Mr Mohan
(Coffee Board of India)
January 2024
Provided strategic guidance during initial project ideation. Emphasized the importance of improving coffee yields over targeting weeds, which helped refine the project’s objectives to be more impactful for the coffee industry.
January - October 2024
Played a crucial role in understanding and explaining the biological mechanisms in the project, helping the team effectively navigate complex concepts in synthetic biology. Provided hands-on assistance in the wet lab, contributing to the design of experiments and troubleshooting issues, significantly improving the project's experimental rigour. We have maintained consistent communication with the team, offering assistance wherever needed throughout the project. Facilitated access to institutional resources and managed logistics, ensuring smooth project progress. .
Dr. Ritu Raval (Associate Professor in Biotechnology, MIT, Manipal)
Dr. Praveen Kumar
(Assistant Professor - Selection Grade, MIT, Manipal)
January 2024
Contributed to the team by specifying the different cell signalling processes for the team to ideate upon various antifungal mechanisms using bacteria. Offered insights into antibiosis, enriching the team’s understanding of microbial interactions and informing the selection of potential biocontrol agents. The team later used this as a base to narrow down the antifungal of choice.
January 2024
Expanded the team’s network within the agricultural research community. Provided valuable insights on current farming practices and research trends that informed the project’s direction. The team gained knowledge about existing farming practices, including the use of chemical fungicides to answer fungal infections. This led the team to start background research on biocontrol agents as an alternative, considering chemical fungicides often results in soil leaching.
Dr. Salmataj S A
(Assistant Professor - Selection Grade, MIT, Manipal)
Dr. Somanna Kolimada (Executive at Coffee Planters Association)
January 2024
Shared expertise on the interactions between bacteria and fungi, mainly related to the pathogen Coffee Leaf Rust, providing critical background information for developing effective biocontrol strategies. Helped outline essential wet lab experiments, including but not limited to antifungal assays, ensuring the team was well-prepared to conduct meaningful research. The team gained an idea about potential experimentation to be carried out with the biocontrol agent of choice.
February 2024
Offered her knowledge of various computational tools and methodologies applicable in the Dry Lab, such as Schrodinger, alpha fold and Hdock, enhancing the team’s capacity for data analysis and experimental design. She shared her experience as a former iGEM participant, providing advice on project management and presentation skills that were invaluable for the team's overall development.
Ms. Anusha
(Research Associate, Dr. Reddy's Laboratory)
Dr. Nagaraj (Agronomist)
&
Dr. Manjunath (Entomologist).
Visit to Coffee Research Substation, Chettalli, March 2024
Learned about the use of Bordeaux mixture and systemic fungicides, which informed the project’s approach to disease management and helped identify gaps for biotechnological interventions. This validated the team’s idea to carry forward with a biocontrol agent in the form of iturin A as an alternative to existing Bordeaux mixtures and system chemical fungicides.
March 2024
She emphasized the difficulty of early detection for Hemileia vastatrix (HV) due to its close genetic similarity to other fungi, which results in low numbers of detectable proteins, making separation from other fungi challenging. She discussed the potential for HV to develop resistance to iturin, concluding that single gene mutations are unlikely to result in resistance due to iturin’s complex mechanism, granting the product long-term effectiveness. Athina highlighted the co-evolutionary relationship between iturin and rust fungi, clarifying that the presence of HV on plants doesn't necessarily indicate disease and orange spores on the back of the leaf are the best indicator for initiating fungicide application. She pointed out that environmental factors, particularly disease pressure, strongly influence the severity of HV infection. Her insights about iturin’s complex mechanism and gene mutations gave the team the idea to choose B. subtilis and replace the bacteria’s native promoter with a stronger dual promoter.
Dr. Athina Koutouleas
(pHD., University of Coppenhagen)
Maurice D’Moss
(Former iGEM Participant)
April 2024
Highlighted the issue of coffee bean adulteration when selling the harvest to roasters, which results in the beans being sold at a lower cost.This meeting was pivotal for our project as it directed us towards the machine learning realm to help farmers predict the yield of coffee.
May 2024
Helped them check the open reading frames (ORF) with dual promoters to ensure that the itu synthetase genes are correctly transcribed by investigating RNA polymerase structure in Bacillus subtilis, focusing on potential transcription hindrance due to transcription factors. Helped simulate the docking of sigma factors from the holoenzyme state and learned about the potential role of stem-loops in halting RNA polymerase progression in some cases.
Dr S Balaji
(Head of Department, Biotechnology, MIT, Manipal)
Dr. Shaik Mohammad Abdul Fayaz (Assistant Professor - Selection Grade Department of Biotechnology, MIT, Manipal)
May - October 2024
Dr. Fayaz helped the team find conceptual clarity behind the working of our promoter and helped us realise we may not be able to make our dual promoter work with the repressible promoter being closest to the gene. We were also suggested we add a spacer between the two promoters if there was any hinderance caused by the adjacent sequence of the promoter region it being a transcription factor binding site. We encountered errors in our docking to large lengths of our fragment which was realised during the conversation with him and hence only the core region was docked. He has also helped us in generation of 3D structures required for docking and recommended various docking webtools to try and interpret the results of them all. He is presently guiding us to perform molecular docking simulation for the sigma factors and our promoter fragments.
June - September 2024
Dr. Sabari highlighted the strong constitutive pVEG promoter, which is frequently used in his lab for GFP expression, where green fluorescence can be seen on the plate. Bacillus subtilis is cold-sensitive, thriving between 20-25°C, with an optimal growth temperature of 37°C, and grows well on LB agar, similar to E. coli. He recommended homology flanks between 500-1kb for transformation, as shorter ones (~350bp) yield low success rates, and offered protocols for transformations and media preparation. Dr. Sabari emphasized proper storage in 50% glycerol at -80°C, as Bacillus subtilis is cold-sensitive, and advised managing cell density to prevent sporulation after extended periods. Also assisted in designing the protocol for our 6-hour bacterial growth curve experiment by guiding us in selecting the appropriate dilution factors and providing support in troubleshooting issues encountered during our previous growth curve attempts.
Dr. Sabari Sankar
(Assistant Professor Grade I Biology, IISER TVM)
Meeting with Karnataka Planters Association
July 2024
Discussed the factors influencing farmer acceptance of biocontrol agents, emphasizing the importance of user-friendly instructions and addressing farmer perceptions. Further went into the key parameters to be considered Suggested conducting field trials to demonstrate the efficacy of the biocontrol product before engaging farmers, which informed the team’s strategy for community outreach. Clarified the team’s doubts over follow-up calls and meetings related to blossom and monsoon rainfall of coffee cultivation which was utilized in the team’s machine learning model. Helped us identify the impact of yield prediction on supply-chain of coffee. Explained how the yield is currently estimated solely based on visual estimation.
July-August 2024
Assisted in optimizing our 24-hour bacterial growth curve protocols by providing comprehensive guidance on experimental design, including the selection of appropriate time intervals and dilution factors. Additionally, he played a key role in troubleshooting experimental challenges, ensuring accurate data collection and analysis.
Mr. Rajesh KM
(PhD Scholar, MIT, Manipal)
Mrs. Atheena PV
(PhD Scholar, PMRF fellow, MIT, Manipal)
July-September 2024
Played a crucial role in helping us understand the laboratory environment and safety protocols. She also provided significant support in troubleshooting various experiments and offered valuable insights and guidance throughout the process.
July 2024
Advised testing two constructs, PbacA and P43, focusing on GFP for quantifying promoter strengths. He explained the influence of the strength of the Ribosome Binding Site (RBS) on downstream gene expression. This was incorporated in the team’s dry lab efforts toward studying the dual promoter’s efficacy using the two suggested constructs. Discussed the Polarity effect, noting that dual promoter systems may not always produce cumulative effects but could show synergistic expression in certain constructs. This helped the team formulate a coherent DBTL cycle as the team’s dual promoter construct caused a synergistic effort and also made the team look into whether the construct was multiplicative or additive in nature. Highlighted the importance of a wettable product formulation and suggested using CPEc as a cheaper alternative to Gibson Assembly.
Dr. Aditya Sarnaik
(Postdoctoral research scientist, Arizona State University)
Meeting with Ms. Sathya D
(Harley Plantations)
September 2024
Provided critical insights into existing pest control methods and the role of Bordeaux mixture, highlighting the need for the new product to offer clear advantages over established practices. Emphasized the importance of ensuring that the biocontrol agent does not leave harmful residues, guiding product development toward safer formulations. Suggested and stressed the significance of field trials, which informed the project’s implementation and testing strategies.
September 2024
Emphasized the need to open options for broader disease management by targeting additional fungal diseases such as Nursery Rot, Black Rot, Berry Stem Rot, and Fruit Rot. Explained how fluctuating temperatures and high moisture during the Oct-Nov season promote the growth of HV spores, leading to plant defoliation and reduced yields, stressing the importance of considering these conditions in antifungal testing. Recommended to test the antifungal compound against 2-3 more pathogens and establish antagonistic relationships with fungal spores. Advised isolating and identifying rust species from different coffee plantations, particularly distinguishing between Arabica and Robusta varieties, to assess the compound’s effectiveness. Provided critical parameters for the machine learning model, such as post-monsoon data, berries per node, and losses after the monsoon season. The team planned its future goals upon Dr. Jeena’s advise to test iturin A as a biocontrol agent against other fungal pathogens affecting coffee.
Dr. Jeena Devasia
(Divisional Head - Plant Breeding & Genetics, Central Coffee Research Institute, Coffee Board of India)
Dr. Bharath Raja Guru
(Professor, Dept. of Biotechnology, MIT, Manipal)
September 2024
He assisted us by providing access to his HPLC machine and facilitating our connection with Nayana. Additionally, he offered us the contact information of a PhD scholar from whom we can obtain MTT.
September 2024
Assisted us in understanding and optimizing our HPLC protocols for both the standard and extracted Iturin. With her guidance, we gained a deeper understanding of the peak analysis necessary for constructing the standard curve. Additionally, she provided valuable insights into interpreting our data and results.
Ms. Nayana Elizabeth Subash
(Research Scholar)