CRISPR-Cas-Based Biomonitoring for Marine Environments: Toward CRISPR RNA Design Optimization Via Deep Learning.

Journal: The CRISPR journal
Published Date: Jul 12, 2023

Abstract

Almost all of Earth's oceans are now impacted by multiple anthropogenic stressors, including the spread of nonindigenous species, harmful algal blooms, and pathogens. Early detection is critical to manage these stressors effectively and to protect marine systems and the ecosystem services they provide. Molecular tools have emerged as a promising solution for marine biomonitoring. One of the latest advancements involves utilizing CRISPR-Cas technology to build programmable, rapid, ultrasensitive, and specific diagnostics. CRISPR-based diagnostics (CRISPR-Dx) has the potential to allow robust, reliable, and cost-effective biomonitoring in near real time. However, several challenges must be overcome before CRISPR-Dx can be established as a mainstream tool for marine biomonitoring. A critical unmet challenge is the need to design, optimize, and experimentally validate CRISPR-Dx assays. Artificial intelligence has recently been presented as a potential approach to tackle this challenge. This perspective synthesizes recent advances in CRISPR-Dx and machine learning modeling approaches, showcasing CRISPR-Dx potential to progress as a rising molecular tool candidate for marine biomonitoring applications.

Authors

  • Benjamín Durán-Vinet
    Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA.
  • Karla Araya-Castro
    Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco, Chile; Berkeley, Berkeley, California, USA.
  • Anastasija Zaiko
    Cawthron Institute, Nelson, New Zealand; Berkeley, Berkeley, California, USA.
  • Xavier Pochon
    Cawthron Institute, Nelson, New Zealand; Berkeley, Berkeley, California, USA.
  • Susanna A Wood
    Cawthron Institute, Nelson, New Zealand; Berkeley, Berkeley, California, USA.
  • Jo-Ann L Stanton
    Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA.
  • Gert-Jan Jeunen
    Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA.
  • Michelle Scriver
    Cawthron Institute, Nelson, New Zealand; Berkeley, Berkeley, California, USA.
  • Anya Kardailsky
    Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA.
  • Tzu-Chiao Chao
    Institute of Environmental Change and Society, Department of Biology, University of Regina, Regina, Canada; Berkeley, Berkeley, California, USA.
  • Deependra K Ban
    Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Berkeley, Berkeley, California, USA.
  • Maryam Moarefian
    Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Berkeley, Berkeley, California, USA.
  • Kiana Aran
    Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Berkeley, Berkeley, California, USA.
  • Neil J Gemmell
    Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA.

Keywords

External Resources

Popular Topics
Recent Journals