii. 10O + 7J + pSB1C3

3. Ligation
a. 10O + 6P
b. 10O + 7J
c. 10O + 6P + pSB1C3
d. 10O + 7J + pSB1C3
4. Transformations
Prove IDDP Theory by checking O.D every 30 minutes. RFP 2 expresses color first.
Gel Electrophoresis
Discussions
1. IDDP Theory
a. Graphs
b. Tables
2. Part Improvement
3. Project Improvement
4. Protocols page for wiki.