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Notebook

Following is the journal containing information regarding our weekly activities from the beginning to the end of the cycle:

We ordered our DNA aptamers from IDT as two µmole DNA oligo in standard desalting conditions. We resuspended the lyophilized aptamer with 0.1 molar PBS. Then we measured the Cyclic voltammetry and impedance of the bare Glassy Carbon electrode before modifying it with GO/PANI solution.

Ideation Stage

  • May 3 – May 7, 2023
    1. Final Team Formation and Role Assignment.
    2. Consultations with Mentors, Advisors, and Instructors for Project Discussion.
    3. The Wet Lab team started looking for the literature on DNAzymes.

  • May 8 – May 14, 2023
    1. Sub-Team Creation for Project Initiatives.
    2. Human Practices and Outreach Team Goal Setting.
    3. Conversing about overall operational details and anticipations.

  • May 15- May 21
    1. The fundraising team started their search for sponsors.
    2. Team had a meeting for how to do collaboration and started looking for teams which should be suitable to collab with as they had similar area of research to us this year, and also last year.
    3. The software and dry lab teams initiated the process of defining their initial objectives.

  • May 22- May 28, 2023
    1. The team initiated conversations regarding the project's name and the creation of a team logo.
    2. The wet lab team has initiated the process of generating sequences for the relevant DNAzymes.
    3. The human rights team had a meeting to organize various events for local IISER, mohali students.

  • May 29- June 4, 2023
    1. The team decided to work with a colorblind-friendly palette throughout the season (as IISER mohali iGEM team did last year).
    2. The team started working survey questionnaire.
    3. Dry lab started looking for volunteers to help in aptamer data and their FASTA sequences.

  • June 5- June 11, 2023
    1. The wet lab team ordered dsDNAzyme sequences and primers for their initial asymmetric PCR.
    2. The outreach team started contacting other iGEM team for collaboration.
    3. The team had another meeting to make the final decisions on our logo and also deliberated on the prospect of commencing the sharing of our work on social media platforms.

  • June 12- June 18, 2023
    1. The team had a meeting to strategize how we can elevate our project to a nationwide scale in India and raise awareness among a larger audience.
    2. The outreach team had its first meeting with a potential sponsor.

  • June 19- June 25, 2023
    1. The team met with Volunteers and explained their work to them.
    2. The outreach team decided to take interview of Doctors from various part of covid effect areas of India.

  • June 26- July 2, 2023
    1. The outreach team took an interview with doctor from rajasthan.
    2. The wet lab team received the primers and DNAzyme sequences in powdered form, subsequently preparing solutions from them.
    3. Following this, the wet lab team initiated their first PCR by employing the received primers and DNAzyme sequences, ensuring the specificity of the primers.
    4. The team had meeting to set future goals of what to be done by the end on July.

  • July 3- July 10, 2023
    1. The wet lab team again set a symmetric PCR reaction and a set of them were also run on agarose gel to make stock for their future experiments.
    2. The wet lab team order primers for further asymmetric PCR.
    3. The team made a keto funding page.
    4. The team has initiated talking with fellow Indian teams concerning the All India iGEM Meet scheduled for 2023.

  • March 20 – March 26
    1. Meeting with Prof. Satyajit Jena, our Primary PI, to discuss our project to seek his guidance and support.
    2. Meeting with Prof. Ananth Venkatesan to help us with plasma ion sputtering of our neural chip.
    3. Meeting with Prof. Samarjit Bhattacharyya to seek his guidance and support for neural chip development.

  • March 27 - April 2
    1. Another meeting with Prof. Satyajit Jena, our Primary PI, to discuss neural chip development and training process.

  • April 3- April 9
    1. Meeting with Prof. Ramendra Sunder Dey to discuss the project's aptamer aspect and seek his support in developing the aptasensor.

  • April 10 – April 16
    1. In preparation for the final meeting with the institutional iGEM committee, we met our mentors and instructors to refine our project idea further.

  • April 17-April 23
    1. Final meeting with the iGEM committee to discuss the chosen idea.
    2. Our idea got approved to work with, but only if we made a small modification to our initial plan.

  • April 24- April 30
    1. Break due to Midsemester exams.

Getting Started

  • May 1 – May 7
    1. Formation of the team and assignment of team roles.
    2. Meeting with mentors, advisors, and instructors to discuss our project idea and initial plans.
    3. Discussing general logistics and expectations.
    4. Everyone joins sub-teams to begin working on the project.
    5. Human Practices and Outreach teams decided their long-term goals and the list of professionals and events they will be managing the whole season.
    6. The Wet Lab team determined the aptamer sequences against the respective microbes and an initial protocol for neural chip development.

  • May 8 – May 14
    1. Reaching out to the IISER, Mohali community to see what we can do to have a local impact.
    2. The hardware and dry lab teams started setting their initial goals.

  • May 15- May 21
    1. The fundraising team started looking for sponsorship.
    2. The team started discussions for Team-Logo and the name of the Project.
    3. We started our discussion for collaboration, and we collaborated with Team iGEM Patras to develop a video discussing iGEM, Synthetic Biology, Wet Lab and Dry Lab, and the Survey on GMO and Syn-Bio.
    4. The Wet Lab team started looking for alternatives to thiol-modified aptamers and did an extensive literature search and discussion with experts to attach unmodified aptamers to GO.
    5. The dry lab Team started the discussion to perform GROMACS simulations of the proteins against our aptamer sequences.

  • May 22 – May 28
    1. The team decided to work with a colorblind-friendly palette throughout the season and decided on our logo.
    2. The team started working on our collaborations with iGEM Team-Patras and finalized our application for Promega Grant.
    3. The team started out working on Outreach and Human practices activities.

  • May 29 – June 4
    1. The team finalized the Logo for the project and submitted the survey questionnaire for review to Institutional Ethics committee member Anu Sabhlok.
    2. The team applied for Beckman Coulter free reagent kits.
    3. Team also started having discussions with other Indian Teams regarding the All India iGEM Meet 2022.

Summer

  • June 5 – June 11
    1. The team discussed with Science communicator Ipsa Jain and received valuable feedback from her regarding our Communication and Education work.
    2. The team had another meeting to finalize our Logo and discussed starting out sharing our work on social media.
    3. We discussed having a potential meeting with Team iGEM Berhampur who was also working with Aptamers this year.
    4. We also finalized ordering our custom DNA oligo from IDT for our Aptamer experiments.

  • June 12 – June 18
    1. The team had its meeting with iGEM Team IISER Berhampur and discussed potential collaborations with them.
    2. Wet Lab Co-head met with Anca from iGEM 2021 Team- Rochester to gain insights into attaching unmodified aptamers over GO and perform the electrochemical discussion method.
    3. We started discussions regarding Collaboration with other iGEM Teams.
    4. The Wet Lab team was notified about an issue we could face while using a neural chip to detect the initially chosen microbes. The Wet Lab team decided to work with Penicillin to sort out the problems that could have arisen.
    5. The social media team had a meeting to kick off the season over our social media handles officially.
    6. Team also decided on our mascot Monsieur Neurapurr.
    7. The team met to finalize our application for Impact Grant Award 2022.

  • June 19 – June 25
    1. The team had its initial meeting with Team AFCM Egypt and Team Linkoping Sweden and discussed potential collaboration.
    2. The team decided on the goals for fulfilling medal criteria and planned work accordingly.
    3. The team finalized the preliminary safety form for submission and met with advisors and mentors over it.
    4. The team finalized their plan to host the Syn-Bio camp and discussed it with volunteers.

  • June 26 – July 2
    1. The team met with Volunteers, brainstormed together for the conduction of the Syn-Bio camp, and also launched posters for registration.
    2. The team discussed our participation in AIIM 2022 and got two Researchers on board for the Virtual Talk Series.
    3. The team again met to discuss the Impact Grant Applications.
    4. Syn-Bio Workshop plans finalized.
    5. The team had an initial collaboration meeting with High School Team ASIJ Tokyo.
    6. The marketing and fundraising team started a massive campaign to raise funds.
    7. The outreach Team collaborated with Team- IISER TVM to develop a lab tour video.

  • July 3 – July 9
    1. Brochures and infographics designed by the design team.
    2. The team had review meetings to analyze the work and plan for the goals.
    3. The human Practices and Wet Lab team met with Dr. Richa Sharma and Dr. Raghavarao to discuss some of the electrochemical sensing aspects of the aptasensor.

  • July 10 – July 16
    1. The team met with volunteers to prepare for Syn-Bio workshops.
    2. The hardware team finalized the design to sputter for the neural chip.
    3. The marketing and Fundraising team reached out to sponsors
    4. The team decided on track selection for the project.
    5. The team received the distribution kit.

  • July 17 – July 23
    1. The neural chip development team placed an order for Retinoic acid.
    2. Initial designs for the Neural chip got sputtered and tested out.
    3. The team had a meeting and finalized the presentation for AIIM 2022.
    4. The design team got done with the 3D rendering of our prototype.
    5. The team successfully conducted the Syn-Bio workshop for high school students.
    6. The human Practices team met Prof. Anu Sabhlok to discuss the social and ethical aspects of the Project.
    7. The team started the survey on GMOs and Syn-bio to understand the general public's perspective on GMOs and Syn-Bio.

  • July 24 – July 30
    1. The team attended the AIIM 2022.
    2. Aptamers received from IDT.
    3. We had a meeting with iGEM Team Montpellier to discuss our collaboration.
    4. The dry Lab team finalized its goals for docking and figured out its work.

  • July 31 – Aug 6
    1. The team received Impact Grant Award.
    2. We had our first meeting with our collaborator iGEM Thessaloniki, Greece.
    3. The wet lab team met to finalize the protocol and start the experiments related to Aptasensors.
    4. The team visited Verka Milk Plant, Chandigarh.
    5. The Wet Lab team started InterLab Calibration Experiments.
    6. The team placed an order for neural cell lines.
    7. The team scheduled the meeting with engineers from BLACKROCK NEUROTECH.
    8. The team successfully concluded its virtual talk series event.
    9. The team submitted IBSC Application to get BSL-2 clearance from Insitute’s BioSafety Committee.
    10. The team decided on the script for Project's Promotional Video.
    11. InterLab study calibration done.

  • Aug 7 – Aug 13
    1. The team received sponsorship from INDUS PROTECH.
    2. The team completed the Inter-Lab study measurements.
    3. The team completed shooting clips for Project's Promotional
    4. The wet Team successfully modified Glassy Carbon electrodes with GO/PANI mixture.
    5. The human Practices team met Prof. Indranil Banerjee to discuss the project.
    6. The human Practices team met Prof. TVR from IISc to discuss the sustainability aspect of the project.
    7. The comic Strip development team finalized the story to work upon.

  • Aug 14- Aug 20
    1. The human Practices Team visited PBTI, Chandigarh.
    2. The Design Team completed the animation for Project's Promotional Video.
    3. Wiki Team started designing the basic templates for the Wiki.
    4. The team met Nanjiang-WorldShaper High School students and discussed a potential collaboration.
    5. Wet Lab Team successfully attached Aptamer over GO/PANI modified GC.
    6. The team got BSL-2 clearance from Insitute’s BioSafety Committee to work with cell lines and S. typhimurium.
    7. The human Practices team visited Dr. Archana at PGIMER to discuss some of the aspects of the project.
    8. The dry Lab team finalized the parameters for running MDS.

  • Aug 21- Aug 27
    1. The wet Lab team successfully tested aptamer for E.coli.
    2. The human Practices and Dry lab team met with the CEO of Cortical Labs to discuss some aspects of neural chip development.
    3. The dry Lab team finalized its plans to develop our software-” KAMI.”

Closing the loop

  • Aug 28- Sept 3
    1. The wet Lab Team placed an order for Penicillium chrysogenum and S. typhimurium.
    2. The dry Lab Team, under the guidance of our Instructor Soumadeep, started the development of the software -” KAMI.”

  • Sept 4 – Sept 10
    1. The wet Lab Team received N2A and SH-SY5Y cell lines.
    2. The human Practices team visited KVK, Mohali.
    3. The team received sponsorship of $1250 from Blue Copper Technology Pvt. Ltd.

  • Sept 11- Sept 17
    1. The wet Lab Team started to culture N2A and SH-SY5Y cell lines.
    2. The team delivered student talk over iGEM and our Project to the BS-MS community of IACS, Kolkata.
    3. The team finalized the development of “Book on Aptamers” with Team Linkoping Sweden and others.

  • Sept 18- Sept 24
    1. The wet Lab Team received Penicillium chrysogenum and S. typhimurium.
    2. Wet Lab Team tested aptamers for Penicillin G as well.
    3. The wiki team finalized their plans regarding the web design and started working on it.
    4. Comic strip development finalized the illustrations for the comic.
    5. The dry Lab team finalized the Docking and almost completed it.

  • Sept 25 – Oct 1
    1. The wet lab team tested the sensitivity of aptamers against E. coli and S. typhimrium.
    2. The wet lab team started two different cell lines.
    3. The dry Lab team performed MDS and finalized modeling work related to the project.
    4. The outreach team conducted Synthetic Biology based demonstration for middle and High school students on the occasion of 16th Foundation Day.
    5. The wiki Team tested uploading and extensively worked on Wiki development.
    6. The comic strip development team started collating the panels for the comic and did some final editing.
    7. Gold medal criteria of long-term partnership achieved and discussed with iGEM Team Montpellier.
    8. The dry Lab Team wrapped up the development of the software-” KAMI” successfully.

  • Oct 2 – Oct 8
    1. The dry Lab team wrapped up their work.
    2. The comic strip got published on our social media handles and sent out to high school students we met during Syn-Bio Workshop.
    3. Boi–Safety video final editing is done and released over our YouTube channel and social media pages.
    4. The team received a sponsorship offer of $500 from ACS Publication.
    5. The team extensively documented the work, and Wiki Team worked on Wiki development and uploading.
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