Detection and differentiation of respiratory syncytial virus subgroups A and B with colorimetric toehold switch sensors in a paper-based cell-free system

A Novel Approach Using LuxSit-i Enhanced Toehold Switches for the Rapid Detection of Vibrio parahaemolyticus

Vibrio parahaemolyticus (V. parahaemolyticus) is a significant concern, as it can cause severe infections and hemolytic trauma. Given its prevalence in seawater and coastal seafood, it poses a substantial risk as a foodborne pathogen. Biosensor-based detection technology has been continuously evolving, and toehold switches have emerged as a promising area within it, especially in the detection of RNA viruses. Here, we have developed a cell-free toehold switch sensor for V. parahaemolyticus detection. Traditional toehold switch detection methods usually use green fluorescent protein (GFP) or enzyme LacZ as the output signal, with an incubation time as long as 2 h, and are also mainly applied to the detection of RNA viruses. In this study, we introduced a novel, artificially designed luciferase (LuxSit-i) as an output signal and constructed toehold switches with two different output signals (sfGFP, LuxSit-i), aimed at reducing the incubation time of toehold switches. Moreover, to further improve the detection process, we separately utilize recombinase polymerase amplification (RPA) and nucleic acid sequence-based amplification (NASBA) to amplify dead and live bacterial suspensions for detection and attempt to distinguish between dead and live bacteria. This study provided a convenient, rapid, and accurate method for the on-site detection of V. parahaemolyticus, especially beneficial for resource-limited settings. By eliminating the requirement for specialized facilities and personnel, this system has the potential to be a valuable tool in improving public health responses, especially in developing regions.

Cell-Free Gene Expression: Methods and Applications

Cell-free gene expression (CFE) systems empower synthetic biologists to build biological molecules and processes outside of living intact cells. The foundational principle is that precise, complex biomolecular transformations can be conducted in purified enzyme or crude cell lysate systems. This concept circumvents mechanisms that have evolved to facilitate species survival, bypasses limitations on molecular transport across the cell wall, and provides a significant departure from traditional, cell-based processes that rely on microscopic cellular "reactors." In addition, cell-free systems are inherently distributable through freeze-drying, which allows simple distribution before rehydration at the point-of-use. Furthermore, as cell-free systems are nonliving, they provide built-in safeguards for biocontainment without the constraints attendant on genetically modified organisms. These features have led to a significant increase in the development and use of CFE systems over the past two decades. Here, we discuss recent advances in CFE systems and highlight how they are transforming efforts to build cells, control genetic networks, and manufacture biobased products.

Assembly of functional microbial ecosystems: from molecular circuits to communities

Microbes compete and cooperate with each other via a variety of chemicals and circuits. Recently, to decipher, simulate, or reconstruct microbial communities, many researches have been engaged in engineering microbiomes with bottom-up synthetic biology approaches for diverse applications. However, they have been separately focused on individual perspectives including genetic circuits, communications tools, microbiome engineering, or promising applications. The strategies for coordinating microbial ecosystems based on different regulation circuits have not been systematically summarized, which calls for a more comprehensive framework for the assembly of microbial communities. In this review, we summarize diverse cross-talk and orthogonal regulation modules for de novo bottom-up assembling functional microbial ecosystems, thus promoting further consortia-based applications. First, we review the cross-talk communication-based regulations among various microbial communities from intra-species and inter-species aspects. Then, orthogonal regulations are summarized at metabolites, transcription, translation, and post-translation levels, respectively. Furthermore, to give more details for better design and optimize various microbial ecosystems, we propose a more comprehensive design-build-test-learn procedure including function specification, chassis selection, interaction design, system build, performance test, modeling analysis, and global optimization. Finally, current challenges and opportunities are discussed for the further development and application of microbial ecosystems.

Construction of multilayered gene circuits using de-novo-designed synthetic transcriptional regulators in cell-free systems

BACKGROUND

De-novo-designed synthetic transcriptional regulators have great potential as the genetic parts for constructing complex multilayered gene circuits. The design flexibility afforded by advanced nucleic acid sequence design tools vastly expands the repertoire of regulatory elements for circuit design. In principle, the design space of synthetic regulators should allow for the construction of regulatory circuits of arbitrary complexity; still, the orthogonality and robustness of such components have not been fully elucidated, thereby limiting the depth and width of synthetic circuits.

RESULTS

In this work, we systematically explored the design strategy of synthetic transcriptional regulators, termed switchable transcription terminators. Specifically, by redesigning key sequence domains, we created a high-performance switchable transcription terminator with a maximum fold change of 283.11 upon activation by its cognate input RNA. Further, an automated design algorithm was developed for these elements to improve orthogonality for a complex multi-layered circuit construction. The resulting orthogonal switchable transcription terminators could be used to construct a three-layer cascade circuit and a two-input three-layer OR gate.

CONCLUSIONS

We demonstrated a practical strategy for designing standardized regulatory elements and assembling modular gene circuits, ultimately laying the foundation for the streamlined construction of complex synthetic gene circuits.

Electrochemiluminescence Biosensor for Ascorbic Acid Based on Target Transformation of Cell-Free RNA Transcription System and Duplex-Specific Nuclease-Assisted Recycling Amplification

A cell-free RNA transcription system had been coupled with electrochemiluminescence (ECL) detection technology for the first time to develop an ascorbic acid (AA, acting as a model target) biosensor. The biosensor is composed of single-stranded DNA (ssDNA) sequences modified with alkynyl and azido groups, respectively, alongside an incomplete gene circuit framework. The addition of target AA and copper ions will cause the linkage of the two ssDNA sequences through a click chemistry reaction. This results in the subsequent reconstruction of a complete gene circuit. The reconstituted gene circuit, in conjunction with the T7 RNA polymerase, drives the transcription of substantial quantities of RNA. ssDNA labeled with ferrocene (Fc) (Fc-DNA) had been immobilized on a tris(2,2'-bipyridyl) ruthenium(II) chloride hexahydrate-doped SiO2 nanoparticle (Ru@SiO2 NPs) modified electrode first. The quenching effect of Fc on Ru@SiO2 causes the low ECL detected. The transcribed RNA sequence assisted double-stranded specific nuclease (DSN) to cut the ssDNA-Fc and the ECL of the system was enhanced. Optimal experimental conditions reveal that the ECL signal exhibits a linear correlation with the logarithmic concentration of AA, spanning a detection range from 100 nM to 1 mM, with a detection limit of 45 nM. This innovative methodology expands the utility of a cell-free RNA transcription system within the realm of biosensing applications.

Peptide-Based electrochemical potential Scanning: A novel approach for disulfide manipulation in pediatric Respiratory syncytial virus detection

Respiratory syncytial virus (RSV) poses a significant risk to children under two years old, necessitating rapid and accurate diagnostic methods. This study introduces an innovative approach using peptides and electrochemical potential scanning for RSV detection. By replacing enzymatic catalysis with electrochemical scanning, the method simplifies the process and reduces costs. Unbound peptides undergo potential-induced disulfide bridge opening, while target-bound peptides remain protected. After removing the target protein, copper ions and a reduced short peptide promote disulfide bridge formation, leading to crosslinking and passivation of the electrode surface. The degree of polymerization and passivation correlates with the target protein levels, generating a signal. This novel method offers enhanced sensitivity, specificity, and scalability, potentially revolutionizing RSV diagnostics in children under two years old. By addressing the limitations of traditional assays, it provides a cost-effective, rapid, and efficient approach for early RSV detection and improved clinical outcomes in this vulnerable population.

Specific separation and sensitive detection of foodborne pathogens by phage-derived bacterial-binding protein-nano magnetic beads coupled with smartphone-assisted paper sensor

Foodborne pathogen infection poses a significant threat to public health and is considered as one of the most serious hazards in global food safety. Herein, a sensitive and efficient method for on-site monitoring of foodborne pathogens was developed by using a smartphone-assisted paper-sensor combined with phage-derived bacterial-binding proteins-nano magnetic beads (PBPs-MBs). PBPs including tail fiber protein (TFP:gp13), cell-wall binding domain (CBD) of endolysin and tailspike protein (TSP) coated on the surface of MBs were applied for rapid separation and enrichment of targeted bacteria (Escherichia coli O157:H7, Staphylococcus aureus and Salmonella typhimurium, respectively) from food samples in 20 min before detection on paper-based sensors. The paper-based sensor was loaded with the lytic agent (polymyxin B) to induce bacterial lysis and release specific endogenous enzymes. Subsequently, three distinct chromogenic substrates were hydrolyzed by their corresponding enzymes, resulting in characteristic color changes on the paper, respectively. In addition, a smartphone APP for red-green-blue (RGB) color analysis of paper was able to directly detect three foodborne pathogens. As a result, the limit of detection (LOD) values for three foodborne pathogens were found to be 2.44 × 102, 2.68 × 104 and 4.62 × 103 CFU/mL, respectively, which were much lower than other studies (106-108 CFU/mL) based on enzymes. Moreover, the feasibility of this approach was further assessed through the successful detection of targeted bacteria in real samples with satisfactory recovery rates. In conclusion, this smartphone-assisted biosensor offers promising application potential for point-of-care testing (POCT) of foodborne pathogens in resource-scarce areas.

Toehold switch plus signal amplification enables rapid detection

Recent world events have led to an increased interest in developing rapid and inexpensive clinical diagnostic platforms for viral detection. Here, the development of a cell-free toehold switch-based biosensor, which does not require upstream amplification of target RNA, is described for the detection of RNA viruses. Toehold switches were designed to avoid interfering secondary structure in the viral RNA binding region, mutational hotspots, and cross-reacting sequences of other coronaviruses. Using these design criteria, toehold switches were targeted to a low mutation region of the SARS-CoV-2 genome nonstructural protein 2 (nsp2). The designs were tested in a cell-free system using trigger RNA based on the viral genome and a highly sensitive fluorescent reporter gene, mNeonGreen. The detection sensitivity of our best toehold design, CSU 08, was in the low picomolar range of target (trigger) RNA. To increase the sensitivity of our cell-free biosensor to a clinically relevant level, we developed a modular downstream amplification system that utilizes toehold switch activation of tobacco etch virus (TEV) protease expression. The TEV protease cleaves a quenched fluorescent reporter, both increasing the signal fold change between control and sample and increasing the sensitivity to a clinically relevant low femtomolar range for target RNA detection.

Development of a cell-free toehold switch for hepatitis A virus type I on-site detection

Picornavirus hepatitis A virus (HAV) is a common cause of hepatitis worldwide. It is spread primarily through contaminated food and water or person-to-person contact. HAV I has been identified as the most common type of human HAV infection. Here, we have developed a cell-free toehold switch sensor for HAV I detection. We screened 10 suitable toehold switch sequences using NUPACK software, and the VP1 gene was used as the target gene. The optimal toehold switch sequence was selected by in vivo expression. The best toehold switch concentration was further found to be 20 nM in a cell-free system. 5 nM trigger RNA activated the toehold switch to generate visible green fluorescence. The minimum detection concentration decreased to 1 pM once combined with NASBA. HAV I trigger RNA could be detected accurately with excellent specificity. In addition, the cell-free toehold switch sensor was verified in HAV I entities. The successful construction of the cell-free toehold switch sensor provided a convenient, rapid, and accurate method for HAV I on-site detection, especially in developing countries, without the involvement of expensive facilities and additional professional operators.

Recent Uses of Paper Microfluidics in Isothermal Nucleic Acid Amplification Tests

Isothermal nucleic acid amplification tests have recently gained popularity over polymerase chain reaction (PCR), as they only require a constant temperature and significantly simplify nucleic acid amplification. Recently, numerous attempts have been made to incorporate paper microfluidics into these isothermal amplification tests. Paper microfluidics (including lateral flow strips) have been used to extract nucleic acids, amplify the target gene, and detect amplified products, all toward automating the process. We investigated the literature from 2020 to the present, i.e., since the onset of the COVID-19 pandemic, during which a significant surge in isothermal amplification tests has been observed. Paper microfluidic detection has been used extensively for recombinase polymerase amplification (RPA) and its related methods, along with loop-mediated isothermal amplification (LAMP) and rolling circle amplification (RCA). Detection was conducted primarily with colorimetric and fluorometric methods, although a few publications demonstrated flow distance- and surface-enhanced Raman spectroscopic (SERS)-based detection. A good number of publications could be found that demonstrated both amplification and detection on paper microfluidic platforms. A small number of publications could be found that showed extraction or all three procedures (i.e., fully integrated systems) on paper microfluidic platforms, necessitating the need for future work.

Paper-based colorimetric sensors for point-of-care testing

By eliminating the need for sample transportation and centralized laboratory analysis, point-of-care testing (POCT) enables on-the-spot testing, with results available within minutes, leading to improved patient management and overall healthcare efficiency. Motivated by the rapid development of POCT, paper-based colorimetric sensing, a powerful analytical technique that exploits the changes in color or absorbance of a chemical species to detect and quantify analytes of interest, has garnered increasing attention. In this review, we strive to provide a bird's eye view of the development landscape of paper-based colorimetric sensors that harness the unique properties of paper to create low-cost, easy-to-use, and disposable analytical devices, thematically covering both fundamental aspects and categorized applications. In the end, we authors summarized the review with the remaining challenges and emerging opportunities. Hopefully, this review will ignite new research endeavors in the realm of paper-based colorimetric sensors.

Diagnostic techniques for critical respiratory infections: Update on current methods

Respiratory infections, whether chronic or acute, are frequent in both children and adults and result in an economic burden in health care systems. In particular, for an immunocompromised patient, respiratory infection leads to acute hypoxemic respiratory failure, a leading cause of intensive care unit (ICU) admission. Most respiratory infections are caused by bacteria, viruses, parasites, smoking, or air pollution. Over the last two decades, considerable improvements have been made in understanding and identifying respiratory infections. Various biosensing techniques have been developed with a range of targets to identify the infection at earlier stages. Recently, nanomaterials have been effectively applied to improve biosensors and their analytical performances. This review discusses recent biosensor developments for identifying respiratory infections caused by viruses and bacteria assisted by different types of nanomaterials and target molecules.

Paper-based diagnostic chips for viral detection

Viruses cause various diseases in humans, and pose serious health risks to individuals and populations worldwide. As a result, various diagnostic procedures and methods have been developed to prevent, manage, and reduce the burden of viral diseases, each with its own benefits and drawbacks. Among these, paper-based diagnostic chips are becoming increasingly common because of their speed, accuracy, convenience, and economical and environmental friendliness. These paper-based diagnostic tests have ideal point-of-care (POC) diagnostic applications, particularly in personalized healthcare. Paper-based diagnostics have emerged as innovative and low-cost solutions for diagnosing viral diseases in remote and underdeveloped regions where traditional diagnostic methods are not readily available. These tests are easy to use, require minimal equipment, and can be performed by nonspecialized personnel, making them accessible even in resource-constrained settings. In this review, we discuss recent developments in paper-based diagnostic chips, the importance of improved methods for identifying viral pathogens, drawbacks of traditional detection techniques, and challenges and prospects of paper-based diagnostic chips for the detection of viruses.

Challenges and perspectives of multi-virus biosensing techniques: A review

In the context of globalization, individuals have an increased chance of being infected by multiple viruses simultaneously, thereby highlighting the importance of developing multiplexed devices. In addition to sufficient sensitivity and rapid response, multi-virus sensing techniques are expected to offer additional advantages including high throughput, one-time sampling for parallel analysis, and full automation with data visualization. In this paper, we review the optical, electrochemical, and mechanical platforms that enable multi-virus biosensing. The working mechanisms of each platform, including the detection principle, transducer configuration, bio-interface design, and detected signals, are reviewed. The advantages and limitations, as well as the challenges in implementing various detection strategies in real-life scenarios, were evaluated. Future perspectives on multiplexed biosensing techniques are critically discussed. Earlier access to multi-virus biosensors will efficiently serve for immediate pandemic control, such as in emerging SARS-CoV-2 and monkeypox cases.

Synthetic biology-based bioreactor and its application in biochemical analysis

In the past few years, synthetic biologists have established some biological elements and bioreactors composed of nucleotides under the guidance of engineering methods. Following the concept of engineering, the common bioreactor components in recent years are introduced and compared. At present, biosensors based on synthetic biology have been applied to water pollution monitoring, disease diagnosis, epidemiological monitoring, biochemical analysis and other detection fields. In this paper, the biosensor components based on synthetic bioreactors and reporters are reviewed. In addition, the applications of biosensors based on cell system and cell-free system in the detection of heavy metal ions, nucleic acid, antibiotics and other substances are presented. Finally, the bottlenecks faced by biosensors and the direction of optimization are also discussed.

Development of Toehold Switches as a Novel Ribodiagnostic Method for West Nile Virus

West Nile virus (WNV) is an emerging neurotropic RNA virus and a member of the genus Flavivirus. Naturally, the virus is maintained in an enzootic cycle involving mosquitoes as vectors and birds that are the principal amplifying virus hosts. In humans, the incubation period for WNV disease ranges from 3 to 14 days, with an estimated 80% of infected persons being asymptomatic, around 19% developing a mild febrile infection and less than 1% developing neuroinvasive disease. Laboratory diagnosis of WNV infection is generally accomplished by cross-reacting serological methods or highly sensitive yet expensive molecular approaches. Therefore, current diagnostic tools hinder widespread surveillance of WNV in birds and mosquitoes that serve as viral reservoirs for infecting secondary hosts, such as humans and equines. We have developed a synthetic biology-based method for sensitive and low-cost detection of WNV. This method relies on toehold riboswitches designed to detect WNV genomic RNA as transcriptional input and process it to GFP fluorescence as translational output. Our methodology offers a non-invasive tool with reduced operating cost and high diagnostic value that can be used for field surveillance of WNV in humans as well as in bird and mosquito populations.

Solid-Phase Cell-Free Protein Synthesis and Its Applications in Biotechnology

Cell-free systems for the in vitro production of proteins have revolutionized the synthetic biology field. In the last decade, this technology is gaining momentum in molecular biology, biotechnology, biomedicine and even education. Materials science has burst into the field of in vitro protein synthesis to empower the value of existing tools and expand its applications. In this sense, the combination of solid materials (normally functionalized with different biomacromolecules) together with cell-free components has made this technology more versatile and robust. In this chapter, we discuss the combination of solid materials with DNA and transcription-translation machinery to synthesize proteins within compartments, to immobilize and purify in situ the nascent protein, to transcribe and transduce DNAs immobilized on solid surfaces, and the combination of all or some of these strategies.

Low-cost, point-of-care biomarker quantification

Low-cost, point-of-care (POC) devices that allow fast, on-site disease diagnosis could have a major global health impact, particularly if they can provide quantitative measurement of molecules indicative of a diseased state (biomarkers). Accurate quantification of biomarkers in patient samples is already challenging when research-grade, sophisticated equipment is available; it is even more difficult when constrained to simple, cost-effective POC platforms. Here, we summarize the main challenges to accurate, low-cost POC biomarker quantification. We also review recent efforts to develop and implement POC tools beyond qualitative readouts, and we conclude by identifying important future research directions.

Evaluation of real-time NASBA assay for the detection of SARS-CoV-2 compared with real-time PCR

Purpose

In January 2020, the COVID-19 pandemic started and has severely affected all countries around the world. The clinical symptoms alone are not sufficient for a proper diagnosis. Thus, molecular tests are required. Various institutes and researchers developed real-time PCR-based methods for the detection of the virus. However, the method needs expensive equipment. In the present study, we developed a real-time NASBA assay for the detection of SARS-CoV-2.

Methods

Primers and molecular beacon probes for RdRp and N genes were designed. In silico analysis showed that primers and the probes were specific for SARS-CoV-2. The standard samples with known copy numbers of the virus were tested using the NASBA assay and an FDA-approved real-time PCR kit. A series of standard samples were prepared and tested. Clinical sensitivity, precision analysis, and clinical assessment of the assay were performed.

Results

The limit of detection of the assay was 200 copies/mL. The clinical sensitivity of the assay was 97.64%. The intra-assay and inter-assay for both N and RdRp genes were less than 5% and 10%, respectively. Clinical assessment of the assay showed that the positive agreement rate and negative agreement rate of the assays were determined to be 97.64% and 100%, respectively.

Conclusions

The results of the present study show that the developed real-time NASBA is a sensitive and specific method for the detection of SARS-CoV-2 and is comparable with real-time PCR. NASBA is an isothermal signal amplification method, and if stand-alone fluorescent readers are available, the real-time NASBA can be used without the need for expensive thermocyclers. In addition compared to other isothermal methods like LAMP, the primer design is straightforward. Thus, real-time NASBA could be a suitable method for inexpensive SARS-CoV-2 detection.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s11845-022-03046-2.

Toward Mail-in-Sensors for SARS-CoV-2 Detection: Interfacing Gel Switch Resonators with Cell-Free Toehold Switches

The COVID-19 pandemic has emphasized the importance of widespread testing to control the spread of infectious diseases. The rapid development, scale-up, and deployment of viral and antibody detection methods since the beginning of the pandemic have greatly increased testing capacity. Desirable attributes of detection methods are low product costs, self-administered protocols, and the ability to be mailed in sealed envelopes for the safe analysis and subsequent logging to public health databases. Herein, such a platform is demonstrated with a screen-printed, inductor-capacitor (LC) resonator as a transducer and a toehold switch coupled with cell-free expression as the biological selective recognition element. In the presence of the N-gene from SARS-CoV-2, the toehold switch relaxes, protease enzyme is expressed, and it degrades a gelatin switch that ultimately shifts the resonant frequency of the planar resonant sensor. The gelatin switch resonator (GSR) can be analyzed through a sealed envelope allowing for assessment without the need for careful sample handling with personal protective equipment or the need for workup with other reagents. The toehold switch used in this sensor demonstrated selectivity to SARS-CoV-2 virus over three seasonal coronaviruses and SARS-CoV-1, with a limit of detection of 100 copies/μL. The functionality of the platform and assessment in a sealed envelope with an automated scanner is shown with overnight shipment, and further improvements are discussed to increase signal stability and further simplify user protocols toward a mail-in platform.

Recent advances in the biosensors application for the detection of bacteria and viruses in wastewater

The presence of disease-causing pathogens in wastewater can provide an excellent diagnostic tool for infectious diseases. Biosensors are far superior to conventional methods used for regular infection screening and surveillance testing. They are rapid, sensitive, inexpensive portable and carry no risk of exposure in their detection schemes. In this context, this review summarizes the most recently developed biosensors for the detection of bacteria and viruses in wastewater. The review also provides information on the new detection methods aimed at screening for SARS-CoV-2, which has now caused more than 4 million deaths. In addition, the review highlights the potential behind on-line and real-time detection of pathogens in wastewater pipelines. Most of the biosensors reported were not targeted to wastewater samples due to the complexity of the matrix. However, this review highlights on the performance factors of recently developed biosensors and discusses the importance of nanotechnology in amplifying the output signals, which in turn increases the accuracy and reliability of biosensors. Current research on the applicability of biosensors in wastewater promises a dramatic change to the conventional approach in the field of medical screening.

Paper-based analytical devices for virus detection: Recent strategies for current and future pandemics

The importance of user-friendly, inexpensive, sensitive, and selective detection of viruses has been highlighted again due to the recent Coronavirus disease 2019 (COVID-19) pandemic. Among the analytical tools, paper-based devices (PADs) have become a leading alternative for point-of-care (POC) testing. In this review, we discuss the recent development strategies and applications in nucleic acid-based, antibody/antigen-based and other affinity-based PADs using optical and electrochemical detection methods for sensing viruses. In addition, advantages and drawbacks of presented PADs are identified. Current state and insights towards future perspectives are presented regarding developing POC diagnosis platform for COVID-19. This review considers state-of-the-art technologies for further development and improvement in PADs performance for virus detection.