Team:IISER-Pune-India/Notebook

January

  • 2nd January - We finalised our team members and started brainstorming ideas.

  • 18th January - We had our first HP meeting in which we decided to take part in “Spread The Smile”(STS). It is a program organised by Disha, a social outreach club at IISER Pune.

  • 20th-22nd January - We made a module for STS. It included very basic scientific information along with a few activities to teach children about synthetic biology and antibiotic resistance.

  • 30th January - In the meeting with our PI and Faculty Advisor Dr Sanjeev Galande we discussed various possible project ideas and finalised one.


February

  • 7th February - As a part of the activities that we had planned for the kids the whole team sat together for a few hours to make Tangrams.

  • The team performed an extensive literature search for our then project idea regarding biolasers for the entirety of the month.


March

  • 23rd March - In a team meeting all the team members along with PhD mentors decided to change the project idea due to lack of literature and resources available.

  • 26th March - Sponsorship meeting with Delta Faucet Company.

  • 30th March - Sponsorship meeting with Scivic Engineering India Pvt. Ltd.

  • 31st March - The team came up with the new idea of developing a drug against Malaria which later was finalised after a meeting with our PI.


April

  • 2nd April - Distribution of work and discussion regarding preparing the iBEC (Indian Biological Engineering Competition) proposal for sponsorship.

  • 10th April - Literature search for potential interactions to target.

  • 19th April - We had a HP meeting to discuss future plans and to decide on possible things we could do, which included building on our STS module to modify it for high school students, engaging the public through social media to create awareness about malaria, conducting a survey etc.

  • 21st April - According to their feasibility, the human and parasite protein interactions were shortlisted and different experimental methods were studied.

  • 22nd April - Meeting for deciding the possible experiments to perform.

  • 23nd-25th April - Designing the three modules for the proposal i.e.

    • Module 1: Cloning and biobrick

    • Module 2: Expression and purification

    • Module 3: Drug efficacy and toxicity check assay

  • 25th April - Confirmation meeting with mentors regarding all three modules.

  • 27th April - Submission of the iBEC proposal after validation from our PI.


May

  • 11th May - We had a HP meeting to finalize a survey to gauge public awareness levels regarding malaria.

  • 12th-16th May - Making of the HP survey questions and conversion into an appropriate format.

  • 13th May - Collaboration meeting with team Aalto Helsinki. Talked about possible wet lab and drylab collaborations.

  • 17th- 23rd May - Continued work on the HP survey.

  • 20th May - Collaboration meeting with Team USP-Brazil 2019. Got us in touch with Team UPCH_Peru 2020 since their team wasn’t going to be participating in this year’s competition.

  • We had our first meeting to decide upon the wiki.

  • 21st May - Tutorial on UCSF Chimera for dry lab members.

  • 23rd May - Collaboration meeting with UPCH Peru. Got us in touch with Dr Dionicia Gamboa, Peruvian parasitologist and associate professor at Institute of Tropical Medicine Alexander von Humboldt, Cayetano Heredia University. Her research focuses on Plasmodium vivax, major malaria parasite species in South America. (Here’s the link to her article.)

  • 25th May - Collaboration meeting with Team Düsseldorf 2020. Discussed possible wet lab collaboration and the postcard project.

  • 26th May - Collaboration meeting with Team Tuebingen 2020 and got in touch with Dr Velavan from the Institute of Tropical Diseases in Tübingen, Germany.

  • 27th May - Started figuring out the use of Javascript for the wiki.

  • 28th May - Collaboration meeting with Team BITSPilani-Goa_India 2020. Talked about possible collaborations. Helped us get in touch with Dr Shruti Vembar, faculty scientist at Institute of Bioinformatics and Applied Biotechnology (IBAB).

    On the same day we got sponsorship approval from Snapgene.

  • 29th May - Sponsorship: Geneious Prime.

  • 31st May - Meeting with Akashwani station director for a possible radio show.


June

  • 2nd June - We formed the diagnostics department.

  • 3rd June - We had a meeting with the HP members to discuss the radio show details.

  • 8th June - We had a meeting where we discussed work done by past iGEM teams and what methods we could use to build the diagnostics kit.

  • 9th-14th June - Radio show script writing and discussion.

  • 10th-14th June - Tutorials for biobrick building (snapgene, geneious, benchling).

  • 15th June - A rough layout of the landing page was decided.

  • 15th-20th June - Continuation of tutorials for biobrick building (snapgene, geneious, benchling).

  • 15th-18th June - Radio show script writing and discussion.

  • 16th June - Circulated the HP survey on different social media platforms.

  • 21st June - Started designing biobrick for 5MZA interaction.

  • 21st June - Meeting with Akashwani station director to finalize the radio show script.

  • 22nd-23rd June - Designing of biobrick for 5MZA interaction.

  • 22nd-28th June - Search for the precursors of host and parasite proteins involved in the interaction and building sample biobricks.

  • 23rd June - Started working on safety form. Made a preliminary draft for all sections.

  • 24th June - Meeting regarding safety issues with mentors.

  • 25th June - Finished with the final draft of the safety form and got it checked from our PhD mentors and PI.

  • 26th June - Submission of the preliminary draft of the safety form.

  • 28th June - The ‘Team Page’ was set up for the wiki.


July

  • 1st July - Had a discussion about whether to use a web based or an offline tool for the software to be developed for the diagnostics section of the project.

  • 1st-4th July - Deciding on the cyclotide i.e. choosing between Kalata B1 and MCoTI-II and addressing the issue of haemolytic activity of cyclotides.

  • 29th June-5th July - Inhibitor modelling and Saturated Mutagenesis done for 2-3 molecules. 22 new molecules were shortlisted from a possible list of 46 interactions from PDB.

  • 29th June-5th July - Scoring of inhibitory peptide models and saturated mutagenesis models using FoldX.

  • 6th July - Collaboration meeting with Team IISER_Berhampur 2020.

    Collaboration meeting with Team OhioState 2020. Possibility of them helping us out with drug disposal methods.

  • 9th July - Collaboration meeting with Team MSP-Maastricht 2020, submitted an abstract of our project in Proceedings Journal.

  • 6th-12th July - Scoring of inhibitory peptide models and saturated mutagenesis models using FoldX.

  • 5th-9th July- Choosing the assembling technique.

  • Started working on the malaria song.

  • Started working on the promotion video.

  • 12th-16th July - In silico primer designing tutorials.

  • 13th July - MD Simulations for proteins started.

  • 14th July - Had a discussion about the cost of different magnification tools, particularly those that would enable us to take microscopic images using a smartphone camera.

  • 18th-22st July - Deciding on expression and purification techniques.

  • 23rd July - Recording of the radio show in the Akashwani Radio Station.

  • 20th July - Amended dry lab protocol was given out, obtained PARAM brahma credentials.

  • 27th July - Airing of the radio show which was broadcasted in Mount Abu, Rajasthan, India.

  • 28th July - Tutorial on how to run GROMACS on the supercomputer cluster by Tejashree Kanitkar, our PhD dry lab mentor and started working on dry lab presentation for the All India iGEM Meet.

  • 25th-30th July - Designing and deciding the experimental details of module 3 i.e. efficacy and toxicity checks.

  • 31st July - Attended the All India iGEM Meet and presented our project in it.


August

  • 1st August - Attended the All India iGEM Meet.

  • 2nd-6th August - Addressing the issue of circularization of cyclotides.

  • 3rd-9th August - MD simulations were run on the Param Brahma Cluster.

  • 3rd August - Second meeting with IISER Berhampur to discuss a possible collaboration.

  • 3rd August - Found a cheap and efficient way to take microscopic images using smartphones developed by Dr Manu Prakash for our diagnostic tool.

  • 4th August - Had a meeting with a senior from college, Gulzar to discuss a new homepage idea. This meeting helped us revamp the entire design of the frontpage. Also discussed Protein NGL viewer to have a 3-D structure of a protein on the wiki.

  • 5th August - Collaboration with Team Pittsburgh 2020. We were invited as a guest on their Podcast.

  • 9th August - Finished training our first CNN (convolutional neural networks) model for diagnostics and obtained an accuracy of 94.5%.

  • Illustrations for the website were made and finalized.

  • 8th-14th August - Grafting the inhibitory peptide sequence in cyclotide and designing the biobrick.

  • 9th-15th August - Script writing and preparation for webinar.

  • 10th August -Sponsorship: Reliance Industries Ltd.

  • 10th-16th August - MD simulations were run on the Param Brahma Cluster.

  • 11th August - Had a meeting to discuss updates and how to move forward with creating a diagnostics kit/tool.

  • 13th August - Collaboration meeting with TAS Taipei. Drylab discussions on image processing and analysis for the diagnostic tool.

  • 12th-18th August - Building biobricks for synthesizing host and parasite protein.

  • 16th August - Hosted a webinar in partnership with IISER Berhampur. It was an hour long webinar meant for students aged between 13-16 years.

    Frontpage of the wiki was finished.

  • 17th-18th August - Continuation of building biobricks for synthesizing host and parasite protein.

  • 17th August - Had a meeting and discussed additions to the NGL viewer in order to have a download feature for the PDB file of the protein.

  • 18th-22nd August -RFC criteria check.

  • Started with write ups for wiki.

  • 29th August - Meeting with PI, Dr Sanjeev Galande for updates.

  • 30th August - As a part of collaboration with MSP Maastricht, we published a paper in a peer reviewed journal, Proceedings Journal.


September

  • 2nd-6th September - Documenting biobricks for 5MZA, 4V3E etc.

  • 3rd September - Meeting with Dr Shanti Kalipatnapu in order to get articles printed in newspapers for public engagement.

  • 5th-6th September - Attended the iGEMeetParis and presented our project.

  • 6th September - Team meeting

  • Ordered DNA from IDT and Twist Bioscience.

  • 7th-13th September - Documenting biobricks for different interactions.

  • 10th September - Safety form was submitted.

  • Finalised wiki subpage layout.

  • Design team started working on designs and illustrations for protocols.

  • 14th-15th September - Documenting biobricks for different interactions.

  • 19th September - Therapeutics meet up organised by Team KCL_UK 2020.

  • 19th September - Wet lab experiments began.

  • Started uploading pages to the wiki.

  • 20th-26th September - Project title and abstract finalization.

  • 22nd September - First gradient PCR was run.

  • 22nd September - As a part of collaboration with iGEM IISER Berhampur, CCU iGEM Taiwan, members participated in a survey conducted.

  • 23rd September - Hindi conversion of the promotion video.

  • 23rd September - Second PCR was done.

  • 25th September - Uploaded the promotion video.

  • 25th September - Gel extraction using PCR -2 product.

  • 28th-29th September - Third PCR and Cell transformation.


October

  • 2nd October - Team meeting.

  • 2nd October - Colony PCR.

  • 3rd October - Gel electrophoresis, alkaline lysis and second transformation.

  • 3rd October - Received the foldscope.

  • 3rd October - Meeting with Mr. Abhishek Kanyal to discuss the analysis of IC50 assay.

  • 1st-4th October - 4V3E biobrick construction.

  • 5th October-Surveys in 13 different languages were circulated everywhere.

  • 5th-9th October - Making of Diagnostic kit user manual.

  • 5th-10th October - Documentation of Engineering success.

  • 7th October - Shared our promotion video on various social media handles.

  • 9th October - Two team members gave a short interview to Pune Mirror for a newspaper article that was published on 10th October.

  • 10th October - Presentation script writing.

  • 10th-12th October - Making of Diagnostic kit user manual.

  • 11th October - Shared the malaria song on our social media handles.

  • 13th October-Sent out the first review of the user manual of the diagnostic kit to PHC (Primary Healthcare) workers.

  • 14th October - Finalization of standardisation protocol of IC50 assay.

  • 14th-16th October - Uploading biobricks on registry.

  • 17th-20th October - Uploading biobricks on registry.

  • 23rd October -Interview with molecular cloud.

  • 23rd October - We received DNA from IDT.

  • 23rd - 26th October:

    1. 1. A gradient PCR and a normal PCR for RF cloning was run.

    2. 2. Transformation in e.coli dh5 alpha.

    3. 3. Plasmid extraction.

    4. 4. Re-transformation in E.coli bl21(de3).

    5. 5. Protein expression.


Wet-lab Journal

You can view our wet-lab journal here.



Team IISER Pune India