Notebook

Here you can follow our team's journey from our first meeting to our final week.

Week 49 2018

We had our first meeting! The team members were introduced to each other and to our PIs. We are all very excited to be apart of LiU iGEM 2019!

Week 50 2018

We had our second meeting this week. The team was introduced to the different groups they could be apart of. For our team, this includes Laboratory work, Human Practice, Wiki, and Modeling. We also discussed what the next year’s project was going to be.

Week 51 2018

This week, we have started to look into antimicrobial peptides. Currently, we are planning on having a project that revolves around this. We also talked about how we can integrate Vibrio natriegens as a chassis for this year’s project.

Week 5

We have started to read up on the laboratory methods, and how plasmids are designed.

Week 6

We have decided to focus our project on antimicrobial peptides.

Week 7

We have reached out to companies that work with antimicrobial peptides in order to gain feedback on our project. We also had a plasmid design meeting and talked about different parts of plasmids.

Week 10

We have made our first models for antimicrobial prediction. We have had our first meeting with Dr. Johan Junker from the Center for Disaster Medicine and Traumatology (KMC). We discussed our project and received important feedback.

Week 11

We have had our first meeting with Mårten Skog, COO from S2Medical, a local company specializing in wound treatment and healing. We have also started to prepare for the Nordic iGEM Conference.

Week 14

We have talked to first responders (EMTs) in order to learn about burn care. Even though our project focuses more on the healing process it's good to gain an understanding of the entire process of burn care. We have also visited the Burn Care Center (BRIVA) in Linköping and talked to the research experts and staff. They supplied us with a cellulose bandage that we could use in our experiments.

Week 15

We have decided on which specific peptides we want to analyse. The peptides that were chosen were LL-37, Magainin 2, PlyF307, Pln1 and LysK.

Week 16

We had our laboratory safety introduction. We have also ordered one of our DNA sequences CBD-asPink.

Week 21

We attended the Nordic iGEM Conference. Where we met teams from all over the northern part of Europe. During our time there we connected with other teams, exchanged ideas and enjoyed good company. The conference also included an "iGEM-like" competition where the teams presented their project ideas and were judged. Our project managed to win the "Judges' Award" and good times were had. We look forward to meeting the teams again in Boston and seeing their progress.

Week 23

Summer has begun!! We are thrilled to initiate our lab work! We started with the cloning process of the CBD-fusion protein and then continued working with the selection plasmid (CBD-pCons AsPink). However, no ligations were successful this week.

Week 24

We redid all our ligations and tried different restriction enzymes. Still no success. Through Linköping University, some of our team members were involved in leading experiments for young students in the 7th and 8th grades, as part of a Summer Science School Program. The experiment was DNA extraction from bananas and we also talked about synthetic biology and what we aimed to accomplish with our research. During a Skype meeting with Aalto-Helsinki iGEM Team we engaged in some troubleshooting regarding our projects, how to use V.natriegens, what antibiotics and backbones to use for V.natriegens and much more. We also decided to switch parts for verification.

Week 25

We have tried new methods this week since we have had problems with the ligation processes. Troubleshooting regarding our failed ligations were conducted. We have also ordered our model peptides from Caslo which they provided us as a sponsorship.

Week 26

We realized that the overhangs in our inserts were too short and that this created problems for ligation. We therefor ordered new primers with longer overhangs and in the meantime continued with different ligation attempts. We tried "Gibson Assembly" and successfully ligated CBD-AsPink. A large culture was done for protein production. We then ran a cellulose binding assay and thrombin activity assay.

Week 27

We successfully ligated some of the antimicrobial peptides with the cellulose binding domain (CBD). The first episode of our podcast is out! Take a look!

Week 28

We have produced the antimicrobial peptides fused with CBD and started to prepare for antimicrobial activity assays. We were contacted by Bilkent-UNAMBG iGEM Team regarding a collaboration. They had written a children's book that talked about how synthetic biology can be used to make our lives better. We translated the storybook to Swedish so that the message could reach people and children in Sweden as well. The book has also been translated to other languages and is able to reach people in many different countries.

Week 29

This week, we have continued experiments with the antimicrobial peptides that had not successfully been ligated. SDS-PAGEs were conducted in order to confirm all the steps in thrombin cleavage assays activity of sfGFP. The protein production of the antimicrobial peptides fused to the cellulose-binding domain was initiated, and the activity of the model peptide Parseq beta was tested in the lab. The second episode of our podcast is out! We also conducted a phone-interview with the former fire fighter Lasse Gustavsson, who survived a major burn trauma. Listening to his stories and experiences was very insightful and humbling. Take a look!

Week 30

We tested the binding capacity of the cellulose bandage, this was measured with sfGFP as a marker. The antimicrobial activity of PlyF307 was analysed. Our mNG improvement was analysed and compared with the original part. New stocks of the antimicrobial peptides were produced. The activity of the model peptide Parseq alpha was tested in the lab.

Week 31

This week we tested the antimicrobial activity of Pln1. LL37 and Magainin 2 was purified. Ligation and colony-screening of the model parseq peptides were conducted. Induction series of sfGFP and mNG was conducted. The fluorescence of EforRed was measured. Thrombin cleavage of LL37, Magainin 2, Pln1 and PlyF307 were analysed on an SDS page. LL37, PlyF307, Magainin 2 and Pln1 was cloned into pUC19 and sent to Aalto-Helsinki iGEM Team. During this week we also had the wonderful opportunity to visit the Burn Care Center (BRIVA) in Linköping and observe the the care and treatment of burn wounds. During this visit we talked with the staff, observed the changing of wound dressings and watched a transplantation with skin grafts. The third episode of our podcast is out! Take a look!

Week 32

We have analysed the antimicrobial activity of LL37 and Magainin 2. Induction gradients of sfGFP were conducted. New attempts on LysK cloning was conducted and CHAP was cloned and placed in pSB1C3 and pUC19. The binding of the amorphous cellulose was analysed. The antimicrobial activity of the recombinant parseq peptides was analysed, however these experiments failed.

Week 33

We investigated the antimicrobial activity LL37, CHAP, Magainin 2, Pln1 and PlyF307 on B.subtilis to determine their effect on gram-positive bacteria. A new CBD purification method was investigated. The fourth episode of our podcast is out! Take a look!

Week 34

We started to analyse the antimicrobial activity of the peptides without the cellulose binding domain attached to the peptide.

Week 35

We talked about our project and LiU iGEM at the annual welcome fair for new students. During this week some of our team members also headed down to the Linköping City Festival. There we handed out informative pamphlets regarding antibiotic resistance and the threat it poses to medicine and society. It was great to talk to people in the community about this major problem. The fifth episode of our podcast is out! Take a look!

Week 36

We have started to analyse the activity of the antimicrobial peptides when they are attached to the cellulose bandage. Our assay is meant to mimic the release and activity of our peptides in the wound. Results look dandy!

Week 37

We have, as all other iGEM teams, handed in our safety from. The sixth and final episode of our podcast is out! Take a look!

Week 38

We are conducting some of our final experiments and we are working hard on our text for our wiki page.

Week 41

We have received word from Aalto-Helsinki iGEM Team that they succeeded in verifying our sampels that we sent to them. Unfortunately, their samples did not reach us in time. Bilkent-UNAMBG iGEM Team sent us the finished, illustrated storybook and now it can be view on our wiki under collaborations.

Week 42

We have been working hard on our wiki texts and we have just had a practice presentation of our project at our univeristy. A lot of people showed up and we received great responses and feedback. We had a really good time and now we are very excited for Boston and looking forward to meeting you all!