OUR AIM
Building a network that connects experts working in various fields and sectors and our stakeholders together and developing a two-way interaction with everyone was one of our primary goals and targets that we wanted to achieve.
THE HUMAN-PRACTICES MODEL
The 3’R “Reflection - Responsibility - Responsiveness” has been a model we had chosen to work with to shape the idea into an ideal kit.
This cycle helped us create an effective dialogue between different domains and merge them to give an appropriate solution for the issue to be tackled. Working towards making a kit that has the potential to become an integral part of the modern world, this dialogue always played a vital role in directing our flow of thoughts on making this project a better version of itself.
During the brainstorming sessions, the team discussed the issues creating local and global concerns. The team interacted with the Biology department of IISER Tirupati to discuss the solutions made for the concerned problems using synthetic biology.
During those sessions, the team realised that PCOS is one of the significant concerns with increasing prevalence worldwide.
The team was involved in multiple iterations and thought processes to develop a solution to make the kit more user-friendly and a feasible diagnostic option for our stakeholders.
Value assessment
We conducted a stakeholder value matrix assessment after considering various factors and values that must be considered while making the analysis.
The impact on the environment, feasibility, user privacy, environmental impact, and other values that must be considered while making a diagnostic kit was analysed.
The value assessment helped the team guide the project to make it more user-friendly.
Table qualitatively comparing different stakeholders and values to be addressed
SWOT analysis
After completing the project design, the team went for a comprehensive situation analysis to have deep knowledge of the impact the kit would create in our society.
The analysis helped the team concentrate on the aspects that required attention to make the kit user-friendly for all Ovary Owners.
The team had always considered the social aspects and values to modulate the project and practice efficient interaction with stakeholders.
Selection of appropriate stakeholders
The team analysed all the potential stakeholders and examined the impact the kit would create when brought into use.
Safe and responsible research
The team concentrated on the safety aspects of the project, laboratory, and during oher outreach events.
The team followed proper lab safety protocols and state guidelines for covid prevention and individual safety.
Ethical aspects
The team analysed the importance of ethical aspects associated with synthetic biology research while interacting with our stakeholders.
The team got complete ethical approval from the institutional ethical committee and conducted the PCOS awareness survey.
The team released the ethics in synthetic biology podcast series to support researchers in understanding the importance of ethical aspects while building a project.
Interactions with experts and Stakeholders
The team interacted with various experts throughout the project and with the stakeholders at the appropriate time and throught the project.
The team also went to Primary health care centres, fertility clinics and pathological labs in the vicinity to gain knowledge of the situation and analyse the impact.
Closing the loop
The team made infographic images with the results collected from the survey. Opinions from various field works were documented and used to reflect the views to modulate the project accordingly.
The team analysed all the documented data to create a design and make a feasible design. The team also interacted with the stakeholders to analyse the current design.
HOW iHP MODULATED APTASTELES
Developing a complete network interlinking stakeholders and experts together has helped the team gather the collective opinions from all possible stakeholders and experts parallelly and incorporate their suggestions into the project.
The entire AptaSteles journey was always directionalised by the impact that would be by it on the society and was optimally moulded by the inputs gained from experts and stakeholders.
Interactions with stakeholders
General PCOS Awareness Survey:
The survey to analyse the impact of our kit, the team created a general PCOS awareness survey.Through this survey, the team analysed the requirements and expectations of our stakeholders. The survey was ethically approved by the institutional ethics committee and was made according to the guidance of Dr Suchi Goel.
Click below to download the results and analysis of the survey
Visit to Primary Healthcare Centers (PHC)
The team visited the PHCs near tirupati and interacted with the doctors and nurses to analyse the situation that prevails at the ground level.
The team interacted with the doctors and nurses of PHC Mangalam about the number of people who reached out to the PHCs having symptoms associated with PCOS. The authorities mentioned that there had been a significant increase in the number of individuals who show up with the symptoms, and atleast more than five people visit the hospital in a week for the same currently.
During further discussions, the team learned that though many individuals had the symptoms, there was no proper setup available for diagnosis, and the individual had to travel to the nearby city to have a complete checkup. The team immediately analysed the available resources in the hospital and collected the details of the feasible storage conditions.
Storage refrigerators of -20°Celcius were available to store vaccines, and proper discarding bins and biohazard management followed. With this input, the team modulated the kit design by lyophilizing the substances and storing it at -20°Celcius. The team also developed the discarding mechanism according to the available discarding options at the PHC by incorporating a biohazard bag with the kit.
Visit to the Fertility Clinics
While visiting the fertility centers, we got to know that the prevalence of speculated PCOS cases is high in Tirupati. Additionally, as per clinical labs, there are 10-15 cases of polycystic ovaries diagnosed in a week, which might be positive cases for PCOS.
An important insight that we was emphasized received while visiting the fertility centers was that a diagnostic kit for PCOS would aid in early diagnosis. During our meeting with Dr Lavanya, senior doctor at Lavanaya fertility clinic, she suggested to target the adolescent age group for PCOS diagnosis, as the reproductive age group will be more aware of the syndrome.
Visit to the Pathological labs and Pharmacies
The team did fieldwork on local pharmacies and pathophysiological labs to analyse if the storage and distribution conditions were met by them,
The initial plan was to develop a home-based diagnostic kit. However, the kit requires special storage conditions like -20° C or -80° C refrigerators due to the reagents stored in the kit. So, to check if the storage and distribution conditions necessary for the kit are available, we set on fieldwork at pharmacies found in Tirupati, our immediate locality. On investigation, it was known that home-based kits like the self-testing pregnancy kits are sold at those pharmacies. They have refrigerators with a temperature range of 2-8°C to store the kits. These pharmacies purchase kits from dealers; if the kits expire, they are returned. On analysing the situation from the fieldwork, it was evident that a home-based kit was difficult to achieve.
So we shifted our focus to making the kit a lab-based one. So we went to pathophysiological labs to ascertain the storage and distribution conditions required for the kit. We found many of them have a -20°C or -80°C refrigerator. Additionally, the labs also had an elaborate sample and kit discarding mechanism. These pathophysiological labs were also accessible to the people in terms of location. The evolution of the kit from a home to a lab based kit was hinged upon the input we got from pharmacies and labs.
The Initial Idea
The team was initially working on various real-world problems. Meets with the IISER-Tirupati Biology department, helped the team choose to work on PCOS Diagnosis. The discussion sessions with Dr Shumathe K R helped the team understand the syndrome and channelise our approach.
IISER-Tirupati Bio-Dept.
The team met with the biology department of IISER Tirupati to modulate their synthetic biology solutions for selected real-world problems. It helped the team to build feasible solutions for the chosen issue. Diagnosis of PCOS was a real-life world problem chosen after a complete analysis of the statistical data and the feasibility of the proposed solution.
Dr Shunmathe K R
The team started its initial interactions with Dr Shunmathe K R, a general physician at Chennai, who explained to the team the syndrome and its symptoms, which aided the team in choosing the list of biomarkers and emphasizing the comorbidities and involving ourselves in making people aware of this syndrome. She also mentioned the existing diagnostic techniques and the inaccessibility of the same to a large set of population.
The Project Design
The team was in constant touch with Dr Ashwani Sharma, who modulated our designs of trigger-target and FASTmiR and Dr Harikrishna, who also suggested modifying the spinach aptamer.
The team also had discussions with experts at Aptalition, where we planned to raise aptamers for two of the selected biomarkers after the discussion.
Dr Ashwani Sharma
Dr Ashwani Sharma, Assistant professor, Department of Chemistry and Biology, IISER Tirupati modulated the trigger target approach, helped design the blocker according to the complementarity and the energy of binding, and suggested modifications in the trials of SELEX to get optimal results.
The team, under the guidance of Dr Ashwani Sharma, was able to develop the protocol of SELEX, and his suggestion of creating a blocker of length 10-15 nucleotides to ensure the modularity of our design was tested and incorporated while designing.
Dr Harikrishna S
The team was connected with Dr HariKrishna S, senior scientist at Syngene who suggested building and modifying the tetraloop region along with the stem regions and simulating the structures to visualise the same and analyse the interactions. The meetings with Dr. Hari Krishna helped the team build the project and virtually modify the aptamer to know about the stability of the G-quadruplex and its stability.
Dr Nibedita Pal
Meeting Dr Nibeditha Pal, Assistant Professor, Department of Biology, IISER Tirupati gave us the breakthrough required for our project. Dr Pal gave us insights into fluorescence and quenching. She explained the interpretation of fluorescence versus time graph. We understood from her about how we could find the intensity of fluorescence as a function of time. With this input, we identified how we would distinguish PCOS from non PCOS cases and solidified our project design.
Aptalition
The team had a great chance to interact with all aptamer enthusiasts in a common forum, the talks from Dr Banani Chakraborty and Dr Sarah Shigdar helped us realise the potential of using aptamers for the diagnosis along with the immobilisation options like Biotin-Streptavidin pulldown and various other applications. The team also interacted with the panellists on day 2 of the event where the suggestions to block the binding site of the aptamer using trigger would aid in release of the trigger while binding with the ligand. These suggestions were adapted into our designs and were modulated accordingly.
The Hardware
The designing and building of our hardware was a dynamic process. The meets with Dr Dileep Mampallil helped us revise our designs. Interactions with Dr Prosenjit Sen and Dr Manoj Varma helped us find the loopholes in our designs and improvise them. Dr Kanagasekaran T helped us build the optical detection components of our kit.
Dr Dileep Mampallil
Interaction withDr Dileep Mampallil, Assistant Professor, Department of Physics, IISER Tirupati, has been instrumental in developing the design for our kit and printing a prototype. He proposed incorporating passive valves in the form of capillary soft valves in the system. This helped us define chambers for the storage of the various reagents in the kit.
Dr Prosenjit Sen
Dr Prosenjit Sen, Associate Professor, Centre of Nanoscience and Engineering, gave us valuable input about making our hardware simpler and feasible.He pointed out the complexities in the circuit design and how we could improve on it. He suggested us to go for a single prototype and parallelising it to rest of them. This helped us come up with up a replicable prototype.
Dr Manoj Varma
Dr Manoj Kumar Varma helped us identify few loopholes in our design and also gave us a direction to find their solutions. Right from the valves to the storage of the reagents and the optical detection, he breezed us through different components that would be useful to our kit. He informed us about the photomultiplier for the detection of fluorescence, miniaturised solenoid valves, which gave us an idea about the specific components we had to look for our kit.
Dr Kanagasekaran T
Dr Kanagasekaran, Assistant Professor, Department of Physics, IISER Tirupati, constantly guided us throughout the development of the optical detection module. He recommended to use PIN photodiodes as it a better option for our system. It was then integrated into the hardware as a sensor for detecting fluorescence.
The Safety Aspects
The team was always keen to develop a safe and efficient method for the diagnosis of PCOS, for which the team verified the same with Dr Vibha Ahuja and also developed a discarding technique involving a biohazard pouch that could be used to discard the microfluidic chip after discussing with Dr Vijayalakshmi Subramanian.
Dr Vijayalakshmi Subramanian
Dr Vijayalakshmi Subramanian, Assistant professor Biology department, IISER Tirupati, is also a member of the safety committee at the institute and was the one to help us design the discarding mechanisms can be applied to make the kit more user-friendly and also a safer to be used.
The team incorporated her suggestions and modulated our approach by adding a biohazard bag and making it according to the availability of biohazard discards available in the nearby Primary healthcare centres, fertility clinics, and pathological labs in the vicinity.
Dr. Vibha Ahuja
The team met with Dr Vibha Ahuja, Chief General Manager of Biotech Consortium India Ltd., and theteam had a veryelaborate discussion about our designs and the safety aspects of the same. After the discussion, she verified our techniques and approaches were safe and that the diagnostic kit would be safe to use if used for diagnosis as it's a complete in-vitro system without involving any genetically modified organisms.
Communication
Interacting with our stakeholders was one of our primary motivations to communicate. Various experts gave suggestions and ideas to be incorporated into our workflow to communicate effectively, build a two-way dialogue, and facilitate our stakeholders.
Ms. Roshni Shangvi, a nutritionist, guided us in making an effective awareness brochure and verified the same. Dr Surbhi Singh, gynecologist and founder of NGO Sacchi Saheli, guided us to conduct various interactive sessions and also gave us insights on the syndrome.
Ms. Roshini Sanghvi
While developing the awareness brochure, the team had input from Roshni Shangvi about the diet plan and the effective fitness routine. With her input on making the brochure and spreading awareness on the same suggested to make some Instagram posters to spread awareness which was also executed during the PCOS awareness month.
Dr Surbhi Singh
The team had its very first interactions with Dr Surbhi Singh and got to know briefly about the syndrome and the symptoms common among people with PCOS. The team did a biomarker analysis according to the symptoms suggested by her. During further interactions with her, the team learned about the importance of communication and spreading awareness and suggested having discussion sessions with the people, which the team executed during the PCOS awareness month events.
Increasing Accessibility
The team was always determined to include the right stakeholders and make the project accessible for a large population. The team interacted with the iGEM family of IISER Tirupati and got to know that all Ovary owners are our stakeholders. The team also discussed with Dr Rasna Kishor and Dr Surbhi Singh and modulated our list of stakeholders. The team also interacted with Dyslexia associations in the vicinity to make the awareness brochure dyslexic friendly.
Dyslexia Association
The team interacted with the Madras Dyslexia association and Pondycherry dyslexia association to modulate the aftercare brochure with separate and differentiated reading sections and prescribed fonts ( the Sans family). The team worked to incorporate an image-based representation of data to make the brochure dyslexic-friendly and easy to read. The team also integrated other inputs, like making a light colour background and contrast fonts were also included.
Ovicloak
The team was in constant discussion with team iGEM IISER Tirupati 2021, who suggested that even intersex people and people from the transmasculine spectrum can also be prone to PCOS. This was also later confirmed from the interactions with other gynaecologists. With this input, the team expanded the stakeholders from women to all Ovary-Owners.
Modelling
The team developed modules for the modelling, taking reference from the literature. The team approached Dr Tapan Chandra Adhyapak and Dr Jatish Kumar to verify our modules. The suggestions from the experts were analysed and incorporated into our modules.
Dr Tapan Chandra Adhyapak
Dr Tapan Chandra Adhyapak,Assistant Professor,Department of Physics, IISER Tirupati helped with the math modelling. He verified the equations and asked the team to check certain factors in the system like the diffusion barrier in our system and explained how it could be modelled. In this light, it was verified that there is no diffusion barrier in the system, as the aptamers are in excess.
Dr Jatish Kumar
Dr Jatish Kumar, Assistant Professor, Department of Chemistry, IISER Tirupati played a key role in validating the rate law equations of the Reaction Kinetics module. He suggested to look up Chain Reaction Kinetics for the steps of looping. Dr Kumar aided us in simplifying the model. Putting together all the pieces of tips he gave, the Reaction Kinetic module was completed.
Implementation
The team discussed with various experts the aspects of our kit that were potentially analysed by our team and were incorporated into multiple modules of our project.
Dr Rasna Kishore suggested the implementation cycle, and the round-table meeting during the All India iGEM Meet 2022 with the startup company founders helped the team develop a preliminary marketing strategy for our product.
The interactions with Dr Shibdas Banerjee helped the team develop strategies for cohort studies, analyze the biomarkers' levels, and modulate the kit accordingly.
Dr Rasna Kishor
The team interacted with Dr Rasna Kishor, who suggested the team create an implementation cycle of Educate-Diagnosis-Modulate.
The discussion sessions with Dr Rasna Kishor made us understand that PCOS is a more prevalent syndrome and needs optimal lifestyle modifications to maintain a healthy lifestyle. Dr Rasna Kishor answered the questions collected from the stakeholders on the syndrome, which was also added to the awareness brochure in the FAQ session.
Her suggestion of educating the large-scale population about the syndrome would help people was incorporated into the workflow, and awareness sessions were conducted parallelly during the laboratory sessions.
Dr Shibdas Banerjee
Dr Shibdas Banerjee enlightened the team with the steps included in biomarker selection based on experimental data and how it can be extrapolated using machine learning. He taught how a dataset is built, and the model is built and validated on the basis of the dataset. This set the basis for biomarker analysis and how it could be implemented in the future to test the sensitivity and specificity of the kit.
The team had a great opportunity to discuss with various start-up companies' CEOs and founders and interact about bringing AptaSteles into the world.
The team discussed the project and kit design that could help the team build a feasible and realistic timeline accommodating the various phases through which the kit would be going through while bringing it to the real world as a complete diagnostic kit.
GALLERY
