Team:IISER Berhampur/Project/Notebook
January
3rd Jan
Participants submitted their proposals to the iGEM selection committee of our institute.
10th Jan
13 projects were screened and reviewed by experts of our Institute.
February
4th Feb
First meeting for all the applicants. All the 13 participating teams were invited to provide a brief overview of the projects.
25th Feb
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.
March
11th March
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)
17th March
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).
20th March
As the pandemic hit the Indian subcontinent, the Institute suspended the classes (till further orders) and everyone was asked to return to home.
April
8th April
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.
May
13th May
Data mining and literature survey started to collect data on Protein-Protein interactions for each DENV Non-structural protein.
15th May
A National Survey form for Dengue was released.
June
12th June
Presented our project to Director Dr. K V R Chary and other faculties of Department of Biological Sciences.
23rd June
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.
July
6th July
Meeting with team iGEM IISER Pune for possible collaboration.
7th July
iGEM Headquarters accepted our application for participating in iGEM 2020.
11th July
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.
13th July
We decided to participate in All Indian iGEM Meet (AIIM) to be conducted on July 31st - Aug 1st.
19th July
We discussed conducting an online quiz for AIIM.
22nd July
Team meeting- we discussed conducting more collaboration.
23rd July
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.
24th July
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
25th July
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).
26th July
Team meeting with the PI. Based on the ranking done, interaction between DENV NS5 and hSTAT2 was selected as our target PPI.
29th July
Conducted a Webinar for students in IISER Berhampur. “iGEM Student Meet”.
30th July
We had a mock presentation of our Sci-Pop Quiz.
31st July
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.
August
1st August
Second day of All India iGEM Meet: Presented a scientific poster and the recent work progress.
2nd August
We went through the reviews and feedback that we got from the judges of AIIM.
5th August
An interview with Dr. Sudheer Krishna and his team. Using Molecular Dynamic Simulations for our project was proposed by Dr. Meenakshi and Dr. Arun.
8th August
Team meeting with PI - discussion about the AIIM experience. Proposal to work on Molecular Dynamic Simulations for our project was approved.
9th August
Gave our proposal to conduct two fun events for iGEM global meet.
10th August
Interview with Dr. Meher a computational biologist from Berhampur University.
11th August
iGEM account of the team members have been accepted
12th August
Team meeting.
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
15th August
Team Meeting with PI.
16th August
Attack of Mosquitoes:Warriors Assemble - a webinar for school students conducted in collaboration with iGEM IISER Pune.
17th August
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.
18th August
Meeting with MSP Maastricht - Possible collaboration for a YouTube video.
19th August
Weekly team meeting
20th August
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.
21st August
Presented poster which signifies our team spirit for global meetup.
22nd August
Weekly team meeting - we discussed the Global Meetup experience and discussed the docking results which the modeling team generated.
24th August
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.
25th August
Team meeting - discussion about Wiki page.
26th August
Meeting with PI - Designing the plasmid and protein-protein interactions.
Meeting with CCU Taiwan iGEM Team - Global Survey form.
27th August
Discussed about communicating our project through various science blogs.
29th August
Team meeting – discussion focused on individual work progress.
30th August
Invited fellow students of IISER to collaborate for Science Communication – our Synthetic Biology Blog.
31st August
Decided to start a crowdfunding initiative to help the at risk (Dengue) population of Berhampur.
We got Snapgene Subscription.
September
1st Sept
A meeting with the Perkin Elmer team as a part of Integrated Human Practice.
2nd Sept
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.
3rd Sept
Made a base script for the Promotional Video.
As part of Science Communication we started making comics on Synthetic biology.
4th Sept
Team meeting - We edited and decided on the script for Promo Video.
5th Sept
Wrote the description for crowdfunding.
Finalised the name for our project as FRaPPe.
6th Sept
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.
7th Sept
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).
8th Sept
Made the poster for Crowdfunding.
9th Sept
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.
10th Sept
We Interviewed District Malaria Officer of Berhampur Dr.R Jagadeesh Pattnaik.
Meeting with PI.
12th Sept
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.
13th Sept
As a part of Science Communication – the first article/blog was published on The Qrius Rhino blog.
15th Sept
Had a meeting with the UC Davis team.
16th Sept
Team meeting. Regular updates.
17th Sept
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.
19th Sept
An interview with G Hussain Syed.
Team meeting with PI
20th Sept
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
21st Sept
Launched our Science Communication blog “Syntillate”
22nd Sept
Promotional video is ready.
23rd Sept
Pamphlets for Human Practices are created.
GROMACS was installed in the remote computer and we checked if everything works fine.
24th Sept
We started our simulation.
Team meeting ,Updated the participation track:, Foundational Advancement , Open ,Therapeutic
25th Sept
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.
26th Sept
Team meeting with PI - we discussed the interviews we had with other professionals.
Energy minimization before adding water and ions was done.
27th Sept
Started making the team page.
28th Sept
Energy minimization after adding water and ions was done.
29th Sept
Discussion about the script for presentation video.
30th Sept
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.
October
1st Oct
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.
3rd Oct
In collaboration with iGEM MSP- Maastricht we launched a video on YouTube on Protein-Protein interaction.
4th Oct
Final MD simulation results were obtained.
5th Oct
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.
1. literature reviews, ( Engineering!) 2. discussing with experts in the field ( Human Practices!) 3. computational modelling (modeling ).
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.
6th Oct
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.
7th Oct
Weekly team meeting - discussion on Wiki Page and Presentation Video
Orders for custom genes (NS5 and hSTAT2) and plasmids were initiated.
8th Oct
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.
9th Oct
MD analysis was done and then we started documentation.
14th Oct
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.
17th Oct
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.
18th Oct
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.
19th Oct
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.
20th Oct
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.
21st Oct
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.
22nd Oct
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.
23rd Oct
Restriction digested plasmids were subjected to electrophoresis on 0.8% agarose gel.
Reagents for cloning and plasmid purification were received from NEB.
24th Oct
Cell culture media was prepared and incubated in the cell culture incubator for sterility check.
25th Oct
HEK293 cells were recovered from previously cryopreserved vials.
Plasmid restriction digestion was repeated with 1µg of pCKI.
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