Team:US AFRL CarrollHS/Notebook
Week 1
Monday (06/04/18)
Lab1
The students brainstormed ideas on project goals and ideas. After briefing many ideas, the students and Mike ultimately decided to bring a “sense and attack” approach to the project. In theory, the module would be able to move naturally towards jet fuel biofilms via chemotaxis, and a higher concentration of biofilms would allow the module to swim towards biofilms before attacking the biofilm and nullifying it before it destroys the jet fuel. Researchers and students alike were excited at the idea and eager to begin the research.
Lab 2
Tuesday (06/05/18)
Lab1
In an effort to reintroduce the students the lab after the break, they began the day by making LB Media. This was also another way to ingratiate the new members of the team to become familiar with real world lab experience and excite them in pursuing the project. Later, the students spent time researching possible project ideas and ways of utilizing quorum sensing and chemotaxis. They spent the day researching in literature and beginning preliminary wiki work.
Lab 2
Wednesday (06/06/18)
Lab1
The students spent most of the day brainstorming ideas in order to host a meet-up for nearby iGEM teams. At the meeting with their mentor, the students discussed the viability of different “search and attack” mechanisms and current research being done to possibly implement into the project. The team brainstormed and looked into different ways of being able to sense fungi.
Lab 2
Thursday (06/07/18)
Lab1
The LabPats began the day by making plates with chloramphenicol resistance. The students plated their old E. coli cells from last year and letting it settle in incubation. Later in the afternoon, the students and mentors discussed the viability of their project idea and creating a basic plasmid outline to begin sequencing through IDT.
Lab 2
Friday (06/08/18)
Lab1
Early in the morning the students listened to a presentation given by Vanessa about fungal contamination on aircraft. The students were very excited as they themselves were working with biofilm contamination in aircraft fuel tanks and it was very eye-opening to listen to their own mentors talk about her own research in the area. The students were able to learn a lot and absorbed new information on how to approach their project and design their own plasmid module. Next, the plates with the old colonies from last year were put in the fridge to be grown as a cell culture on Monday. Afterwards the students began introductory MatLab courses on modelling and how to model synthetic biology in order to enhance their project this year.
Lab 2
Week 2
Monday (06/11/18)
Lab1
The day began with an early lab meeting. The goal of the meeting was to ingratiate the new members with basic lab rules and procedures. Afterwards, the students prepared a presentation about a current project proposal to present to the other half of the team as well as practicing to a few mentors who had been on vacation. Later in the afternoon, the students grew up the Prhl_GFP cells from last year and also streaked plates of a “RhlR” plasmid from Dr. Goodson.
Lab 2
Tuesday (06/12/18)
Lab1
Early the next morning, the students began by performing a mini-prep on the grown up Phrl_GFP cells in order to retrieve the plasmids. After viewing fluorescence under a UV light, they were able to determine that last year’s glycerol stock solution was still usable. Next, they picked colonies from Dr. Goodson’s “RhlR” in order to begin growing up in the incubator. After a quick lunch, the students headed to the meeting with their mentors and USAFA team in order to give a short briefing about their current project proposal and method of approach.
Lab 2
Wednesday (06/13/18)
Lab1
The LabPats began the day by performing a mini-prep on the RhlR cultures in order to extract the plasmid for later transformations and digestions. Before they could continue with their project, the students needed to find primers and utilize the Gibson Assembly in order to continue on with their plasmid design. After a long day in the lab, the students began research on the specifics of the Gibson Assembly and how to design their own primers. Annie also began preliminary Wiki work, Yazmin emailed a professor to acquire a certain E. coli strain with the CheZ gene knocked out. Jason continued learning about mathematical modelling.
Lab 2
Thursday (06/14/18)
Lab1
Dr. Breedon assisted the LabPats in designing primers and sequencing their plasmid for IDT to make. They discussed plans on trying to make their own plasmid from scratch via Gibson Assembly, as well as double checking the final product with the IDT construct. They ordered many primers and parts, like different ribosome binding sites attached to the CheZ gene.
Lab 2
Friday (06/15/18)
Lab1
Lab 2
Week 3
Lab1
The students began bright and early with their first presentation to the lab. The lab meeting included many prominent scientists from around the department excited to hear about the summer intern’s development with a new iGEM project. The team heard a stellar presentation by USAFA iGEM before giving their own and receiving praise as well. The LabPats are still currently waiting for their sequenced parts and primers to arrive before proceding with further lab work. Thus, they took this opportunity to learn more about wiki development and modelling, with Annie deciding to implement bootstrap into their wiki design.
Lab 2
Tuesday (06/19/18)
Lab1
Early on the workday, the students took the overnight cultures of the “Rhl” plasmid and tested the fluorescence level to ensure the GFP still worked and that the plasmid wasn’t corrupted. It worked exactly as intended, and the students were able to obtain great fluorescence and pictures. They wanted to have a backup for later just in case, and created a glycerol stock of their “Rhl” plasmid. They then performed a genomic sequence protocol to extract the DNA from the Rhl plasmid so that they can amplify the CheZ gene later when designing the various plasmids.
Lab 2
Wednesday (06/20/18)
Lab1
Lab 2
Thursday (06/21/18)
Lab1
With DNA sequences still coming in, the students were out of the lab for today. Today they learned a lot about DNA sequencing programs and further modelling methods.
Lab 2
Friday (06/22/18)
Lab1
The students are still currently waiting for DNA sequences to come in. Mentor Dr. Varaljay thought it would be a perfect opportunity to use NCBI Blast as a method of analyzing DNA sequences with proteins and nucleotides. She gave a quick lesson on how to use it and how to discover more about unknown surface proteins pertaining to the project.
Lab 2