Paris Real-Time LAMP hardware residence

[FranQuero]

Good evening all!

This week starts the hardware residencies at the Learning Planet Institute (Former CRI, Paris) for real-time isothermal amplification analysis supported by the 2022 Collaborative Development Program.

These residencies aim to exchange knowledge and share solutions that different groups working with real-time nucleic acid amplification hardware have found separetely during this last years. The idea is to document which technologies work better for the different applications while we benchmark the different pros and cons of each one. At the end of the residency, we will record a series of new designs and solutions that the rest of the community can replicate/adapt for their own purposes.

Some of the most relevant projects of the residents who will join us locally and remotely are described here.

In a nutshell, locally we will count with @gaudi (Switzerland) @Hail_Harry (Ghana), Boris Orostica (Chile) and Yanwu Guo (Oslo). Remotely will join @shingohisakawa (Japan), @dusjagr (Indonesia), @scientist (Ireland), Smitha S Hegde (Denmark) and Fernan Federici (Chile).

As a brief description of our program, we will be doing the following activities:

On Monday the 13th, 9am-10am CEST (room 5.08, 5th floor)
Kick-off presentations
Link to join on google meet.

From Monday the 13th to Friday the 17th, 11am-7pm CEST (Student Lab, room 1.16, 1st floor)
Hands-on experimentation. We will stream the lab activity on twitch, where we will interact with our viewers by answering questions and listening to feedback.

Saturday, the 18th, starting 3pm CEST (Learning Extension Center, Room 0.06, ground floor)
Final presentations of the obtained results and discussion with invited GOSH guests @jcm80 (Open Bioeconomy Lab, Cambridge node), Jim Haseloff (OpenPlant initiative, Cambridge University) and @Rachel (Hackuarium, Switzerland)
Link to join on google meet.

During the week, we will be offering different training sessions on LAMP, real-time amplifier sensors, and other technologies, but the program may be subjected to day-before-adaptations we may need to make to compatibilize experiments, presentations… Stay tuned to the project page on the hackteria wiki, where we will be documenting all the progress and updating the schedule, and join the globalLAMP telegram channel where we are normally chatting about this technologies and events.

See you soon!

[FranQuero]

Here it comes, the update!

In spite of the diverse problems with the EU Visas’ of some residents and the Paris extreme prices in the high turism season, the residence has finished successfully! We have been working on three new prototypes of Open-Source Real-Time nucleic acid amplification equipment and we are now happy to share them with the community!

As explained in the grant application, these technologies are critical for both, low resources diagnostics and research, as they allow to study the different kinetics of nucleic acid amplification reactions. In general, this is interesting for two main different goals. In one hand it will enable measuring the difference of target concentrations (Virus/Bacterial DNA, for example) quantitatively, as when the target is more concentrated in the sample, the kinetics/speed of the reaction will be faster. Practically this serves to spot false positives that won’t be possible to detect with endpoint (yes/no) methods. A second application is also to enable carrying out reaction optimization protocols to find the best reaction conditions (Temperature, different reagents combinations…). This will allow, for example, to try primers for new targets without the need of a 10k€ qPCR machine.

Personally It was a pleasure to share this intense work week with all the residents. Now we are in the documenting phase. All the schedule we followed and the event’s outcomes are already in the hackteria wiki, where we will keep uploading some information.

Two of the three devices are already documented in Gitlab. The WebCam qLAMP will take a bit more as @gaudi started to work recently on it but it’s pretty promising for extremelly affordable hardware that eventually will allow multiplexing different fluorescences.

The production prices of WebCam qLAMP and open qLAMP are expected to be around 30-50€ meanwhile the ChiliLAMP, with much more precise optics and a raspberryPi inside, will be a bit more.

We are now thinking about scaling the production of the reactions and the hardware helped by @guo 's network in the biology part and @gaudi #Boris Orostica and mine for the hardware. Meanwhile, @Hail_Harry keeps exploring which are the subsequent applications now that the pandemic is apparently ending. We are also considering moving from CoronaVirus detection to agricultural/animal diagnosis, as human diseases are always much more regulated and therefore more difficult/expensive to have a real impact. If you have any idea/interest/need, you are welcome to join the global LAMP telegram group or just drop it in a comment in this thread.

We will be happy to see new people joining with new ideas!