Notebook

04/16/22

Brainstormed ways to build upon the Lipid A Phighter project from last year

Decided upon a diagnostic approach using phage

Built off of a conversation with Dr. Ahmer, who identified bacteriophage as a rapid way to indentify bacteria

N/A

04/06/22

Brainstormed HP ideas and looked at past winners of human practice awards

Began searching for potential sepsis contacts

05/14/22

Focused on setting up a permanent iGEM space for future teams

Secured funding from CFAES and ordered a set full set of microbio laboratory equipment

Secured permanent location in professor Rowan's lab, but couldn't be set up because of supply chain delays and issues

05/ 28/22

Began researching strong promoter sequences: a strong promoter would translate more quickly, creating more fluorophore, thus allowing sepsis to be more quickly diagnosed

05/18/22

Selected four projects to pursue

Phage-Bacteria population model

Bioreactor design

Cellular automata model to show the benefits of a phage cocktail

Sepsis detection device as a physical model that can detect fluorescence and report it

05/25/22

Each project was further planned out and it was decided what would be in and out of scope for each

05/17/22

Discussed summer camp ideas to make it more specific to our project and sepsis

Looked into potential collaborations with local teams to have a summer camp or event at science museums

05/24/22

Developed Instagram posts for general synthetic biology education

06/24/22

Found a lab space in Dr. Wood's lab in the chemical engineering department

Transported equipment from the lab used last year (microbiology department) to the new lab

Set a timeline for PCR: Satvik perform PCR over the weekend and then do cleanup and train Elijah next week

PCR clean up next week

06/27/22

Satvik finished PCR cleanup with Elijah and gel extracted all protein inserts for use in phage cloning

06/08/22

Split into teams to tackle each project concurrently

Preliminary research was conducted by each team for their selected project

06/15/22

Each team presented preliminary research for their respective projects

Presentations were analyzed and next steps for each project discussed

06/22/22

Assigned research roles for each project

Began looking into different professionals that could help provide insight into our bioreactor design

06/29/22

Researched optimal bioreactor design based on optimal pH, temperature, and agitation conditions

Discussed the ideal type of bioreactor, either a stirred tank or airlift

06/10/22

Corresponded with Wright State iGEM team to plan events at COSI/Boonshoft

06/13/22

Ryan, Emily, and Angela met with the University of Washington iGEM team to discuss our 2021 project and share both 2022 projects

06/23/22

Ryan, Fesume, and Angela video called with Wright State to form a collaboration and create more specific plans for COSI/Boonshoft

07/06/22

Elijah completed nanodrops

Satvik determined nucleic acid profiles recorded were not sufficient to continue with cloning

Satvik switched wet lab's focus to this year's clones

Promoter research led Satvik to use constitutive promoters which would not be inhibited by the bacteria

07/16/22

Satvik, Elijah, and Ankit are still the only members allowed to work in Dr. Wood's lab

Satvik ordered parts from IDT so he could begin on this year's construct

07/31/22

Satvik performed a miniprep on the lab-provided backbone but failed

Have to re-streak and attempt to re-isolate the backbone

07/06/22

Brainstormed questions to ask bioreactor specialists

Sent emails out to these specialists

07/13/22

Discussed current bioreactor design

Began research regarding each bioreactor's medium and how pH and temperature could be controlled

Began thinking about wiki design and coding

07/20/22

Discussed resarch regarding medium and controls and how to apply it to the bioreactor

Basic SolidWorks bioreactor model was created and displayed

07/13/22

Angela met with Christina Harsch to understand the Ohio Department of Education standards

Christina also helped with creating our lesson plans for our outreach events

07/21/22

Ryan, Emily, and Angela spoke with William Lynes about his challenging sepsis experience

Dr. Lynes described the lack of sepsis knowledge among patients and doctors in the hospital

From this meeting, started to brianstorm some ideas to combat this lack of knowledge

07/28/21

Ryan and Angela discussed an outreach project with Laurie Miller from COSI and the Wright State iGEM team

Decided on October 9^th for the event at COSI and finalized what synbio experiments we would do

Strawberry DNA lab, Phage puzzle, fluorescing bacteria, and a microscope activity were designed

07/31/21

Angela talked with Christina Harsch about cognitive benefits of 2D versus 3D puzzles to help us design the phage puzzle

Decided that a 2D pahge puzzle would engage more types of learners

Ryan worked on the protocol for the phage puzzle

08/06/22

Satvik is having trouble isolating the backbone and is now the only current team member in the lab

The backbone was determined to be contaminated after 2 weeks of isolation attempts

08/16/22

Satvik isolated the backbone and begane ligation process

Ligation and transformation process carried out until we have viable colonies with our contruct cloned in

08/29/22

Backbone was used up after only 2 ligation attempts

Satvik had to reisolate to ensure the backbone was fresh and not contaminated (took about 3 days to get back on track)

08/03/22

Fesume presented his finished population model

Discussed potentially using the model to predict the population of phage that is cultivated in a bioreactor

08/10/22

Emily presented further research into how to quantify fluorescence intensity using the sepsis detection device

Could use image sensors to take a picture of the petri dish and then use software to calculate intensity

Could use Beer's law and look at absorbance of fluorescence

08/02/22

Angela created a sepsis awareness poster to put in hospitals to teach patients about sepsis and how to prevent it

08/15/22

Angela updated activity protocols for the science museums

08/21/21

Angela reserached ICU pyschosis and post sepsis syndrome

08/26/21

Fesume, Angela, Ryan, Elijah, and Kaya recorded the promotional video

09/10/22

Satvik is still attempting ligations for bacterial clones

Attempt 3 and 4 failed: after consulting with Sophia and Nate, Satvik re-streaked and re-isolated the backbone to ensure he was using fresh DNA for his ligations

The grad students recommended that Satvik do this before all future attempts

Attempts 5 and 6 also failed: Satvik used a newer T4 ligase buffer from New England Biolabs in case an expired buffer was to blame

Thus far, all attempts proved negative, with every attempt having no colony growth

N/A

09/10/22

Fesume 3D printed the 2D phage puzzle to use at Boonshoft and COSI

09/25/22

Angela, Fesume, and Ryan traveled to the Boonshoft Museum alongside Wright State to teach listeners about DNA, synbio, and sepsis

10/02/22

Satvik continued to attempt cloning with no success

Attempt 7: grad students suggested using a backbone isolated from a different strain

Swtiched from pET28a backbone to a pET29a backbone

10/09/22

Attempt 7 failed, leaving wet lab without results or proof of concept

N/A

10/09/22

Angela and Fesume traveled to COSI with Wright State to educate visitors about synthetic biology and sepsis

09/25/22

The strawberry DNA protocol was posted on Instagram to allow others to conduct this experiment at home