Collaborative Developement of Isothermal Amplification & Devices
June 11. - 19, 2022 Paris
Scope of the Project
Quantitative real-time DNA amplification is at the heart of either diagnosing infectious disease or any section of biology research. Use of these devices has been limited due its cost and availability, therefore, refuting to elaborate and end-point methods like gel-electrophoresis. This project will change accessibility and affordability of this device to specially low-income countries either for POC or teaching purposes. Furthermore, the core of the project includes researchers and collaborators from diverse geographical backgrounds, professional expertise and socioeconomic origins, either at the development stage or at the end-user level at the next phases.
[Project Application ]
- Francisco Javier Quero (France)
- Urs Gaudenz (Switzerland)
- Yanwu Guo (Oslo)
- Fernán Federici Noe (Chile)
- Boris Enrique Orstica Navarrete (Chile)
- Harry Akligoh (Ghana)
- Ganga Chinna Rao Devarapu (remote)
- Smitha S Hegde (remote)
- Marc Dusseiller (remote / Indonesia)
- Shingo Hisakawa (remote Japan)
Saturday, June 11th 2022
● Visiting the different labs
● Bringing materials to the lab
● Taking over the house
● Welcome beers ● Lot's of bicycle riding
Sunday, June 12th
● chilling in the house
● defining program for the week
● tourist tour
● prepare kick-off presentation
Monday, June 13th – Sharing Knowledge
● Kick-Off presentation Setting up the lab
● Sensor Lab
● Lyophilization Intro
● Show and tell with prototypes
Tuesday, June 14th – Work Sessions
● Lab work session
● Hands On Workshops
● Amplification benchmark
Wednesday, June 15th – Networking
● Visiting local Hackerspaces / Fablabs
● Broadcasting from the lab
● Connecting with other GOSH communities
● Exchange with potential production partners
Thursday, June 16th – Design Sprints
● Rapid Prototyping
Friday, June 17th – Future Outlook
● Assessment of achievements
● Minimal viable products
● Global potential analysis
● Potential collaboration partners
● Planing for phase 2
● Open Houses Vincennes
Saturday, June 18th – Guests & Celebrities
More to come:
One day of lectures
Invite and connect to other GOSH communities
Public / broadcasted event / time for broadcast in the lab
Seeed and some of the production companies?
- Future outlook session (where do we want to go with our project / applications / specifications)
- Field trip (going out to nature) to test devices / protocols in the field
- Induction heating - PocketPCR / Pocket qPCR - open qLAMP - Webcam PCR - GMO/Corona Detective - Chili LAMP
- Program for the week - How to collaborate in the future - Say hello with Marc (Indonesia) and Shingo (Japan)
LPI (Learning Planet Institute) formerly CRI (Center for Research and Interdisciplinarity)
LPI is co-constructing and sharing new ways of learning, teaching, conducting research and mobilizing collective intelligence in the fields of life, learning and digital sciences, in order to address the UN’s sustainable development goals (SDGs).
Address: Learning Planet Institute, 8bis rue Charles V, 75004, Paris.
House in the city with backyard, hosted by Alexandra
49 Rue de la Liberté, Vincennes, Île-de-France 94300, France
At the end of the workshop we compared the ability of the three prototypes (webcam qLAMP, chili qLAMP and open qLAMP) to amplify 200 SARS-CoV-2 inactivated viral units using the CoronaDetective protocol in the green channel and the [GMO detective https://gmodetective.com/] in the red channel. The GMO should generate less signal as the filters we're using are for green fluorescence, which filters the vast majority of the red signal.
Pros and cons of each equipment
From our experience Chili qLAMP is a really sensible piece of hardware. It really reach levels of sensitivity that the other two machines struggle to sense, but it still require some calibration to find a compromise between detecting low levels of product fluorescence without getting saturated by the negative controls.
With a price of 20€ per each photodiode, Boris will work in the short term to find a greater price without sacrificing the high sensitivity.
Also, the inclusion of a Raspberry Pi inside of the machine allows to do a high level processing of results and connect with other devices in the network.
Eventhought it's still early in its development, the webcam qlamp have demosntrated the ability to generate really good results just using a 2/3$ camera as the sensor unit.
This machine is really promising for future applications as measuring multiplexed fluorescences in one single tube (Different wavelengths for measuring different things at the same time in one reaction), or scaling the format to 96/384 plates without an additional cost.
The open qLAMP is a middle point between the two previous machines. It uses an photodiode analog circuit but by the price range of the webcam qlamp.
It's the most ready for production device at the time of this residence. It still require some adjustments as including an small screen for controlling the machine when a local network is not available and developing an standard and quicker calibration procedure.
Last days' topic consisted in how to move forward into real world applications. The following questions arose:
- The system comprises two main parts, the lyophilized reactions and the hardware. Yanwu has contacts in the Chinese production ecosystem and will explore how to scale the reactions production. For the Hardware, Boris, Urs and Fran will study how to build the devices on a mid to large-scale and sell them.
- Regarding the application, we discussed RED (Research, Education and Diagnosys) applications. Initially, Research and Education would be more straightforward targets. Still, we believe that open source affordable devices can impact decentralized diagnostics. For Education, we can always use the GMO detective.
- For choosing a new target (as the pandemic is apparently ending), Harry will study the needs in Ghana. We talked about typhoid fever. As pointed here, there is a need for a cheap and specific diagnosis. The current Widal test is unspecific and can generate many false positives, leading to unnecessary treatments and increased antibiotic resistance to the standard treatment. A test that costs less than 4$ per person is needed. DNA detective reactions cost 0.5€ to be produced.
- Plant or animal diagnosis are easier to have a certified than human diseases diagnosys. Funghi detective, developed at CRI (For the pathogens generating the Ink Disease in trees), can be an example. Still, we will need feedback on which agricultural diseases - are essential to be diagnosed on time.
- How we will organize it? For round 2, we will create an association where we can transparently receive the funds, and everyone has control over them. For the future, we think the better way is a local company network where different participants create different open-source products required by others in the network. In this way, for example, Urs, Fran or Boris will build the hardware, Yanwu will produce the reactions that will be sent to Duplex Bioscience, the local company Harry has created to distribute in Ghana the technology.
Event Funded by:
- GOSH Collaborative Development Program
- Shuttleworth Foundation Flash Grants
- Tsinghua University, Materials sponsor
- CRI, Center for Research and Interdisciplinarity
Thank you to our sponsors