Participants submitted their proposals to the iGEM selection committee of our institute.
13 projects were screened and reviewed by experts of our Institute.
First meeting for all the applicants. All the 13 participating teams were invited to provide a brief overview of the projects.
Details of the iGEM competition were discussed.
The participating teams were requested to vote for their top 3 teams.
Project comments from the expert panel were also discussed.
The project with the most votes was selected as the IISER Berhampur iGEM team project for 2020.
This day marked the divisions of members in to sub-teams to coordinate and to effectively work on specific aspects of the project. Bio-modelling, Math-modelling and Outreach & Public affairs were the three sub-teams.
We received the information from the Government of India, regarding the funding support from Department of Biotechnology on Indian Biological Engineering Competition (iBEC, 2020)
An extensive meeting took place to place the application for the iBEC funding. This discussion choked out the timeline of the project, written state of purpose and project specifications.
The discussion further moved to discuss the possibility of a brief presentation to Prof. K.V.R Chary (Director, IISER Berhampur).
As the pandemic hit the Indian subcontinent, the Institute suspended the classes (till further orders) and everyone was asked to return to home.
Each sub-team started their respective works and discussed the progress in the first virtual team meeting. The modeling team presented the literature review they had done for different DENV Non-structural proteins and also presented the epidemiological data on dengue that they have collected. They also presented the analysis they have done comparing peptide inhibitors with small molecules and biologics.
Data mining and literature survey started to collect data on Protein-Protein interactions for each DENV Non-structural protein.
A National Survey form for Dengue was released.
Presented our project to Director Dr. K V R Chary and other faculties of Department of Biological Sciences.
Preliminary Safety form was filled. The modeling team was continuing its previous tasks, and in addition was exploring what other modeling components can be added to refine the project further.
Meeting with team iGEM IISER Pune for possible collaboration.
iGEM Headquarters accepted our application for participating in iGEM 2020.
Team meeting with PI. Several aspects regarding peptide inhibitor designing,evolutionary analysis to justify our choice of NS Proteins, epidemiology modeling and reporter system modeling were discussed.
We decided to participate in All Indian iGEM Meet (AIIM) to be conducted on July 31st - Aug 1st.
We discussed conducting an online quiz for AIIM.
Team meeting- we discussed conducting more collaboration.
iGEM Headquarters accepted our application for participating in iGEM 2020.
Meeting with iGEM MSP, Maastricht University for possible YouTube collaboration.
We launched an initiative called iMASK. For promoting the use of masks during this pandemic.
Modeling team discussed with Dr Malay Kumar Rana regarding peptide inhibitor designing and possible collaboration.
Modelling team ranked the several Protein-Protein Interactions they have listed based on the amount of structural data available and how important the particular PPI is in DENV pathogenesis.
We registered to participate in All India iGEM Meet
Meeting with CCU iGEM - We exchanged our ideas for possible collaboration.
Official google site for iGEM IISER Berhampur was launched by Dr. Rohit Soni (Assistant Professor and Coordinator of Students’ Affairs, IISER Berhampur).
Team meeting with the PI. Based on the ranking done, interaction between DENV NS5 and hSTAT2 was selected as our target PPI.
Conducted a Webinar for students in IISER Berhampur. “iGEM Student Meet”.
We had a mock presentation of our Sci-Pop Quiz.
Hosted and participated in the All India iGEM Meet (AIIM) 2020 and presented the project proposal with the Indian iGEM community. All Indian Teams came together and exchanged ideas, knowledge and visions of Synthetic Biology. We also interacted with iGEM Alumni and got to know about their stories and experiences.
Second day of All India iGEM Meet: Presented a scientific poster and the recent work progress.
We went through the reviews and feedback that we got from the judges of AIIM.
An interview with Dr. Sudheer Krishna and his team. Using Molecular Dynamic Simulations for our project was proposed by Dr. Meenakshi and Dr. Arun.
Team meeting with PI - discussion about the AIIM experience. Proposal to work on Molecular Dynamic Simulations for our project was approved.
Gave our proposal to conduct two fun events for iGEM global meet.
Interview with Dr. Meher a computational biologist from Berhampur University.
iGEM account of the team members have been accepted
Interview with Dr. Rindu Raveendran, Assistant Professor, DMWIMS Medical College to understand the depth of the issue from a person working in a dengue prone rural area
Team Meeting with PI.
Attack of Mosquitoes:Warriors Assemble - a webinar for school students conducted in collaboration with iGEM IISER Pune.
Meeting with Dr. Sunita Patel from CEBS, Mumbai. For possible collaboration. We pitched in our idea and she agreed to help us in Molecular Dynamics simulations. She also gave us a few tasks, i.e., to learn the principle of molecular dynamics and decide which force field to choose, to go ahead with the MD simulations.
Meeting with MSP Maastricht - Possible collaboration for a YouTube video.
Weekly team meeting
Created an official slack channel for better communications within and across iGEM community and various teams.
We conducted two fun events for other iGEM teams. One is Riff Off - where a random theme will be selected and a team has to sing a song based on it. Second one - What do you Meme? - meme making challenge on iGEM and we got to meet and greet teams who became our collaborators later.
Participated in iGEM Global Meetups. Different members attended different talks.
Presented poster which signifies our team spirit for global meetup.
Weekly team meeting - we discussed the Global Meetup experience and discussed the docking results which the modeling team generated.
We had another meeting with Dr. Sunita Patel and this time we presented her whatever we have learned related to MD and also kept the justification for choosing GROMOS G4a7 force field.
Team meeting - discussion about Wiki page.
Meeting with PI - Designing the plasmid and protein-protein interactions.
Meeting with CCU Taiwan iGEM Team - Global Survey form.
Discussed about communicating our project through various science blogs.
Team meeting – discussion focused on individual work progress.
Invited fellow students of IISER to collaborate for Science Communication – our Synthetic Biology Blog.
Decided to start a crowdfunding initiative to help the at risk (Dengue) population of Berhampur.
We got Snapgene Subscription.
A meeting with the Perkin Elmer team as a part of Integrated Human Practice.
Made the video on Protein-Protein Interaction in collaboration with iGEM MSP Maastricht.
Molecular Cloud (Genscript) interviewed our team.
We named our Science Communication blog to Syntillate.
Made a base script for the Promotional Video.
As part of Science Communication we started making comics on Synthetic biology.
Team meeting - We edited and decided on the script for Promo Video.
Wrote the description for crowdfunding.
Finalised the name for our project as FRaPPe.
We attended iGEM Worldwide Virtual Meet up by Parisian Teams. We pitched our Poster in the meet up. And we got second place in poster presentation.
Team meeting - Promo Video making.
We had another meeting with Dr. Sunita Patel and this time, we finalised the codes that would be required for the simulation while using GROMACS(software package which we chose to do our MD simulation).
Made the poster for Crowdfunding.
Launched a crowdfunding campaign to procure funds to buy Mosquito Nets that to be distributed to the local community to spread awareness and the basic importance of safety measures. This Outreach activity aims to collaborate directly with the mosquito net workers which also help them to overcome their decline in business hit by the pandemic.
We got permission from our parent institute for remotely accessing a high performance computer to carry out the MD simulation.
Released the Global Survey Form on Dengue in collaboration with iGEM CCU Taiwan.
We Interviewed District Malaria Officer of Berhampur Dr.R Jagadeesh Pattnaik.
Meeting with PI.
Meeting with Mr. Tribhuban Parida(one of the Phd students working with Dr. Sandeep), regarding the techniques that are required to remotely handle the high performance computer. He gave us a few tasks related to learning about how to carry out basic functions in command prompt while accessing the computer remotely.
As a part of Science Communication – the first article/blog was published on The Qrius Rhino blog.
Had a meeting with the UC Davis team.
Team meeting. Regular updates.
Published another Synthetic Blog in Next Gen Scientists Foundation titled ‘What I cannot create, I do not understand’
Another meeting with Mr. Tribhuban Parida where we discussed with him whatever we have learned. He also taught us a few techniques.
An interview with G Hussain Syed.
Team meeting with PI
This was the first day where we actually started working remotely and transferred all the necessary files from our computers to the remotely handled computer
Launched our Science Communication blog “Syntillate”
Promotional video is ready.
Pamphlets for Human Practices are created.
GROMACS was installed in the remote computer and we checked if everything works fine.
We started our simulation.
Team meeting ,Updated the participation track:, Foundational Advancement , Open ,Therapeutic
An interview with Dr. Puja Singh from CCMB, Hyderabad. She told about the background that is created due to the Transfection and suggested to go for transduction. And instead of using two plasmid constructs she suggested to use a single plasmid with P2A linker.
Team meeting with PI - we discussed the interviews we had with other professionals.
Energy minimization before adding water and ions was done.
Started making the team page.
Energy minimization after adding water and ions was done.
Discussion about the script for presentation video.
Weekly team meeting where all the subteam update their progress.
An interview with Dr. Bharath Srinivasan from AstraZeneca. For his views on FRaPPe.
NVT and NPT equilibration steps were completed.
We won the Molecular cloud sponsorship for the month of September.
Started the Cloning Strategy Design. Chalked out the possible wet lab FRaPPe constructs that are to be transformed in E.coli and then transfected into the mammalian HEK293 cells. Out of the initial 36 possibilities, we narrowed it down to 4 control and 4 test constructs based on inputs from modelling.
Team meeting with our PI- Discussion about documentation of our project. Feasibility of wet lab was assessed and constructs to be cloned were finalised. Combined CID-FRET plasmids from Addgene were explored and decided upon.
In collaboration with iGEM MSP- Maastricht we launched a video on YouTube on Protein-Protein interaction.
Final MD simulation results were obtained.
Due to the Covid pandemic, we had to re strategise our project. Due to the lockdown, the team could not access the lab till the beginning of October. And due to the same reason, reagents could not reach us on time either.
However, we decided to utilize this time in planning and revisiting our experiments through.
And this made us realise that instead of waiting for the reagents to arrive and then start optimizing protocols and techniques, as soon as we could access the lab, we should start working on trial experiments to optimize our cloning, transfection and FRET approaches.
The process of analysing the results of MD simulation started.
We received a gift hamper from MolecularCloud which had bags and pins for the members.
Using the plasmids from Addgene, restriction enzymes were selected to be used for subcloning the genes of interest into the backbones. We decided to get both the genes synthesized directly. The coding sequences for DENV NS-5 and hSTAT2 were customised by appending the Restriction enzyme sites.
Weekly team meeting - discussion on Wiki Page and Presentation Video
Orders for custom genes (NS5 and hSTAT2) and plasmids were initiated.
To ensure the ease of synthesis, the design for the genes (NS-5 and hSTAT2) to be synthesized and cloned into the Addgene plasmids was revised to include Splicing using Overlap Extension (SOE).
Quotes raised with Addgene for CFP-FKBP and YFP-FRB plasmids.
Meeting with PI - Updated about the progress of the subteams.
MD analysis was done and then we started documentation.
Weekly team meeting - updated the progress on MDS simulation, wiki page and presentation video.
Documentation was done and sent to Dr. Sunita and Dr. Selvi for review.
pCKI plasmid was kindly provided by Dr. Vinay Bulusu.
Agar media and plates were prepared and ampicillin was spread over the plate.
Transformation of the pCKI plasmid and DH5α competent cells was performed.
Transformed cells were plated on LB-Ampicillin agar plate along with an additional control plate for the competent cells. These plates were incubated at 37°C for 12 hours.
There were few colonies on the plates, which suggested that the transformation process had not gone well. So, we decided to repeat the process.
This could be because of problems with the cells or the culture media
The LB media and LB-Amp agar plates were prepared freshly. After transformation of the plasmid and competent cells, the cells were plated and incubated at 37°C for 12 hours.
We used two different plasmid concentrations.
With the completion of 12 hours incubation, we were successful in witnessing the colonies in both plates. Stored these plates at 4°C to proceed further.
A single colony was added to a falcon tube containing 5 mL of LB Broth media with different concentrations of Ampicillin and two replicates were taken for each concentration. A pipette tip was used to scoop out a single colony. The falcon tubes were placed in a shaking incubator with 100 rpm for 12 hours at 37°C.
We were able to observe the dense colour of the media signifying the growth.
Cells were processed for plasmid extraction. Plasmids that were extracted were stored in -20o C
MD analysis was done and then we started documentation.
Team meeting with PI - Updates on the documentation, reviewing and editing all the pages that goes into the wiki page.
Reviewing was done and we uploaded the document to our wiki page.
Restriction digestion of the plasmid was done to confirm the plasmid.
Single enzyme digests and Double enzyme digests using 250ng of plasmid were performed at 37°C for 1 hour.
Restriction digested plasmids were subjected to electrophoresis on 0.8% agarose gel.
Reagents for cloning and plasmid purification were received from NEB.
Cell culture media was prepared and incubated in the cell culture incubator for sterility check.
HEK293 cells were recovered from previously cryopreserved vials.
Plasmid restriction digestion was repeated with 1µg of pCKI.