Aptamer-Based Biosensors to Detect Aquatic Phycotoxins and Cyanotoxins

Cyanotoxins availability and detection methods in wastewater treatment plants: A review

Research interest in ecological significance, toxicity, and potential applications of cyanobacterial metabolites has grown as a result of the current extensive cyanobacterial blooms in water bodies. Under favourable conditions, specific cyanobacterial species release cyanotoxins, hepatotoxins, dermatoxins, neurotoxins, and cytotoxins, creating a heightened threat to aquatic ecosystems and human health. Wastewater treatment plants (WWTPs) offer one of the best culture media for cyanobacterial development and synthesis of cyanotoxins by providing optimum environmental conditions, including temperature, light intensity, lengthy water residence time, and nutrient-rich habitat. To discover the intricate relationships between cyanobacterial populations and other living organisms, it is important to comprehend the cyanobacterial communities in the ecology of WWTPs. Monitoring strategies of these cyanotoxins typically involved combined assessments of biological, biochemical, and physicochemical methodologies. Microscopic observations and physicochemical factors analysis cannot be carried out for toxicity potential analysis of blooms. Due to their high sensitivity, molecular-based approaches allow for the early detection of toxic cyanobacteria, while biological analysis is carried out by using water bloom material and cell extracts to screen cyanotoxins build up in organisms. As each approach has benefits and drawbacks, the development of an integrated multi-method laboratory system is essential to obtain trustworthy results and accurate detection of cyanotoxin levels in WWTPs allowing us to take necessary proactive and preventative approaches for effective wastewater treatment.

Rapid and Easy Detection of Microcystin-LR Using a Bioactivated Multi-Walled Carbon Nanotube-Based Field-Effect Transistor Sensor

In this study, we developed a multi-walled carbon nanotube (MWCNT)-based field-effect transistor (MWCNT-FET) sensor with high sensitivity and selectivity for microcystin-LR (MC-LR). Carboxylated MWCNTs were activated with an MC-LR-targeting aptamer (MCTA). Subsequently the bioactivated MWCNTs were immobilized between interdigitated drain (D) and source (S) electrodes through self-assembly. The top-gated MWCNT-FET sensor was configured by dropping the sample solution onto the D and S electrodes and immersing a Ag/AgCl electrode in the sample solution as a gate (G) electrode. We believe that the FET sensor's conduction path arises from the interplay between the MCTAs, with the applied gate potential modulating this path. Using standard instruments and a personal computer, the sensor's response was detected in real-time within a 10 min time frame. This label-free FET sensor demonstrated an impressive detection capability for MC-LR in the concentration range of 0.1-0.5 ng/mL, exhibiting a lower detection limit of 0.11 ng/mL. Additionally, the MWCNT-FET sensor displayed consistent reproducibility, a robust selectivity for MC-LR over its congeners, and minimal matrix interferences. Given these attributes, this easily mass-producible FET sensor is a promising tool for rapid, straightforward, and sensitive MC-LR detection in freshwater environments.

A review on aquatic toxins - Do we really know it all regarding the environmental risk posed by phytoplankton neurotoxins?

Aquatic toxins are potent natural toxins produced by certain cyanobacteria and marine algae species during harmful cyanobacterial and algal blooms (CyanoHABs and HABs, respectively). These harmful bloom events and the toxins produced during these events are a human and environmental health concern worldwide, with occurrence, frequency and severity of CyanoHABs and HABs being predicted to keep increasing due to ongoing climate change scenarios. These contexts, as well as human health consequences of some toxins produced during bloom events have been thoroughly reviewed before. Conversely, the wider picture that includes the non-human biota in the assessment of noxious effects of toxins is much less covered in the literature and barely covered by review works. Despite direct human exposure to aquatic toxins and related deleterious effects being responsible for the majority of the public attention to the blooms' problematic, it constitutes a very limited fraction of the real environmental risk posed by these toxins. The disruption of ecological and trophic interactions caused by these toxins in the aquatic biota building on deleterious effects they may induce in different species is paramount as a modulator of the overall magnitude of the environmental risk potentially involved, thus necessarily constraining the quality and efficiency of the management strategies that should be placed. In this way, this review aims at updating and consolidating current knowledge regarding the adverse effects of aquatic toxins, attempting to going beyond their main toxicity pathways in human and related models' health, i.e., also focusing on ecologically relevant model organisms. For conciseness and considering the severity in terms of documented human health risks as a reference, we restricted the detailed revision work to neurotoxic cyanotoxins and marine toxins. This comprehensive revision of the systemic effects of aquatic neurotoxins provides a broad overview of the exposure and the hazard that these compounds pose to human and environmental health. Regulatory approaches they are given worldwide, as well as (eco)toxicity data available were hence thoroughly reviewed. Critical research gaps were identified particularly regarding (i) the toxic effects other than those typical of the recognized disease/disorder each toxin causes following acute exposure in humans and also in other biota; and (ii) alternative detection tools capable of being early-warning signals for aquatic toxins occurrence and therefore provide better human and environmental safety insurance. Future directions on aquatic toxins research are discussed in face of the existent knowledge, with particular emphasis on the much-needed development and implementation of effective alternative (eco)toxicological biomarkers for these toxins. The wide-spanning approach followed herein will hopefully stimulate future research more broadly addressing the environmental hazardous potential of aquatic toxins.

Rapid electrochemical biosensor composed of DNA probe/iridium nanoparticle bilayer for Aphanizomenon flos-aquae detection in fresh water

Toxic cyanobacteria pose a serious threat to aquatic ecosystems and require adequate detection and control systems. Aphanizomenon flos-aquae is a harmful cyanobacterium that produces the toxicant saxitoxin. Therefore, it is necessary to detect the presence of A. flos-aquae in lakes and rivers. We proposed a rapid electrochemical biosensor composed of DNA primer/iridium nanoparticles (IrNP) bilyer for the detection of A. flos-aquae in freshwater. The extracted A. flos-aquae gene (rbcL-rbcX) is used as a target, and it was fixed to the electrode using a 5'-thiolated DNA primer (capture probe). Then, Avidin@IrNPs complex for amplification of electrical signals was bound to the target through a 3'-biotinylated DNA primer (detection probe). To rapidly detect the target, an alternating current electrothermal flow technique was introduced in the detection step, which could reduce the detection time to within 20 min. To confirm the biosensor fabrication, atomic force microscopy was used to investigate the surface morphology. To evaluate the biosensor performance, cyclic voltammetry and electrochemical impedance spectroscopy were used. The target gene was detected at a concentration of 9.99 pg/mL in tap water, and the detection range was 0.1 ng/mL to 10³ ng/mL with high selectivity. Based on the combined system, we employed A. flos-aquae in tap water. This rapid cyanobacteria detection system is a powerful tool for CyanoHABs in the field.

Recent Advances in Aptasensing Strategies for Monitoring Phycotoxins: Promising for Food Safety

Phycotoxins or marine toxins cause massive harm to humans, livestock, and pets. Current strategies based on ordinary methods are long time-wise and require expert operators, and are not reliable for on-site and real-time use. Therefore, it is urgent to exploit new detection methods for marine toxins with high sensitivity and specificity, low detection limits, convenience, and high efficiency. Conversely, biosensors can distinguish poisons with less response time and higher selectivity than the common strategies. Aptamer-based biosensors (aptasensors) are potent for environmental monitoring, especially for on-site and real-time determination of marine toxins and freshwater microorganisms, and with a degree of superiority over other biosensors, making them worth considering. This article reviews the designed aptasensors based on the different strategies for detecting the various phycotoxins.

Aptamer-based biosensors for virus protein detection

Virus threatens life health seriously. The accurate early diagnosis of the virus is vital for clinical control and treatment of virus infection. Aptamers are small single-stranded oligonucleotides (DNAs or RNAs). In this review, we summarized aptasensors for virus detection in recent years according to the classification of the viral target protein, and illustrated common detection mechanisms in the aptasensors (colorimetry, fluorescence assay, surface plasmon resonance (SPR), surface-enhanced raman spectroscopy (SERS), electrochemical detection, and field-effect transistor (FET)). Furthermore, aptamers against different target proteins of viruses were summarized. The relationships between the different biomarkers of the viruses and the detection methods, and their performances were revealed. In addition, the challenges and future directions of aptasensors were discussed. This review will provide valuable references for constructing on-site aptasensors for detecting viruses, especially the SARS-CoV-2.

Analysis of Total-Forms of Cyanotoxins Microcystins in Biological Matrices: A Methodological Review

Microcystins (MCs) are cyclic heptapeptidic toxins produced by many cyanobacteria. Microcystins can be accumulated in various matrices in two forms: a free cellular fraction and a covalently protein-bound form. To detect and quantify the concentration of microcystins, a panel of techniques on various matrices (water, sediments, and animal tissues) is available. The analysis of MCs can concern the free or the total (free plus covalently bound) fractions. Free-form analyses of MCs are the most common and easiest to detect, whereas total-form analyses are much less frequent and more complex to achieve. The objective of this review is to summarize the different methods of extraction and analysis that have been developed for total forms. Four extraction methods were identified: MMPB (2-methyl-3-methoxy-4-phenylbutyric acid) method, deconjugation at basic pH, ozonolysis, and laser irradiation desorption. The study of the bibliography on the methods of extraction and analysis of the total forms of MCs showed that the reference method for the subject remains the MMPB method even if alternative methods and, in particular, deconjugation at basic pH, showed results encouraging the continuation of the methodological development on different matrices and on naturally-contaminated samples.

Aptamer-Based Sensors for Thrombin Detection Application

Thrombin facilitates the aggregation of platelet in hemostatic processes and participates in the regulation of cell signaling. Therefore, the development of thrombin sensors is conducive to comprehending the role of thrombin in the course of a disease. Biosensors based on aptamers screened by SELEX have exhibited superiority for thrombin detection. In this review, we summarized the aptamer-based sensors for thrombin detection which rely on the specific recognitions between thrombin and aptamer. Meanwhile, the unique advantages of different sensors including optical and electrochemical sensors were also highlighted. Especially, these sensors based on electrochemistry have the potential to be miniaturized, and thus have gained comprehensive attention. Furthermore, concerns about aptamer-based sensors for thrombin detection, prospects of the future and promising avenues in this field were also presented.

Environmental monitoring tools and strategies in salmon net-pen aquaculture

As global salmon production accelerates in response to higher consumer demand for seafood, so does the need for sophisticated monitoring strategies to enable and maintain ethically sound, productive, and environmentally friendly production of fish. Innovative technologies are needed to ensure proper water quality, react to unfavorable hydrodynamic conditions, monitor for changes in fish health, and minimize ecological interactions with indigenous aquatic life, including fish escapes. Automated sensors connected wirelessly to data stations, visualization aids, and acoustic and physical tagging technologies are emerging tools capable of detecting environmental stress and its associated behavioral changes in farmed fish. Computer modeling of the monitoring data collected from a single salmon farm or collection of farms sharing a data network can be used to spot environmental trends vital for anticipating some of the consequences of climate change. Environmental regulations governing salmon farming in coastal areas are becoming more stringent in response to public pressures to protect coastal and ocean resources and to provide for multipurpose use of marine resources. As net-pen salmon aquaculture expands globally, new technologies will be essential to collect and interpret the anticipated larger volumes of data needed to meet these stringent regulatory requirements and to safeguard the high investment costs inherent in salmon farming. Integr Environ Assess Manag 2022;18:950-963. © SETAC.

Recent advances in nanomaterials-based optical and electrochemical aptasensors for detection of cyanotoxins

The existence of cyanotoxins poses serious threats to human health, it is highly desirable to develop specific and sensitive methods for rapid detection of cyanotoxins in food and water. Due to the distinct advantages of aptamer including high specificity, good stability and easy preparation, various aptamer-based sensors (aptasensors) have been proposed to promote the detection of cyanotoxins. In this review, we summarize recent advance in optical and electrochemical aptasensors for cyanotoxins sensing by integrating with versatile nanomaterials or innovative sensing strategies, such as colorimetric aptasensors, fluorescent aptasensors, surface enhancement Raman spectroscopy-based aptasensors, voltammetric aptasensors, electrochemical impedance spectroscopy-based aptasensors and photoelectrochemical aptasensors. We highlight the accomplishments and advancements of aptasensors with improved performance. Furthermore, the current challenges and future prospects in cyanotoxins detection are discussed from our perspectives, which we hope to provide more ideas for future researchers.

A Review of Apta-POF-Sensors: The Successful Coupling between Aptamers and Plastic Optical Fibers for Biosensing Applications

Aptamers represent the next frontier as biorecognition elements in biosensors thanks to a smaller size and lower molecular weight with respect to antibodies, more structural flexibility with the possibility to be regenerated, reduced batch-to-batch variation, and a potentially lower cost. Their high specificity and small size are particularly interesting for their application in optical biosensors since the perturbation of the evanescent field are low. Apart from the conventional plasmonic optical sensors, platforms based on silica and plastic optical fibers represent an interesting class of devices for point-of-care testing (POCT) in different applications. The first example of the coupling between aptamers and silica optical fibers was reported by Pollet in 2009 for the detection of IgE molecules. Six years later, the first example was published using a plastic optical fiber (POF) for the detection of Vascular Endothelial Growth Factor (VEGF). The excellent flexibility, great numerical aperture, and the large diameter make POFs extremely promising to be coupled to aptamers for the development of a sensitive platform easily integrable in portable, small-size, and simple devices. Starting from silica fiber-based surface plasmon resonance devices, here, a focus on significant biological applications based on aptamers, combined with plasmonic-POF probes, is reported.

Recent advances in the potential applications of luminescence-based, SPR-based, and carbon-based biosensors

Abstract

The need for biosensors has evolved in the detection of molecules, diseases, and pollution from various sources. This requirement has headed to the development of accurate and powerful equipment for analysis using biological sensing component as a biosensor. Biosensors have the advantage of rapid detection that can beat the conventional methods for the detection of the same molecules. Bio-chemiluminescence-based sensors are very sensitive during use in biological immune assay systems. Optical biosensors are emerging with time as they have the advantage that they act with a change in the refractive index. Carbon nanotube-based sensors are another area that has an important role in the biosensor field. Bioluminescence gives much higher quantum yields than classical chemiluminescence. Electro-generated bioluminescence has the advantage of miniature size and can produce a high signal-to-noise ratio and the controlled emission. Recent advances in biological techniques and instrumentation involving fluorescence tag to nanomaterials have increased the sensitivity limit of biosensors. Integrated approaches provided a better perspective for developing specific and sensitive biosensors with high regenerative potentials. This paper mainly focuses on sensors that are important for the detection of multiple molecules related to clinical and environmental applications.

Key points

• The review focusses on the applications of luminescence-based, surface plasmon resonance-based, carbon nanotube-based, and graphene-based biosensors

• Potential clinical, environmental, agricultural, and food industry applications/uses of biosensors have been critically reviewed

• The current limitations in this field are discussed, as well as the prospects for future advancement

CRISPR-Cas12a-Based Aptasensor for On-Site and Highly Sensitive Detection of Microcystin-LR in Freshwater

On-site monitoring of trace organic pollutants with facile methods is critical to environmental pollutant prevention and control. Herein, we proposed a CRISPR-Cas12a-based aptasensor platform (named as MC-LR-Casor) for on-site and sensitive detection of microcystin-LR (MC-LR). After hybridization with blocker DNA, the MC-LR aptamers were conjugated to magnetic beads (MBs) to get the MB aptasensor. In the presence of MC-LR, their interactions with aptamers were triggered and the specific binding caused the release of blocker DNA. Using the programmability of the CRISPR-Cas system, the released blocker DNA was designed to activate a Cas12a-crRNA complex. Single strand DNA reporters were rapidly cleaved by the complex. Signal readout could be achieved by fluorometer or lateral flow strips, which were positively correlated to MC-LR concentration. Benefiting from the CRISPR-Cas12a amplification system, the proposed sensing platform exhibited high sensitivity and reached the limit of detection of ∼3 × 10^-6 μg/L (fluorescence method) or 1 × 10^-3 μg/L (lateral flow assay). In addition, the MC-LR-Casor showed excellent selectivity and good recovery rates, demonstrating their good applicability for real water sample analysis. During the whole assay, only two steps of incubation at a constant temperature were required and the results could be visualized when employing flow strips. Therefore, the proposed assay offered a simple and convenient alternative for in situ MC-LR monitoring, which may hold great promise for future environmental surveillance.

Aptamers functionalized hybrid nanomaterials for algal toxins detection and decontamination in aquatic system: Current progress, opportunities, and challenges

Purification and detection of algal toxins is the most effective technique to ensure that people have clean and safe drinking water. To achieve these objectives, various state-of-the-art technologies were designed and fabricated to decontaminate and detect algal toxins in aquatic environments. Amongst these technologies, aptamer-functionalized hybrid nanomaterials conjugates have received significant consideration as a result of their several benefits over other methods, such as good controllable selectivity, low immunogenicity, and biocompatibility. Because of their excellent properties, aptamer-functionalized hybrid nanomaterials conjugates are one of several remarkable agents. Several isolated aptamer sequences for algal toxins are addressed in this review, as well as aptasensor and decontamination aptamer functionalized metal nanoparticle-derived hybrid nanocomposites applications. In addition, we present diverse aptamer-functionalized hybrid nanomaterial conjugates designs and their applications for sensing and decontamination.

Spectroscopic ellipsometry methods for brevetoxin detection

The spectroscopic ellipsometry (SE), and attenuated internal reflection spectroscopic ellipsometry (TIRE) are promising methods in label-free biosensing applications. An ellipsometer running under surface plasmon resonance (SPR) conditions has unique advantages over other SPR-based methods in terms of sensitivity and real-time/label-free measurement capability. In this study, both SE and TIRE-based brevetoxin B (BTX) sensors were developed using two anti-BTX aptamers reported before. A new aptamer sequence was also derived from these two antiBTX aptamers using predictive modeling tools and an exclusion method. All three antiBTX aptamers' analytical performances were quite competitive in terms of both detecting range and detection limits. However, the selectivity of the previously reported aptamers against analogs of BTX was poor at low detection ranges, especially for okadaic acid. Furthermore, the selectivity of the derived aptamer was lower than its predecessors. The sensors were capable of detecting BTX in the range of 0.05 nM-1600 nM in the TIRE and 0.5 nM-2000 nM in the SE configuration. The detection limits of the sensors were 1.48 nM (1.32 ng/mL) and 0.80 nM (0.72 ng/mL) for SE and TIRE configurations, respectively. Both configurations have been used successfully to detect BTX standards spiked into real fish and shrimp samples.

3D Impedimetric Biosensor for Cyanobacteria Detection in Natural Water Sources

The excessive growth of cyanobacteria in freshwater sources produces the development of toxic blooms mainly due to the production of cyanotoxins. Here, a novel impedimetric biosensor based on a three-dimensional interdigitated electrode array (3D-IDEA) for detection of cyanobacteria cells is reported. The 3D-IDEA sensor surface biofunctionalization was performed by means of the layer-by-layer method using polyethyleneimine (PEI) as the anchoring layer and concanavalin A (Con A) as the bioreceptor to lipopolysaccharides of cyanobacteria cells. The developed PEI-Con A 3D-IDEA sensors show a linear response (R2 = 0.992) of the impedance changes (RS) versus the logarithm of cyanobacteria concentrations in the range of 102–105 cells·mL−1 with the detection limit of 100 cells·mL−1. Moreover, to prevent the interference from components that may be present in real water samples and minimize a possible sample matrix effect, a filtration methodology to recover cyanobacterial cells was developed. The proposed methodology allows 91.2% bacteria recovery, permitting to obtain results similar to controlled assays. The developed system can be used in aquatic environments to detect cyanobacteria and consequently to prevent the formation of blooms and the production of cyanotoxins. Con A can bind to most polysaccharides and so react with other types of bacteria. However, currently, on the market, it is not possible to find specific biorecognition elements for cyanobacteria. Taking into consideration the specificity of samples to be analyzed (natural water resources), it is difficult to expect high concentration of other bacteria. In this sense, the developed methodology may be used as an alarm system to select samples for more thorough and precise laboratory analysis.

Improving Biosensors by the Use of Different Nanomaterials: Case Study with Microcystins as Target Analytes

The eutrophication of lakes and rivers without adequate rainfall leads to excessive growth of cyanobacterial harmful algal blooms (CyanoHABs) that produce toxicants, green tides, and unpleasant odors. The rapid growth of CyanoHABs owing to global warming, climate change, and the development of rainforests and dams without considering the environmental concern towards lakes and rivers is a serious issue. Humans and livestock consuming the toxicant-contaminated water that originated from CyanoHABs suffer severe health problems. Among the various toxicants produced by CyanoHABs, microcystins (MCs) are the most harmful. Excess accumulation of MC within living organisms can result in liver failure and hepatocirrhosis, eventually leading to death. Therefore, it is essential to precisely detect MCs in water samples. To date, the liquid chromatography-mass spectrometry (LC-MS) and enzyme-linked immunosorbent assay (ELISA) have been the standard methods for the detection of MC and provide precise results with high reliability. However, these methods require heavy instruments and complicated operation steps that could hamper the portability and field-readiness of the detection system. Therefore, in order for this goal to be achieved, the biosensor has been attracted to a powerful alternative for MC detection. Thus far, several types of MC biosensor have been proposed to detect MC in freshwater sample. The introduction of material is a useful option in order to improve the biosensor performance and construct new types of biosensors. Introducing nanomaterials to the biosensor interface provides new phenomena or enhances the sensitivity. In recent times, different types of nanomaterials, such as metallic, carbon-based, and transition metal dichalcogenide-based nanomaterials, have been developed and used to fabricate biosensors for MC detection. This study reviews the recent advancements in different nanomaterial-based MC biosensors.

Neutralization of Daboxin P activities by rationally designed aptamers

Inefficacy and associated risks of current antivenom has raised the need for alternative approaches of snakebite management. Aptamers are one such alternative which is being pursued for therapeutic interventions as well as for design of diagnostic kits due to its high specificity. Present study focussed on designing and validating nucleic acid aptamers against snake venom PLA_2, a hydrolytic enzyme present in all venomous snakes. The aptamers were designed by adding nucleic acid chain on the surface of Daboxin P, a major PLA₂ enzyme of Daboia russelii venom. Binding characteristics of the aptamers were confirmed by docking to Daboxin P as well as acidic and basic PLA₂s from different snake species using in silico docking. The aptamers folded into different tertiary structures and bound to the active and Ca²⁺ binding site of PLA₂ enzymes. Molecular dynamics simulation analysis of Daboxin P-aptamer complexes showed that the complexes were stable in an aqueous environment. The electrophoretic mobility shift assay further confirmed the binding of the synthetic aptamers to Daboxin P and other snake venom PLA₂ enzymes. The aptamers inhibited the sPLA₂ activity with an IC₅₀ value ranging between 0.52 μM and 0.77 μM as well as the anticoagulant activity of Daboxin P. The aptamers could also inhibit the PLA₂ activity of Echis carinatus crude venom and anti-coagulant activity of Bungarus caeruleus crude venom, members of big four snakes. However, the aptamers didn't inhibit fibrinogenolytic or proteolytic activity of big four venom as well as the coagulation and hemolytic activities. Thus, aptamers can be rationally designed to inhibit the biochemical and biological activities of snake venom proteins.

Selective and easy detection of microcystin-LR in freshwater using a bioactivated sensor based on multiwalled carbon nanotubes on filter paper

Microcystin-LR (MC-LR) is a cyanobacterial toxin produced as a result of eutrophication in polluted water in warm weather conditions. The MC-LR could cause health problems in mammal organs such as the liver, heart, and muscle. Therefore, the World Health Organization (WHO) has stipulated a limit of <1.0 ng/mL in drinking water. Thus, detection and quantification are vital, but current techniques require complex and expensive offsite analysis. We have developed an inexpensive, sensitive, and field-deployable sensor based on bioactivated multiwalled carbon nanotubes (MWCNTs, diameter 20 nm) and micropore filter paper (0.45-μm pore size) for the detection of MC-LR. A specially designed DNA oligonucleotide (5-NH₂-C₆-AN₆) was used as the MC-LR targeting aptamer (MCTA). For bioactivation, MCTA was immobilized on the carboxylated MWCNTs via the formation of amide bonds. The bioactivated MWCNTs were deposited on the micropore filter paper by suction filtering. The detection of MC-LR in freshwater was possible within 1.5 h, achieved by measuring the changes in electrical resistance caused by the selective MC-LR and MCTA interactions. Despite suffering from some matrix effects, the detection limit of the sensor was 0.19 ng/mL for low-concentration MC-LR (≤0.5 ng/mL). This method is much cheaper (biosensor price: < $2.5) than liquid chromatography coupled with tandem mass spectroscopy analysis (ca. $50/sample) which is a standard method for MC-LR detection in a modern laboratory. Thus, this cheap and straightforward MC-LR sensor has applications for detection in remote locations.

Current Trends and Challenges for Rapid SMART Diagnostics at Point-of-Site Testing for Marine Toxins

In the past twenty years marine biotoxin analysis in routine regulatory monitoring has advanced significantly in Europe (EU) and other regions from the use of the mouse bioassay (MBA) towards the high-end analytical techniques such as high-performance liquid chromatography (HPLC) with tandem mass spectrometry (MS). Previously, acceptance of these advanced methods, in progressing away from the MBA, was hindered by a lack of commercial certified analytical standards for method development and validation. This has now been addressed whereby the availability of a wide range of analytical standards from several companies in the EU, North America and Asia has enhanced the development and validation of methods to the required regulatory standards. However, the cost of the high-end analytical equipment, lengthy procedures and the need for qualified personnel to perform analysis can still be a challenge for routine monitoring laboratories. In developing regions, aquaculture production is increasing and alternative inexpensive Sensitive, Measurable, Accurate and Real-Time (SMART) rapid point-of-site testing (POST) methods suitable for novice end users that can be validated and internationally accepted remain an objective for both regulators and the industry. The range of commercial testing kits on the market for marine toxin analysis remains limited and even more so those meeting the requirements for use in regulatory control. Individual assays include enzyme-linked immunosorbent assays (ELISA) and lateral flow membrane-based immunoassays (LFIA) for EU-regulated toxins, such as okadaic acid (OA) and dinophysistoxins (DTXs), saxitoxin (STX) and its analogues and domoic acid (DA) in the form of three separate tests offering varying costs and benefits for the industry. It can be observed from the literature that not only are developments and improvements ongoing for these assays, but there are also novel assays being developed using upcoming state-of-the-art biosensor technology. This review focuses on both currently available methods and recent advances in innovative methods for marine biotoxin testing and the end-user practicalities that need to be observed. Furthermore, it highlights trends that are influencing assay developments such as multiplexing capabilities and rapid POST, indicating potential detection methods that will shape the future market.

Mathematical Modelling of Biosensing Platforms Applied for Environmental Monitoring

In recent years, mathematical modelling has known an overwhelming integration in different scientific fields. In general, modelling is used to obtain new insights and achieve more quantitative and qualitative information about systems by programming language, manipulating matrices, creating algorithms and tracing functions and data. Researchers have been inspired by these techniques to explore several methods to solve many problems with high precision. In this direction, simulation and modelling have been employed for the development of sensitive and selective detection tools in different fields including environmental control. Emerging pollutants such as pesticides, heavy metals and pharmaceuticals are contaminating water resources, thus threatening wildlife. As a consequence, various biosensors using modelling have been reported in the literature for efficient environmental monitoring. In this review paper, the recent biosensors inspired by modelling and applied for environmental monitoring will be overviewed. Moreover, the level of success and the analytical performances of each modelling-biosensor will be discussed. Finally, current challenges in this field will be highlighted.

Translational control of enzyme scavenger expression with toxin-induced micro RNA switches

Biological computation requires in vivo control of molecular behavior to progress development of autonomous devices. miRNA switches represent excellent, easily engineerable synthetic biology tools to achieve user-defined gene regulation. Here we present the construction of a synthetic network to implement detoxification functionality. We employed a modular design strategy by engineering toxin-induced control of an enzyme scavenger. Our miRNA switch results show moderate synthetic expression control over a biologically active detoxification enzyme molecule, using an established design protocol. However, following a new design approach, we demonstrated an evolutionarily designed miRNA switch to more effectively activate enzyme activity than synthetically designed versions, allowing markedly improved extrinsic user-defined control with a toxin as inducer. Our straightforward new design approach is simple to implement and uses easily accessible web-based databases and prediction tools. The ability to exert control of toxicity demonstrates potential for modular detoxification systems that provide a pathway to new therapeutic and biocomputing applications.

Impedimetric Microcystin-LR Aptasensor Prepared with Sulfonated Poly(2,5-dimethoxyaniline)–Silver Nanocomposite

This paper presents a novel impedimetric aptasensor for cyanobacterial microcystin-LR (L, l-leucine; R, l-arginine) (MC-LR) containing a 5′ thiolated 60-mer DNA aptamer (i.e., 5′-SH-(CH2)6GGCGCCAAACAGGACCACCATGACAATTACCCATACCACCTCATTATGCCCCATCT CCGC-3′). A nanocomposite electrode platform comprising biocompatible poly(2,5-dimethoxyaniline) (PDMA)-poly(vinylsulfonate) (PVS) and silver nanoparticle (Ag0) on a glassy carbon electrode (GCE), i.e., (GCE/PDMA–PVS–Ag0) was used in the biosensor development. Small-angle X-ray scattering (SAXS) spectroscopic analysis revealed that the PDMA–PVS–Ag0 nanocomposites were polydispersed and contained embedded Ag0. Electrochemical impedance spectroscopy (EIS) responses of the aptasensor gave a dynamic linear range (DLR) and limit of detection (LOD) values of 0.01–0.1 ng L−1 MC-LR and 0.003 ng L−1 MC-LR, respectively. The cross-reactivity studies, which was validated with enzyme-linked immunosorbent assay (ELISA), showed that the aptasensor possesses excellent selectivity for MC-LR.

Saxitoxin aptasensor based on attenuated internal reflection ellipsometry for seafood

In this study, we proposed label-free saxitoxin (STX) sensor using STX specific aptamer in combination with spectroscopic ellipsometry (SE) and attenuated internal reflection (AIR) spectroscopic ellipsometry method which is operated under surface plasmon resonance (SPR) conditions. Besides the other surface plasmon resonance-based applications, AIR-SE applications have unique advantages in terms of sensitivity and it was used herein for real-time detection of STX in real samples. Another method, SE, was also used and compared with AIR-SE. Analytical performances were satisfactory with low detection limits and a wide detection range. Limit of detection was 0.01 ng/mL for AIR-SE and 0.11 ng/mL for SE. Both proposed sensors were operable in 0.01 nM-1000 nM STX range. These methods were also used for the accurate, selective, and sensitive detection of STX from fish and shrimp samples.

FSBC: fast string-based clustering for HT-SELEX data

BACKGROUND

The combination of systematic evolution of ligands by exponential enrichment (SELEX) and deep sequencing is termed high-throughput (HT)-SELEX, which enables searching aptamer candidates from a massive amount of oligonucleotide sequences. A clustering method is an important procedure to identify sequence groups including aptamer candidates for evaluation with experimental analysis. In general, aptamer includes a specific target binding region, which is necessary for binding to the target molecules. The length of the target binding region varies depending on the target molecules and/or binding styles. Currently available clustering methods for HT-SELEX only estimate clusters based on the similarity of full-length sequences or limited length of motifs as target binding regions. Hence, a clustering method considering the target binding region with different lengths is required. Moreover, to handle such huge data and to save sequencing cost, a clustering method with fast calculation from a single round of HT-SELEX data, not multiple rounds, is also preferred.

RESULTS

We developed fast string-based clustering (FSBC) for HT-SELEX data. FSBC was designed to estimate clusters by searching various lengths of over-represented strings as target binding regions. FSBC was also designed for fast calculation with search space reduction from a single round, typically the final round, of HT-SELEX data considering imbalanced nucleobases of the aptamer selection process. The calculation time and clustering accuracy of FSBC were compared with those of four conventional clustering methods, FASTAptamer, AptaCluster, APTANI, and AptaTRACE, using HT-SELEX data (>15 million oligonucleotide sequences). FSBC, AptaCluster, and AptaTRACE could complete the clustering for all sequence data, and FSBC and AptaTRACE performed higher clustering accuracy. FSBC showed the highest clustering accuracy and had the second fastest calculation speed among all methods compared.

CONCLUSION

FSBC is applicable to a large HT-SELEX dataset, which can facilitate the accurate identification of groups including aptamer candidates.

AVAILABILITY OF DATA AND MATERIALS

FSBC is available at http://www.aoki.ecei.tohoku.ac.jp/fsbc/.

Aptamer-Based Biosensors for Environmental Monitoring

Due to their relative synthetic and chemical simplicity compared to antibodies, aptamers afford enhanced stability and functionality for the detection of environmental contaminants and for use in environmental monitoring. Furthermore, nucleic acid aptamers can be selected for toxic targets which may prove difficult for antibody development. Of particular relevance, aptamers have been selected and used to develop biosensors for environmental contaminants such as heavy metals, small-molecule agricultural toxins, and water-borne bacterial pathogens. This review will focus on recent aptamer-based developments for the detection of diverse environmental contaminants. Within this domain, aptamers have been combined with other technologies to develop biosensors with various signal outputs. The goal of much of this work is to develop cost-effective, user-friendly detection methods that can complement or replace traditional environmental monitoring strategies. This review will highlight recent examples in this area. Additionally, with innovative developments such as wearable devices, sentinel materials, and lab-on-a-chip designs, there exists significant potential for the development of multifunctional aptamer-based biosensors for environmental monitoring. Examples of these technologies will also be highlighted. Finally, a critical perspective on the field, and thoughts on future research directions will be offered.

Sensors, Biosensors, and Analytical Technologies for Aquaculture Water Quality

In aquaculture industry, fish, shellfish, and aquatic plants are cultivated in fresh, salt, or brackish waters. The increasing demand of aquatic products has stimulated the rapid growth of aquaculture industries. How to effectively monitor and control water quality is one of the key concerns for aquaculture industry to ensure high productivity and high quality. There are four major categories of water quality concerns that affect aquaculture cultivations, namely, (1) physical parameters, e.g., pH, temperature, dissolved oxygen, and salinity, (2) organic contaminants, (3) biochemical hazards, e.g., cyanotoxins, and (4) biological contaminants, i.e., pathogens. While the physical parameters are affected by climate changes, the latter three are considered as environmental factors. In this review, we provide a comprehensive summary of sensors, biosensors, and analytical technologies available for monitoring aquaculture water quality. They include low-cost commercial sensors and sensor network setups for physical parameters. They also include chromatography, mass spectrometry, biochemistry, and molecular methods (e.g., immunoassays and polymerase chain reaction assays), culture-based method, and biophysical technologies (e.g., biosensors and nanosensors) for environmental contamination factors. According to the different levels of sophistication of various analytical techniques and the information they can provide (either fine fingerprint, highly accurate quantification, semiquantification, qualitative detection, or fast screening), we will comment on how they may be used as complementary tools, as well as their potential and gaps toward current demand of real-time, online, and/or onsite detection.

Marine Toxins Detection by Biosensors Based on Aptamers

Marine toxins cause great harm to human health through seafood, therefore, it is urgent to exploit new marine toxins detection methods with the merits of high sensitivity and specificity, low detection limit, convenience, and high efficiency. Aptasensors have emerged to replace classical detection methods for marine toxins detection. The rapid development of molecular biological approaches, sequencing technology, material science, electronics and chemical science boost the preparation and application of aptasensors. Taken together, the aptamer-based biosensors would be the best candidate for detection of the marine toxins with the merits of high sensitivity and specificity, convenience, time-saving, relatively low cost, extremely low detection limit, and high throughput, which have reduced the detection limit of marine toxins from nM to fM. This article reviews the detection of marine toxins by aptamer-based biosensors, as well as the selection approach for the systematic evolution of ligands by exponential enrichment (SELEX), the aptamer sequences. Moreover, the newest aptasensors and the future prospective are also discussed, which would provide thereotical basis for the future development of marine toxins detection by aptasensors.

The Diversity of Cyanobacterial Toxins on Structural Characterization, Distribution and Identification: A Systematic Review

The widespread distribution of cyanobacteria in the aquatic environment is increasing the risk of water pollution caused by cyanotoxins, which poses a serious threat to human health. However, the structural characterization, distribution and identification techniques of cyanotoxins have not been comprehensively reviewed in previous studies. This paper aims to elaborate the existing information systematically on the diversity of cyanotoxins to identify valuable research avenues. According to the chemical structure, cyanotoxins are mainly classified into cyclic peptides, alkaloids, lipopeptides, nonprotein amino acids and lipoglycans. In terms of global distribution, the amount of cyanotoxins are unbalanced in different areas. The diversity of cyanotoxins is more obviously found in many developed countries than that in undeveloped countries. Moreover, the threat of cyanotoxins has promoted the development of identification and detection technology. Many emerging methods have been developed to detect cyanotoxins in the environment. This communication provides a comprehensive review of the diversity of cyanotoxins, and the detection and identification technology was discussed. This detailed information will be a valuable resource for identifying the various types of cyanotoxins which threaten the environment of different areas. The ability to accurately identify specific cyanotoxins is an obvious and essential aspect of cyanobacterial research.

An automated 3D-printed smartphone platform integrated with optoelectrowetting (OEW) microfluidic chip for on-site monitoring of viable algae in water

A sudden increase of algae and their associated toxins in aquatic ecosystems can detrimentally affect the quality of the water, causing serious socio-economic and public health problems. To prevent the spread of harmful algae in aquatic ecosystems, it is essential to track the water's quality through rapid and in-situ monitoring systems. Conventional methods of algae quantification such as microscopy, hemocytometry, and UV-vis spectroscopy, however, are often unsuitable or inconvenient for in-situ assessment as they require skilled labor and expensive equipment. In this study, we developed a three-dimensional (3D)-printed smartphone platform integrated with a light-driven microfluidic chip operated by optoelectrowetting (OEW). This OEW-driven microfluidic chip not only allows multiplexed drop-wise functions such as droplet transportation, merging, mixing, immobilization on a detection zone, for on-chip water sample preparation but also fluorescent detection and counting of target algae cells using a commercially-available smartphone. Two freshwater algae (C. reinhardtii and M. aeruginosa) and two marine water algae (Amphiprora sp and C. closterium) were employed to validate the 3D-printed smartphone platform in this study. The fluorescence images of viable algae and the cell counting from the microfluidic chip were comparable to the results from a hemocytometer (P > 0.05). We have further conducted tests with spiked samples using freshwater and marine water that were directly collected from environmental samples, showing the same order of magnitude of cell numbers in the spiked and control cultures of algae cells (10⁶ cell/mL, P > 0.05). Unlike traditional quantification methods, the 3D-printed smartphone platform integrated with the OEW offers a highly portable, user-friendly, low-cost tool that enables simple on-chip sample preparation and detection of viable algae. Thus, this stand-alone technology has the potential for rapid and in-situ monitoring of water quality, while using the smartphone's wireless communication capabilities to report the quality of the water in real-time.

Heavy Metal/Toxins Detection Using Electronic Tongues

The growing concern for sustainability and environmental preservation has increased the demand for reliable, fast response, and low-cost devices to monitor the existence of heavy metals and toxins in water resources. An electronic tongue (e-tongue) is a multisensory array mostly based on electroanalytical methods and multivariate statistical techniques to facilitate information visualization in a qualitative and/or quantitative way. E-tongues are promising analytical devices having simple operation, fast response, low cost, easy integration with other systems (microfluidic, optical, etc) to enable miniaturization and provide a high sensitivity for measurements in complex liquid media, providing an interesting alternative to address many of the existing environmental monitoring challenges, specifically relevant emerging pollutants such as heavy metals and toxins.

Two colorimetric ampicillin sensing schemes based on the interaction of aptamers with gold nanoparticles

Two kinds of aptasensors for ampicillin (AMP) are described. The assay strategies include the use of gold nanoparticles (AuNPs) that were modified with (a) a thiolated aptamer (T-Apt), and (b) a non-thiolated polyadenine aptamer (polyA Apt). The AuNPs and the aptamers were brought to interaction prior to addition of AMP. T-Apt and polyA Apt are adsorbed on the AuNPs by different mechanisms. The adsorbed aptamer was able to bind the target while preventing non-specific interactions. Remarkably different optical absorbances (measured at 520 and 680 nm) are produced the absence and presence of AMP. The assay can selectively recognize AMP even in the presence of species of similar chemical structure. The T-Apt based assay has a linear response in the 1-600 nM AMP concentration range and a 0.1 nM limit of detection. The respective data for the polyA Apt assay are 1-400 nM and 0.49 nM. Graphical abstract Schematic presentation of the colorimetric aptasensor for ampicillin detection using two kinds of anti-ampicillin aptamers and gold nanoparticles. Polydiallyldimethylammonium chloride (PDDA) acts as aggregation agent.

Aptamer-Based Fluorescent Sensor Array for Multiplexed Detection of Cyanotoxins on a Smartphone

Developing easy-to-use and miniaturized detectors is essential for in-field monitoring of environmentally hazardous substances, such as the cyanotoxins. We demonstrated a differential fluorescent sensor array made of aptamers and single-stranded DNA (ssDNA) dyes for multiplexed detection and discrimination of four common cyanotoxins with an ordinary smartphone within 5 min of reaction. The assay reagents were preloaded and dried in a microfluidic chip with a long shelf life over 60 days. Upon the addition of analyte solutions, competitive binding of cyanotoxin to the specific aptamer-dye conjugate occurred. A zone-specific and concentration-dependent reduction in the green fluorescence was observed as a result of the aptamer conformation change. The aptasensors are fully optimized by quantification of their dissociation constants, tuning the stoichiometric ratios of reaction mixtures, and implementation of an internal intensity correction step. The fluorescent sensor array allowed for accurate identification and measurement of four important cyanotoxins, including anatoxin-a (ATX), cylindrospermopsin (CYN), nodularin (NOD), and microcystin-LR (MC-LR), in parallel, with the limit of detection (LOD) down to a few nanomolar (<3 nM), which is close to the World Health Organization's guideline for the maximum concentration allowed in drinking water. The smartphone-based sensor platform also showed remarkable chemical specificity against potential interfering agents in water. The performance of the system was tested and validated with real lake water samples that were contaminated with trace levels of individual cyanotoxins as well as binary, ternary, and quaternary mixtures. Finally, a smartphone app interface has been developed for rapid on-site data processing and result display.

A Comprehensive Review: Development of Electrochemical Biosensors for Detection of Cyanotoxins in Freshwater

Cyanobacteria harmful algal blooms are increasing in frequency and cyanotoxins have become an environmental and public concern in the U.S. and worldwide. In this Review, the majority of reported studies and developments of electrochemical affinity biosensors for cyanotoxins are critically reviewed and discussed. Essential background information about cyanobacterial toxins and electrochemical biosensors is combined with the rapidly moving development of electrochemical biosensors for these toxins. Current issues and future challenges for the development of useful electrochemical biosensors for cyanotoxin detection that meet the demands for applications in field freshwater samples are discussed. The major aspects of the entire review article in a prescribed sequence include (i) the state-of-the-art knowledge of the toxicity of cyanotoxins, (ii) important harmful algal bloom events, (iii) advisories, guidelines, and regulations, (iv) conventional analytical methods for determination of cyanotoxins, (v) electrochemical transduction, (vi) recognition receptors, (vii) reported electrochemical biosensors for cyanotoxins, (viii) summary of analytical performance, and (ix) recent advances and future trends. Discussion includes electrochemical techniques and devices, biomolecules with high affinity, numerous array designs, various detection approaches, and research strategies in tailoring the properties of the transducer-biomolecule interface. Scientific and engineering aspects are presented in depth. This review aims to serve as a valuable source to scientists and engineers entering the interdisciplinary field of electrochemical biosensors for detection of cyanotoxins in freshwaters.

An Alternative Medical Diagnosis Method: Biosensors for Virus Detection

Infectious diseases still pose an omnipresent threat to global and public health, especially in many countries and rural areas of cities. Underlying reasons of such serious maladies can be summarized as the paucity of appropriate analysis methods and subsequent treatment strategies due to the limited access of centralized and equipped health care facilities for diagnosis. Biosensors hold great impact to turn our current analytical methods into diagnostic strategies by restructuring their sensing module for the detection of biomolecules, especially nano-sized objects such as protein biomarkers and viruses. Unquestionably, current sensing platforms require continuous updates to address growing challenges in the diagnosis of viruses as viruses change quickly and spread largely from person-to-person, indicating the urgency of early diagnosis. Some of the challenges can be classified in biological barriers (specificity, low number of targets, and biological matrices) and technological limitations (detection limit, linear dynamic range, stability, and reliability), as well as economical aspects that limit their implementation into resource-scarce settings. In this review, the principle and types of biosensors and their applications in the diagnosis of distinct infectious diseases were comprehensively explained. The deployment of current biosensors into resource-scarce settings is further discussed for virus detection by elaborating the pros and cons of existing methods as a conclusion and future perspective.

Exonuclease I-assisted fluorescent method for ochratoxin A detection using iron-doped porous carbon, nitrogen-doped graphene quantum dots, and double magnetic separation

In this paper, a fluorescent method was developed for ochratoxin A (OTA) detection that uses iron-doped porous carbon (MPC) and aptamer-functionalized nitrogen-doped graphene quantum dots (NGQDs-Apt) as probes. In this method, the adsorbance of the NGQDs-Apt on the MPC due to a π-π interaction between the aptamer and the MPC results in the quenching of the fluorescence of the NGQDs-Apt. However, since OTA interacts strongly with the aptamer, the presence of OTA leads to the detachment of the NGQDs-Apt from the MPC, resulting in the resumption of fluorescence from the NGQDs-Apt. When exonuclease I (Exo I) is also added to the solution, this exonuclease specifically digests the aptamer, leading to the release of the OTA back into the solution. This free OTA then interacts with another MPC-NGQDs-Apt system, inducing the release of more NGQDs into the solution, which enhances the fluorescent intensity compared to that of the system with no Exo I. Utilizing this behavior of OTA in the presence of NGQDs-Apt, it was possible to detect concentrations of OTA ranging from 10 to 5000 nM, with a limit of detection of 2.28 nM. Our method was tested by applying it to the detection of OTA in wheat and corn samples. This method has four advantages: (1) the magnetic porous carbon is easy to prepare, its porosity enhances its loading capacity for NGQDs, it highly efficiently quenches the fluorescence of the NGQDs, and its magnetic properties facilitate the separation of the MPC from other species in solution; (2) applying double magnetic separation decreases the background signal; (3) Exo I digests the free aptamer effectively, which allows the resulting free OTA to induce the release of more NGQDs-Apt, ultimately enhancing the fluorescent signal; and (4) the proposed method presented high sensitivity and a wide linear detection range. This method may prove helpful in food safety analysis and new biosensor development (achieved by using different aptamer sequences to that used in the present work). Graphical abstract Exonuclease I (Exo I)-assisted fluorescent method for ochratoxin A (OTA) detection using magnetic porous carbon (MPC), nitrogen-doped graphene quantum dots (NGQDs), and double magnetic separation.

Aptamers and Aptasensors for Highly Specific Recognition and Sensitive Detection of Marine Biotoxins: Recent Advances and Perspectives

Marine biotoxins distribute widely, have high toxicity, and can be easily accumulated in water or seafood, exposing a serious threat to consumer health. Achieving specific and sensitive detection is the most effective way to prevent emergent issues caused by marine biotoxins; however, the previous detection methods cannot meet the requirements because of ethical or technical drawbacks. Aptamers, a kind of novel recognition element with high affinity and specificity, can be used to fabricate various aptasensors (aptamer-based biosensors) for sensitive and rapid detection. In recent years, an increasing number of aptamers and aptasensors have greatly promoted the development of marine biotoxins detection. In this review, we summarized the recent aptamer-related advances for marine biotoxins detection and discussed their perspectives. Firstly, we summarized the sequences, selection methods, affinity, secondary structures, and the ion conditions of all aptamers to provide a database-like information; secondly, we summarized the reported aptasensors for marine biotoxins, including principles, detection sensitivity, linear detection range, etc.; thirdly, on the basis of the existing reports and our own research experience, we forecast the development prospects of aptamers and aptasensors for marine biotoxins detection. We hope this review not only provides a comprehensive summary of aptamer selection and aptasensor development for marine biotoxins, but also arouses a broad readership amongst academic researchers and industrial chemists.