AIIM
What is AIIM?
The All India iGEM Meet (AIIM) is a premier annual event where iGEM teams from across India come together to exchange ideas, showcase innovations, and learn from each other. Hosted by a different team each year, AIIM fosters collaboration and knowledge-sharing, with the 2024 edition organized by the IISc Bangalore team. Alongside insightful talks by leading experts from academia, industry, and entrepreneurship, the meet offers an exceptional opportunity for teams to connect and grow. In 2024, the IISc-Software team led an exciting workshop on "Computational Biology and Structural Visualization of Proteins," delving into specialized topics such as protein electrostatics and statistical mechanics. AIIM served as a dynamic platform for sparking new ideas, building networks, and deepening participants' understanding of these cutting-edge fields.
Workshop Summary
The primary goal of this workshop was to share our knowledge on protein electrostatics and statistical mechanics—topics that are often unfamiliar to undergraduate students. Recognizing this gap, we aimed to provide a comprehensive introduction and offer valuable resources to help participants gain a deeper understanding of these advanced subjects. All the codes, and hands-on exercises were shared with the participants in the form of a github repository. The link to the website is here.
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Protein Structure Visualization with PyMol:
We demonstrated some basics of PyMol, talked about commonly used file formats like PDB and PQR, alongside advanced features like alignment, morphing, and mutagenesis. The focus protein, NCC, was used to explain ion channels and their mutations, which cause the Gitelman Syndrome.
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Python Automation and APBS Electrostatics:
We covered automating PyMol tasks using Python and introduced participants to the APBS command-line tools and web-server for calculating electrostatic potentials, making the topic more approachable.
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Statistical Mechanics for Molecular Dynamics:
Here we shared an overview of molecular simulations, underlying algorithms, limitations in their biological applications, and best practices for conducting simulations. The goal of this presentation was to highlight the potential of these methods in synthetic biology.
Reviews
The workshop was well-received by a diverse audience, including students from other iGEM teams, IISc undergraduates, and MTech students from the CDS department. Participants praised the practical insights into APBS and molecular simulations, expressing interest in similar future sessions. iGEM teams from IISER TVM and IIT Bombay were particularly enthusiastic, with many eager to explore these advanced topics further.
Talk by Dr. Debnath Pal - Our Primary PI
In the talk titled "Snippets from Computing on COVID", Debnath sir delved into the critical role of computational biology in understanding the complexities of SARS-CoV-2, especially when experimental data and observations were conflicting during the pandemic. The central question addressed was, "Why is SARS-CoV-2 so contagious?" Drawing from previous experiments and ongoing research, sir explained how computational models have been essential in reconciling divergent findings from lab-based experiments. One key focus was the infection initiation model, which helps explain the virus's heightened transmissibility compared to other coronaviruses. Current results from computational studies have provided insights into the virus's mechanisms of infection, such as its efficient binding to host receptors, which underpins its contagiousness. The talk concluded by emphasizing how computational approaches continue to be invaluable for filling gaps where traditional experiments fall short, ultimately advancing our understanding of COVID-19.
School Visit to NPS Rajajinagar
To teach high school students about synthetic and computational biology, we began by introducing DNA and proteins, giving them a solid foundational understanding. This was followed by a hands-on DNA extraction experiment using papaya, allowing students to reinforce their knowledge through practical experience. Next, we conducted a quiz on molecular biology concepts to deepen their comprehension of synthetic biology. Finally, we demonstrated how scientists use software like PyMOL to visualize protein structures and biomolecules, enhancing the students' understanding of computational biology.
Our team tailored the explanations for the students at a 10th-grade level, ensuring that the material on key biomolecular segments and relevant biophysical concepts was understandable. We did this after consulting with Mrs. Sushma Ravikiran, a biology faculty member at Carmel School, to make sure the content was appropriate for their educational level.
Demonstration of DNA
The students were highly responsive, showing genuine curiosity and asking many insightful questions about how and why things work in biology. They were especially fascinated by the revolutionary potential of synthetic biology, which sparked their interest in exploring more about the field.
Demonstration of Proteins
Next, we introduced the students to protein structures, focusing on Keratin and Haemoglobin, two proteins that are familiar to the students.
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Keratin
We explained keratin as a structural protein found in hair, nails, and skin. The focus was on the difference between alpha-keratin in hair and beta-keratin in nails, linking the vertical lines in nails to the arrangement of beta-keratin.
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Haemoglobin
We explored Haemoglobin's role in oxygen transport and used the 1a3n.pdb file to visualize its tetrameric structure. Through PyMOL, we demonstrated how iron binds to oxygen and the structural changes during oxygen binding and release, giving students a clear view of this essential process.
The students were highly responsive, showing genuine curiosity and asking many insightful questions about how and why things work in biology. They were especially fascinated by the revolutionary potential of synthetic biology, which sparked their interest in exploring more about the field.
BioComp-Bytes
We organised BioComp-Bytes, a series of talks where professors from all over the world known for their works in Computational Biology, Bioinformatics and other aspects of Biological Sciences present and interact with the audience.
These talks are aimed at providing a platform for the students and researchers to learn about the latest advancements in the field of Computational Biology and Bioinformatics. This series is also intended to spread awareness about the different computational tools and techniques that are being used in the field of Biological Sciences, for Protein Structure Prediction, Drug Discovery, Protein Analysis and more.
Speakers
IISc-Software Team organised four talks in the BioComp-Bytes series. The speakers for the talks were:
- "Solving 3D Biomolecular Puzzles by Integrative Modelling" by Professor Dr. A.M.J.J. (Alexandre) Bonvin, Utrecht University, Netherlands.
- "Structural Map of the Human Proteome Using AlphaFold" given by Professor Arne Elofsson from Stockholm University, Sweden.
- "Cellular consequences of genetic variation" given by Professor Pedro Beltrao from ETH Zurich, Switzerland.
- "RNA Structure and Prediction" given by Professor Janusz M. Bujnicki, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw.
Audience and Participation
The talks were attended by students from IISc, and other institutions across India. A google form was sent across iGEM India community, iGEM Slack and other platforms to register for the event. We had multiple registrations with 50+ registrations for each talk. We also had students from various other countries, like China and the UK. The talk was conducted via Google Meets with great audience participation and interaction with the speaker.
Command Line Interface - BEPT
BEPT (Beginner-friendly Electrostatics for Protein analysis Tool) is a command-line tool that integrates the functionalities of the pdb2pqr and APBS tools, streamlining their usage for beginners. With Bept, users can explore these powerful tools without the need to delve into complex documentation, making the learning process smoother and more accessible.
Bept is developed by the IISc-Software Team, in collaboration with future undergraduate iGEMers at IISc Bengaluru, under the guidance of our Principal Investigator (PI).
Who is Bept created for?
Bept is designed for anyone interested in studying protein electrostatics, especially APBS Electrostatics. It caters to a wide audience, including students, research professionals, and industrialists. The intuitive and interactive interface makes it accessible to all, regardless of their prior experience with command-line tools.
With Bept, users can confidently pursue research in protein electrostatics, contributing to faster scientific development and discovery globally. For more information, visit our official Github Page.
Beyond The Microscope
In September, our team, alongside volunteers from the foundations, conducted online and hybrid sessions for the “Beyond The Microscope” initiative for grades 9th to 12th. The hybrid session engaged students from Madhya Pradesh and Ladakh, with participants attending from their school computer labs during school hours. This included schools where access to cutting-edge educational resources is often limited. The online sessions took place in the evenings, allowing students to join from their laptops and phones.
These sessions focused on key concepts related to the conversion of DNA to proteins and the visualization of common protein structures, such as keratin and Haemoglobin, using PyMOL. We incorporated hands-on activities to illustrate DNA-to-protein conversion through online web servers. The protein visualization provided students with a deeper understanding of how these structures function within the body.
The interactions during the sessions were engaging, and the feedback from students was overwhelmingly positive. Many expressed a desire for additional sessions and resources to further explore the topics discussed, demonstrating the impact of our initiative in inspiring interest in the field of synthetic biology.
BIOMANIA
We organized an engaging online session for students in grades 5th to 8th, in collaboration with the STEAM Vision Foundation. The students were from schools across the country. This interactive session introduced young participants to the fundamentals of molecular biology and illustrated how these concepts are applied in synthetic biology. To enhance their experience, we incorporated fun art and craft activities that encouraged creativity and hands-on learning.
In the sessions, we focussed on an introduction to the molecular biology of DNA and Proteins. This gave them a better understanding of the importance of DNA in heredity and Proteins in our body. Each participant received our made synthetic biology booklet and bookmarks as a reward for their active involvement in the session. Volunteers from the STEAM Vision Foundation played a crucial role in facilitating the crafts and ensuring that all students were actively engaged throughout the event. The students actively participated in making the DNA models with pencils, colored sticks and tapes. This initiative sparked interest in science while fostering community and collaboration in exploring synthetic biology.
TechBio Ideathon
We organized a synthetic and computational biology ideathon aimed at fostering interest and engagement in synthetic biology among undergraduate students nationwide. The problem statements were carefully designed to reflect real-life challenges, encouraging participants to explore the practical applications of synthetic biology in addressing these issues. The panel of judges comprised experts from a diverse range of fields, including healthcare, biosensing, materials science, entrepreneurship, environmental science, and other relevant disciplines. Their broad expertise ensured a comprehensive evaluation of the participants' innovative solutions, providing valuable insights and feedback.
The problem statements were:
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Sustainable Bio-Fabrication for Circular Textiles
Develop biodegradable and sustainable textiles using engineered microbes to produce natural fibers, dyes, or binding agents, while utilizing synthetic biology and also promoting a circular economy in the textile industry.
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Bio-Sensors for Environmental Monitoring
Design scalable, synthetic biology-based biosensors for continuous real-time monitoring of environmental pollutants coupled with advanced data analysis systems to provide actionable environmental insights for informed policy and research decisions.
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Precision Medicine through Synthetic Biology
Design a synthetic biology platform that enables the creation of personalized therapies, including custom gene therapies, engineered probiotics, and targeted drug delivery systems, while utilizing patient data to continuously refine and adapt treatments for optimal effectiveness and responsiveness to the patient’s evolving health status.
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Synthetic Biology driven Vaccine Development
Design a synthetic biology platform that enables the rapid synthesis of antigens and optimizes immune responses, facilitating quick adaptation to emerging pathogens and enhancing vaccine development speed and efficiency in response to global health threats.
Highlights of Ideathon Event
We had around 125 registrations from participants across the country, who sent in their ideas for the problem statement they selected. After careful judging by experts, we had 5 finalists out of them, 1-2 from each idea for the final round. The winner of this ideathon, the best solution award was won by Riya Jain from the Team MedTech Coders. Students presented innovative solutions, demonstrating their creativity and critical thinking skills. The judges were highly impressed by the quality of the ideas generated during the event, underscoring the potential of synthetic biology in solving contemporary problems. We made sure to offer them post-ideathon support regarding any of their ideas on how to make them ready for the real world and connected them to judges who were experts in this field.
