A cantilever biosensor-based assay for toxin-producing cyanobacteria Microcystis aeruginosa using 16S rRNA

CyanoStrainChip: A Novel DNA Microarray Tool for High-Throughput Detection of Environmental Cyanobacteria at the Strain Level

Detecting cyanobacteria in environments is an important concern due to their crucial roles in ecosystems, and they can form blooms with the potential to harm humans and nonhuman entities. However, the most widely used methods for high-throughput detection of environmental cyanobacteria, such as 16S rRNA sequencing, typically provide above-species-level resolution, thereby disregarding intraspecific variation. To address this, we developed a novel DNA microarray tool, termed the CyanoStrainChip, that enables strain-level comprehensive profiling of environmental cyanobacteria. The CyanoStrainChip was designed to target 1277 strains; nearly all major groups of cyanobacteria are included by implementing 43,666 genome-wide, strain-specific probes. It demonstrated strong specificity by in vitro mock community experiments. The high correlation (Pearson's R > 0.97) between probe fluorescence intensities and the corresponding DNA amounts (ranging from 1-100 ng) indicated excellent quantitative capability. Consistent cyanobacterial profiles of field samples were observed by both the CyanoStrainChip and next-generation sequencing methods. Furthermore, CyanoStrainChip analysis of surface water samples in Lake Chaohu uncovered a high intraspecific variation of abundance change within the genus Microcystis between different severity levels of cyanobacterial blooms, highlighting two toxic Microcystis strains that are of critical concern for Lake Chaohu harmful blooms suppression. Overall, these results suggest a potential for CyanoStrainChip as a valuable tool for cyanobacterial ecological research and harmful bloom monitoring to supplement existing techniques.

Fabrication of graphene oxide-based pretreatment filter and Electrochemical-CRISPR biosensor for the field-ready cyanobacteria monitoring system

Microcystis aeruginosa (M. aeruginosa) cause the eutrophication of lakes and rivers. To effectively control the overgrowth of M. aeruginosa, a suitable measurement method should be required in the aquatic fields. To address this, we developed a field-ready cyanobacterial pretreatment device and an electrochemical clustered regularly interspaced short palindromic repeats (EC-CRISPR) biosensor. The cyanobacterial pretreatment device consists of a syringe, glass bead, and graphene oxide (GO) bead. Then, the M. aeruginosa dissolved in the freshwater sample was added to fabricated filter. After filtration, the purified gene was loaded onto a CRISPR-based electrochemical biosensor chip to detect M. aeruginosa gene fragments. The biosensor was composed of CRISPR/Cpf1 protein conjugated with MXene on an Au microgap electrode (AuMGE) integrated into a printed circuit board (PCB). This AuMGE/PCB system maximizes the signal-to-noise ratio, which controls the working and counter electrode areas requiring only 3 μL samples to obtain high reliability. Using the extracted M. aeruginosa gene with a pre-treatment filter, the CRISPR biosensor showed a limit of detection of 0.089 pg/μl in fresh water. Moreover, selectivity test and matrix condition test carried out using the EC-CRISPR biosensor. These handheld pre-treatment kit and biosensors can enable field-ready detection of CyanoHABs.

Cyanobacterial Algal Bloom Monitoring: Molecular Methods and Technologies for Freshwater Ecosystems

Cyanobacteria (blue-green algae) can accumulate to form harmful algal blooms (HABs) on the surface of freshwater ecosystems under eutrophic conditions. Extensive HAB events can threaten local wildlife, public health, and the utilization of recreational waters. For the detection/quantification of cyanobacteria and cyanotoxins, both the United States Environmental Protection Agency (USEPA) and Health Canada increasingly indicate that molecular methods can be useful. However, each molecular detection method has specific advantages and limitations for monitoring HABs in recreational water ecosystems. Rapidly developing modern technologies, including satellite imaging, biosensors, and machine learning/artificial intelligence, can be integrated with standard/conventional methods to overcome the limitations associated with traditional cyanobacterial detection methodology. We examine advances in cyanobacterial cell lysis methodology and conventional/modern molecular detection methods, including imaging techniques, polymerase chain reaction (PCR)/DNA sequencing, enzyme-linked immunosorbent assays (ELISA), mass spectrometry, remote sensing, and machine learning/AI-based prediction models. This review focuses specifically on methodologies likely to be employed for recreational water ecosystems, especially in the Great Lakes region of North America.

A Fragile Balance: Does Neutrophil Extracellular Trap Formation Drive Pulmonary Disease Progression?

Neutrophils act as the first line of defense during infection and inflammation. Once activated, they are able to fulfil numerous tasks to fight inflammatory insults while keeping a balanced immune response. Besides well-known functions, such as phagocytosis and degranulation, neutrophils are also able to release "neutrophil extracellular traps" (NETs). In response to most stimuli, the neutrophils release decondensed chromatin in a NADPH oxidase-dependent manner decorated with histones and granule proteins, such as neutrophil elastase, myeloperoxidase, and cathelicidins. Although primarily supposed to prevent microbial dissemination and fight infections, there is increasing evidence that an overwhelming NET response correlates with poor outcome in many diseases. Lung-related diseases especially, such as bacterial pneumonia, cystic fibrosis, chronic obstructive pulmonary disease, aspergillosis, influenza, and COVID-19, are often affected by massive NET formation. Highly vascularized areas as in the lung are susceptible to immunothrombotic events promoted by chromatin fibers. Keeping this fragile equilibrium seems to be the key for an appropriate immune response. Therapies targeting dysregulated NET formation might positively influence many disease progressions. This review highlights recent findings on the pathophysiological influence of NET formation in different bacterial, viral, and non-infectious lung diseases and summarizes medical treatment strategies.

Development of Electrochemical DNA Biosensor for Equine Hindgut Acidosis Detection

The pH drop in the hindgut of the horse is caused by lactic acid-producing bacteria which are abundant when a horse’s feeding regime is excessively carbohydrate rich. This drop in pH below six causes hindgut acidosis and may lead to laminitis. Lactic acid-producing bacteria Streptococcus equinus and Mitsuokella jalaludinii have been found to produce high amounts of L-lactate and D-lactate, respectively. Early detection of increased levels of these bacteria could allow the horse owner to tailor the horse’s diet to avoid hindgut acidosis and subsequent laminitis. Therefore, 16s ribosomal ribonucleic acid (rRNA) sequences were identified and modified to obtain target single stranded deoxyribonucleic acid (DNA) from these bacteria. Complementary single stranded DNAs were designed from the modified target sequences to form capture probes. Binding between capture probe and target single stranded deoxyribonucleic acid (ssDNA) in solution has been studied by gel electrophoresis. Among pairs of different capture probes and target single stranded DNA, hybridization of Streptococcus equinus capture probe 1 (SECP1) and Streptococcus equinus target 1 (SET1) was portrayed as gel electrophoresis. Adsorptive stripping voltammetry was utilized to study the binding of thiol modified SECP1 over gold on glass substrates and these studies showed a consistent binding signal of thiol modified SECP1 and their hybridization with SET1 over the gold working electrode. Cyclic voltammetry and electrochemical impedance spectroscopy were employed to examine the binding of thiol modified SECP1 on the gold working electrode and hybridization of thiol modified SECP1 with the target single stranded DNA. Both demonstrated the gold working electrode surface was modified with a capture probe layer and hybridization of the thiol bound ssDNA probe with target DNA was indicated. Therefore, the proposed electrochemical biosensor has the potential to be used for the detection of the non-synthetic bacterial DNA target responsible for equine hindgut acidosis.

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.

Using photocatalyst powder to enhance the coagulation and sedimentation of cyanobacterial cells and enable the sludge to be self-purified under visible light

Removing harmful cyanobacteria intact by coagulation can prevent cell lysis and toxin release, which provides many benefits for drinking water production, including reduction of the burden on subsequent processes and guaranteeing the water quality. But the electronegativity and buoyancy of cyanobacterial cells make them settle slowly and their accumulation and concentration in flocs would still have severe adverse effects. In this study, we introduced a photocatalyst powder to act as a ballasting agent in the coagulation process and to degrade the cells and cyanotoxins during sludge storage. Results showed that adding N-TiO₂ would decrease the coagulant dose to half of the conventional value, and also allow Microcystis aeruginosa cells to completely settle within 10 min. During sludge storage, the algal cells, cyanotoxins and other organics in sludge would be degraded to safe levels after 32 h' visible-light irradiation. Meanwhile, the N-TiO₂, water and some of the coagulant in purified sludge will be directly and safely reused. Thus, this is an environmentally friendly and cost-effective technology which incorporates photocatalyst in algal flocs to enhance coagulation and sedimentation and to enable the sludge produced to be self-purified under visible-light.

Study of Alzheimer's Disease-Related Biophysical Kinetics with a Microslit-Embedded Cantilever Sensor in a Liquid Environment

A microsized slit-embedded cantilever sensor (slit cantilever) was fabricated and evaluated as a biosensing platform in a liquid environment. In order to minimize the degradation caused by viscous damping, a 300 × 100 µm² (length × width) sized cantilever was released by a 5 µm gap-surrounding and vibrated by an internal piezoelectric-driven self-actuator. Owing to the structure, when the single side of the slit cantilever was exposed to liquid a significant quality factor (Q = 35) could be achieved. To assess the sensing performance, the slit cantilever was exploited to study the biophysical kinetics related to Aβ peptide. First, the quantification of Aβ peptide with a concentration of 10 pg/mL to 1 μg/mL was performed. The resonant responses exhibited a dynamic range from 100 pg/mL to 100 ng/mL (−56.5 to −774 ΔHz) and a dissociation constant (K_D) of binding affinity was calculated as 1.75 nM. Finally, the Aβ self-aggregation associated with AD pathogenesis was monitored by adding monomeric Aβ peptides. As the concentration of added analyte increased from 100 ng/mL to 10 µg/mL, both the frequency shift values (−813 to −1804 ΔHz) and associate time constant increased. These results showed the excellent sensing performance of the slit cantilever overcoming a major drawback in liquid environments to become a promising diagnostic tool candidate.

Effect of Distributed Mass on the Node, Frequency, and Sensitivity of Resonant-Mode Based Cantilevers

We derived an analytical expression for a resonant-mode based bi-layered cantilever with distributed mass load. The behavior of mode of vibration, nodal position, frequency shift, as well as sensitivity under different mass load distributions was theoretically studied. The theoretical results suggested that asymmetric mass load distribution leads to the shift of nodes as well as the sensitive regions of a resonant-mode based cantilever. n - 1 local maximal sensitivities and n - 1 local minimal sensitivities are observed when the cantilever vibrates in the nth-order resonance. The maximal sensitivity is found at the first local maximal sensitivity and the behavior of mass load length as a function of the maximal sensitivity follows the rule of an exponent decaying function. The sensitivity increases as the load mass increases for the same mass load distribution, but the corresponding slopes are different.

Piezoelectric Cantilever Biosensors for Label-free, Real-time Detection of DNA and RNA

This chapter reviews the design, fabrication, characterization, and application of piezoelectric-excited millimeter-sized cantilever (PEMC) sensors. The sensor transduction mechanism, sensing principle, and mode of operation are discussed. Bio-recognition strategies and surface functionalization methods for detection of DNA and RNA are discussed with a focus on self-assembly-based approaches. Methods for the verification of biosensor response via secondary binding assays, reversible binding assays, and the integration of complementary transduction mechanisms are presented. Sensing applications for medical diagnostics, food safety, and environmental monitoring are provided. PEMC sensor technology provides a robust platform for the real-time, label-free detection of DNA and RNA in complex matrices over nanomolar (nM) to attomolar (aM) concentration ranges.

Acoustofluidic particle trapping, manipulation, and release using dynamic-mode cantilever sensors

Active and programmable mixing, trapping, separation, manipulation and release of suspended particles in liquids using dynamic-mode cantilever sensors.

Hybrid integrated label-free chemical and biological sensors

Label-free sensors based on electrical, mechanical and optical transduction methods have potential applications in numerous areas of society, ranging from healthcare to environmental monitoring. Initial research in the field focused on the development and optimization of various sensor platforms fabricated from a single material system, such as fiber-based optical sensors and silicon nanowire-based electrical sensors. However, more recent research efforts have explored designing sensors fabricated from multiple materials. For example, synthetic materials and/or biomaterials can also be added to the sensor to improve its response toward analytes of interest. By leveraging the properties of the different material systems, these hybrid sensing devices can have significantly improved performance over their single-material counterparts (better sensitivity, specificity, signal to noise, and/or detection limits). This review will briefly discuss some of the methods for creating these multi-material sensor platforms and the advances enabled by this design approach.