The application of CRISPR-Cas for single species identification from environmental DNA.

  title={The application of CRISPR-Cas for single species identification from environmental DNA.},
  author={Molly A. Williams and Joyce O'Grady and Bernard Ball and Jens Carlsson and Elvira de Eyto and Philip McGinnity and Eleanor Jennings and Fiona Regan and Anne Parle‐McDermott},
  journal={Molecular ecology resources},
We report the first application of CRISPR-Cas technology to single species detection from environmental DNA (eDNA). Organisms shed and excrete DNA into their environment such as in skin cells and faeces, referred to as environmental DNA (eDNA). Utilising eDNA allows non-invasive monitoring with increased specificity and sensitivity. Current methods primarily employ PCR-based techniques to detect a given species from eDNA samples, posing a logistical challenge for on-site monitoring and… 

Advice to consider when developing a CRISPR-Cas assay for single species detection using eDNA

An isothermal CRISPR-Cas based detection assay for single-species assessment of Salmo salar as a route to a simple, cost-effective biosensor device and highlighted critical steps to consider and pitfalls to avoid when designing such isothermal assays.

Comparing CRISPR‐Cas and qPCR eDNA assays for the detection of Atlantic salmon ( Salmo salar L.)

It is demonstrated that overall, the CRISPR-Cas assay performs similarly to qPCR for assessing the presence or absence of S. salar from eDNA and provides a viable alternative approach to a simple, cost-effective biosensor device.

Advances in Field Detection Based on CRISPR/Cas System.

An emerging nucleic acid detection method based on the CRISPR/Cas system has reduced the reliance on qPCR and has several important features that make it suitable for on-site POCT (point-of-care testing), including short detection cycles, low cost, high sensitivity, and the ability to be combined with different readout methods.

Label-Free Detection of Transgenic Crops Using an Isothermal Amplification Reporting CRISPR/Cas12 Assay.

The isoCRISPR assay will enrich the toolbox for transgenic crop identification and broaden the application of CRISPR/Cas in food authenticity and safety.

Increasing eDNA capabilities with CRISPR technology for real‐time monitoring of ecosystem biodiversity

The accelerating pace of scientific discovery is being driven by the development of transformative technologies that are expanding traditional scientific boundaries. In ecology, the concept that

Novel nucleic acid detection strategies based on CRISPR‐Cas systems: From construction to application

The CRISPR‐Cas systems used for the recognition and detection of specific nucleic acids for different purposes are summarized, including the detection of genomic DNA, nongenomic DNA, RNA, and pathogenic microbe genomes.

Rapid and accurate species identification for ecological studies and monitoring using CRISPR‐based SHERLOCK

SHERLOCK’s ease of field deployment is improved by combining the previously demonstrated rapid isothermal amplification and CRISPR genetic identification with a minimally invasive and extraction‐free DNA collection protocol, as well as the option of instrument‐free lateral flow detection.

CRISPR-Cas12a-Based Diagnostics of Wheat Fungal Diseases.

A clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a-based nucleic acid assay for an early and rapid diagnosis of wheat FHB promises the molecular diagnosis of crop diseases and broadens the application of CRISPR tools.



Nucleic acid detection with CRISPR-Cas13a/C2c2

A Cas13a-based molecular detection platform, termed Specific High-Sensitivity Enzymatic Reporter UnLOCKing (SHERLOCK), is used to detect specific strains of Zika and Dengue virus, distinguish pathogenic bacteria, genotype human DNA, and identify mutations in cell-free tumor DNA.

Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6

SHERLOCKv2 can detect Dengue or Zika virus single-stranded RNA as well as mutations in patient liquid biopsy samples via lateral flow, highlighting its potential as a multiplexable, portable, rapid, and quantitative detection platform of nucleic acids.

CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity

It is shown that RNA-guided DNA binding unleashes indiscriminate single-stranded DNA cleavage activity by Cas12a that completely degrades ssDNA molecules, which is also a property of other type V CRISPR-Cas12 enzymes.

Robust Detection of Rare Species Using Environmental DNA: The Importance of Primer Specificity

Environmental DNA (eDNA) is being rapidly adopted as a tool to detect rare animals. Quantitative PCR (qPCR) using probe-based chemistries may represent a particularly powerful tool because of the

DNA Detection Using Recombination Proteins

RPA couples isothermal recombinase polymerase-driven primer targeting of template material with strand-displacement DNA synthesis and achieves exponential amplification with no need for pretreatment of sample DNA, thereby establishing an instrument-free DNA testing system.

The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA

It is shown that type V-A Cpf1 from Francisella novicida is a dual-nuclease that is specific to crRNA biogenesis and target DNA interference and constitutes the most minimalistic of the CRISPR–Cas systems so far described.

Species detection using environmental DNA from water samples

A novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water, using specific primers that amplify short mitochondrial DNA sequences to track the existence of a frog in controlled environments and natural wetlands.

Environmental DNA (eDNA) From the Wake of the Whales: Droplet Digital PCR for Detection and Species Identification

Droplet digital (dd)PCR technology for detection and species identification of cetaceans using environmental (e)DNA collected from seawater is adopted, with a focus on identification of known killer whale ecotypes.