Human Practices
Every year, 1.3 billion tons of food are wasted globally—over one-third of all food produced. This generates 8-10% of global greenhouse gas emissions, causes about one trillion dollars in economic loss, and deepens inequality as millions face hunger. In Japan, food loss reached 4.64 million tons in 2023. Many fruits and vegetables are discarded despite being edible, often due to minor imperfections or strict retail standards. PreserVEG aims to reduce such waste by enhancing produce safety and visualizing freshness and deterioration.
Even when still edible, produce is often discarded over concerns about appearance, freshness, or safety. In Japan, an especially strict demand for freshness further drives this tendency.
Climacteric produce like bananas, apples, and tomatoes release ethylene gas during ripening, accelerating deterioration of nearby items and shortening overall shelf life.
The lack of simple, objective criteria for judging deterioration forces reliance on appearance and smell, leading to premature or delayed disposal and increased food waste.
To clearly illustrate the progress of our project, we created a roadmap summarizing each phase—from identifying the problem to proposing a solution and considering social implementation. This roadmap visually shows how our idea evolved and was shaped into a project that takes both social and scientific responsibility into account. You can click on each apple pin to jump to the corresponding section.
The AREA Framework is a structured approach to achieving “Responsible Innovation,” with the aim of effectively integrating stakeholder dialogue and feedback into projects. Originally proposed by Professor Richard Owen, the framework is guided by the principle of promoting science and innovation that are socially desirable and in public interest. It is now widely adopted by research funding agencies and academic projects as a method to support responsible decision-making and has also been employed by numerous iGEM teams in recent years. Notably, the TU Eindhoven 2022 team pragmatically optimized the AREA Framework, restructuring it into the following four phases. Our team followed this approach and redefined each phase as follows to better suit our project:
Reflect → Purpose
Engage → Contribution
Act → Implementation
Anticipate → Outlook
This change aims to provide a clearer and more intuitive understanding of the role each AREA phase played in the actual project. Click on the segmented parts of the circle in the diagram below to see details about each phase.
Following the process described above, we have redefined the four phases of AREA as follows. For example, “Reflect” was a process for deeply exploring the motivation and social significance of the activity. By redefining it as “Purpose,” we made it possible to clearly express why that dialogue was important. Similarly, “Engage” has been reorganized to focus more on the resulting “Contribution” rather than the actual interactions themselves. “Act” demonstrates how the gathered opinions were translated into “Implementation,” while “Anticipate” is now expressed as a “Outlook” for future actions based on anticipated challenges and impacts, linking more directly to concrete steps. Organizing it this way allows the AREA framework to be used not merely as a concept, but as a clear, practical guideline for advancing projects step-by step.
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Human Practices are an essential element in all iGEM projects. Understanding the people affected by our activities and those who provide valuable perspectives is crucial not only for assessing scientific feasibility but also for designing socially meaningful solutions. Throughout this project, we gathered input from individuals in various roles, including university professors and industry experts. To organize these stakeholders, we categorized them into seven distinct groups. This framework enabled us to identify the concerns and expectations held by each group and incorporate them into our project design. The roles and characteristics of each stakeholder group are summarized in the diagram.
Based on information from our stakeholder analysis, we categorized seven stakeholders. We used the “Power-Interest Grid” below for this purpose. This framework positions stakeholders on two axes—Power and Interest—to determine the optimal approach for engagement. We visualized the analysis results as a matrix and placed each stakeholder within it.
Using this matrix allows us to adjust our approach and focus for each stakeholder based on their specific characteristics, rather than treating all stakeholders uniformly. We organized objectives and approaches into the following four quadrants
High Power × High Interest
We engaged to gather broad input, ranging from specialized questions to on-site challenges.
High Power × Low Interest
We are engaged to ensure appropriate information sharing and understanding in critical situations, and to clarify what improvements could increase their interest.
Low Power × High Interest
Since many lack specialized knowledge, we prioritized clarifying on-site challenges over
Low authority × Low interest
Since many individuals lacked specialized knowledge, we prioritized clarifying on-site challenges without imposing excessive burdens during our engagement.
To ensure that our Human Practices are meaningful and effective, it is essential to accurately understand the relationships among all stakeholders involved in the project. Therefore, we organized and analyzed the interconnections between each stakeholder group. The diagram above illustrates the relationships among seven distinct stakeholder groups, depicting the progression from the foundational stage to the applied stage. By visualizing this flow, we were able to gain a clearer understanding of the connections and interactions among stakeholders. In addition, the diagram presents the specific Human Practices conducted with each group, through which we were able to further clarify and refine the overall direction of our project.
To investigate the challenges faced in the field regarding the goal of reducing food waste, we conducted Human Practice. The results revealed that a large amount of food waste occurs from the pre-shipment stage through the wholesale and retail stages. Consequently, we focused the target of this project on those stages and set the project goal as developing packaging materials that coat produce.
Institution: Ministry of Agriculture, Forestry and Fisheries
Stakeholder: Government, Localities
Expertise: Regional branch office of the Ministry of Agriculture, Forestry and Fisheries implementing policies for agricultural development in the Tokai region
The Tokai Regional Agricultural Administration Bureau works in cooperation with local governments to promote the recycling of food waste and reduce food loss, while also managing the safe use of pesticides. Building on the insights gained through this interview regarding the current situation and countermeasures for food loss, the bureau intends to focus its efforts on wholesalers and retailers handling fresh produce. Moving forward, it aims to develop coating technologies to minimize produce loss during distribution and sales, while continuing HP activities to acquire further technical knowledge.
The Tokai Regional Agricultural Administration Bureau collaborates with local governments to reduce food waste through initiatives such as supporting the recycling of food residues from food-related businesses and implementing measures to prevent food loss during distribution and consumption.
In addition, it oversees the safe management of pesticides used for quality preservation against pests in agricultural fields and other settings.
We contacted the bureau to discuss the current situation regarding food loss and the corresponding countermeasures.
Food loss in the wholesale and retail sectors amounts to approximately 570,000 tons annually. Although food loss accounts for about 20% of the total food waste generated by the entire food industry, the proportion is relatively high in the wholesale and retail stages. Specifically, wholesalers generate around 90,000 tons of food loss out of an annual 160,000 tons of food waste, while retailers produce about 480,000 tons out of 910,000 tons. (1)
To address this issue, the Ministry of Agriculture, Forestry and Fisheries (MAFF) is promoting more sustainable consumer purchasing behavior through measures such as reviewing commercial practices, encouraging the donation of unused food, and promoting sales in line with demand. Furthermore, by sponsoring and supporting the “Food Industry Mottainai Awards,” MAFF aims to achieve a 60% reduction in food loss at both the distribution and consumption stages.
Regarding food waste recycling rates, MAFF has set targets of 75% for wholesalers and 65% for retailers. The current average rates—74% and 66%, respectively—are close to these goals. However, when focusing solely on fresh produce, the recycling rates are substantially lower: 59% for wholesalers and 41% for retailers, indicating a major challenge in the overall management of food waste. (2)
The significant volume of produce loss represents one of the key challenges in addressing food waste. As the recycling and reuse of produce are less developed than for other food categories, minimizing produce loss is seen as a critical step toward reducing overall food waste
h the approach of coating fresh produce, with the primary goal of reducing losses occurring at wholesale and retail sites. Moving forward, we will conduct Human Practice to gain technical insights for project implementation.
Future projects will focus on initiatives targeting wholesalers and retailers within the produce handling industry. Fresh produce experiences significant losses during distribution and sales, and its recycling rate tends to be lower compared to other food products.
Therefore, we have decided to proceed wit
Company: Riken Technos group
Stakeholder: Industry
Expertise: A material solutions company applying resin compounding and processing technologies to compounds, films, and food packaging
Human Practices were conducted to seek advice on the functionality of a fruit and vegetable coating material made from biocellulose, leveraging Riken Technos Corporation's film processing technology. The results highlighted the need to focus on moisture, oxygen, and carbon dioxide permeability while also utilizing its water retention and safety properties. However, considering food hygiene and the potential burden on the produce, we decided to proceed with development as a wrap or film type packaging material rather than a direct coating.
Riken Technos Corporation possesses cutting-edge film processing technology in the medical and food sectors. We contacted them to seek advice on the direction the bio-cellulose film produced in this project should take, as well as to exchange opinions.
Regarding the relationship between handling vegetables and fruits and the film, it was noted that coating can block moisture exchange, potentially leading to spoilage, so moderate moisture permeability is necessary. We received advice that it is beneficial to investigate moisture permeability, ethylene gas, and the permeability of carbon dioxide and oxygen during the development stage. However, since the appropriate oxygen permeability value differs depending on the type of produce, we were advised that narrowing down the target produce is advisable. Furthermore, when using coating agents, direct coating is difficult because they must meet the standards of the Food Sanitation Act. Regarding antimicrobial properties, focusing on biodegradability is also considered an effective perspective.
To implement this project, we first determined it necessary to focus on maintaining freshness and reducing food loss, discussing food that becomes waste during the storage period before distribution. Furthermore, since coating has certain limitations, we need to consider alternatives like plastic wrap or film for non-sealed applications. We also gained insights into the need to prioritize sustainable materials over antimicrobial properties, focusing on biodegradability.
Based on advice derived from Riken Technos Corporation's expertise in film development technology, this project must proceed with particular focus on moisture, oxygen, and carbon dioxide permeability. We also considered that the properties of bacterial cellulose, such as its water retention, water absorption, and safety, could be leveraged here. Regarding the form of the project product, directly coating produce would require compliance with the Food Sanitation Act and could potentially stress the produce during the heating and drying processes involved in application. Therefore, we decided to explore creating packaging materials such as wraps or films instead of a form applied directly to the produce.
Building on Section 1, we decided to create packaging materials using bacterial cellulose. In Section 2, we conducted Human Practice with companies and professors to seek technical advice. As a result, many technical challenges related to the development of bacterial cellulose as a packaging material were identified.
Company: Kinjirushi Group
Stakeholder: Industry
Expertise: A company handling everything from wasabi variety development to manufacturing, utilizing technologies such as freshness-preserving films while establishing a thorough quality control system.
Through discussions with Kinjirushi Corporation, it became clear that packaging materials with flexibility, barrier properties, and antibacterial properties are crucial for maintaining the quality of fresh produce. While replacing conventional materials with bacterial cellulose is effective for extending shelf life, challenges exist in adapting it to storage and transportation under the current logistics system.
Kinjirushi Corporation possesses advanced technology concerning packaging materials for fresh produce, including freshness-preserving films. Therefore, with the aim of clarifying the relationship between food loss in produce and packaging materials, discussions were held regarding the effectiveness of packaging materials in maintaining food quality and challenges within the production process.
At Kinjirushi Corporation, increased waste from plastic packaging material usage is a challenge, and the company is working to improve this through in-house development. We also received feedback that three key requirements for fresh produce packaging materials are flexibility, barrier properties, and antimicrobial properties. Properly controlling the respiration rate and moisture balance of fresh produce contributes to quality preservation and safety assurance.
From an economic perspective, it was pointed out that companies are required to allocate costs commensurate with the price of the target fresh produce and to enhance productivity.
Furthermore, while replacing packaging materials with bacterial cellulose is expected to extend shelf life, it was noted that current logistics systems face challenges in accommodating storage requirements.
Considering the challenges of plastic packaging materials, we are advancing the adoption of bacterial cellulose, which combines flexibility and biodegradability. To address the lack of barrier properties and antimicrobial effects, we are exploring designs that incorporate these functionalities. Additionally, insufficient resistance to transport impacts has been identified as a challenge, indicating room for structural improvements. Furthermore, since applying this to all produce is impractical, development is prioritizing items with high market value that deteriorate quickly and are prone to loss.
Based on advice from Kinjirushi Corporation, this project is exploring coating bacterial cellulose with substances that prevent fruit and vegetable quality degradation to enhance quality retention functions. This includes considering the addition of antimicrobial, repellent, and plant hormone absorption capabilities. This is expected to contribute to preventing fruit and vegetable deterioration and reducing waste volume. Additionally, to address cost challenges, we plan to improve bacterial cellulose yield through genetic engineering techniques for promoter optimization and increased expression of cellulose synthesis-promoting factors. However, bacterial cellulose is vulnerable to impact during transport, which could cause damage or degradation. If intended for use during transport, it is necessary to consider measuring the impact resistance of the bacterial cellulose.
Institute: Gifu University
Stakeholder: Academia
Expertise: : Postharvest Engineering (Prof.Nakano)
Food fermentation science(Assistant Prof. Nakagawa)
Through discussions with Professor Nakano and Assistant Professor Nakagawa, we evaluated the usefulness and novelty of coating fresh produce with microbially derived cellulose. We found that similar studies using plant-based cellulose nanofibres already exist and that technical issues such as coating stability remain unsolved. Moreover, since some fruits and vegetables do not show visible signs of deterioration, the professors suggested that visualising freshness using pigments or microbial metabolism could be effective in reducing food loss. This insight marked a turning point, shifting our project’s focus from packaging materials to a freshness visualisation system.
Professor Nakano is an expert in post-harvest engineering and is working on the development of freshness preservation and freshness evaluation technologies for fruits and vegetables. And assistant professor Nakagawa conducts research on utilizing substances produced by microorganisms such as sugars, lipids, and enzymes for industrial and domestic applications. We aimed to discuss the usefulness and novelty of this project's concept – coating fresh produce with cellulose derived from microorganisms – by comparing it with existing freshness preservation technologies.
It was found that research already exists on the use of plant-derived cellulose nanofibres to coat fruit and vegetables. Furthermore, as nanocellulose coatings are prone to cracking during drying, it became clear that there are many challenges in terms of materials and technology, such as coating methods and the amount of water in the cellulose. We also learned that some fruits and vegetables may not show any visible changes even when they deteriorate or reach their optimal eating stage. We understood that this can potentially lead to the disposal of produce. Based on these facts, the professors suggested that tools utilising pigment components and microbial metabolism to visualise the condition of fresh produce could also be effective in addressing FLW.
The concept of this project presents challenges in differentiating it from existing research, and we have recognised that numerous technical issues remain that cannot be resolved by synthetic biology alone. Furthermore, in order to understand the reality of food loss and propose solutions with a view to social implementation, it was considered necessary to incorporate the perspectives of both consumers and producers of fresh produce.
We gained a new perspective on tackling food waste by visualising the condition of fresh produce. From this idea, we realised that harnessing microbial metabolic functions to indicate produce deterioration could help reduce food loss.This discussion marked a turning point, shifting the project’s focus from developing packaging materials to creating a freshness visualisation system.
From the advice received from post-harvest and microbiology specialists, we decided to devise a more realistic and distinctive solution based on the approach of visualising the condition of fresh produce. Furthermore, it is necessary to conduct public surveys and interviews with farmers to get feedback and understand end-user opinions, in order to assess the social impact of new projects.
Institution: Professor, Gifu University
Stakeholder: Academia
Expertise: Molecular and Cellular Biology
We aimed to design a genetic circuit using the Cre/loxP system to simultaneously achieve bacterial cellulose synthesis and prevent quality degradation. However, discussions with Prof. Nakagawa pointed out that the necessity of using the Cre/loxP system for phased gene expression was not sufficiently justified, and that using two different bacterial strains might be a more efficient approach. Furthermore, we received the idea of replacing Cre expression with a circuit activated by microorganisms reacting to food surface components. It was also suggested to use simpler molecules, such as antibacterial peptides, instead of complex pathways. We examined the necessity of the Cre/loxP system and decided to design a simpler, more environmentally responsive circuit for quality maintenance.
Prof. Nakagawa is engaged in research using genome editing technology and cultured cells to elucidate the roles played by post-translational modifications of proteins. We designed a genetic circuit using the Cre/loxP system to simultaneously achieve bacterial cellulose synthesis and prevent quality degradation. Based on the project's objectives, we aimed to have this circuit design evaluated for its validity and to receive advice for its improvement.
Insert1 ex) cellulose synthesis enhancer
Insert2 ex) antibacterial agents, insect repellents
It was pointed out that the necessity of using the Cre/loxP system to achieve phased gene expression for the dual purposes (bacterial cellulose synthesis and functional enhancement) has not been sufficiently demonstrated. At present, it was revealed that using two types of bacterial cells may be more efficient than deliberately inducing phased gene expression.
Additionally, we also received advice on a new approach. This is the concept that instead of adding IPTG to induce Cre expression, the circuit is activated when the microorganism detects components on the food surface.
Regarding methods to prevent quality deterioration, it was pointed out that synthesizing antibacterial substances or insect repellents may require complex metabolic pathways, potentially making substrate supply difficult.
Through this discussion, we felt it necessary to reexamine the significance of introducing the Cre/loxP system. We realized that this system offers few advantages unless there is a need for phased gene expression. Therefore, the conventional design requires revision.
Furthermore, we began to consider that incorporating a new mechanism for inducing Cre expression could enhance the novelty of the project. Additionally, regarding quality control, we decided to consider candidates such as antibacterial peptides, which can be synthesized relatively simply, rather than complex chemical substances.
First, to clarify the reason for introducing the Cre/loxP system, we decided to redesign the genetic circuit. If the necessity for the system is limited, we will also consider switching to a simpler design. Additionally, to develop a new Cre expression induction system, we will explore an environmentally responsive genetic circuit based on the characteristics of fresh produce. Furthermore, for the quality deterioration prevention function, we will specifically consider utilizing antibacterial peptides with relatively simple synthetic pathways.
Based on the activities described in Section 2, it became clear that implementing packaging materials made from bacterial cellulose was technically challenging. Therefore, the project shifted its focus toward developing a bio spray with functions to visualize and prevent the deterioration of fresh produce.
Stakeholder: General public
Survey location: Online and Open campus
Following revising our project policy, we conducted a public survey to understand societal perceptions and implementation challenges regarding ethylene-induced deterioration in fresh produce. The results revealed that balancing safety with quality preservation (maintaining taste and aroma) is a key future challenge. Therefore, we are using Nisin, a food additive approved for safety, and are investigating safety management measures through interviews with farmers and companies. Additionally, we decided to interview coating companies to address quality preservation and are currently conducting experiments on processing methods.
After revising our project policy, we conducted a survey targeting the general public to confirm how ethylene-induced deterioration of produce is perceived in society and to identify challenges for implementation.
Approximately 85% of people have experienced not being able to eat fruits and vegetables due to spoilage. It was found that they often notice the spoilage only when it has already progressed significantly, such as when discoloration or mold growth occurs. Additionally, nearly half of the respondents expressed reluctance to use biosprays developed using genetic modification technology. Key concerns cited for this project include safety, impact on taste and aroma, and cost.
Survey results indicate that the project's biospray prevents the spread of ethylene-induced deterioration, thereby reducing produce loss, suggesting this project could contribute to that goal. Furthermore, since bacterial cellulose incurs significant costs for synthesis and processing, (3) from a financial perspective, biosprays are more effective than creating packaging materials using bacterial cellulose for fruits and vegetables in terms of widespread adoption by the general public. To implement and popularize biosprays, it is essential that they are safe and do not affect taste or aroma.
Future activities must ensure two key points: ensuring safety of the project and maintaining the original taste and aroma of the produce remain unchanged. Therefore, regarding safety, we have opted to use nisin, an antimicrobial peptide that is also used as a food additive and has minimal impact on the body's natural bacterial flora. The safety of nisin is guaranteed by national authorities. (4) Furthermore, to gain insights into the safety management practices employed by those in the produce handling industry, we decided to conduct field visits to farms and companies. Additionally, to explore methods for minimizing impacts on taste and aroma, we will conduct human practice activities with companies specializing in coating to gain knowledge on processing method innovations and proceed with experiments.
Company: Fig farmer tete.
Stakeholder: Farmer
Expertise: A fig farm selling fresh figs and processed fig products.
Through interviews with tete. , an organic fig farmer, it became clear that quality control for fresh produce relies heavily on sensory judgment, with labor shortages and inconsistent standards posing significant challenges. Furthermore, we learned that when introducing biosensors, setting appropriate thresholds to prevent increased food waste and designing sensors that do not compromise product appearance are critical considerations.
To assess the social utility and concerns of this project, we conducted an interview with fig farmer tete.. Tete. is dedicated to reducing environmental impact through pesticide-free fig cultivation and utilizing unsellable fruits in processed goods. From this perspective as a farmer and seller, we asked how our project might be perceived and what opinions or concerns exist regarding safety and quality control. This provided valuable insights into the challenge of food loss in fresh produce.
Tete. strives to ensure safety and consumer trust through safety management practices such as storing harvested figs in low-humidity cold storage at 13-15°C and strictly avoiding pesticides and herbicides.
However, determining harvest timing and deterioration relies on sensory judgment, such as manually assessing fig firmness, presenting challenges due to labor shortages and inconsistent standards.
Furthermore, when introducing biosensors, it was pointed out that excessive labeling indicating “unfit for consumption” could paradoxically lead to increased food loss, making it crucial to set appropriate thresholds. Additionally, advice was received that since biosensors can alter the product's inherent texture, potentially reducing consumer purchasing interest, it is necessary to devise methods that do not compromise the product's appearance.
We believe the project's biosensor is effective in solving the challenges faced by tete.: labor shortages caused by manual fig condition checks, inconsistent harvesting standards, and deterioration resulting from handling the figs by hand. However, concerns exist that introducing the biosensor may lead to excessive waste due to the visualization of product deterioration levels and a decline in consumer purchasing interest.
Future activities require the selection of an appropriate ethylene threshold. Furthermore, since biosensor specifications could potentially lead to reduced consumer purchasing interest and excessive food loss, the project biosensor's color change detectable under black light illumination.
Institute: Professor, Gifu University
Stakeholder: Academia
Expertise: Postharvest Engineering
Our purpose in contacting him was to have him reevaluate this technique from the perspective of climacteric fruit ripening. Based on his advice, this study revealed that while the technique is effective for fruits where ethylene concentration increases until full ripeness, it is unsuitable for fruits where ethylene decreases thereafter—though its function as a “ripeness marker” remains viable. The GFP-based ripeness indicator proposed by Professor Nakano shows high practicality, but the precise control of GFP expression remains a key technical challenge for future development.
Professor Nakano provided advice even before the project change. (Link to Professor's interview card) The new approach of creating markers for deterioration originated from that HP. Therefore, the goal was to have him reevaluate the new approach of visualizing produce deterioration using a biospray from the perspective of climacteric produce ripening. Furthermore, based on the advice received, we decided to consider which climacteric produce this tool could be applied to
During this exchange, we received advice that “there are various types of climacteric fruits” and that “the timing of ethylene release differs by type and should be considered.” Additionally, we received the suggestion that a system “visualizing optimal eating time based on GFP expression levels” could be useful, not just for timing decay.
We investigated climacteric fruits in detail. Our findings suggest this project could be effective for fruits exhibiting pronounced climacteric ripening. Regarding the suggestion that a “system visualizing fruit ripeness based on GFP expression levels” could be useful, while GFP expression is currently achievable, precisely controlling its expression levels remains technically challenging. However, we recognize this as an important challenge for future development.
Based on the points raised by Professor Nakano, we conducted a detailed investigation into the characteristics of climacteric fruits. The results revealed that this project is effective for fruits where ethylene concentration continues to rise from harvest until they reach optimal ripeness. Conversely, it was found that detecting deterioration is difficult for fruits where ethylene concentration decreases after they pass their optimal ripeness. However, even for this type of fruit, it is considered possible that it could function as a “marker to visualize ripeness.”
Furthermore, the system proposed by Professor Nakano, which “indicates fruit ripeness based on GFP expression levels,” could be a highly practical technology if realized. However, while GFP expression itself is currently achievable, freely controlling its quantity remains a technical challenge at this stage. This is an important issue that should be addressed for future development, and we intend to explore its potential going forward.
Company: Kanesue Group Corporation
Stakeholder: Access
Expertise: Specialty supermarket for organic and natural foods
Through interviews with the organic food specialty store Shunrakuzen, we identified the current situation and challenges related to produce loss.
The use of genetically modified organisms is difficult for safety-conscious consumers to accept.
Furthermore, because the assessment of produce deterioration relies on visual inspection, issues such as inconsistent disposal standards and increased workloads have arisen.
These findings highlight the need for technological development that can visualize the condition of produce and support appropriate disposal decisions.
Shunrakuzen is a specialty store for organic and natural foods operating primarily in Aichi Prefecture. Particularly for fresh produce, it establishes clear labeling standards based on cultivation methods, providing an environment where consumers can confidently select products.
In this activity, we conducted Human Practices with Mr. Katsuhiko Goto, who is responsible for product management. From Shunrakuzen’s perspective, which maintains strict handling standards for fresh produce, we received specific feedback on the project’s safety and usefulness. We also discussed the current situation and challenges related to produce loss at retail stores.
We received feedback that using genetically modified organisms (GMOs) as raw materials may be difficult for consumers with high food safety awareness to accept.
Furthermore, since the rate of deterioration varies depending on the type of produce, disposal decisions rely on employees’ visual inspections. This results in inconsistent judgment criteria and increased labor costs, which have been identified as challenges.
As a countermeasure, some general retailers adopt open dating (expiration date labeling); however, this sometimes results in the disposal of still-edible produce, ultimately increasing the overall waste rate.
Furthermore, Shunrakuzen reported a high waste rate for vegetables and fruits, with produce waste accounting for approximately half of the total food waste.
Providing safety information based on scientific evidence is crucial for reducing psychological barriers to the use of genetically modified organisms. Furthermore, for challenges that are difficult to solve with existing methods, visualization technology using blacklight irradiation with biosensors was confirmed to be an effective approach that enables anyone to accurately assess the condition of produce.
Fresh produce constitutes a significant portion of food waste, and preventing its loss is considered to directly contribute to reducing overall food waste.
Based on advice from Shunrakuzen, we created a new website for experts to help promote social acceptance of genetically modified organisms and provide accurate information to consumers.
While we demonstrated the usefulness of biosensors, establishing clear disposal criteria based on ethylene concentration is considered a key future challenge for achieving more accurate reductions in produce loss.
Institute: Professor, Gifu University
Stakeholder: Academia
Expertise: molecular biology
In this Human Practice, we sought advice from Professor Yokogawa, an expert in protein research, to identify the causes of experimental failure and improve the experimental system. For the Cre/loxP system, we obtained solutions including revising the plasmid structure, re-evaluating control settings, and confirming recombination in vivo. Through this advice, we were able to re-run the experiments and lay the groundwork for establishing a loxP plasmid recombination system using Cre recombinase. (HumanPractice①) In the Petn expression system, it was suggested that insufficient expression of the transcription factor EtnR2 and codon usage bias might be factors contributing to the undetectable fluorescence. We recognized the importance of confirming protein expression via SDS-PAGE and optimizing expression conditions. (HumanPractice②)
① Professor Yokogawa specializes in artificially manipulating the mechanism that produces proteins from genetic information. He creates new functional molecules and develops applied technologies based on the precise control of biological information, demonstrating deep expertise in proteins. Therefore, we consulted Professor Yokokawa regarding issues arising when the loxP plasmid was not cleaved by Cre recombinase. Our goal was to receive advice on how to proceed with future experiments and methods for verification.
②We also sought advice on the cause of the lack of GFP fluorescence, which should have been observed if EtnR1/R2 were functioning normally.
① We consulted Professor Yokogawa regarding the issue where the loxP plasmid was not cleaved by purified Cre recombinase. He pointed out that we needed to confirm factors related to the plasmid's nucleotide sequence and structure as potential causes for the reaction not proceeding. He also advised on the importance of appropriately incorporating positive and negative controls to correctly evaluate the reaction conditions. Additionally, he advised that since reactions may proceed more readily in vivo than in vitro, evaluating recombination success within E. coli would be effective. He further advised that considering induction conditions is crucial for subsequent experimental systems, as adding IPTG increases the load on protein synthesis, potentially leaving insufficient resources for GFP expression.
② He advised us that since EtnR1/R2 might not be expressed at all, we should first confirm their expression via SDS-PAGE. However, our lab lacked the reagents and equipment necessary to perform SDS-PAGE. When we conveyed this situation, the professor kindly offered to let us conduct the experiment in his laboratory. He also pointed out that the lack of codon optimization might be reducing translation efficiency, potentially hindering successful GFP protein expression.
① Following advice from Professor Yokogawa, we revised our experimental design to establish the Cre/loxP system. First, suspecting factors like the supercoiled structure of the plasmid, we considered changing the substrate format. Additionally, when confirming cleavage via electrophoresis, we decided to evaluate both a positive control and a negative control without added Cre enzyme in parallel. Furthermore, based on the advice that enzyme reaction assays may be more readily established in vivo than in vitro, we adopted a strategy to perform recombination verification within cells. Additionally, considering that excessive IPTG induction in the protein expression system could become a burden and potentially impair GFP output, we incorporated the optimization of induction conditions starting from low concentrations as a task. Incorporating this advice from him clarified the troubleshooting flow when problems arise.
② Following the professor's advice, we proceeded with confirming EtnR1/R2 expression via SDS-PAGE.
Regarding codon optimization, we analyzed the codon usage frequency of the sequence to assess its optimality.
This allowed us to identify regions potentially affecting translation efficiency. However, since it would require reordering parts, we did not implement codon optimization.
Through this advice, we clarified that insufficient expression of EtnR1/R2 was one possible reason for the lack of fluorescence detection. This enabled us to establish a more concrete verification plan moving forward
① We incorporated the professor's advice into our action plan and compared the reactivity of supercoiled DNA and linearized DNA. Furthermore, we conducted in vivo recombination assessments to more accurately understand the behavior of the Cre/loxP system within cells. Concurrently, we investigated IPTG induction conditions to determine the IPTG concentration yielding maximum GFP fluorescence. These efforts aimed to ensure reproducibility of the Cre/loxP system and establish a foundation for implementing a circuit to visualize fruits and vegetables deterioration.
② We planned to evaluate the presence and expression levels of EtnR1/R2 via SDS-PAGE to determine whether the lack of detectable GFP fluorescence stemmed from expression defects. Based on these results, we would implement codon optimization as a future task if necessary.
Institution: Professor, Gifu University
Stakeholder: Academia
Expertise: Biomolecular Functionology
Professor Atsuhiro Shimada at Gifu University researches the cytochrome oxidase reaction mechanism at the atomic level. Based on his expertise, we consulted him about (1) the reaction mechanism of TOM toward ethylene and (2) co-culture simulation of E. coli expressing EtnR1/R2 and TOM. He advised that TOM and its mutants share the same mechanism and that factors such as expression burden, membrane permeability, and gene integration should be considered. Following his feedback, we obtained biomass data under IPTG induction and included concentration gradients in our model. Next, we will analyze TOM mutants through docking, refine parameters, and optimize our model through genome integration.
Professor Atsuhiro Shimada of Gifu University conducts research aimed at elucidating the reaction mechanism of cytochrome oxidase, a terminal enzyme in the respiratory chain, at the atomic level.
With this background in mind, we asked him questions related to the following two topics that our Dry Lab team is currently pursuing:
1.Prediction of the reaction mechanism of TOM (toluene o-xylene monooxygenase) toward ethylene and the resulting concentration changes
2.Co-culture simulation of E. coli expressing EtnR1/R2 and E. coli expressing TOM
Regarding the aforementioned topic (1) on the reaction mechanism of TOM, Professor Shimada explained that the difference between TOM and its mutants A113F and V106F lies solely in the substrate specificity of the enzymes, while the fundamental reaction mechanism remains the same.
For topic (2), the co-culture simulation of E. coli expressing EtnR1/R2 and E. coli expressing TOM, we received valuable feedback on several aspects, including the effects of protein expression burden, the number of parameters, the intracellular localization of substances in E. coli, and the forms of gene introduction.
When we asked whether there might be any major factors overlooked in our model construction, Professor Shimada pointed out that:
・If a protein is expressed in large quantities, it may be necessary to independently consider the expression burden.
・Although the expressed Tom protein and the produced ethylene oxide were treated as being at equal concentrations in both strains, differences in membrane permeability are likely to cause concentration imbalances, which should also be taken into account.
・To improve the model’s accuracy, it is important to increase the number of parameters and collect a wider variety of experimental data to measure them precisely.
Furthermore, he suggested that, rather than relying on a co-culture system, it may be more effective to design a single E. coli strain capable of expressing all relevant genes, considering not only plasmid-based expression but also genomic integration as a potential approach.
Although limited prior research is available on the reaction mechanism of TOM, obtaining reliable feedback has allowed us to gain a deeper understanding of this protein and explore the possibility of developing a more advanced design.
To account for protein expression burden, we designed our experiments for determining the biomass growth parameters in the Monod equation such that IPTG induction was continuously applied, thereby ensuring parameter acquisition under conditions where the expression burden was present.
Additionally, the consideration of concentration gradients among substances was described in the model explanation section and presented as an improvement strategy for achieving a more accurate and realistic model construction.
To further deepen our understanding of TOM A113F and V106F, for which available information remains limited, it will be essential to conduct docking simulations and enzyme assays.
In order to enhance the accuracy of the co-culture model, it is also necessary to incorporate equations and parameters that describe phenomena such as protein expression burden and transport across cell membranes, as well as to design experiments and collect diverse datasets for parameter estimation.
Furthermore, to avoid overly complex designs, the genomic integration of target genes should be considered, taking into account factors such as protein expression levels and cellular regulatory mechanisms.
Considering the future potential and applicability of bacterial cellulose as a material, we explored a practical implementation combining bacterial cellulose with the bio spray. This aimed to address existing challenges and enhance the functionality of the bio spray. We conducted Human Practices to obtain advice on the form of the envisioned final product and its potential for societal implementation.
Institution: Professor, Gifu University
Stakeholder: Academia
Expertise: Environmental Microorganisms
In this Human Practice, we sought advice from Professor Kohei Nakamura of Environmental Microbiology regarding the social implementation and safety of a project aiming to reduce food loss. We received feedback that the biospray method, which directly sprays genetically modified microorganisms, presents significant challenges in terms of safety and social acceptance. Consequently, we revised the design to apply the microorganisms by immobilizing them on bacterial cellulose in an “enveloping” form. Concurrently, we reaffirmed that defining specifications for ethylene detection—including target concentration range, detection limits, and reproducibility—is essential. Moving forward, we plan to advance the concretization of a safer, more acceptable implementation model through literature review and target value setting.
Professor Kohei Nakamura is an expert in environmental microbiology. Specifically, he is focusing on elucidating microbial communities and methanogenic symbiotic systems, their application to environmental remediation and resource recovery, and genomic analysis of degradative bacteria. Based on this expertise, we aimed to explain the project's overall vision and seek his advice on the nature of the final deliverables with an eye toward societal implementation, as well as their feasibility.
We sought feedback on our project's overall vision and the biospray we vision as the final deliverable. The professor pointed out that while our project aims to reduce food loss as its goal, the method of directly spraying the recombinant spray onto carries safety concerns. This could lead to the disposal of items that are inherently edible, potentially increasing waste and creating contradiction. Looking toward societal implementation, the professor advised that we should not assume the current product form of a biospray at this stage. Instead, we need to re-examine the design for an implementation form that prioritizes safety. Additionally, regarding ethylene detection, the professor suggested it would be beneficial to specify the measurement design concretely. This should clarify not just whether detection is possible, but also the target concentration range, the detection limit required, and the level of reproducibility needed for evaluation.
After consulting with a professor specializing in microbiology, we reaffirmed that spraying recombinant organisms directly onto produce in the form of a biospray is impractical from a safety perspective. Based on this, we determined it necessary to revise our approach, prioritizing safety by not limiting the final product to a sprayable form. Furthermore, regarding ethylene detection, we recognized that it is essential not merely to determine detectability, but to clearly define the target concentration range and reproducibility. Clarifying these specifications is considered a critical task for the future development of this project.
Based on the professor's feedback, we have established a policy to pursue social implementation by incorporating detection functions into the bio-cellulose and wrapping produce, as the final form prioritizing safety. Since this approach does not require spraying, it enables operation without directly applying bacteria to food surfaces, thereby lowering psychological and hygienic barriers during handling. While aspects like the detection threshold for ethylene concentration require further study, advancing to actual testing at this stage is challenging. However, as this is a critical issue directly linked to future development, we will first focus on organizing literature information and setting target values. Through these steps, we aim to concrete the implementation vision for reducing food loss.
Company: Nichiban Group
Stakeholder: Industry
Expertise: A manufacturer offering a wide range of products centered on adhesive tape, from medical and healthcare applications to daily necessities.
To explore the potential and applications of bacterial cellulose, we held discussions with Nichiban corporation and gained valuable insights regarding its potential for medical products leveraging its water retention properties and for environmental contributions. At the same time, we learned that managing physical properties such as water absorption rate and thickness remains a challenge. Furthermore, we learned that process stability, cost, processability, and functionality are crucial for practical implementation.
To explain the relevance and motivation for interacting with stakeholders involved in the issue Nichiban Corporation's Research and Development Division manufactures products for diverse industries including medical, healthcare, and food, utilizing nonwoven fabrics, cellophane, urethane, and other materials based on its proprietary adhesive and bonding technologies. Therefore, we sought opinions on the future potential and possible applications of bacterial cellulose as a material, which was considered for use in this project.
Stakeholder Opinions, Our Interactions, and Discussions Bacterial cellulose possesses water retention properties that are absent in plant-derived nanocellulose, which is water-sensitive and degrades quickly. Leveraging this characteristic in the medical field could enable applications such as “moist healing formulations” that absorb exudate and promote natural healing. Regarding further functionalities and potential applications of bacterial cellulose in product development, we received opinions suggesting its use in medical products like bandage and dressing pads, as well as in industrial and office settings to reduce plastic usage and contribute to carbon neutrality.
However, we were also informed that managing physical properties such as water absorption rate, degradability, thickness, and hardness adjustability remains a challenge. Additionally, from a corporate perspective, when evaluating the future potential of new materials like bacterial cellulose, companies tend to prioritize four key factors:
① Process, supply, and long-term stability;
② Cost;
③ Processability and ease of handling; and
④ Functionality as a differentiating feature.
How feedback was implemented and its impact on the project We believed that using bacterial cellulose, which combines water absorption and retention properties, in our project could address the challenges within our team regarding changes in taste and aroma, as well as safety concerns. Furthermore, by leveraging the water absorption and retention properties of bacterial cellulose, we could also consider an application method where the bio spray would adhere more easily to fresh produce. To implement this in the project, we determined it was necessary to begin material design considering machinability and processability and develop prototypes with the production process in mind.
Steps to be taken became clear following advice from Nichiban Corporation's R&D headquarters, which possesses extensive expertise in material development. One step involves evaluating whether utilizing the water absorption and retention properties of bacterial cellulose can mitigate the challenging changes in taste and aroma. Additionally, it is necessary to explore methods for more effectively depositing the bio-spray onto the surface of fruits and vegetables using bacterial cellulose. Moving forward, we will focus on material design considering machinability and processability and proceed with prototype development with the production process in mind.
Mr. Yoshikawa of the OKB Research Institute, who supported our Human Practices, provided advice on the overall project summary and future prospects. Based on his advice, we clarified our future direction.
Company: OKB Group
Stakeholder: Localities
Expertise: As Agri Director of OKB SCLAMB, which supports venture startups, providing support and advice to farmers for sixth-sector industrialization and income improvement
As the project manager, Mr. Yoshikawa played a key role in coordinating outreach efforts with companies and farmers. After receiving his overall evaluation of the project, we decided to begin considering the handover of our research, the expansion of our target demographics, and potential demand in international markets.
Mr. Yoshikawa worked diligently as the project coordinator to enable our HP activities with various companies and farmers. We interviewed Mr. Yoshikawa, who has observed our activities as project director, to receive his overall evaluation of the project.
Through Human Practices, we discovered that the initial bacterial cellulose packaging material did not meet market needs and that implementing a bio-cellulose coating was difficult. The ability to quickly pivot the project direction based on this insight was a positive outcome of effectively utilizing Human Practices. However, we received feedback that it would be a great waste to end the project at this stage of basic research alone, and that moving towards social implementation would be beneficial.
Challenges identified for the social implementation of the project's biospray include shifting research content, obtaining patents, and expanding the target audience.
We decided to consider who among the members, professors, or companies should take over the research, and to explore where demand exists, including overseas markets, to expand the target audience.
We participated in the Japan Meetups, which were held twice — once in spring and once in summer. Through interactions with other teams, we gained inspiring ideas and fresh perspectives. Furthermore, the Q&A sessions during each team’s project presentations provided valuable opportunities to identify areas for improvement in our own project and to deepen our analysis.
We held a joint event with Kinjirushi Corporation. The main purpose of this event was to interact with our project sponsors and deepen our understanding of wasabi, a type of fresh produce.
We learned basic information such as the process through which wasabi develops its pungency, and also experienced grinding fresh wasabi ourselves.
Through this event, we were able to help our sponsors gain a deeper understanding of the iGEM sci-net project.
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