A CRISPR-based and post-amplification coupled SARS-CoV-2 detection with a portable evanescent wave biosensor

A temperature compensated fiber probe for highly sensitive detection in virus gene biosensing

This research presents an innovative reflective fiber optic probe structure, mutinously designed to detect H7N9 avian influenza virus gene precisely. This innovative structure skillfully combines multimode fiber (MMF) with a thin-diameter seven-core photonic crystal fiber (SCF-PCF), forming a semi-open Fabry-Pérot (FPI) cavity. This structure has demonstrated exceptional sensitivity in light intensity-refractive index (RI) response through rigorous theoretical and experimental validation. The development of a quasi-distributed parallel sensor array, which provides temperature compensation during measurements, has achieved a remarkable RI response sensitivity of up to 532.7 dB/RIU. The probe-type fiber optic sensitive unit, expertly functionalized with streptavidin, offers high specificity in detecting H7N9 avian influenza virus gene, with an impressively low detection limit of 10-2 pM. The development of this biosensor marks a significant development in biological detection, offering a practical engineering solution for achieving high sensitivity and specificity in light-intensity-modulated biosensing. Its potential for wide-ranging applications in various fields is now well-established.

Improving trans-cleavage activity of CRISPR-Cas13a using engineered crRNA with a uridinylate-rich 5'-overhang

The engieering of Cas13a crRNA to enhance its binding affinity with the Cas enzyme or target is a promising method of improving the collateral cleavage efficiency of CRISPR-Cas13a systems, thereby amplifying the sensitivity of nucleic acid detection. An examination of the top-performing engineered crRNA (24 nt 5'7U LbuCas13a crRNA, where the 5'-end was extended using 7-mer uridinylates) and optimized conditions revealed an increased rate of LbuCas13a-mediated collateral cleavage activity that was up to seven-fold higher than that of the original crRNA. Particularly, the 7-mer uridinylates extension to crRNA was determined to be spacer-independent for enhancing the LbuCas13a-mediacted collateral cleavage activity, and also benefited the LwaCas13a system. The improved trans-cleavage activity was explained by the interactions between crRNA and LbuCas13a at the molecular level, i.e. the 5'-overhangs were anchored in the cleft formed between the Helical-1 and HEPN2 domains with the consequence of more stable complex, and experimentally verified. Consequently, the improved CRISPR-Cas13a system detected the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA with a sensitivity of 2.36 fM that was 160-times higher than that of the original system. Using isothermal amplification via reverse transcription-recombinase polymerase amplification (RT-RPA), the system was capable to detect SARS-CoV-2 with attomolar sensitivity and accurately identified the SARS-CoV-2 Omicron variant (20/21 agreement) in clinical samples within 40 min.

A group-targeting biosensor for sensitive and rapid detection of quinolones in water samples

BACKGROUND

Quinolones (QNs) widely exist in the environment due to their wide range of applications and poor metabolic properties, resulting in the generation and spread of resistance genes, posing a potential threat to human health. Traditional analytical methods cannot detect all broad ranges of QNs simultaneously. The development of facile, efficient and reliable method for quantification and assessment of the total QNs is a long-lasting challenge.

RESULTS

We hereby provide a simple, sensitive and instantaneous group-targeting biosensor for the detection of total QNs in environmental water samples. The biosensor is based on a group-specific antibodies with high affinity against QNs. Fluorescent labeled antibodies bound to the coated antigen modified on the surface of the transducer, and excited by the evanescent waves. The detected fluorescent signal is inversely proportional to the QNs concentration. This biosensor exhibited excellent performance with detection limits lower than 0.15 μg L-1 for all five QNs variants, and even lower than 0.075 μg L-1 for ciprofloxacin (CIP) and ofloxacin (OFL). Environmental water samples can be detected after simple pretreatment, and all detection steps can be completed in 10 min. The transducer has a high regenerative capacity and shows no significant signal degradation after two hundred detection cycles. The recoveries of QNs in a variety of wastewater range from 105 to 119%, confirming its application potential in the measurement of total QNs in reality.

SIGNIFICANCE

The biosensor can realize rapid and sensitive detection of total QNs in water samples by simple pretreatment, which overcomes the disadvantage of the traditional methods that require complex pretreatment and time-consuming, and pave the groundwork for expansive development centered around this technology.

RNA-Based Sensor Systems for Affordable Diagnostics in the Age of Pandemics

In the era of the COVID-19 pandemic, the significance of point-of-care (POC) diagnostic tools has become increasingly vital, driven by the need for quick and precise virus identification. RNA-based sensors, particularly toehold sensors, have emerged as promising candidates for POC detection systems due to their selectivity and sensitivity. Toehold sensors operate by employing an RNA switch that changes the conformation when it binds to a target RNA molecule, resulting in a detectable signal. This review focuses on the development and deployment of RNA-based sensors for POC viral RNA detection with a particular emphasis on toehold sensors. The benefits and limits of toehold sensors are explored, and obstacles and future directions for improving their performance within POC detection systems are presented. The use of RNA-based sensors as a technology for rapid and sensitive detection of viral RNA holds great potential for effectively managing (dealing/coping) with present and future pandemics in resource-constrained settings.

Phages modified hydrogel pellet assembled in 3D printed both-in-one device for detecting Pseudomonas aeruginosa based on colorimetric and pressure readout modes

Pseudomonas aeruginosa (P. aeruginosa) with noticeable drug-resistance profile is one of the most pernicious pathogens that attracts major public health concerns. Herein, a 3D printed device combined with hydrogel pellet modified with phages was designed for point-of-care testing (POCT) of this pathogen with both colorimetric and pressure readout modes. A P. aeruginosa phage belonging to the family of Podoviridae was isolated from river water and noted as vB_PaeP-JZ1 (JZ1). Due to its host specificity, phage JZ1 was used as a recognizing agent for modifying the hydrogel pellet, and the modified hydrogel pellet was assembled into the 3D printed device to act as the sensing interface. Polymyxin B (PMB) was tagged with Pd@Pt core-shell nanodendrites (Pd@PtNDs) showing excellent peroxidase-like activity to act as the colorimetric and pressure signal tracer. P. aeruginosa can be quantified within the concentration ranges of 2.6 × 103 cfu mL-1 - 2.6 × 108 cfu mL-1 and 2.6 × 102 cfu mL-1 - 2.6 × 107 cfu mL-1 with colorimetric and pressure readout modes, respectively. The both modes can achieve quantitation of P. aeruginosa within 25 min. Thus the "both-in-one" 3D printed device with dual-mode readout function offers a rapid, sensitive, and specific platform for POCT of pathogenic bacteria.

Application of CRISPR/Cas13a-based biosensors in serum marker detection

The detection of serum markers is important for the early diagnosis and monitoring of diseases, but conventional detection methods have the problem of low specificity or sensitivity. CRISPR/Cas13a-based biosensors have the characteristics of simple detection methods and high sensitivity, which have a certain potential to solve the problems of conventional detection. This paper focuses on the research progress of CRISPR/Cas13a-based biosensors in serum marker detection, introduces the principles and applications of fluorescence, electrochemistry, colorimetric, and other biosensors based on CRISPR/Cas13a in the detection of serum markers, compares and analyzes the differences between the above CRISPR/Cas13a-based biosensors, and looks forward to the future development direction of CRISPR/Cas13a-based biosensors.

Combination of nucleic acid amplification and CRISPR/Cas technology in pathogen detection

Major health events caused by pathogenic microorganisms are increasing, seriously jeopardizing human lives. Currently PCR and ITA are widely used for rapid testing in food, medicine, industry and agriculture. However, due to the non-specificity of the amplification process, researchers have proposed the combination of nucleic acid amplification technology with the novel technology CRISPR for detection, which improves the specificity and credibility of results. This paper summarizes the research progress of nucleic acid amplification technology in conjunction with CRISPR/Cas technology for the detection of pathogens, which provides a reference and theoretical basis for the subsequent application of nucleic acid amplification technology in the field of pathogen detection.

Advanced technologies towards improved HPV diagnostics

Persistent infection with high-risk types of human papillomaviruses (HPV) is a major cause of cervical cancer, and an important factor in other malignancies, for example, head and neck cancer. Despite recent progress in screening and vaccination, the incidence and mortality are still relatively high, especially in low-income countries. The mortality and financial burden associated with the treatment could be decreased if a simple, rapid, and inexpensive technology for HPV testing becomes available, targeting individuals for further monitoring with increased risk of developing cancer. Commercial HPV tests available in the market are often relatively expensive, time-consuming, and require sophisticated instrumentation, which limits their more widespread utilization. To address these challenges, novel technologies are being implemented also for HPV diagnostics that include for example, isothermal amplification techniques, lateral flow assays, CRISPR-Cas-based systems, as well as microfluidics, paperfluidics and lab-on-a-chip devices, ideal for point-of-care testing in decentralized settings. In this review, we first evaluate current commercial HPV tests, followed by a description of advanced technologies, explanation of their principles, critical evaluation of their strengths and weaknesses, and suggestions for their possible implementation into medical diagnostics.

Ultrasensitive miRNA Detection Based on Magnetic Upconversion Nanoparticle Enhancement and CRISPR/Cas13a-Driven Signal Amplification

MicroRNAs (miRNAs), a class of small molecules with important regulatory functions, have been widely used in the field of biosensing as biomarkers for the early diagnosis of various diseases. Therefore, it is crucial to develop an miRNA detection platform with high sensitivity and specificity. Here, we have designed a CRISPR/Cas13-based enzymatic cyclic amplification system and regarded the magnetic upconversion nanoparticles (MUCNPs) as a biosensor of outputting the detection signal for the highly sensitive and high-fidelity detection of miRNAs. MUCNPs were composed of UCNPs (fluorescence donors) and Fe3O4@AuNPs (fluorescence acceptors) through double-stranded DNA hybrid coupling. The target miRNA acted as an activator, which could activate the trans-cleavage activity of Cas13a to the well-designed Trigger containing two uracil ribonucleotides (rU) in its loop and trigger a strand displacement reaction to generate a large amount of single-stranded DNA, resulting in the release of the UCNPs from MUCNPs. Benefiting from the high fidelity and high selectivity of CRISPR/Cas13a, the great effect of triggered enzymatic cycle amplification, and the high-intensity luminescent signal of MUCNPs, this method possessed miRNA detection capability with high sensitivity and specificity even in the complex environment with 10% fetal bovine serum (FBS) and a serum sample. Meanwhile, the detection limit could be as low as 83.2 fM. In addition, this method effectively reduced the effect of photobleaching and maintained high stability, which was expected to achieve efficient and sensitive miRNA detection.

Association of wastewater SARS-CoV-2 load with confirmed COVID-19 cases at a university hospital in Sapporo, Japan during the period from February 2021 to February 2023

Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been used to monitor trends in SARS-CoV-2 prevalence in a community without being influenced by clinical testing resources or healthcare-seeking behaviors. Since the rate of mortality from COVID-19 is higher in elderly patients with comorbidities, it is important to protect hospitalized patients from nosocomial infections caused by SARS-CoV-2. SARS-CoV-2 dissemination within a hospital ward was mostly mediated by healthcare workers (HCWs) and patients. HCWs need to understand the occurrence of COVID-19 and reflect this in their infection control measures. The aim of the present study was to determine the potential of SARS-CoV-2 RNA in wastewater as a leading indicator of confirmed COVID-19 cases at a university hospital. The trend of the geometric mean RNA concentrations in wastewater collected in Sapporo corresponded well with that of the number of newly confirmed COVID-19 cases at Hokkaido University Hospital between February 15, 2021 and February 26, 2023 (Pearson's r = 0.8823, p < 0.0001). Our results showed that monitoring SARS-CoV-2 RNA in municipal wastewater was useful for estimating the number of COVID-19 patients in healthcare facilities in the city.

Advances in the application of CRISPR-Cas technology in rapid detection of pathogen nucleic acid

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) are widely used as gene editing tools in biology, microbiology, and other fields. CRISPR is composed of highly conserved repetitive sequences and spacer sequences in tandem. The spacer sequence has homology with foreign nucleic acids such as viruses and plasmids; Cas effector proteins have endonucleases, and become a hotspot in the field of molecular diagnosis because they recognize and cut specific DNA or RNA sequences. Researchers have developed many diagnostic platforms with high sensitivity, high specificity, and low cost by using Cas proteins (Cas9, Cas12, Cas13, Cas14, etc.) in combination with signal amplification and transformation technologies (fluorescence method, lateral flow technology, etc.), providing a new way for rapid detection of pathogen nucleic acid. This paper introduces the biological mechanism and classification of CRISPR-Cas technology, summarizes the existing rapid detection technology for pathogen nucleic acid based on the trans cleavage activity of Cas, describes its characteristics, functions, and application scenarios, and prospects the future application of this technology.

Fabrication of MIL-101(Cr)/silver nanocomposites as SERS substrate for sensitive determination of malachite green and crystal violet in tilapia

Nanocomposites with multiple functions have attracted much attention in designing novel SERS substrates. In this report, the enrichment ability of MIL-101(Cr) and the local surface plasma resonance (LSPR) of silver nanoparticles are combined to fabricate a SERS substrate denoted as MIL-101-MA@Ag, which can simultaneously produce high-density and uniformly distributed hot spots. Moreover, the enrichment ability of MIL-101(Cr) can further improve the sensitivity by concentrating and transferring the analytes in the vicinity of hot spots. Under optimal conditions, MIL-101-MA@Ag showed good SERS activity for malachite green (MG) and crystal violet (CV), with detection limits as low as 9.5×10-11 M and 9.2×10-12 M at 1616 cm-1, respectively. The prepared substrate has been successfully applied to detect MG and CV in tilapia, the recovery rate of fish tissue extract was 86.4~102%, and the relative standard deviation (RSD) was 8.9~15%. The results demonstrate that MOF-based nanocomposites are expected to be useful SERS substrates and have a universal applicability for the detection of other hazardous molecules.

Biomedical equipments, vaccine and drug in the prevention, diagnosis and treatment of COVID-19

SARS-CoV-2 virus caused an infectious disease, named COVID-19. Biomedical equipments, vaccine and drug have played a crucial role in the prevention, diagnosis and treatment. Nevertheless, up to now, there still has been no literature summarizing the diagnosis, prevention and treatment of this infectious disease from the perspective of biomedical equipments. Thus, this review wants to give an overview on the biomedical equipments, vaccine and drug in the prevention, diagnosis and treatment of this disease, and avoids the overlap with previous research, more emphasis on biomedical equipments, and less emphasis on biomaterials. The existing problems in the current research and application were summarized, and the future research direction was proposed, so as to provide reference to deal with similar viral infections in the future.

A SERS-signalled, CRISPR/Cas-powered bioassay for amplification-free and anti-interference detection of SARS-CoV-2 in foods and environmental samples using a single tube-in-tube vessel

The pandemic of COVID-19 creates an imperative need for sensitive and portable detection of SARS-CoV-2. We devised a SERS-read, CRISPR/Cas-powered nanobioassay, termed as OVER-SARS-CoV-2 (One-Vessel Enhanced RNA test on SARS-CoV-2), which enabled supersensitive, ultrafast, accurate and portable detection of SARS-CoV-2 in a single vessel in an amplification-free and anti-interference manner. The SERS nanoprobes were constructed by conjugating gold nanoparticles with Raman reporting molecular and single-stranded DNA (ssDNA) probes, whose aggregation-to-dispersion changes can be finely tuned by target-activated Cas12a though trans-cleavage of linker ssDNA. As such, the nucleic acid signals could be dexterously converted and amplified to SERS signals. By customizing an ingenious vessel, the steps of RNA reverse transcription, Cas12a trans-cleavage and SERS nanoprobes crosslinking can be integrated into a single and disposal vessel. It was proved that our proposed nanobioassay was able to detect SARS-CoV-2 as low as 200 copies/mL without any pre-amplification within 45 min. In addition, the proposed nanobioassay was confirmed by clinical swab samples and challenged for SARS-CoV-2 detection in simulated complex environmental and food samples. This work enriches the arsenal of CRISPR-based diagnostics (CRISPR-Dx) and provides a novel and robust platform for SARS-CoV-2 decentralized detection, which can be put into practice in the near future.

Entropy-driven assisted T7 RNA polymerase amplification-activated CRISPR/Cas13a activity for SARS-CoV-2 detection in human pharyngeal swabs and environment by an electrochemiluminescence biosensor

In this study, we introduce an electrochemiluminescence (ECL) sensing platform based on the "Entropy-driven triggered T7 amplification-CRISPR/Cas13a system" (EDT-Cas). This platform combines a programmable entropy-driven cycling strategy, T7 RNA polymerase, and the CRISPR/Cas13a system to amplify the determination of the SARS-CoV-2 RdRp gene. The Ti₃C₂T_x-compliant ECL signaling molecule offers unique benefits when used with the ECL sensing platform to increase the assay sensitivity and the electrode surface modifiability. To obtain the T7 promoter, the SARS-CoV-2 RdRp gene may first initiate an entropy-driven cyclic amplification response. Then, after recognizing the T7 promoter sequence on the newly created dsDNA, T7 RNA polymerase starts transcription, resulting in the production of many single-stranded RNAs (ssRNAs), which in turn trigger the action of CRISPR/Cas13a. Finally, Cas13a/crRNA identifies the transcribed ssRNA. When it cleaves the ssRNA, many DNA reporter probes carrying -U-U- are cleaved on the electrode surface, increasing the ECL signal and allowing for the rapid and highly sensitive detection of SARS-CoV-2. With a detection limit of 7.39 aM, our method enables us to locate the SARS-CoV-2 RdRp gene in clinical samples. The detection method also demonstrates excellent repeatability and stability. The SARS-CoV-2 RdRp gene was discovered using the "Entropy-driven triggered T7 amplification-CRISPR/Cas13a system" (EDT-Cas). The developed ECL test had excellent recoveries in pharyngeal swabs and environmental samples. It is anticipated to offer an early clinical diagnosis of SARS-CoV-2 and further control the spread of the pandemic.

Two-dimensional material-enhanced surface plasmon resonance for antibiotic sensing

Two-dimensional (2D) materials attract attention from the academic community due to their excellent properties, and their wide application in sensing is expected to revolutionize environmental monitoring, medical diagnostics, and food safety. In this work, we systematically evaluate the effects of 2D materials on the Au chip surface plasmon resonance (SPR) sensor. The results reveal that 2D materials cannot improve the sensitivity of intensity-modulated SPR sensors. However, there exists an optimal real part of RI of 3.5-4.0 and optimal thickness when choosing nanomaterials for sensitivity enhancement of SPR sensors in angular modulation. In addition, the smaller the imaginary part of the nanomaterial RI, the higher the sensitivity of the proposed Au SPR sensor. The 2D material's thickness needed for the highest sensitivity decreases with increasing real part and imaginary part of the RI. As a case study, we developed a 5 nm-thickness MoS₂-enhanced SPR biosensor, which exhibited a low sulfonamides (SAs) detection limit of 0.05 μg/L based on a group-targeting indirect competitive immunoassay, nearly 12-fold lower than that of the bare Au SPR system. The proposed criteria help to shed light on the 2D material-Au surface interaction, which has greatly promoted the development of novel SPR biosensing with outstanding sensitivity.

An ultra-sensitive one-pot RNA-templated DNA ligation rolling circle amplification-assisted CRISPR/Cas12a detector assay for rapid detection of SARS-CoV-2

Rapid, sensitive, and one-pot diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays an extremely important role in point-of-care testing (POCT). Herein, we report an ultra-sensitive and rapid one-pot enzyme-catalyzed rolling circle amplification-assisted CRISPR/FnCas12a assay, termed OPERATOR. OPERATOR employs a single well-designed single-strand padlock DNA, containing a protospacer adjacent motif (PAM) site and a sequence complementary to the target RNA which procedure converts and amplifies genomic RNA to DNA by RNA-templated DNA ligation and multiply-primed rolling circle amplification (MRCA). The MRCA amplicon of single-stranded DNA is cleaved by the FnCas12a/crRNA complex and detected via a fluorescence reader or lateral flow strip. OPERATOR presents outstanding advantages including ultra-sensitivity (1.625 copies per reaction), high specificity (100%), rapid reaction speed (∼30 min), easy operation, low cost, and on-spot visualization. Furthermore, we established a POCT platform by combining OPERATOR with rapid RNA release and a lateral flow strip without professional equipment. The high performance of OPERATOR in SARS-CoV-2 tests was confirmed using both reference materials and clinical samples, and the results suggest that is readily adaptable for point-of-care testing of other RNA viruses.

Facile and Unplugged Surface Plasmon Resonance Biosensor with NIR-Emitting Perovskite Nanocomposites for Fast Detection of SARS-CoV-2

The emergence of the coronavirus disease 2019 (COVID-19) pandemic prompted researchers to develop portable biosensing platforms, anticipating to detect the analyte in a label-free, direct, and simple manner, for deploying on site to prevent the spread of the infectious disease. Herein, we developed a facile wavelength-based SPR sensor built with the aid of a 3D printing technology and synthesized air-stable NIR-emitting perovskite nanocomposites as the light source. The simple synthesis processes for the perovskite quantum dots enabled low-cost and large-area production and good emission stability. The integration of the two technologies enabled the proposed SPR sensor to exhibit the characteristics of lightweight, compactness, and being without a plug, just fitting the requirements of on-site detection. Experimentally, the detection limit of the proposed NIR SPR biosensor for refractive index change reached the 10-6 RIU level, comparable with that of state-of-the-art portable SPR sensors. In addition, the bio-applicability of the platform was validated by incorporating a homemade high-affinity polyclonal antibody toward the SARS-CoV-2 spike protein. The results demonstrated that the proposed system was capable of discriminating between clinical swab samples collected from COVID-19 patients and healthy subjects because the used polyclonal antibody exhibited high specificity against SARS-CoV-2. Most importantly, the whole measurement process not only took less than 15 min but also needed no complex procedures or multiple reagents. We believe that the findings disclosed in this work can open an avenue in the field of on-site detection for highly pathogenic viruses.

Application of Hybridization Chain Reaction/CRISPR-Cas12a for the Detection of SARS-CoV-2 Infection

Globally, the emergence of the coronavirus disease (COVID-19) has had a significant impact on life. The need for ongoing SARS-CoV-2 screening employing inexpensive and quick diagnostic approaches is undeniable, given the ongoing pandemic and variations in vaccine administration in resource-constrained regions. This study presents results as proof of concept to use hybridization chain reaction (HCR) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a complex for detecting SARS-CoV-2. HCR hairpin probes were designed using the NUPACK web-based program and further used to amplify the SARS-CoV-2 N gene in archived nasopharyngeal samples. The results were visualized using agarose gels and CRISPR Cas12a-based lateral flow strips. The assay was evaluated using the gold standard, real-time polymerase chain reaction (RT-PCR), as recommended by the World Health Organization (WHO). The results show the comparative efficiency of HCR to RT-PCR. This study shows that HCR and CRISPR are viable alternatives for diagnosing SARS-CoV-2 in samples.

Conductive Ink-Coated Paper-Based Supersandwich DNA Biosensor for Ultrasensitive Detection of Neisseria gonorrhoeae

Herein, we report results of the studies relating to the development of an impedimetric, magnetic bead-assisted supersandwich DNA hybridization assay for ultrasensitive detection of Neisseria gonorrhoeae, the causative agent of a sexually transmitted infection (STI), gonorrhea. First, a conductive ink was formulated by homogenously dispersing carboxylated multiwalled carbon nanotubes (cMWCNTs) in a stable emulsion of terpineol and an aqueous suspension of carboxymethyl cellulose (CMC). The ink, labeled C5, was coated onto paper substrates to fabricate C5@paper conductive electrodes. Thereafter, a magnetic bead (MB)-assisted supersandwich DNA hybridization assay was optimized against the porA pseudogene of N. gonorrhoeae. For this purpose, a pair of specific 5' aminated capture probes (SCP) and supersandwich detector probes (SDP) was designed, which allowed the enrichment of target gonorrheal DNA sequence from a milieu of substances. The SD probe was designed such that instead of 1:1 binding, it allowed the binding of more than one T strand, leading to a 'ladder-like' DNA supersandwich structure. The MB-assisted supersandwich assay was integrated into the C5@paper electrodes for electrochemical analysis. The C5@paper electrodes were found to be highly conductive by a four-probe conductivity method (maximum conductivity of 10.1 S·cm^-1). Further, the biosensing assay displayed a wide linear range of 100 aM-100 nM (10⁹ orders of magnitude) with an excellent sensitivity of 22.6 kΩ·(log[concentration])^-1. The clinical applicability of the biosensing assay was assessed by detecting genomic DNA extracted from N. gonorrhoeae in the presence of DNA from different non-gonorrheal bacterial species. In conclusion, this study demonstrates a highly sensitive, cost-effective, and label-free paper-based device for STI diagnostics. The ink formulation prepared for the study was found to be highly thixotropic, which indicates that the paper electrodes can be screen-printed in a reproducible and scalable manner.

Microplastics in household fecal sewage treatment facilities of rural China

Fecal sewage (FS), composed of human feces and wastewater, potentially contains microplastics (MPs) that are prone to environmental pollution. In this study, 65 FS samples, as collected from 65 villages in 27 Chinese provinces, have been employed to investigate the characteristics of MPs in three kinds of household FS treatment facilities of rural regions, and the possibility of FS irrigation as the source of MPs in farmlands. As a result, seven physicochemical properties and microbial community of FS were detected, and pertinent social statistical data were collected to determine influencing factors of MPs. The abundance of FS-based MPs ranged from 47.16 to 143.05 particles L^-1, with an average 90.38 ± 20.63 particles L^-1. The FS from northern China had higher MPs abundance than that from southern and northwestern China. Average MPs abundance was cesspit (101.33) > septic tank (86.54) > biogas digester (84.11). The estimated mass of FS-based MPs entering farmlands in China was 7.8 × 10³-5.6 × 10⁴ tons a year. Chemical oxygen demand and genus Phascolarctobacterium might mainly affected MPs abundance in FS, while some other factors such as suspended substance, ambient temperature, and medical care spending were also significantly correlated with FS-based MPs abundance.

CRISPR/Cas12a-powered evanescent wave fluorescence nanobiosensing platform for nucleic acid amplification-free detection of Staphylococcus aureus with multiple signal enhancements

Although CRISPR-based biosensors for pathogenic detection are highly specific, they not sensitive enough and nucleic acid amplification is generally required to improve their sensitivity. However, this allows only binary operations and significantly limits practical applications. Here, a CRISPR/Cas12a-powered Evanescent wAve fluorescence nanobiosensing plaTform (CREAT) was developed for ultrasensitive nucleic acid amplification-free quantitative detection of pathogens with multiple signal enhancements. In addition to collateral cleavage amplification of the CRISPR/Cas12a system, we constructed nanophotonic structure-based evanescent wave fluorescence enhancement, Mg²⁺ or DNA-mediated fluorescence enhancement, and air-displacement fluorescence enhancement strategies for ultrasensitive detection of Staphylococcus aureus (S. aureus). Especially, the fluorescence signal detected by CREAT can be significantly enhanced by adding a simple air displacement step, thus improving detection sensitivity. This nanobiosensor detected real samples containing S. aureus, with a detection limit of 592 CFU/mL and 13.2 CFU/mL in 45 min and 90 min, respectively, which are comparable to those of RT-qPCR. This paves a new way for simple, rapid, sensitive, robust, and flexible on-site detection of S. aureus as well as other pathogens.

Recent Progress in Functional-Nucleic-Acid-Based Fluorescent Fiber-Optic Evanescent Wave Biosensors

Biosensors capable of onsite and continuous detection of environmental and food pollutants and biomarkers are highly desired, but only a few sensing platforms meet the "2-SAR" requirements (sensitivity, specificity, affordability, automation, rapidity, and reusability). A fiber optic evanescent wave (FOEW) sensor is an attractive type of portable device that has the advantages of high sensitivity, low cost, good reusability, and long-term stability. By utilizing functional nucleic acids (FNAs) such as aptamers, DNAzymes, and rational designed nucleic acid probes as specific recognition ligands, the FOEW sensor has been demonstrated to be a general sensing platform for the onsite and continuous detection of various targets ranging from small molecules and heavy metal ions to proteins, nucleic acids, and pathogens. In this review, we cover the progress of the fluorescent FNA-based FOEW biosensor since its first report in 1995. We focus on the chemical modification of the optical fiber and the sensing mechanisms for the five above-mentioned types of targets. The challenges and prospects on the isolation of high-quality aptamers, reagent-free detection, long-term stability under application conditions, and high throughput are also included in this review to highlight the future trends for the development of FOEW biosensors capable of onsite and continuous detection.

An Ultrasensitive Colorimetric Foodborne Pathogenic Detection Method Using a CRISPR/Cas12a Mediated Strand Displacement/Hybridization Chain Reaction

Accurate, rapid, and sensitive pathogenic detections play an important role in food safety. Herein, we developed a novel CRISPR/Cas12a mediated strand displacement/hybridization chain reaction (CSDHCR) nucleic acid assay for foodborne pathogenic colorimetric detection. A biotinylated DNA toehold is coupled on avidin magnetic beads and acts as an initiator strand to trigger the SDHCR. The SDHCR amplification allowed the formation of long hemin/G-quadruplex-based DNAzyme products to catalyze the TMB-H₂O₂ reaction. In the presence of the DNA targets, the trans-cleavage activity of CRISPR/Cas12a was activated to cleave the initiator DNA, resulting in the failure of SDHCR and no color change. Under optimal conditions, the CSDHCR has a satisfactory linear detection of DNA targets with a regression equation Y = 0.0531*X - 0.0091 (R² = 0.9903) in the range of 10 fM to 1 nM, and the limit of detection was determined as 4.54 fM. In addition, Vibrio vulnificus, one foodborne pathogen, was used to verify the practical application of the method, and it showed satisfactory specificity and sensitivity with a limit of detection at 1.0 × 10⁰ CFU/mL coupling with recombinase polymerase amplification. Our proposed CSDHCR biosensor could be a promising alternative method for ultrasensitive and visual detection of nucleic acids and the practical application of foodborne pathogens.

Highly Specific Antibiotic Detection on Water-Stable Black Phosphorus Field-Effect Transistors

Two-dimensional (2D) black phosphorus (BP) has been reported to have appealing semiconducting properties as the sensing channel in field-effect transistor (FET) sensors. However, the intrinsic instability of BP in water greatly hinders its application, and little is known about its sensing performance and mechanism in aqueous medium. Herein, a water-stable BP FET sensor for antibiotic detection is reported. A novel surface engineering strategy with Ag⁺ coordination and melamine cyanurate (MC) supramolecular passivation is utilized to enhance the stability and transistor performance of BP. With molecularly imprinted polymers (MIPs) as the detection probe for tetracycline, the BP_Ag(+)/MC/MIPs sensor shows high sensitivity to tetracycline with a detection limit of 7.94 nM and a quick response within 6 s as well as high selectivity against other antibiotics with similar molecular structures. A new sensing mechanism relying on the conjugation effect of the probe structure is proposed, and new knowledge about alkalinity-enhanced and ionic strength-related response from the electrostatic gating effect is given based on the solution chemistry impact study. This work offers an efficient surface engineering strategy to enable the application of 2D BP for antibiotic detection in aqueous medium and presents a new sensing mechanism in chemical analysis by FET sensors.

Aptamer-based CRISPR-Cas powered diagnostics of diverse biomarkers and small molecule targets

CRISPR-Cas systems have been widely used in genome editing and transcriptional regulation. Recently, CRISPR-Cas effectors are adopted for biosensor construction due to its adjustable properties, such as simplicity of design, easy operation, collateral cleavage activity, and high biocompatibility. Aptamers' excellent sensitivity, specificity, in vitro synthesis, base-pairing, labeling, modification, and programmability has made them an attractive molecular recognition element for inclusion in CRISPR-Cas systems. Here, we review current advances in aptamer-based CRISPR-Cas sensors. We briefly discuss aptamers and the knowledge of Cas effector proteins, crRNA, reporter probes, analytes, and applications of target-specific aptamers. Next, we provide fabrication strategies, molecular binding, and detection using fluorescence, electrochemical, colorimetric, nanomaterials, Rayleigh, and Raman scattering. The application of CRISPR-Cas systems in aptamer-based sensing of a wide range of biomarkers (disease and pathogens) and toxic contaminants is growing. This review provides an update and offers novel insights into developing CRISPR-Cas-based sensors using ssDNA aptamers with high efficiency and specificity for point-of-care setting diagnostics.

Dual nucleases-assisted cyclic amplification using polydopamine nanospheres-based biosensors for one-pot detection of microRNAs

The accurate detection of microRNAs (miRNAs) is essential in the early diagnosis and treatment of cancers. Existing miRNA detection methods represented by nucleic acid amplification (NAA) techniques, such as qRT-PCR, suffer from the small size of miRNAs and lead to limited practicability. CRISPR Cas13a system, another valuable toolbox for nucleic acid detection, relies heavily on the behaviors of accompanying isothermal NAA techniques, which prompts similar deficiencies in miRNA detection. In this study, a dual nucleases-assisted cyclic amplification (DUNCAN) strategy has been established to replace NAA techniques for one-pot detection of miRNAs. The DUNCAN strategy contained an initial reaction based on CRISPR Cas13a for target recognition, and an accompanied cyclic reaction using DNA probes protected by polydopamine nanospheres (PDANSs) for signal amplification and result readout. Exemplified by miR-19b, which has been confirmed to be related to several tumors, the quantitative detection through the DUNCAN strategy was achieved in the dynamic range of 10-10⁶ fM, with a calculated detection limit of 1.27 fM. Besides, the DUNCAN strategy presented well selectivity and anti-interference performance for accurate detection of miR-19b in complex miRNA mixtures, different cell lines and clinical samples compared with qRT-PCR. All these performances demonstrated the promising potential of the DUNCAN strategy in clinical miRNA detection and diagnosis.

A novel cascade signal amplification strategy integrating CRISPR/Cas13a and branched hybridization chain reaction for ultra-sensitive and specific SERS detection of disease-related nucleic acids

The molecular diagnosis of disease by high-sensitively and specifically detecting extremely trace amounts of nucleic acid biomarkers in biological samples is still a great challenge, and the powerful sensing strategy has become an urgent need for basic researches and clinical applications. Herein, a novel one-pot cascade signal amplification strategy (Cas13a-bHCR) integrating CRISPR/Cas13a system (Cas13a) and branched hybridization chain reaction (bHCR) was proposed for ultra-highly sensitive and specific SERS assay of disease-related nucleic acids on SERS-active silver nanorods sensing chips. The Cas13a-bHCR based SERS assay of gastric cancer-related miRNA-106a (miR-106a) can be achieved within 60 min and output significantly enhanced SERS signal due to the multiple signal amplification, which possesses a good linear calibration curve from 10 aM to 1 nM with the limit of detection (LOD) low to 8.55 aM for detecting gastric cancer-related miR-106a in human serum. The Cas13a-bHCR based SERS sensing also shows good specificity, uniformity, repeatability and reliability, and has good practicability for detection of miR-106a in clinical samples, which can provide a potential powerful tool for SERS detection of disease-related nucleic acids and promise brighter prospects in the field of clinical diagnosis of early disease.

MXene-based composites against antibiotic-resistant bacteria: current trends and future perspectives

Today, finding novel nanomaterial-based strategies to combat bacterial resistance is an important field of science. MXene-based composites have shown excellent antimicrobial potential owing to their fascinating properties such as excellent photothermal effects, highly active sites, large interlayer spacing, unique chemical structures, and hydrophilicity; they have great potential to damage the bacterial cells by rupturing the bacterial cell membranes, enhancing the permeability across the membrane, causing DNA damages, reducing the metabolic activity, and generating oxidative stress. After inserting into or attaching on the surface of pathogenic bacteria, these two-dimensional structures can cause bacterial membrane disruption and cell content leakage owing to their sharp edges. Remarkably, MXenes and their composites with excellent photothermal performance have been studied in photothermal antibacterial therapy to combat antibiotic-resistant bacteria and suppress chronic wound infections, thus providing new opportunities for multidrug-resistant bacteria-infected wound healing. But, details about the possible interactions between MXene-based nanosystems and bacterial cell membranes are rather scarce. Also, the mechanisms of photothermal antibacterial therapy as well as synergistic tactics including photothermal, photodynamic or chemo-photothermal therapy still need to be uncovered. This review endeavors to delineate critical issues pertaining to the application of MXene-based composites against antibiotic-resistant bacteria, focusing on their photocatalytic inactivation, physical damage, and photothermal antibacterial therapy.

This review endeavors to delineate critical issues pertaining to the application of MXene-based composites against antibiotic-resistant bacteria.

CRISPR-Cas based molecular diagnostics for foodborne pathogens

Foodborne pathogenic infection has brought multifaceted issues to human life, leading to an urgent demand for advanced detection technologies. CRISPR/Cas-based biosensors have the potential to address various challenges that exist in conventional assays such as insensitivity, long turnaround time and complex pretreatments. In this perspective, we review the relevant strategies of CRISPR/Cas-assisted diagnostics on foodborne pathogens, focusing on biosensing platforms for foodborne pathogens based on fluorescence, colorimetric, (electro)chemiluminescence, electrochemical, and surface-enhanced Raman scattering detection. It summarizes their detection principles by the clarification of foodborne pathogenic bacteria, fungi, and viruses. Finally, we discuss the current challenges or technical barriers of these methods against broad application, and put forward alternative solutions to improve CRISPR/Cas potential for food safety.

CRISPR-Cas13a system: A novel tool for molecular diagnostics

The clustered regularly interspaced short palindromic repeats (CRISPR) system is a natural adaptive immune system of prokaryotes. The CRISPR-Cas system is currently divided into two classes and six types: types I, III, and IV in class 1 systems and types II, V, and VI in class 2 systems. Among the CRISPR-Cas type VI systems, the CRISPR/Cas13a system has been the most widely characterized for its application in molecular diagnostics, gene therapy, gene editing, and RNA imaging. Moreover, because of the trans-cleavage activity of Cas13a and the high specificity of its CRISPR RNA, the CRISPR/Cas13a system has enormous potential in the field of molecular diagnostics. Herein, we summarize the applications of the CRISPR/Cas13a system in the detection of pathogens, including viruses, bacteria, parasites, chlamydia, and fungus; biomarkers, such as microRNAs, lncRNAs, and circRNAs; and some non-nucleic acid targets, including proteins, ions, and methyl groups. Meanwhile, we highlight the working principles of some novel Cas13a-based detection methods, including the Specific High-Sensitivity Enzymatic Reporter UnLOCKing (SHERLOCK) and its improved versions, Cas13a-based nucleic acid amplification-free biosensors, and Cas13a-based biosensors for non-nucleic acid target detection. Finally, we focus on some issues that need to be solved and the development prospects of the CRISPR/Cas13a system.

Paper-Based Biosensors for the Detection of Nucleic Acids from Pathogens

Paper-based biosensors are microfluidic analytical devices used for the detection of biochemical substances. The unique properties of paper-based biosensors, including low cost, portability, disposability, and ease of use, make them an excellent tool for point-of-care testing. Among all analyte detection methods, nucleic acid-based pathogen detection offers versatility due to the ease of nucleic acid synthesis. In a point-of-care testing context, the combination of nucleic acid detection and a paper-based platform allows for accurate detection. This review offers an overview of contemporary paper-based biosensors for detecting nucleic acids from pathogens. The methods and limitations of implementing an integrated portable paper-based platform are discussed. The review concludes with potential directions for future research in the development of paper-based biosensors.

Rapid Detection of Attomolar SARS-CoV-2 Nucleic Acids in All-Dielectric Metasurface Biosensors

Worldwide infection due to SARS-CoV-2 revealed that short-time and extremely high-sensitivity detection of nucleic acids is a crucial technique for human beings. Polymerase chain reactions have been mainly used for the SARS-CoV-2 detection over the years. However, an advancement in quantification of the detection and shortening runtime is important for present and future use. Here, we report a rapid detection scheme that is a combination of nucleic acid amplification and a highly efficient fluorescence biosensor, that is, a metasurface biosensor composed of a pair of an all-dielectric metasurface and a microfluidic transparent chip. In the present scheme, we show a series of proof-of-concept experimental results that the metasurface biosensors detected amplicons originating from attomolar SARS-CoV-2 nucleic acids and that the amplification was implemented within 1 h. Furthermore, this detection capability substantially satisfies an official requirement of 100 RNA copies/140 μL, which is a criterion for the reliable infection tests.

Theoretical study of glycoluril by highly symmetrical magnesium oxide Mg12O12 nanostructure: adsorption, detection, SERS enhancement, and electrical conductivity study

Using metal substrates that are nanoscale in size, surface-enhanced Raman scattering (SERS) is a technique for enhancing the Raman signal of biomolecules. Numerous industries including sensing materials, adsorption and medical devices, use nanomaterials like nanocages and nanoclusters. To discover a possible novel sensor platform involving a small metal cluster and a curved rigid substrate, we used density functional theoretical (DFT) simulations to explore the adsorption of glycoluril (GLC), a prospective drug intermediate, on a pure magnesium oxide cage (Mg₁₂O₁₂). This well defined cage was used as (i) an exact probable structure that could be used as well as (ii) a general model for MgO nanostructures. We also investigated the mono Al-doped Mg₁₂O₁₂ nanocage version Mg₁₁AlO₁₂. All computations were performed at the M06-2X level of theory. The GLC binds to the Mg₁₂O₁₂ nanocage by way of strong donor-acceptor interactions. The adsorption is releasing - 45.80 kcal mol^-1 of energy. Due to Al doping, the energy gap of GLC-Mg₁₁AlO₁₂ (1.91 eV) is reduced from that of GLC-Mg₁₂O₁₂ (4.28 eV) and hence there is an increase in electrical conductivity of GLC-Mg₁₁AlO₁₂. The electronic change in the nanocage's conductivity can be transformed into an electrical signal which can be used to detect the presence of the drug analyte. In addition, when a GLC molecule is present, the work function of the nanocage is also reduced. The MgO nanocage, we conclude, is a work function type as well as a possible electronic sensor for GLC drug detection. GLC desorption from the Mg₁₁AlO₁₂ surface recovers more quickly in comparison with Mg₁₂O₁₂ recovery time. The AIM and NCIs assessed in this study were performed to help analyze the electronic structures of the complexes. Our findings pave the possibility for Mg₁₁AlO₁₂ nanostructures to be used in drug recognition.

SARS-CoV-2 detection methods: A comprehensive review

The ongoing novel COVID-19 has remained the center of attention, since its declaration as a pandemic in March 2020, due to its rapid and uncontrollable worldwide spread. Diagnostic tests are the first line of defense against the transmission of this infectious disease among individuals, with reverse-transcription quantitative polymerase chain reaction (RT-qPCR) being the approved gold standard for showing high sensitivity and specificity in detecting SARS-CoV-2. However, alternative tests are being invested due to the global demand for facilities, reagents, and healthcare workers needed for rapid population-based testing. Also, the rapid evolution of the viral genome and the emergence of new variants necessitates updating the existing methods. Scientists are aiming to improve tests to be affordable, simple, fast, and at the same time accurate, and efficient, as well as friendly user testing. The current diagnostic methods are either molecular-based that detect nucleic acids abundance, like RT-qPCR and reverse-transcription loop-mediated isothermal amplification (RT-LAMP); or immunologically based that detect the presence of antigens or antibodies in patients’ specimens, like enzyme-linked immunosorbent assay (ELISA), lateral flow assay (LFA), chemiluminescent immunoassay (CLIA), and neutralization assay. In addition to these strategies, sensor-based or CRISPR applications are promising tools for the rapid detection of SARS-CoV-2. This review summarizes the most recent updates on the SARS-CoV-2 detection methods with their limitations. It will guide researchers, epidemiologists, and clinicians in identifying a more rapid, reliable, and sensitive method of diagnosing SARS-CoV-2 including the most recent variant of concern Omicron.

A Framework for Biosensors Assisted by Multiphoton Effects and Machine Learning

The ability to interpret information through automatic sensors is one of the most important pillars of modern technology. In particular, the potential of biosensors has been used to evaluate biological information of living organisms, and to detect danger or predict urgent situations in a battlefield, as in the invasion of SARS-CoV-2 in this era. This work is devoted to describing a panoramic overview of optical biosensors that can be improved by the assistance of nonlinear optics and machine learning methods. Optical biosensors have demonstrated their effectiveness in detecting a diverse range of viruses. Specifically, the SARS-CoV-2 virus has generated disturbance all over the world, and biosensors have emerged as a key for providing an analysis based on physical and chemical phenomena. In this perspective, we highlight how multiphoton interactions can be responsible for an enhancement in sensibility exhibited by biosensors. The nonlinear optical effects open up a series of options to expand the applications of optical biosensors. Nonlinearities together with computer tools are suitable for the identification of complex low-dimensional agents. Machine learning methods can approximate functions to reveal patterns in the detection of dynamic objects in the human body and determine viruses, harmful entities, or strange kinetics in cells.

In Silico Evaluation of CRISPR-Based Assays for Effective Detection of SARS-CoV-2

Coronavirus disease (COVID-19) caused by the SARS-CoV-2 has been an outbreak since late 2019 up to now. This pandemic causes rapid development in molecular detection technologies to diagnose viral infection for epidemic prevention. In addition to antigen test kit (ATK) and polymerase chain reaction (PCR), CRISPR-based assays for detection of SARS-CoV-2 have gained attention because it has a simple setup but still maintain high specificity and sensitivity. However, the SARS-CoV-2 has been continuing mutating over the past few years. Thus, molecular tools that rely on matching at the nucleotide level need to be reevaluated to preserve their specificity and sensitivity. Here, we analyzed how mutations in different variants of concern (VOC), including Alpha, Beta, Gamma, Delta, and Omicron strains, could introduce mismatches to the previously reported primers and crRNAs used in the CRISPR-Cas system. Over 40% of the primer sets and 15% of the crRNAs contain mismatches. Hence, primers and crRNAs in nucleic acid-based assays must be chosen carefully to pair up with SARS-CoV-2 variants. In conclusion, the data obtained from this study could be useful in selecting the conserved primers and crRNAs for effective detections against the VOC of SARS-CoV-2.

Impedimetric Detection Based on Label-Free Immunoassay Developed for Targeting Spike S1 Protein of SARS-CoV-2

After the COVID-19 pandemic started all over the world, great importance was placed on the development of sensitive and selective bioanalytical assays for the rapid detection of the highly pathogenic SARS-CoV-2 virus causing COVID-19 disease. In this present work, an impedimetric immunosensor was developed and applied for rapid, reliable, sensitive and selective detection of the SARS-CoV-2 S1 protein. To detect the SARS-CoV-2 virus, targeting of the spike S1 protein was achieved herein by using S1 protein-specific capture antibody (Cab-S1) immobilized screen-printed electrode (SPE) in combination with the electrochemical impedance spectroscopy (EIS) technique. With the impedimetric immunosensor, the detection limit for S1 protein in buffer medium was found to be 0.23 ng/mL (equal to 23.92 amol in 8 µL sample) in the linear concentration range of S1 protein from 0.5 to 10 ng/mL. In the artificial saliva medium, it was found to be 0.09 ng/mL (equals to 9.36 amol in 8 µL sample) in the linear concentration range of S1 protein between 0.1 and 1 ng/mL. The selectivity of the impedimetric immunosensor toward S1 protein was tested against influenza hemagglutinin antigen (HA) in the buffer medium as well as in artificial saliva.

Kinetics of neutralizing antibodies against SARS-CoV-2 infection according to sex, age, and disease severity

Knowledge of the factors affecting the difference in kinetics and longevity of the neutralizing antibody (nAb) response to SARS-CoV-2 is necessary to properly prioritize vaccination. In the present study, from March to December 2020, of the 143 patients who recovered from COVID-19, 87 underwent study visits scheduled every 3 months. Patient demographics and blood samples were collected followed by a plaque reduction neutralization test to analyze nAb titers. A linear mixed model was used to compare the effects of sex, age, and disease severity over time. Results demonstrated a gradual reduction in nAb titers over time with a significant decrease from 6 to 9 months post-COVID-19 infection (p < 0.001). In time-to-sex, age, and disease severity comparisons, reduction in nAb titers over time was unaffected by sex (p = 0.167), age (p = 0.188), or disease severity (p = 0.081). Additionally, the nAb titer was 1.46 times significantly higher in those aged ≥ 50 years than in those aged < 50 years (p = 0.036) irrespective of time Moreover, the nAb titer was 2.41 times higher in the moderate or above than that in the below moderate disease severity group (p < 0.001). However, no significant differences were observed in terms of sex (p = 0.300). Given the reduction in nAbs over time, maintaining protective neutralizing antibodies regardless of sex, age, or disease severity is needed.

The CRISPR-Cas system as a tool for diagnosing and treating infectious diseases

Emerging and relapsing infectious diseases pose a huge health threat to human health and a new challenge to global public health. Rapid, sensitive and simple diagnostic tools are keys to successful management of infectious patients and containment of disease transmission. In recent years, international research on Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-related proteins (Cas) has revolutionized our understanding of biology. The CRISPR-Cas system has the advantages of high specificity, high sensitivity, simple, rapid, low cost, and has begun to be used for molecular diagnosis and treatment of infectious diseases. In this paper, we described the biological principles, application fields and prospects of CRISPR-Cas system in the molecular diagnosis and treatment of infectious diseases, and compared it with existing molecular diagnosis methods, the advantages and disadvantages were summarized.

Electronic and structural computing features of some chromene derivatives and evaluating their anticancer activities

Electronic and structural features of some of representative chromene derivatives were investigated in this work towards recognizing their anticancer roles. Density functional theory (DFT) calculations were performed to obtain five structures of chromene derivatives with the same skeleton of original structure. In addition to obtaining optimized structural geometries, electronic molecular orbital features were evaluated for the models. Energy levels of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) indicated effects of additional R group pf chromene derivatives on electronic features. Based on such results, it was predicted that one of derivatives, L5, could better participate in interactions with other substances in comparison with other ligand structures. This achievement was obtained based on availability of HOMO and LUMO levels in lower energies easily catchable for electron transferring. On the other hand, L5 was assumed to interact in the weakest mode with other substances. Indeed, the main goal of this work was to examine anticancer activity of the investigated chromene derivatives, in which each of L1–L5 chromene derivatives were analyzed first to recognized electronic and structural features. Next, molecular docking (MD) simulations were performed to examine anticancer role of L1–L5 against methyltransferase cancerous enzyme target. The results indicated that formations of ligand-target complexes could be occurred within different types of interactions and surrounding amino acids of central ligand. In agreement with the achievements of analyses of single-standing L1–L5 compounds, L4-Target was seen as the strongest complex among possible complex formations. Moreover, values of binding energies and inhibition constant indicated that all five chromene derivatives could work as inhibitors of methyltransferase cancerous enzyme by the most advantage for L4 ligand. And as a final remark, details of such anticancer activity were recognized by graphical representations of ligand-target complexes showing types of interactions and involving amino acids in interactions.

Formations of bimolecular barbituric acid complexes through hydrogen bonding interactions: DFT analyses of structural and electronic features

Formations of bimolecular barbituric acid (BA) complexes through hydrogen-bonding (HB) interactions were investigated in this work. BA has been known as a starting compound of pharmaceutical compounds developments, in which the molecular and atomic features of parent BA in homo-paring with another BA molecule were investigated here. The models were optimized to reach the stabilized structures and their properties were evaluated at the molecular and atomic scales. Density functional theory (DFT) calculations were performed to provide required information for achieving the goal of this work. Six dimer models were obtained finally according to examining all possible starting dimers configurations for involving in optimization calculations. N-H . . . O and C-H . . . O interactions were also involved in dimers formations besides participation of the X-center of parent BA in interaction. Molecular and atomic scales features were evaluated for characterizing the dimers formations. As a consequence, several configurations of BA dimers were obtained showing the importance of performing such structural analyses for developing further compounds from BA.

Powerful CRISPR-Based Biosensing Techniques and Their Integration With Microfluidic Platforms

In the fight against the worldwide pandemic coronavirus disease 2019 (COVID-19), simple, rapid, and sensitive tools for nucleic acid detection are in urgent need. PCR has been a classic method for nucleic acid detection with high sensitivity and specificity. However, this method still has essential limitations due to the dependence on thermal cycling, which requires costly equipment, professional technicians, and long turnover times. Currently, clustered regularly interspaced short palindromic repeats (CRISPR)-based biosensors have been developed as powerful tools for nucleic acid detection. Moreover, the CRISPR method can be performed at physiological temperature, meaning that it is easy to assemble into point-of-care devices. Microfluidic chips hold promises to integrate sample processing and analysis on a chip, reducing the consumption of sample and reagent and increasing the detection throughput. This review provides an overview of recent advances in the development of CRISPR-based biosensing techniques and their perfect combination with microfluidic platforms. New opportunities and challenges for the improvement of specificity and efficiency signal amplification are outlined. Furthermore, their various applications in healthcare, animal husbandry, agriculture, and forestry are discussed.

Metal oxide nanocage as drug delivery systems for Favipiravir, as an effective drug for the treatment of COVID-19: a computational study

This paper is a summary of research that looks at the potential of fullerene-like (MO)₁₂ nanoclusters (NCs) in drug-carrying systems using density functional theory. Favipiravir/Zn₁₂O₁₂ (− 34.80 kcal/mol), Favipiravir/Mg₁₂O₁₂ (− 34.98 kcal/mol), and Favipiravir/Be₁₂O₁₂ (− 30.22 kcal/mol) were rated in order of drug adsorption degrees. As a result, Favipiravir attachment to (MgO)₁₂ and (ZnO)₁₂ might be simple, increasing Favipiravir loading efficiency. In addition, the quantum theory of atoms in molecules (QTAIM) assessment was utilized to look at the interactions between molecules. The FMO, ESP, NBO, and E_ads reactivity patterns were shown to be in excellent agreement with the QTAIM data. The electrostatic properties of the system with the biggest positive charge on the M atom and the largest E_ads were shown to be the best. This system was shown to be the best attraction site for nucleophilic agents. The findings show that (MgO)₁₂ and (ZnO)₁₂ have great carrier potential and may be used in medication delivery.

Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect?

Here, we report a first comprehensive genomic analysis of SARS-CoV-2 variants circulating in North African countries, including Algeria, Egypt, Libya, Morocco, Sudan and Tunisia, with respect to genomic clades and mutational patterns. As of December 2021, a total of 1669 high-coverage whole-genome sequences submitted to EpiCoV GISAID database were analyzed to infer clades and mutation annotation compared with the wild-type variant Wuhan-Hu-1. Phylogenetic analysis of SARS-CoV-2 genomes revealed the existence of eleven GISAID clades with GR (variant of the spike protein S-D614G and nucleocapsid protein N-G204R), GH (variant of the ORF3a coding protein ORF3a-Q57H) and GK (variant S-T478K) being the most common with 25.9%, 19.9%, and 19.6%, respectively, followed by their parent clade G (variant S-D614G) (10.3%). Lower prevalence was noted for GRY (variant S-N501Y) (5.1%), S (variant ORF8-L84S) (3.1%) and GV (variant of the ORF3a coding protein NS3-G251V) (2.0%). Interestingly, 1.5% of total genomes were assigned as GRA (Omicron), the newly emerged clade. Across the North African countries, 108 SARS-CoV-2 lineages using the Pangolin assignment were identified, whereby most genomes fell within six major lineages and variants of concern (VOC) including B.1, the Delta variants (AY.X, B.1.617.2), C.36, B.1.1.7 and B.1.1. The effect of mutations in SAR-CoV-2 genomes highlighted similar profiles with D614G spike (S) and ORF1b-P314L variants as the most changes found in 95.3% and 87.9% of total sequences, respectively. In addition, mutations affecting other viral proteins appeared frequently including; N:RG203KR, N:G212V, NSP3:T428I, ORF3a:Q57H, S:N501Y, M:I82T and E:V5F. These findings highlight the importance of genomic surveillance for understanding the SARS-CoV-2 genetic diversity and its spread patterns, leading to a better guiding of public health intervention measures. The know-how analysis of the present work could be implemented worldwide in order to overcome this health crisis through harmonized approaches.