Based on the work of EPFL IGEM team in 2019, we developed a new for plant DNA extraction based on the use of a microneedle patch.
1. Microneedles Patch
To optimize the current design of the Microneedles patch, the materials choice and fabrication process need to be refined. The following tasks have to be investigated:
- Optimize the fabrication process to make it reliable, simple and scalable
- Develop a suitable packaging for the Microneedles to protect them during storage, transport and insertion in the manipulator
- Assess the shelf-life of the Microneedles
- Assess the capability of DNA preservation on the Microneedles
- Design new microneedles shape optimized to a specific sample (thin, sharp, hard…)
Keywords: Materials, Fabrication process, Hydrogels, Prototyping and Testing
2. Microneedles stapler
The aim is to design a device that will enable easy handling of the microneedles patch by the operator during the sampling and will protect the patch from contaminations before and after the sampling:
- Develop a hand-held manipulator for the Microneedles to simplify handling
- Reduce variability and contamination risk during the sampling/extraction phase
Keywords: Mechanical design, Prototyping, Ergonomics, Sampling
3. Microneedles platform
To further enhance the performances of the Microneedles, improvements in the DNA extraction process must be investigated.
- Develop a fluidic system for the elution
- Integrate the quantification sensor to the fluidic system
- Labelling function (name, date and description)
- Geo localization
Keywords: Life sciences, Biochemistry, DNA extraction, DNA purification
The GenoRobotics project tackles the challenge of field sequencing. To achieve a solution for autonomous on-site analysis, we work on the following topics:
Nanopore DNA Sequencing
The aim of this work is to be able to sequence four universal plant genes using a Nanopore sequencer for easing the use of DNA barcoding.
- Implement reliable sample multiplexing for sequencing
- Sequence DNA extracted with Microneedles
- Protocol optimization (field compatible and/or microfluidic compatible)
- Sequence RPA output
Keywords: MinION, Nanopore sequencing, Laboratory work, Biology, genomic DNA , Plant DNA barcoding, Environmental & Life sciences
2. Isothermal amplification: RPA
After DNA extraction, DNA has to be amplified to prepare library for Nanopore sequencing. An isothermal amplification pipeline must be designed in order to develop a field compatible tool.
- Reliable RPA: Develop three pairs of primers for plant DNA barcoding
- Enable multiplex amplification (for multiple target genes)
- Interface with Oxford Nanopore’s barcodes for sample multiplexing
Keywords: DNA extraction, DNA amplification, RPA, Biology, Biochemistry, Environmental & Life sciences
3. Nanopore interface
Develop a fluidic interface to automate sample loading and wash process on the Minion flowcell
Keywords: Microfabrication, microfluidics, MinION, Nanopore sequencing, Biology, Environmental & Life sciences
The CoWaS project tackles the challenge of biodiversity monitoring in water bodies. To achieve a solution for autonomous analysis, we work on the following topics:
1. Water Sampling
The aim is to develop a water pumping and filtration system that can be pre-programmed or remotely controlled to ensure an operator-free continuous sampling of a water body at a fixed depth. A first prototype (CoWaS) has been built. We now need to develop:
- Extend the CoWaS to 14 Sterivex
- Design a plug&play cartridge for simple changing of the Sterivex
- Develop the remote communication and control system of the CoWaS
Keywords: Water sampling, Mechanical/Electrical Design, Programming, Communication system, Environmental sampling
2. DNA Extraction
The water samples must then be stored or processed to extract the DNA contained in them. A suitable extraction pipeline must be designed based on the first tests and results that have already been carried out.
- DNA conservation (heating system integrated in cartridge)
- Design a pipeline for DNA extraction from the Sterivex filters
- 16S sequencing protocol
Keywords: DNA extraction, Nanopore DNA sequencing, Biochemistry, Environmental & Life sciences
3. Microfluidics and Miniaturization
To develop an autonomous platform able to monitoring bacterial communities in Leman lake we need to:
- Implement the automated pipeline in a miniaturized and integrated chip
- Interface with the Nanopore DNA sequencer
Keywords: Microfabrication, Microfluidics, Automation, Robotics, Materials, Microfabrication, Microfluidics
The focus here is the development of the biodiversity database with its associated software tools and hardware equipment. It will store the data produced during survey and monitoring expeditions and will propose a set of bioinformatics and analysis tools. We are currently working on the following topics:
1. User interface tools
The aim is to develop software tools (desktop and/or web-based) to enable user-friendly actions such as data upload/download.
Keywords: Software development, User interface, Database
2. Interfacing with international Biodiversity Databases
The current version of the database is not currently linked to standard international Databases such as GenBank. The goal is to design an interface that enables data exchange between these systems.
Keywords: Database management, Data structure, Interfaces
3. Field equipment
The data will be generated mostly during expeditions in harsh environment. It needs to be stored locally until it can be uploaded to the main database. This part of the project focuses on the development of a solution for storing and exchanging data with the database during field expeditions.
Keywords: Field hardware, Data storage, Communication system, Electrical/Mechanical Design, Prototyping
DNA sequencing generate large amount of data which need to be analysed
1. Bioinformatic tools
In order to exploit the data generated by the nanopore sequencer we need to:
- Develop bioinformatic pipelines to analyze the sequences obtained on the Minion
- Implement these pipelines on the database
- Display: monitoring, report, plots…
Keywords: Data science, data alignment, BLAST, Monitoring, Database
The DNA Sensor team works on the development of an integrated DNA quantification sensor. It will be integrated to the instrument to assess the quality of the DNA extraction before sequencing. This implies challenging design constraints to ensure the sensor’s integrability, accuracy and reliability. The following topics are available:
1. Proof of Concept
A first Proof of Concept based on UV absorption is currently being developed and tested assess its performances.
Keywords: Design & Prototyping, Optics, Electronics, DNA quantification
2. Miniaturization and Integration
The current design is a small table-top instrument. The concept should be adapted to an integrated and microfabricated sensor that can interface with a microfluidic system.
Keywords: Microfabrication, Design, Optics, DNA quantification
Communication and promotion
The communication and promotion around the project is focus on the following points:
- Communicate on the project through social media
- Content creation
- Website management
Keywords: Web design, social media, graphic design, content creation
Contact and promote GenoRobotics !
- Develop a sponsoring dossier
- Find yearly sponsors for the association: funds and in kind (equipment, materials, services)
- Find sponsors & partners for specific events (workshops, expedition,…)
- Crowdfunding campaign
Keywords: fundraising, sponsoring, partners, network
The GenoRobotics projects aims at enabling DNA analyse directly in the field in order to facilitate the work of field work. Every prototype is then tested during a yearly scientific expedition with future user in order to review the pros and cons of the last prototypes.
2022 Scientific expedition
The goal of this expedition is to test 2 prototypes: the microneedles stapler and the DNA quantifier as well as to test the nanopore DNA sequencing protocol developed on plants
- Set up a scientific expedition to test the prototypes (localisation, preparation, logistics, budget…)
- Interact with actors in field biology and ecology to find partner projects
- Communication & promotion
Keywords: scientific expedition, ecology, network, funding, logistic, communication
If you didn’t find a suitable project listed but are still interested in joining GenoRobotics, you are most welcome to contact us!
We will do our very best to work something out.