Facilitators: Benjamin Duran Vinet, Gracie Kroos.
Summary
Clustered Repeats Interspaced Short Palindromic Repeats and Associated CRISPR proteins (CRISPR-Cas) systems, initially renowned for gene editing, have now evolved into powerful tools for diagnostics, marking significant advancements in clinical settings. These CRISPR-based diagnostics (CRISPR-Dx) combine the precision of CRISPR with isothermal amplification methods, yielding rapid, specific, and highly sensitive results. Despite these promising developments, the design of CRISPR RNAs (crRNAs), which program and guide the system to its target, remains a challenging and intricate task.
Artificial intelligence (AI) offers a transformative solution to these design challenges. A notable advancement in this area is the development of the neural network namely ADAPT (Activity-informed Design with All-inclusive Patrolling of Targets). This AI tool was pre-trained with 19,000 data points to streamline and accelerate the deployment of CRISPR-Dx. ADAPT provides an end-to-end solution that enhances the efficiency of CRISPR-based diagnostics, demonstrating impressive results in various applications.
The upcoming workshop will focus on the fundamentals of CRISPR-Dx, explaining its core principles and methodologies. Participants will learn how to apply this cutting-edge AI technology in real-world scenarios, such as environmental biosurveillance namely CORSAIR (CRISPR-Based Environmental Biosurveillance Assisted Via Artificial Intelligence guide-RNAs). The workshop will guide attendees through the process of using ADAPT on their local computers, offering hands-on experience in deploying CORSAIR for their own targets of interest.
To solidify practical understanding, the workshop will conclude with a session on designing experiments to validate CORSAIR results. Participants will receive guidance on the essential requirements and potential troubleshooting techniques they may need in the laboratory. This comprehensive approach will equip participants with the knowledge and skills to effectively utilize CORSAIR in their research in environmental biosurveillance, paving the way for innovative applications in environmental biosecurity and beyond.
Workshop objectives
- Integrate ‘off-the-shelf’ state-of-the-art artificial intelligence modelling method for the quick deployment of CRISPR-based biosurveillance for environmental biosecurity.
- Structure a proof-of-concept deployment of CRISPR-based biosurveillance.
Target audience
Early career researchers and seasoned researchers who are studying or with interest in applying emerging CRISPR-Dx technologies for environmental biosurveillance.
Requirements
Knowledge
- Basic molecular biology knowledge is preferred.
- Basic shell knowledge commands are preferred.
Hardware
- A laptop with a working Wi-Fi connection, Intel Core i5 or superior/equivalent, 8GB of RAM or superior, Windows 10 or superior/Mac OS X is required.
Software
- For Windows users: Pre-installed Windows Subsystem for Linux Ubuntu 22.04.4 LTS or superior.
- For Mac users: Terminal is pre-installed by default.
- For all users: Conda must be pre-installed to be able to run all the workshop.
- For all users (optional): Geneious Prime software (https://www.geneious.com/) is extremely handy for the visualization and handling of the results. Free trials are available in the website.
Preparation prior to the workshop
Reading
The following articles are recommended.
- Kaminski, M.M., Abudayyeh, O.O., Gootenberg, J.S. et al. CRISPR-based diagnostics. Nat Biomed Eng 5, 643–656 (2021). https://doi.org/10.1038/s41551-021-00760-7
- Durán-Vinet B, Araya-Castro K, Zaiko A, et al. CRISPR-Cas-Based Biomonitoring for Marine Environments: Toward CRISPR RNA Design Optimization Via Deep Learning. CRISPR J. 2023;6(4):316-324. https://doi.org/10.1089/crispr.2023.0019
Targets
- If the attendee is interested in running their own sequences, it is recommended to have them ready in FASTA format. Only DNA sequences are permitted.
DRAFT PROGRAM
09:00-09:20 | Introduction of attendees and facilitators
09:20-09:50 | Introduction to basic CRISPR and CRISPR-Dx principles
09:50-10:00 | Q&A
10:00-10:15 | Break
10:15-10:30 | CORSAIR deployment examples
10:30-11:30 | ADAPT dependencies install and run with example/own files.
11:30-12:00 | Results rundown and Q&A
11:30-12:00 | Break
13:00-13:30 | Insights and troubleshooting tips
13:30-13:50 | Final remarks and Q&A
13:50-14:00 | Closing