The Small Council
Dr. Vaidhyasubramaniam S., Vice Chancellor - SASTRA Deemed University
Our team is extremely grateful to our management and especially, our Vice Chancellor Dr. Vaidhyasubramaniam S., for his financial support to our entire iGEM venture without which whatever we have accomplished over the past 5 months would not have been possible. Beginning from the iGEM registration (via the SASTRA Student Innovation Fund) to obtaining the cell-free protein synthesis kit for our experiments (via SASTRA Research & Modernisation Fund), his support was incessant.
Dr. Swaminathan S., Dean - Planning & Development
Our team is grateful to Dr. Swaminathan S., for his administrative and infrastructural support to our maiden iGEM venture. He mentored us for the big presentations.
Dr. Rajan K. S., Dean - School of Chemical and Biotechnology
Our team is indebted to Dr. Rajan K.S., Dean of the School of Chemical and Biotechnology in our University, for his continuous moral and administrative support requisite to obtain the funds for our project through the SASTRA Student Innovation Fund (iGEM Team Registration Fee) and Research & Modernization Fund (Cell-free Protein Synthesis Kit). He was the creative head behind launching the SynBio club in our university.
Dr. Uma Maheswari K., Dean - School of Arts, Science and Humanities
Our team is indebted to Dr. Uma Maheswari K., Dean - SASH of our University, for her periodic reviewing of the progress made by our team towards our wet lab experiments in spite of her jam-packed schedule. Her valuable suggestions were incorporated into our experimental work.
Dr. Ashok Palaniappan, Senior Assistant Professor, School of Chemical and Biotechnology
Our team is heartily thankful to our Primary Principal Investigator, Dr. Ashok Palaniappan for his envisaged suggestions and strategies towards the design and implementation of our project, in general. He constantly supported us in each of the steps in our maiden journey and he viewed our project as much with a microscope as a telescope. He fixed every problem that evaded our abilities.
Dr. Adline Princy S., Associate Dean - Research, School of Chemical and Biotechnology
Our team is grateful to our Secondary Primary Investigator, Dr. Adline Princy S., for her infrastructural support of providing us with her lab space in our University. Her unwavering support to our wet lab team members was crucial to carry out our experiments in time.
Hands of the King
Pulling off as a student team leader and managing SASTRA iGEM team’s journey along with his fellow team leader could be the major accomplishment of this member. With his connatural interest in physics and mathematics, he found himself some significant space and time in The House of Modelling and helped them to realize the mass action kinetic model requisite to validate the experimental results from the sensor studies. Apart from this, he was the creative head behind the idea of a SynBio Auction and floated it to be an activity for the Human Practices session and his presence was conspicuous in all of the Human Practices and Integrated Human Practices sessions hosted by our team. The Human Practices session at D. A. V. Public School, Chennai was possible through his efforts.
He could be called the chief architect of the House of Toeholds, because of the very reason of him being the one who introduced the entire team to iGEM and stitched together such a diverse team of 15 members. With his innate interest in minimalistic designs and software development, he headed The House of Software and was instrumental in extracting the toehold secondary structure features, those relating to its structure, sequence and thermodynamics predominantly. The gblocks that we used in our project owes its design and ordering to him as he spearheaded the Twist Biosciences and IDT promotional offers and ensured that they reached us in time. He was also the creative head behind the idea of Primers and floated it to be a collaboration for our Human Practices. The Integrated Human Practices session at PCVC, Chennai was possible through his efforts. The amazing cartoon illustrations that you see in our project video, that is Shiva’s!
Ashwin Kumar Jainarayanan
We would like to thank our team’s advisor, Mr. Ashwin Kumar Jainarayanan, a prospective D. Phil student in Interdisciplinary Bioscience at the University of Oxford for his constant technical and non-technical support on how to go about with our maiden iGEM journey, owing to his experience in leading the IISER-Mohali iGEM team twice in 2017 and 2018.
We would like to thank Mr. Ramit B., an iGEM alumnus from Sri Venkateswara College of Engineering, Chennai for his valuable help with the design of gblocks requisite for our BioBrick characterization.
The House of Wetlab
Of the four houses in the HOUSE OF TOEHOLDS,The House of Wet Lab was instrumental in validating the identified panel of biomarkers, namely hsa-miR-21-5p and hsa-miR-20a-5p obtained from the survival analysis of the panel, through a literature survey. The survival analysis along with validation from the literature survey bolsters the prognostic value of our biomarker choice towards early-stage cervical cancer detection. The other chores performed by this house were,
- Filling up of the iGEM 2019 Safety form after obtaining suggestions from our Institutional Bio-Safety Committee (iBSC), post their certification of carrying out our designed experiments in our labs,
- Performed experiments to study the effect of pH on the promoter activity of the BioBrick Bba_K608011, which has a constitutive medium strength promoter
- Transformation of NEB #C2997I DH5-alpha competent E. coli cells
- Optimization of the transformation protocol
- Selection of transformed cells by chloramphenicol
- Optimization of the chloramphenicol concentration
- Observation of growth in various pH conditions
- Fluorescence measurements
- Design of the PCR experiments and subsequent amplification of the toehold DNA construct to be used for the biosensor experiments (miR-21 and miR-20a toehold DNA constructs were amplified)
- Ordering of the cell-free protein synthesis kit requisite for the characterization of our designed toehold switch for miR-21
As one of our instructors and an experienced ocular microbiologist, she was pivotal in guiding the members of both the House of Wet Lab and House of Sensors with regards to the lab procedures to be followed, safety concerns while performing the experiments and review of the protocols to be employed for the studies of existing BioBrick and new BioBrick characterization.
She headed the wetlab team and was pivotal in the design of experiments for the Bba_K608011 characterization and subsequent collation & interpretation of the obtained results. She helped the sensor team with choosing the appropriate cell-free protein synthesis kit required for the biosensor characterization, through extensive brainstorming sessions with Dr. Bindu Simon. Apart from these, she actively involved herself in the engagement activities as part of our Human Practices sessions and helped the Primers magazine collaboration team with proofreading the received contributions. The sweet voice that you hear in our project video, that is Uttara’s!
She spearheaded the Human Practices & Public engagement drive of our iGEM team, which involved the design of events and sessions for the same. She formulated the Google Form, which our team circulated to gauge the Awareness on Cervical Cancer amongst general public to strengthen the relevance of our project to the society. The Integrated Human Practices session with Dr. M.A. Raja and the Human Practices session at Chettinad Vidyashram, Chennai was possible through her efforts. The hsa-miR-21-5p and hsa-miR-20a-5p toehold DNA amplification, essentially requisite for obtaining enough concentration for the biosensor characterization studies was taken care of by Smriti through PCR experiments, with valuable help from Deeptha.
Apart from significantly helping out Smriti in designing and performing the PCR experiments for the hsa-miR-21-5p and hsa-miR-20a-5p toehold DNA amplification, she was one of the moderators for our Human Practices sessions at D.A.V. Public School, Chennai and Chettinad Vidyashram, Chennai. The Integrated Human Practice session amidst the Repco Microfinance Self Help Group women was possible through her efforts. She was helpful in proofreading the received contributions for our Primers magazine collaboration.
She was actively involved in the transformation of competent cells and its optimization spanning three test runs, which was the primary step in our efforts towards additional characterization of an existing BioBrick part, Bba_K608011. She performed inoculation works associated with the experiments for the effect of pH on the chosen BioBrick. She was an active participant in our Integrated Human Practice sessions and aided in documenting the report for our Integrated Human Practice session at Cancer Institute (W.I.A), Chennai. She was helpful in proofreading the received contributions for our Primers magazine collaboration.
He calls himself the Preserver of Cultures, obviously the microbial ones owing to his valuable contribution towards optimizing the transformation protocol that was requisite for selection of competent cells to be used in the existing BioBrick characterization experiment. When he was not busy culturing the microbes, he introduced the students to the world of Synthetic biology during the school visits as part of our Human Practices. He wishes to take credit for the most terrible pictures that you could see in our wiki page, because he was the one behind the lens!
Dr. Bindu Simon, Assistant Professor (Research), SCBT
A plant biotechnologist by profession and the Principal Investigator of Phytoengineering Lab in our University, she was instrumental in furnishing us with technical advice and gave valuable suggestions such as opting for a cell-free characterization & the appropriate protein synthesis kit for the same and ways to increase the transformation efficiency, to name a few.
Dr. Srinandan C.S., Assistant Professor (Research), SCBT
A microbiologist by profession and the Principal investigator of Biofilm Biology Lab in our University, he provided the necessary infrastructural support in his laboratory to ensure that some of our experiments were performed.
The Central Instrumentation Facility, SASTRA Deemed University
We are grateful to the Central Instrumentation facility of our University for providing us with the necessary infrastructural support such as -80 °C storage facility to store our cell-free protein synthesis kit and the DH5-alpha competent E. coli cells, water bath and incubator shaker that were used in the transformation experiments.
Nanosensors Lab, SASTRA Deemed University
We are extremely thankful to Dr. John Bosco Balaguru R., Principal Investigator, Nanosensors Lab of our University and his lab members for permitting us to use their spectrofluorometer as part of our existing BioBrick characterization experiments.
We would also like to thank Dr. Anbazhagan V., Senior Assistant Professor and his lab members for permitting us to use their spectrofluorometer as well.
Biopharmaceutical Technology Lab, SASTRA Deemed University
We would also like to thank Dr. Senthil Visaga Ambi, Principal Investigator, Biopharmaceutical Technology Lab of our University for providing us with their lab’s fluorescent plate reader to measure O.D values for fixing the cell number density.
Genurem Life Sciences, Thanjavur
We would like to acknowledge the wet lab assistance provided by Genurem Life Sciences, Thanjavur in performing PCR purification and sequencing of the amplified toehold construct.
The House of Sensors
The next house to be attributed is The House of Sensors. They predominantly performed the cell-free transcription & translation for the conversion of toehold DNA to the toehold secondary structure, which is the sensing element of our biosensor. Since a second generation toehold design was employed for our project, the essential incubation of the miR and anti-miR for the hybrid trigger formation in cases of both hsa-miR-21-5p and hsa-miR-20a-5p markers, was performed by this team. The calibration of the fluorescent plate reader for our study was undertaken using the fluorescein provided in the DNA Distribution kit of our iGEM’s registration kit. Finally, the members of this house carried out the requisite fluorescence measurements associated with our BioBrick characterization, which was the design of a biosensor.
The members of this house are Medical Nanotechnologists, who are in their final year of Integrated Master of Technology programme in Medical Nanotechnology. Vishal Kannan, Hariprasad K., Karunya V. and Bavithra I. were the occupants of this house.
He headed this house and was instrumental in formulating the design of experiments associated with our biosensor studies along with the sensor team members. He subsequently collected & interpreted the obtained results from their studies along with his team. Also, he took part in frequent discussions with the modelling team and provided the necessary inputs to the modelling team regarding the experimental design for the biosensor studies. This in turn channelised the modelling aspects to a certain extent and bolstered the work of the modeling team. In addition, the Human Practices session at Natesan Vidyalaya, Chennai was moderated by him.
He played a key role towards formulating the experimental design for our Biobrick characterization along with Vishal, assisted in reagent preparation and fluorescence measurements. The Integrated Human Practices session with Dr. J. S. Malliga and the Human Practices session at Natesan Vidyalaya, Chennai was possible through his efforts. Apart from these, he took care of the overall event coverage of our Human Practices sessions organised at Natesan Vidyalaya and Chettinad Vidyashram, Chennai.
Apart from assisting the sensor team with their experiments, she was pivotal in optimizing the protocols employed for the sensor studies by appropriately identifying the mistakes during the trial runs. She helped the wet lab team with the existing BioBrick part characterization and was an active participant in our Integrated Human Practices sessions at PCVC NGO, Chennai and Repco Microfinance Self Help Group, Trichy. She also aided in documenting the report for our Integrated Human Practice session at PCVC NGO, Chennai.
She assisted the sensor team with their experiments and helped the wet lab team with the existing BioBrick part characterization. She actively engaged herself in our Integrated Human Practices sessions at PCVC NGO, Chennai and Repco Microfinance Self Help Group, Trichy. She helped in documenting the report for our Integrated Human Practice session at Apollo Cancer Institute, Chennai.
Vascular Biology Lab, SASTRA Deemed University
We are extremely thankful to Vascular Biology Lab of our University and the lab members for permitting us to use their fluorescent plate reader as part of our new BioBrick characterization experiments.
National Center for Biological Sciences, Bengaluru
We are extremely grateful to NCBS, Bengaluru for providing us with a 96-well plate with U-bottom to handle 30 µL sample volumes as part of our new BioBrick characterization experiments.
The House of Modelling
The House of Modelling sheltered one of the integral aspects of our project that corroborated the interdisciplinary nature of synthetic biology, ranging from collating and utilising results provided by our software team to giving useful suggestions and insights to the sensor team towards design of experiments & results validation. This facet of the project was supported in part by DST-SERB grant EMR/2017/000470.
The members of this house are Medical Nanotechnologists, who are in their pre-final year of Integrated Master of Technology programme in Medical Nanotechnology. Swetha N. and Raghavv Raghavender Suresh were the occupants of this house
She remained the backbone of the modelling team as she made immense contributions in terms of formulating the differential equations requisite for our model and subsequently coded the same in MATLAB R2017b. Even though she was a late entrant into our team, she was instrumental in the analysis of the output and results obtained from the modelling simulations.
Raghavv Raghavender Suresh
A late entrant to the team, he made significant contributions with the requisite literature survey and documentation for modelling. Apart from this, he aided the team with editing and proof-reading the documents prepared for our team’s wiki page and was extremely instrumental in collating the Primers magazine (a venture as part of our collaboration) and formulated the script for the video.
As one of our instructors, she was instrumental in performing the initial phase of modelling with the miRNA differential expression profiling and survival analysis based on Cox regression models and Kaplan-Meier curves, essential for the choice of our biomarkers to be used in our project.
The House of Software
The House of Software covered the essential aspects of our project which included the gblocks design (second generation toehold switch design for hsa-miR-21-5p and hsa-miR-20a-5p) and extraction of toehold secondary structure features using regression models.
A quirky person and the odd one out in our team (being the lone student from the Department of Information and Communications Technology), he undertook the process of shaping our wiki page single handedly with his web page development skills. Our team logo and our team banner owes its creation to him and our social media pages (Instagram and Medium) owes its maintenance to him. He wishes to take credit for adding humour elements to an otherwise somber iGEM team!
She made immense contributions towards the analysis of secondary structure based features for toehold switch and trigger. She also scripted the secondary structure based features using ViennaRNA package.
Human Practices and Collaborations
We would like to thank the management of D. A. V. Public School, Chennai, Natesan Vidyasala Matriculation School, Chennai and Chettinad Vidyashram, Chennai for providing us with their space and time to host our Human Practices Public Engagement sessions, aimed at disseminating the excitement of Synthetic Biology.
We would also like to thank PCVC, Chennai and Repco Microfinance Self Help Group for allowing us to meet the women sheltered in their NGOs to gauge the significance of our project.
We are grateful to Mr. Ramadorai S., former adviser to the Prime Minister of India - National Council on Skill Development and Chairman of Tata Technologies for agreeing to meet our team leaders and provide his immensely valuable suggestions towards sculpting our project into more proper shape.
We are thankful to Dr. M. A. Raja, Medical Oncologist at the Apollo Cancer Institute, Chennai and Dr. J. S. Malliga, Head of the Preventive Oncology Department at the Cancer Institute (W.I.A), Chennai for their acceptance to meet us as part of our Integrated Human Practice sessions.
We would like to thank Indian Institute of Science Education and Research, Bhopal and the IISER-Bhopal team for hosting us during the All India iGEM Meet 2019.
Design and Web Development
We would like to thank our fellow friends Mr. Muralidhar V and Mr. Krishna Sathyamurthy, IV year Mechanical Engineering students for aiding us in designing our customized iGEM Tees.
We are extremely grateful to Mr. Aravind Ram Seshadri, IV year Mechanical Engineering student and Shivaramakrishna's roommate, for lending us his iPad Pro, which was a cornerstone for our illustrations and project video.
First and foremost, we would like to thank the Web Developer from US AFRL Carroll HS for their tutorial on YouTube on how to style the iGEM Wiki. https://www.youtube.com/playlist?list=PLg5B0YEXzgEorRa8vuZPoHaH5e1jmgVQ6
We would also like to thank Keshav Aditya, graduate student in Computer Science at Stony Brook University. The following list of code snippets and templates from open source websites are heartily acknowledged:
- Shapiro Matron, VB Script to convert Excel tables to HTML Format https://gist.github.com/shapiromatron/5024948
- Emanuele, for their awesome row separators! https://codepen.io/emared/pen/gWGBLR
- Ariel Fresler, for his Smooth Scroll Plugin https://github.com/flesler/jquery.scrollTo
- Charlie Samways. for the Game of Throne Font! https://www.fonts4free.net/game-of-thrones-font.html
- Alvoro Trigo, for the fullpage.js https://alvarotrigo.com/fullPage
- The Bootstrap Team, getbootstrap.com
- The Developers Behind https://wordhtml.com