NavBar

Notebook

Below you will find an overview of the major deliverables, decisions, and brainstorming from each week of our project timeline! Each date is for the week of.

Wet Lab

03/03/21

Bacterial-induced sepsis is the overreaction to a lipid A, a portion of an endotoxin in the bacterial cell membrane. This could be targeted using synthetic biology techniques to neutralize the harmful effects.

Our plan was to insert a phage vector containing a trp promoter into E.coli until we want it to be lytic

Dry Lab

HP

02/01/21

Partnered with SJMS to design 5 days of summer camp materials

03/01/21

Hosted a global meet-up on zoom with over 23 teams present. This allowed teams to swap project ideas and collaborations

04/20/21

Presented our project pitch to ID SCOPE (At the Ohio State University)

Wet Lab

05/03/21

Decided to use FraR so that the system will be off in our lab E. coli and on in wild E. coli to prevent expression of toxic genes.

Dry Lab

05/10/21

Decided which parts of the Model criteria we might be able to fill

05/17/21

Looked into modeling in general

Discussed emailing an OSU professor who teaches modeling (Dr. Friedman) as well as the William & Mary iGEM team as they won best model last year

05/24/21

Discussed the general idea of models

Made sure everyone had Matlab downloaded

Emailed William & Mary iGEM team as they won best model last year for ideas on how to structure our modeling plan

HP

05/10/21

Discussed medal criteria options

Discussed timeline and expected progress in this summer

Start brainstorming for summer camp ideas

05/17/21

Present summer camp ideas in committee meeting these included a strawberry DNA lab and a transformation lab

Met with Evan Boylan from SJMS to update him on our summer camp plans

05/24/21

Committee members presented their own summer camp activities and suggestions (i.e. epidemiology experiment along with how to write up the protocols)

Organize summer camp schedule and materials. We have 7 different protocols to divide over 5 days.

Ryan tested the Strawberry DNA lab at home and found it was successful even without a strainer as long as most of the strawberry chunks did not get into the final solution.

Wet Lab

06/14/21

Met Dr. Gunn and was advised to get rid of eukaryotic protein modifier for lipid A due to difficulty of expression

06/28/21

Cloned Promoters in TOPO

Dry Lab

05/31/21

Dove into more detailed model ideas including genetic circuit, enzyme kinetics (divvied up each enzyme to members to find kinetics), and start to end model of a phage therapy treatment

Discussed professionals to reach out to and had email drafts due at the next meeting

06/07/21

Reviewed email drafts

No one found kinetics of their enzyme binding to lipid A. We were advised it would be difficult to calculate and test kinetics in lab (that would defeat the purpose of modeling anyways)

Erin introduced the idea of using docking to investigate the best protein to use

Everyone will try to find crystal structures of their respective proteins to be used in docking

06/14/21

Crystal structures were found for most of the proteins

Satvik and Ryan met on June 20th and came up with a plethora of model ideas. Marked plausible and pleasant ones in the meeting this week

Each member was assigned a model to look more in depth into

06/28/21

Met with Austin Cool, a graduate student who works with computational biology specifically with docking. We learned that Docking scores cannot be compared between different proteins with the same molecule. So, we can’t compare our binding proteins, but we could compare a single protein and different molecules.

For the binding proteins we could generate contact maps which show the parts of the protein binding to the molecule. This could show important binding interactions that make a good/strong lipid A binder

Presented model proposals: Catheter, Bacteria evolving to be phage resistant, Phage database, Phage therapy modeling with immune system, Docking using crystal structures

HP

05/31/21

Continued presenting summer camp activities to HP committees

Discuss summer camp logistics

06/07/21

Host summer camp at SJMS

Met with FCB_UANL iGEM to discuss a collaboration where we expand on our regulations work from last year.

06/14/21

Brainstormed interviewing patients of sepsis and physicians to target communities and professional perspective

Met with MSU iGEM to offer our advice from our experience working with regulatory work and biocontainment last year.

06/28/21

Met with FCB_UANL (regulation) to discuss how phage therapy could be implemented into other countries, and determine what regulations hinder application of engineered phage therapy

Met with Rochester (children book). Planning on running a panel together during Sepsis Awareness month. We also want to create a children’s book about sepsis. They are also reaching out to physicians and patients so we thought it would be a great opportunity to exchange notes.

Wet Lab

07/5/21

PCR Verification of the Clones

Digestion of TOPO clones

Ligation into reporter plasmid

Dry Lab

07/5/21

Discussed model ideas and narrowed it down to catheter, genetic circuit, docking, and phage database

Completed a quick worksheet for next meeting outlining, inputs, outputs, what medal criteria the model will meet, and how the model will help the overall project

Went over more wet lab concepts on how the phage will actually be working included learning that we have proteins that competitively bind to lipid-A and some that modify it.

Finalized the above 4 selected models

Met with William and Mary iGEM to gain their perspective on how to set up a good modeling project. We found they distribute the work to a primary person, and everyone has a secondary model they help out with. This is similar to how we have been doing it.

07/12/21

Started models and talked about any roadblocks or questions

Set up format of meetings in the future, everyone bringing an update presentation of the work they have done and where they are

Creating github accounts so Lizzie can share her code with us

07/19/21

Database: get units for columns and reach out to phage database to see how they gathered everything

Docking information: Make colorful, neat, and easier to see

Genetic Circuit: Look into low, medium, and high rate ranges

Catheter: keep looking into catheter designs

07/26/21

Database: keep getting units and information to add

Docking: Meet with Austin about docking and attempt an actual simulation

Catheter replacement: look into the business avenue instead of catheter

Met with Dr. Mandell, who mentioned that docking would not give useful outputs due to the approximations required.

Officially dropped catheter idea after meeting with Dr. Adkins and Dr. Mandell

Brainstormed other outside excellence ideas

Dr. Strathdee recommended a database that included receptors of each of the phage targets.

HP

07/12/21

Outreach team: reach out to Dr. Crouser and one patient related to a team member

Regulation team: Continue revising and meeting with FCB_UANL to discuss regulation proposal

07/19/21

Outreach team: Updated email content with Dr. Crouser and Dr. Adkins

Decide library meet up time for children’s book idea

Communicate with Rochester that each of the teams will write-up a draft for the storyline.

Met with Dr. Adkins, a physician in the ICU. We found that a lot of ICU cases involve sepsis, and catheters are a huge risk. However catheters are too off topic from our project so we have decided not to pursue this project further.

07/26/21

Dr. Mandell encouraged our children’s book idea saying “a good way to appeal to adults is through their children”. He also recommended reaching out to the FDA for our regulations work.

Met with Dr. Strathdee and Dr. Patterson, the author and patient of the book “The Perfect Predator”. Dr. Strathdee also mentioned contacting someone at the FDA to gain insight into our regulations work.

Wet Lab

Isolated digested inserts in preparation of phage cloning

Continued to characterize promoters

Due to COVID-19 delays, the phage cloning kit won’t be here for a couple months. We decided to attempt traditional phage cloning

Dry Lab

08/2/21

Gene circuit: waiting on wet lab data to flush out our model

Database: still being filled out, looking into professional database options

Bacteria model: reading and deciphering the paper Dr. Vatsan sent us

08/16/21

Met with Dr. Debnath to discuss model ideas. He confirmed that docking is not an effective route for a model. And recommended a bacterial mutation rate model instead.

Dr. Debnath also suggested ordering the database on the bugs that are most common or popular.

Dr. Raman supported pursuing a model between phage and bacteria and how they evolve together while comparing the effect on various conditions. He thought a mutation model would be less effective due to the high random chance.

HP

08/9/21

Dr. Debnath recommended regulations incorporating aspects such as upscaling and cost.

08/16/21

Met with Brooke Zentmeyer, an OSU law student to discuss our regulations work. She proposed structuring it like a petition with parts that include action items and an objective.

Wet Lab

09/13/21

Isolated unmodified phage vector

Digested phage DNA

Ligation in phage clones

Unsuccessfully screened for phage clones

Dry Lab

08/30/21

Continued work on the phage database

09/13/21

Met with William and Mary iGEM team who recommended looking into epidemiology models (SIR compartmental model) to address why our population control modeling is not showing the expected results.

Worked towards getting experimental data for the genetic circuit model

09/20/21

Made progress on the phage-bacteria system

HP

09/13/21

Completed the illustrations for the children’s book to be ready for review by friends and family

Presented at Rochester Symposium to raise awareness on Sepsis

Wet Lab

Switched to backup plan and lysed clones with anti-lipid A proteins expressed

Tested clone lysates on LAL Assay

Unsuccessful cloning continued

Dry Lab

Met with Dr. Rathman to check to make sure we correctly coded the ODE. Also discussed how to handle the S prime and P prime terms in the system of ODEs

Talked with Dr. Raman about the prime terms and ways to get around them

Worked with Dr. Rathman again to come up with a way around the prime terms using a mass matrix

Finalized model using a steady state assumptions and outputted graphs

HP

Team Operations Timeline

Below you will find our yearly project timeline and materials we used to keep our team organized. We hope that future teams can use this information to structure there teams in a way to complete their project on time and maintain an organized team.

Time Period	Action	What happens	Purpose
December	Recruitment	Create google survey of an application that includes name, major, year, and an essay that shows literature reading and writing capabilities and creative ideas	Limits the number of applicants so we can find the individuals best fit for our team
		Post application on social media, ask professors to send it out	Promotes the team existence and campus awareness
		Deadline is due first Sunday of January, the following week will be hosting interviews for those whose applications matched our criteria	Practices professional development and simulates an actual job interview. Also an opportunity to meet the applicants face to face
January	Meet the team	Host interviews and our first meeting. This time is used to meet the team and gather necessary information. We also introduce them to our platforms we use: Slack, google drive, zotero, and benchling	An introduction to keep our team organized and everyone knows how to communicate and save research findings
February	Welcome to iGEM	Medal Criteria overview	An introduction to the vast idea of iGEM, which is a lot to explain to someone who has no background in it.
	Welcome to iGEM	Past project presentation	This is our first 'assignment' where we pair a new member with a returning member as a sort of mentor/mentee system. This allows new members to explore what previous teams have done and to start generating ideas for our project. Also practices professional development presentation skills. Also gives members a personal connection to someone on the team which is especially hard because we were meeting online
	Brainstorm	After getting a deeper understanding of what iGEM is and what can be done, we begin to brainstorm. We start by having students look for problems that could be addressed, interesting things about science, and anything else that just gets ideas out there. We will then begin to research and narrow down our options by determining what's feasible and what is the largest issue at hand.	Get ideas down for possible iGEM projects to look into
March/April		We narrow down our choices based on everyone's interest. This year we had everyone draft a proposal that included project background, what we would do, and what impact this project would have. We then take the projects that members wrote their proposal on and vote to narrow down to 2 or 3 project ideas.	Determine who is interested in what and to see which ones are our top choices
March/April		After splitting the team based on interest for our top 2 or 3 project ideas, we spend the next month meeting with professionals and finding more research that supports the feasibility and purpose of our top project choices. To conclude this phase teams will submit a written proposal (more in depth that before), project timeline, and create a project presentation that is presented to our entire team and the attendees of an Infectious Disease SCOPE meeting at the Ohio State Battelle Center	Go really in depth into our top choices to see which one is best
May	Project	School has ended and we've voted on our top project choice from the presentations taking into advice from our advisors and ID scope. We then split our team into committees (wet, dry, HP, visual) and go more in depth to planning out our summer
Summer	Meetings	We have a weekly general meeting where everyone attends to discuss team progress and expectations, what is happening in each committee, and then we have a discussion on any troubles each commiittee is having or if they have any work to present
	Meetings	Each committee will have meetings based on material (wet lab generally has 2), Dry and HP has 1, and visual tends to be every other week
	Expectations	To keep everyone accountable and on top of things, and as a way to check our team progress and monitor where everyone's time is going we have everyone filling out weekly timesheets that include hyperlinks to the materials they worked on, a short description, and the hours they spent on that item
	Useful documents	Common documents that we have used throughout the summer are the timesheet spreadsheet where you can download the excel template here (we converted ours to a google spreadsheet to host on our shared Drive). You can also download an the Agenda template we used for our general meetings here. As a large part of the iGEM competition is documenting our project, we have created an excel file that keeps everyone accountable to have an even share in the write-ups. This spreadsheet automatically marks cells when an assignment is late, and records how many write-ups each member has signed up for. This can be downloaded here. Once downloaded it would need to be converted into a google spreadsheet file and the cells with FALSE should be changed to a check box.

Below are examples of our useful documents that we have used to keep our project deliverables organized and no information is lost. The timesheets were especially helpful in keeping track of what each member is working on and how much time spent on each item. This helps make sure we are spending our time where it needs to be. The excel file makes seeing where are time is going easily because it automatically compiles everyone's hours into one graph, but one could still go into each person's timesheet to find the links to the work they focused on that week.

We used the agenda template shown below for our general meetings to keep our meetings organized, on track, and to avoid loosing any ideas or topics addressed at the meetings. We recommend including an agenda that contains topics to be addressed and a action items list to keep everyone aware on what to focus on for that week.

Lastly, we organized a spreadsheet to make dividing the wiki documentation easier. We value this experience of learning how to document the project's progress and wanted to ensure each member got experience! The spreadsheet contains automatic functions that tally how much a person has signed up for, and will turn the cell red when an assignment is marked late.