Hydrogel Digital LAMP with Suppressed Nonspecific Amplification for Rapid Diagnostics of Fungal Disease in Fresh Fruits

Spatial double-layer hydrogels enabled visual detection of Cladobotryum mycophilum based on recombinase-aided amplification - CRISPR/Cas12a

Cladobotryum mycophilum, a pathogen responsible for cobweb disease, caused significant and irreversible losses in the mushroom industry. Effective monitoring and early prevention rely on the development of advanced diagnosis methods. This study introduced a novel hydrogel-based C. mycophilum detection method that integrates recombinase-aided amplification (RAA) with the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) system (CRISPR/Cas12a), referred as RCCH. The RAA reaction occurs within cross-linked PEG hydrogel, which is subsequently overlaid with a CRISPR/Cas12a-functionalized hydrogel. The porous network of the PEG hydrogel traps essential enzymes, facilitating spatial co-localization of target DNA and the CRISPR/Cas12a-crRNA complex. Upon activation of Cas12a's trans-cleavage activity, clear and countable fluorescent spots are generated for visual detection. RCCH demonstrates a limit of detection as low as 1 fg/μL, and exceptional selectivity against common fungi Trichoderma viride and T. harzianum and the host mushroom Lentinula edodes. The entire process is completed in under 40 min, indicating RCCH's potential as a rapid, accurate, and practical detection method for monitoring mushroom diseases. This innovative approach offers significant support for enhancing safety in the mushroom industry.

Multiplex Digital Nucleic Acid Analysis by a LAMP-Argonaute Coupling Assay via a Parallel Droplet Fusion SlipChip

Multiplex digital nucleic acid analysis (NAA) allows the precise quantification of multiple target nucleic acids with single-molecule sensitivity, making it highly appealing for life science research and clinical diagnostics. Nucleic acid-guided endonucleases, such as CRISPR, have demonstrated great potential in digital NAA. However, performing multiplex digital NAA with an endonuclease remains challenging. The thermophilic Argonaute protein (Ago) enables specific targeting of multiple sequences by a single enzyme, exhibiting superior potential in multiplex detection. Here, we developed a multiplex digital NAA by coupling nucleic acid amplification and Ago-specific detection using parallel droplet fusion facilitated by a SlipChip. The SlipChip can generate a series of droplets to perform multiplex digital loop-mediated isothermal amplification (LAMP), followed by a series of droplets containing Ago reagents for parallel mixing and reactions, resulting in three distinct digital fluorescence signals (FAM, ROX, and Cy5) corresponding to each specific target sequence. We performed viral load analysis of respiratory viruses, including influenza A, influenza B, and SARS-CoV-2, within 60 min. In addition, we used this digital LAMP-Ago assay to analyze viral loads in 34 clinical samples. The system provides a multiplex digital NAA capable of precise nucleic acid quantification with high sensitivity and specificity.

Focusing on New Discoveries in Food Technology and Creating a New Future of Nutrition and Health: An Introduction to the 4th International Symposium of Food Science, Nutrition and Health in Dalian, China

The 4th International Symposium on Food Science, Nutrition and Health (ISFSNH) was held at the Shangri-La Hotel in Dalian, China, on May 29-31, 2023. The symposium explored the connotations and needs of "The Great Food Perspective" under the theme "Focusing on new discoveries in food technology and creating a new future of nutrition and health" to better address the global emerging diverse food needs. The ISFSNH covered four areas: (1) food processing theory and technology, (2) food safety and quality control, (3) precision nutrition and health, and (4) creation of nutritious and healthy foods. More than 1000 scholars and entrepreneurs from more than 100 colleges and universities globally attended the conference. This special issue of the Journal of Agricultural and Food Chemistry highlights the important topics of the 4th ISFSNH and includes more than 20 papers.

Nucleic Acid Plate Culture: Label-Free and Naked-Eye-Based Digital Loop-Mediated Isothermal Amplification in Hydrogel with Machine Learning

Digital nucleic acid amplification enables the absolute quantification of single molecules. However, due to the ultrasmall reaction volume in the digital system (i.e., short light path), most digital systems are limited to fluorescence signals, while label-free and naked-eye readout remain challenging. In this work, we report a digital nucleic acid plate culture method for label-free, ultrasimple, and naked-eye nucleic acid analysis. As simple as the bacteria culture, the nanoconfined digital loop-mediated isothermal amplification was performed by using polyacrylamide (PAM) hydrogel as the amplification matrix. The nanoconfinement of PAM hydrogel with an ionic polymer chain can remarkably accelerate the amplification of target nucleic acids and the growth of inorganic byproducts, namely, magnesium pyrophosphate particles (MPPs). Compared to that in aqueous solutions, MPPs trapped in the hydrogel with enhanced light scattering characteristics are clearly visible to the naked eye, forming white "colony" spots that can be simply counted in a label-free and instrument-free manner. The MPPs can also be photographed by a smartphone and automatically counted by a machine-learning algorithm to realize the absolute quantification of antibiotic-resistant pathogens in diverse real samples.