Team:Kyoto/Implementation
Implementation
Overview
We aim to reduce the amount of flower waste in the production stage by helping farmers to diagnose flower virus infections on their farms and to control pests with pesticides that are friendly to both the environment and human beings. In addition, the biomolecular production platform that supports our project is a wonderful system with a broad future potential. In this page, we describe a part of our vision for a sustainable society using these technologies.
Fig.1 Our whole story of Implementation
DLA Cycle-Diseased Leaves Assessment Cycle-
End Users
We have developed a technology that will enable flower farmers to take easier measures against diseases.
What is DLA Cycle?
The DLA Cycle (Diseased Leaves Assessment Cycle) is a system in which we use a combination of DLAEMON, an image-based diagnosis technology, and fluorescence-based viral infection diagnosis technology integrating enzymatic reactions, DLAMI, and NOBITA.
This system will allow farmers to quickly notice and take action when plants are infected with a virus. This will prevent a large number of flowers from being discarded due to disease during the production stage.
This system will allow farmers to quickly notice and take action when plants are infected with a virus. This will prevent a large number of flowers from being discarded due to disease during the production stage.
Diagnostic Imaging
We developed software that can determine whether a leaf is infected with a virus or not from a photograph, and named it DLAEMON (Diseased Leaves Assessment by Efficient Machine-learning On Neural network) .
See the Software page for details
We expect farmers in future to use DLAEMON.
The operations they have to undertake are just three steps.
Fig.2 DLAEMON
The operations they have to undertake are just three steps.
- Take a picture of the leaf they want to diagnose at the farm
- Visit our application, which is open source.
- Select a photo of the leaf and press a button to load it into our AI, DLAEMON
-> Done!
Fluorescence Diagnosis
Farmers can run further diagnostic tests on leaves that were suspected to be positive for virus infection by DLAEMON. Here, we adopt a technology that combines RT-LAMP and CRISPR-Cas12a. Using an enzymatic reaction, only the leaf extract of a sample infected with the virus will fluoresce, visualizing the presence of the virus.The device used in this process is DLAMI (DLA's Machine Interface). With our software NOBITA (Numericalization Of Brightness of Image for one Touch Assessment), the existence of fluorescence can be quantitatively observed.
See enzymatic reaction in detail (Modeling) See DLAMI in detail (Hardware) See NOBITA in detail (Software)
In this diagnosis, the steps to be operated by the farmers are simple.
DLA Cycle has mainly two advantages.
First, the inspection efficiency of NOBITA and reliability will be enhanced when DLAEMON works together. Second, most importantly, DLAEMON will evolve with the feedback by NOBITA. If we continue to have this system run, we someday become able to diagnose sufficiently only with DLAEMON. If so, farmers become able to diagnose plant virus infection only by taking photos with their smartphone and the disease control will dramatically become even easier.
See detailed instructions (Engineering) See the improvement of AI accuracy in the future ( Software )
See enzymatic reaction in detail (Modeling) See DLAMI in detail (Hardware) See NOBITA in detail (Software)
In this diagnosis, the steps to be operated by the farmers are simple.
Fig.3 How to use DLAMI
- Extract RNA from arbitrary leaves, or the leaves identified as positive for virus infection by DLAEMON[1].
- Put the extraction and a reagent for RT-LAMP into a tube.
- Put the tube into a pot, and keep the temperature isothermal(constant) at 63°C.
- Take the tube out of the pot, and add Cas 12a-reagent into the tube.
- Set the tube on our hardware, and take a photo with a smartphone.
- Check whether the fluorescence can be observed in the photo or not with our software.
-> Done!
Fig.4 DLA cycle
First, the inspection efficiency of NOBITA and reliability will be enhanced when DLAEMON works together. Second, most importantly, DLAEMON will evolve with the feedback by NOBITA. If we continue to have this system run, we someday become able to diagnose sufficiently only with DLAEMON. If so, farmers become able to diagnose plant virus infection only by taking photos with their smartphone and the disease control will dramatically become even easier.
See detailed instructions (Engineering) See the improvement of AI accuracy in the future ( Software )
DLAEMON to The Height
We have a dream that in the future, we take the performance of DLAEMON to the highest level and fly DLAEMON in the sky. If DLAEMON gets smart enough to diagnose more complicated images, it might become possible to detect viral infections with much less effort than the method we are proposing now.
The current DLAEMON can only scan one leaf at once. Therefore, farmers need to take a lot of photos, which is troublesome. Therefore, it would be of great help in practical situations to have DLAEMON learn to find suspected infected leaves in an image with multiple leaves in the future.
The diagnostic process at this time is as follows.
The current DLAEMON can only scan one leaf at once. Therefore, farmers need to take a lot of photos, which is troublesome. Therefore, it would be of great help in practical situations to have DLAEMON learn to find suspected infected leaves in an image with multiple leaves in the future.
The diagnostic process at this time is as follows.
- Photograph the entire field from above using a high-definition camera mounted on a drone.
- Load the photos into the advanced DLAEMON.
- Have the upgraded DLAEMON analyze all the photographed leaves simultaneously.
- As a result of the analysis, let DLAEMON point out the location to be examined in detail.
- Perform image diagnosis or fluorescence diagnosis for each leaf in the specified location.
Fig.5 DLAEMON Drone
The Applicability of DLA Cycle
DLA Cycle can play an important role in fields even for vegetable production. Like the methods explained so far, early virus diagnosis for vegetables can prevent production loss. Consequently, this will provide a solution to the food problem that is currently a global challenge.
How about RNAi Pesticide?
We propose an RNAi-based solution to the problem of Western flower thrips, an agricultural pest that is known to carry a virus called TSWV and cause disease. This method can make plants more invulnerable to virus infection.
There are two ways to apply this insecticide.
Fig.6 RNAi
1. Let plants absorb dsRNA
Thrips are so small that they can lurk in the bud and stay attached to the flower all the way. Some consumers hesitate to buy flowers because of such insects. Our hope is that removing them will encourage more people to access the flowers.
If you employ this proposing usage, you would add our dsRNA to the water in which the flowers are kept for wet transport or in stores. Then the dsRNA is absorbed through the cut end of flowers and goes through the conduit to reach the whole plant. The thrips then ingest the dsRNA orally as they devour the leaves, and the dsRNA induces RNAi in the thrips to kill them.
This approach could be extended to hydroponics of vegetables such as tomatoes, one of the victims of thrips. In this case, the plant absorbs the dsRNA from the roots, not from the cut end.
If you employ this proposing usage, you would add our dsRNA to the water in which the flowers are kept for wet transport or in stores. Then the dsRNA is absorbed through the cut end of flowers and goes through the conduit to reach the whole plant. The thrips then ingest the dsRNA orally as they devour the leaves, and the dsRNA induces RNAi in the thrips to kill them.
This approach could be extended to hydroponics of vegetables such as tomatoes, one of the victims of thrips. In this case, the plant absorbs the dsRNA from the roots, not from the cut end.
2. Coat dsRNA to the surface of plants
In the future, we would like to produce pesticides containing this dsRNA to be sprayed on farms. In this process, our dsRNA is attached to the surface of leaves. After this, as in 1., the dsRNA is orally ingested by the thrips to induce RNAi in the body. Note, though, that this method requires a large amount of dsRNA.
We also came up with a product called Thrip Hoi Hoi (a thrip trap) to further apply this usage. The idea is to coat the leaves of the thrip's favorite food with dsRNA and scatter it over entire fields. We aim to have the thrips removed by the surrounding traps before they get to the crops.
We also came up with a product called Thrip Hoi Hoi (a thrip trap) to further apply this usage. The idea is to coat the leaves of the thrip's favorite food with dsRNA and scatter it over entire fields. We aim to have the thrips removed by the surrounding traps before they get to the crops.
Extra - [Transgenic Plants]
There are other ideas for thrip control using RNAi. One of them is a transgenic plant. We cannot make specific suggestions here given the lack of validation on experimental evidence, but we would love to share this idea with you. This plant is incorporated with a gene that produces dsRNA to target essential genes of thrips, and will kill the thrips that feed on this plant. By cultivating these plants throughout the field, we can protect our agricultural products from thrips.
The Future We Envision
How should we implement our technology into society?
To begin with, we would visit communication sites where local farmers share information and give demonstrations on how to use our device for disease and insect control so that the farmers can learn about the new technology. For example, in Japan, we imagine agricultural experiment stations and agricultural extension centers in each prefecture as possible places of interaction. There, we will listen to farmers' feedback on the convenience of use and the functionality, in order to refine our system further.
Additionally, we asked an expert who is actually doing development research on technologies for agricultural fields for advice on the implementation of our project. One of them is to write papers and present at conferences seeking a credible platform to express our research. By doing so, we would like to spread the technology acquired through our project to every stakeholder as well as those who contributed to our project. There, as a foothold, we will have active discussions with domestic stakeholders and become able to get feedback not only from the aforementioned farmers but also from experts. Following this advice, we are planning to write a paper after Jamboree.
Other than that, our project could be more useful in the real world by publishing our diagnostic applications to the world, on the web, and sharing our protocols with an unspecified number of people involved in the floral and agricultural industries.
The steps we need to take in order to realize the future we aspire to, or in other words to implement our project, are as clear as these ! There are, however, several things we need to keep in mind when actually implementing our technology in the real world. This will be discussed later in the "challenge to overcome" paragraph.
To begin with, we would visit communication sites where local farmers share information and give demonstrations on how to use our device for disease and insect control so that the farmers can learn about the new technology. For example, in Japan, we imagine agricultural experiment stations and agricultural extension centers in each prefecture as possible places of interaction. There, we will listen to farmers' feedback on the convenience of use and the functionality, in order to refine our system further.
Additionally, we asked an expert who is actually doing development research on technologies for agricultural fields for advice on the implementation of our project. One of them is to write papers and present at conferences seeking a credible platform to express our research. By doing so, we would like to spread the technology acquired through our project to every stakeholder as well as those who contributed to our project. There, as a foothold, we will have active discussions with domestic stakeholders and become able to get feedback not only from the aforementioned farmers but also from experts. Following this advice, we are planning to write a paper after Jamboree.
Other than that, our project could be more useful in the real world by publishing our diagnostic applications to the world, on the web, and sharing our protocols with an unspecified number of people involved in the floral and agricultural industries.
The steps we need to take in order to realize the future we aspire to, or in other words to implement our project, are as clear as these ! There are, however, several things we need to keep in mind when actually implementing our technology in the real world. This will be discussed later in the "challenge to overcome" paragraph.
BLOOM System is Essential for Us
We intend to make our device more affordable and accessible to a wider audience by making various biomolecules for each component of our projects such as enzymatic reactions and RNAi pesticides. In response, we focused on the asymmetric cell division in E. coli. BLOOM System is a production platform for biomolecules based on this mechanism. This system is necessary for the sustainable society we envision.
See how the production platform works ( Modeling )
BLOOM System overcomes the weaknesses the conventional continuous culture has, and is capable of controlling complex gene expression pathways. In other words, the BLOOM System is the next star of culture methods deriving from the continuous culture with high production efficiency and high affinity to the philosophy of the sustainable society. This production platform is expected to contribute to biomaterial production in such a society in the future.
The strength of this system is that the timing of expression of multiple genes can be freely managed, and their products can be autonomously collected by cell precipitation or lysis. This property allows us to yield a fresh, well-quality end product when inducing cell precipitation as soon as the end product is expressed.
In addition, the following are some of the application examples.
All the user of the BLOOM System has to do is to try to select the appropriate parts. Moreover, to make it something that more and more people will love, we would like to extend our modeling so that it can predict the best tag and repressor to produce the product by inputting the properties of it, thereby rendering even this selection process of parts much easier.
See Modeling for more details
There may be an implementation strategy of distributing modeling programs and plasmids as shared resources or selling them as business resources. It would be beautiful if our BLOOM System could bloom as one of the production platforms in a sustainable society.
Fig.7 Production System
BLOOM System overcomes the weaknesses the conventional continuous culture has, and is capable of controlling complex gene expression pathways. In other words, the BLOOM System is the next star of culture methods deriving from the continuous culture with high production efficiency and high affinity to the philosophy of the sustainable society. This production platform is expected to contribute to biomaterial production in such a society in the future.
The strength of this system is that the timing of expression of multiple genes can be freely managed, and their products can be autonomously collected by cell precipitation or lysis. This property allows us to yield a fresh, well-quality end product when inducing cell precipitation as soon as the end product is expressed.
In addition, the following are some of the application examples.
- Improvement of efficiency production itself
Selecting the most suitable method may increase the efficiency of continuous culture thanks to the wide range of collection methods. -
Combating toxic intermediate products
By generating the repressor earlier, the amount of toxic intermediate products can be suppressed.
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Assurance of biosafety
It is possible to create a system in which E. coli is programmed to self-destruct after the expression and collection steps.
All the user of the BLOOM System has to do is to try to select the appropriate parts. Moreover, to make it something that more and more people will love, we would like to extend our modeling so that it can predict the best tag and repressor to produce the product by inputting the properties of it, thereby rendering even this selection process of parts much easier.
See Modeling for more details
There may be an implementation strategy of distributing modeling programs and plasmids as shared resources or selling them as business resources. It would be beautiful if our BLOOM System could bloom as one of the production platforms in a sustainable society.
Challenges to Overcome
In implementing our project, we will have to overcome several safety issues. We have decided to consider the risks of each of them and list ways to avoid them. Please see below. In all cases, we have a responsibility to ensure that when we release new technologies into the world, we do so with the utmost care for the environment as well as people.
- The risk of the virus escaping back into the environment while on its way to diagnosis.
→We designed the hardware to be sturdy enough. - The risk of harming farmers when they improperly handle enzymes to detect infections.
→We will explain to farmers how to treat them and make sure they fully understand it. - The risk of negatively impacting ecosystems by intensively reducing populations of Western flower thrips with RNAi pesticides
- The risk of causing adverse effects on ecosystems by unintentionally killing other insects that are similar to the target sequence of the RNAi pesticide
→It is critical to fully consider the impact on ecosystems beforehand. To avoid this risk, we will start the implementation by testing this pesticide in a strictly regulated and limited area and make careful decisions.
Reference