Recent advances on CRISPR/Cas system-enabled portable detection devices for on-site agri-food safety assay

Agri-food safety has been considered as one of the most important public concerns worldwide. From farm to table, food crops and foods are extremely vulnerable to the contamination by a variety of pollutants from their growth and processing. Moreover, the SARS-CoV-2 detected in the food supply chain during COVID-19 pandemic has posed a greater challenge for rapid and on-site detection of agri-food contaminants in complex and volatile environments. Therefore, the development of rapid, accurate, and on-site detection technologies and portable detection devices is of great importance to ensure the agri-food security. This review comprehensively summarized the recent advances on the construction of CRISPR/Cas systems-based biosensing technologies and their portable detection devices, as well as their promising applications in the field of agri-food safety. First of all, the classification and working principles of CRISPR/Cas systems were introduced. Then, the latest advances on the CRISPR/Cas system-based on-site detection technologies and portable detection devices were also systematically summarized. Most importantly, the state-of-the-art applications of CRISPR/Cas systems-based on-site detection technologies and portable detection devices in the fields of agri-food safety were comprehensively summarized. Impressively, the future opportunities and challenges in this emerging and promising field were proposed. Emerging CRISPR/Cas system-based on-site detection technologies have showed a great potential in the detection of agri-food safety. Impressively, the integration of CRISPR/Cas systems-based biosensing technologies with portable detection devices (e.g., nanopore-based detection devices, lateral flow assay, smartphone-based detection devices, and microfluidic devices) is very promising for the on-site detection of agri-food contaminants. Additionally, CRISPR/Cas system-based biosensing technologies can be further integrated with much more innovative technologies for the development of novel detection platforms to realize the more reliable on-site detection of agri-food safety.

Programmable Nanostructures Based on Framework-DNA for Applications in Biosensing.

DNA has been actively utilized as bricks to construct exquisite nanostructures due to their unparalleled programmability. Particularly, nanostructures based on framework DNA (F-DNA) with controllable size, tailorable functionality, and precise addressability hold excellent promise for molecular biology studies and versatile tools for biosensor applications. In this review, we provide an overview of the current development of F-DNA-enabled biosensors. Firstly, we summarize the design and working principle of F-DNA-based nanodevices. Then, recent advances in their use in different kinds of target sensing with effectiveness have been exhibited. Finally, we envision potential perspectives on the future opportunities and challenges of biosensing platforms.

Highly Sensitive and Specific SARS-CoV-2 Serological Assay Using a Magnetic Modulation Biosensing System.

Sensitive serological assays are needed to provide valuable information about acute and past viral infections. For example, detection of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgG antibodies could serve as the basis for an "immunity passport" that would enable individuals to travel internationally. Here, utilizing a novel Magnetic Modulation Biosensing (MMB) system and the receptor-binding domain of the SARS-CoV-2 spike protein, we demonstrate a highly sensitive and specific anti-SARS-CoV-2 IgG serological assay. Using anti-SARS-CoV-2 IgG antibodies, RT-qPCR SARS-CoV-2-positive and healthy patients' samples, and vaccinees' samples, we compare the MMB-based SARS-CoV-2 IgG assay's analytical and clinical sensitivities to those of the enzyme-linked immunosorbent assay (ELISA). Compared with ELISA, the MMB-based assay has an ~6-fold lower limit of detection (129 ng/L vs. 817 ng/L), and it detects an increase in the IgG concentration much earlier after vaccination. Using 85 RT-qPCR SARS-CoV-2-positive samples and 79 -negative samples, the MMB-based assay demonstrated similar clinical specificity (98% vs. 99%) and sensitivity (93% vs. 92%) to the ELISA test, but with a much faster turnaround time (45 min vs. 245 min). The high analytical and clinical sensitivity, short turnaround time, and simplicity of the MMB-based assay makes it a preferred method for antibody detection.

Integrating Water Purification with Electrochemical Aptamer Sensing for Detecting SARS-CoV-2 in Wastewater.

Wastewater analysis of pathogens, particularly SARS-CoV-2, is instrumental in tracking and monitoring infectious diseases in a population. This method can be used to generate early warnings regarding the onset of an infectious disease and predict the associated infection trends. Currently, wastewater analysis of SARS-CoV-2 is almost exclusively performed using polymerase chain reaction for the amplification-based detection of viral RNA at centralized laboratories. Despite the development of several biosensing technologies offering point-of-care solutions for analyzing SARS-CoV-2 in clinical samples, these remain elusive for wastewater analysis due to the low levels of the virus and the interference caused by the wastewater matrix. Herein, we integrate an aptamer-based electrochemical chip with a filtration, purification, and extraction (FPE) system for developing an alternate in-field solution for wastewater analysis. The sensing chip employs a dimeric aptamer, which is universally applicable to the wild-type, alpha, delta, and omicron variants of SARS-CoV-2. We demonstrate that the aptamer is stable in the wastewater matrix (diluted to 50%) and its binding affinity is not significantly impacted. The sensing chip demonstrates a limit of detection of 1000 copies/L (1 copy/mL), enabled by the amplification provided by the FPE system. This allows the integrated system to detect trace amounts of the virus in native wastewater and categorize the amount of contamination into trace (<10 copies/mL), medium (10-1000 copies/mL), or high (>1000 copies/mL) levels, providing a viable wastewater analysis solution for in-field use.

Recent Trends in SERS-Based Plasmonic Sensors for Disease Diagnostics, Biomolecules Detection, and Machine Learning Techniques.

Surface-enhanced Raman spectroscopy/scattering (SERS) has evolved into a popular tool for applications in biology and medicine owing to its ease-of-use, non-destructive, and label-free approach. Advances in plasmonics and instrumentation have enabled the realization of SERS's full potential for the trace detection of biomolecules, disease diagnostics, and monitoring. We provide a brief review on the recent developments in the SERS technique for biosensing applications, with a particular focus on machine learning techniques used for the same. Initially, the article discusses the need for plasmonic sensors in biology and the advantage of SERS over existing techniques. In the later sections, the applications are organized as SERS-based biosensing for disease diagnosis focusing on cancer identification and respiratory diseases, including the recent SARS-CoV-2 detection. We then discuss progress in sensing microorganisms, such as bacteria, with a particular focus on plasmonic sensors for detecting biohazardous materials in view of homeland security. At the end of the article, we focus on machine learning techniques for the (a) identification, (b) classification, and (c) quantification in SERS for biology applications. The review covers the work from 2010 onwards, and the language is simplified to suit the needs of the interdisciplinary audience.

Molecular imprinting-based sensors: Lab-on-chip integration and biomedical applications.

The innovative technology of a marketable lab-on-a-chip platform for point-of-care (POC) in vitro detection has recently attracted remarkable attention. The POC tests can significantly enhance the high standard of medicinal care. In the last decade, clinical diagnostic technology has been broadly advanced and successfully performed in several areas. It seems that lab-on-a-chip approaches play a significant role in these technologies. However, high-cost and time-consuming methods are increasing the challenge and the development of a cost-effective, rapid and efficient method for the detection of biomolecules is urgently needed. Recently, polymer-coated sensing platforms have been a promising area that can be employed in medical diagnosis, pharmaceutical bioassays, and environmental monitoring. The designed on-chip sensors are based on molecular imprinting polymers (MIPs) that use label-free detection technology. Molecular imprinting shines out as a potentially promising technique for creating artificial recognition material with molecular recognition sites. MIPs provide unique advantages such as excellent recognition specificity, high selectivity, and good reusability. This review article aims to define several methods using molecular imprinting for biomolecules and their incorporation with several lab-on-chip technologies to describe the most promising methods for the development of sensing systems based on molecularly imprinted polymers. The higher selectivity, more user-friendly operation is believed to provide MIP-based lab-on-a-chip devices with great potential academic and commercial value in on-site clinical diagnostics and other point-of-care assays.

Plasmonic/magnetic nanoarchitectures: From controllable design to biosensing and bioelectronic interfaces.

Controllable design of the nanocrystal-assembled plasmonic/magnetic nanoarchitectures (P/MNAs) inspires abundant methodologies to enhance light-matter interactions and control magnetic-induced effects by means of fine-tuning the morphology and ordered packing of noble metallic or magnetic building blocks. The burgeoning development of multifunctional nanoarchitectures has opened up broad range of interdisciplinary applications including biosensing, in vitro diagnostic devices, point-of-care (POC) platforms, and soft bioelectronics. By taking advantage of their customizability and efficient conjugation with capping biomolecules, various nanoarchitectures have been integrated into high-performance biosensors with remarkable sensitivity and versatility, enabling key features that combined multiplexed detection, ease-of-use and miniaturization. In this review, we provide an overview of the representative developments of nanoarchitectures that being built by plasmonic and magnetic nanoparticles over recent decades. The design principles and key mechanisms for signal amplification and quantitative sensitivity have been explored. We highlight the structure-function programmability and prospects of addressing the main limitations for conventional biosensing strategies in terms of accurate selectivity, sensitivity, throughput, and optoelectronic integration. State-of-the-art strategies to achieve affordable and field-deployable POC devices for early multiplexed detection of infectious diseases such as COVID-19 has been covered in this review. Finally, we discuss the urgent yet challenging issues in nanoarchitectures design and related biosensing application, such as large-scale fabrication and integration with portable devices, and provide perspectives and suggestions on developing smart biosensors that connecting the materials science and biomedical engineering for personal health monitoring.

Reshaping de Novo Protein Switches into Bioresponsive Materials for Biomarker, Toxin, and Viral Detection.

De novo designed protein switches are powerful tools to specifically and sensitively detect diverse targets with simple chemiluminescent readouts. Finding an appropriate material host for de novo designed protein switches without altering their thermodynamics while preserving their intrinsic stability over time would enable the development of a variety of sensing formats to monitor exposure to pathogens, toxins, and for disease diagnosis. Here, a de novo protein-biopolymer hybrid that maintains the detection capabilities induced by the conformational change of the incorporated proteins in response to analytes of interest is generated in multiple, shelf-stable material formats without the need of refrigerated storage conditions. A set of functional demonstrator devices including personal protective equipment such as masks and laboratory gloves, free-standing films, air quality monitors, and wearable devices is presented to illustrate the versatility of the approach. Such formats are designed to be responsive to human epidermal growth factor receptor (HER2), anti-hepatitis B (HBV) antibodies, Botulinum neurotoxin B (BoNT/B), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This combination of form and function offers wide opportunities for ubiquitous sensing in multiple environments by enabling a large class of bio-responsive interfaces of broad utility.

Nanotechnology-Enabled Biosensors: A Review of Fundamentals, Design Principles, Materials, and Applications.

Biosensors are modern engineering tools that can be widely used for various technological applications. In the recent past, biosensors have been widely used in a broad application spectrum including industrial process control, the military, environmental monitoring, health care, microbiology, and food quality control. Biosensors are also used specifically for monitoring environmental pollution, detecting toxic elements' presence, the presence of bio-hazardous viruses or bacteria in organic matter, and biomolecule detection in clinical diagnostics. Moreover, deep medical applications such as well-being monitoring, chronic disease treatment, and in vitro medical examination studies such as the screening of infectious diseases for early detection. The scope for expanding the use of biosensors is very high owing to their inherent advantages such as ease of use, scalability, and simple manufacturing process. Biosensor technology is more prevalent as a large-scale, low cost, and enhanced technology in the modern medical field. Integration of nanotechnology with biosensors has shown the development path for the novel sensing mechanisms and biosensors as they enhance the performance and sensing ability of the currently used biosensors. Nanoscale dimensional integration promotes the formulation of biosensors with simple and rapid detection of molecules along with the detection of single biomolecules where they can also be evaluated and analyzed critically. Nanomaterials are used for the manufacturing of nano-biosensors and the nanomaterials commonly used include nanoparticles, nanowires, carbon nanotubes (CNTs), nanorods, and quantum dots (QDs). Nanomaterials possess various advantages such as color tunability, high detection sensitivity, a large surface area, high carrier capacity, high stability, and high thermal and electrical conductivity. The current review focuses on nanotechnology-enabled biosensors, their fundamentals, and architectural design. The review also expands the view on the materials used for fabricating biosensors and the probable applications of nanotechnology-enabled biosensors.

Deep Learning Optimization for Lens-Free Holographic Imaging and SARS-CoV-2 Biosensing

Rapid biosensing assays to detect SARS-CoV-2 are critical in mitigating the impact of the pandemic. Here, we use a lens-free holographic microscope coupled with deep learning in a rapid and sensitive assay to detect SARS-CoV-2. © 2022 The Author(s)