Electrochemical DNA biosensor for the detection of pathogenic bacteria Aeromonas hydrophila

CRISPR/Cas12-based electrochemical biosensors for clinical diagnostic and food monitoring

Each organism has a unique sequence of nitrogenous bases in in the form of DNA or RNA which distinguish them from other organisms. This characteristic makes nucleic acid-based detection extremely selective and compare to other molecular techniques. In recent years, several nucleic acid-based detection technology methods have been developed, one of which is the electrochemical biosensor. Electrochemical biosensors are known to have high sensitivity and accuracy. In addition, the ease of miniaturization of this electrochemical technique has garnered interest from many researchers. On the other hand, the CRISPR/Cas12 method has been widely used in detecting nucleic acids due to its highly selective nature. The CRISPR/Cas12 method is also reported to increase the sensitivity of electrochemical biosensors through the utilization of modified electrodes. The electrodes can be modified according to detection needs so that the biosensor's performance can be improved. This review discusses the application of CRISPR/Cas12-based electrochemical biosensors, as well as various electrode modifications that have been successfully used to improve the performance of these biosensors in the clinical and food monitoring fields.

Emerging bioanalytical sensors for rapid and close-to-real-time detection of priority abiotic and biotic stressors in aquaculture and culture-based fisheries

Abiotic stresses of various chemical contamination of physical, inorganic, organic and biotoxin origin and biotic stresses of bacterial, viral, parasitic and fungal origins are the significant constraints in achieving higher aquaculture production. Testing and rapid detection of these chemical and microbial contaminants are crucial in identifying and mitigating abiotic and biotic stresses, which has become one of the most challenging aspects in aquaculture and culture-based fisheries. The classical analytical techniques, including titrimetric methods, spectrophotometric, mass spectrometric, spectroscopic, and chromatographic techniques, are tedious and sometimes inaccessible when required. The development of novel and improved bioanalytical methods for rapid, selective and sensitive detection is a wide and dynamic field of research. Biosensors offer precise detection of biotic and abiotic stressors in aquaculture and culture-based fisheries within no time. This review article allows filling the knowledge gap for detection and monitoring of chemical and microbial contaminants of abiotic and biotic origin in aquaculture and culture-based fisheries using nano(bio-) analytical technologies, including nano(bio-)molecular and nano(bio-)sensing techniques.

Recent Advancements in Electrochemical Biosensors for Monitoring the Water Quality

The release of chemicals and microorganisms from various sources, such as industry, agriculture, animal farming, wastewater treatment plants, and flooding, into water systems have caused water pollution in several parts of our world, endangering aquatic ecosystems and individual health. World Health Organization (WHO) has introduced strict standards for the maximum concentration limits for nutrients and chemicals in drinking water, surface water, and groundwater. It is crucial to have rapid, sensitive, and reliable analytical detection systems to monitor the pollution level regularly and meet the standard limit. Electrochemical biosensors are advantageous analytical devices or tools that convert a bio-signal by biorecognition elements into a significant electrical response. Thanks to the micro/nano fabrication techniques, electrochemical biosensors for sensitive, continuous, and real-time detection have attracted increasing attention among researchers and users worldwide. These devices take advantage of easy operation, portability, and rapid response. They can also be miniaturized, have a long-life span and a quick response time, and possess high sensitivity and selectivity and can be considered as portable biosensing assays. They are of special importance due to their great advantages such as affordability, simplicity, portability, and ability to detect at on-site. This review paper is concerned with the basic concepts of electrochemical biosensors and their applications in various water quality monitoring, such as inorganic chemicals, nutrients, microorganisms' pollution, and organic pollutants, especially for developing real-time/online detection systems. The basic concepts of electrochemical biosensors, different surface modification techniques, bio-recognition elements (BRE), detection methods, and specific real-time water quality monitoring applications are reviewed thoroughly in this article.

DNA electrochemical biosensor for detection of Alicyclobacillus acidoterrestris utilizing Hoechst 33258 as indicator

Alicyclobacillus acidoterrestris is an acidophilic and thermophilic bacterium present in the soil, often associated with the spoilage of acidic juices, such as orange juice. Their spores resist pasteurization and, when reactivated, modify the organoleptic properties of the juice, making it unsuitable for consumption, due mainly to production of guaiacol. Biosensors are detection devices that respond quickly and are easy to handle, with great potential for use in the juice production chain. In this context, this work reports an electrochemical genosensor for detection of A. acidoterrestris, based on a graphite electrode modified with electrochemically reduced graphene oxide, a polymer derived from 3-hydroxybenzoic acid and a specific DNA probe sequence complementary with the genomic DNA of A. acidoterrestris. Detection of the target was performed by monitoring the oxidation peak of the Hoechst 33258, a common DNA stainer. The genosensor detection limit was 12 ng mL^-1 and it kept 77% of response after ten weeks, and a test showed that orange juice does not interfere with bacteria lysate detection. This biosensor is the first platform for electrochemical detection of the genomic DNA of A. acidoterrestris in the literature, and the first to use Hoechst 33258 as indicator with whole genomic DNA molecules.

Thermodynamically designed target-specific DNA probe as an electrochemical hybridization biosensor

Applications of molecular techniques to elucidate identity or function using biomarkers still remain highly empirical and biosensors are no exception. In the present study, target-specific oligonucleotide probes for E. coli K12 were designed thermodynamically and applied in an electrochemical DNA biosensor setup. Biosensor was prepared by immobilization of a stem-loop structured probe, modified with a thiol functional group at its 5' end and a biotin molecule at its 3' end, on a gold electrode through self-assembly. Mercaptopropionic acid (MPA) was used to optimize the surface probe density of the electrode. Hybridization between the immobilized probe and the target DNA was detected via the electrochemical response of streptavidin-horseradish peroxidase in the presence of the substrate. The amperometric response showed a linear relationship with the target DNA concentration, ranging from 10 and 400 nM, with a correlation coefficient of 0.989. High selectivity and good repeatability of the biosensor showed that the thermodynamic approach to oligonucleotide probe design can be used in development of electrochemical DNA biosensors.

The Genoprotective Role of Naringin

Since ancient times, fruits and edible plants have played a special role in the human diet for enhancing health and maintaining youthfulness. The aim of our work was to determine the interactions between naringin, a natural ingredient of grapefruits, and DNA using an electrochemical biosensor. Electrochemical methods allow analyzing the damages occurring in the structure of nucleic acids and their interactions with xenobiotics. Our study showed that the changes in the location of electrochemical signals and their intensity resulted from the structural alterations in DNA. The signal of adenine was affected at lower concentrations of naringin, but the signal of guanine was unaffected in the same condition. The dynamics of changes occurring in the peak height and surface of adenine related to naringin concentration was also significantly lower. The complete binding of all adenine bases present in the tested double-stranded DNA solution was observed at naringin concentrations ranging from 8.5 to 10.0 µM. At larger concentrations, this active compound exerted an oxidizing effect on DNA. However, the critical concentrations of naringin were found to be more than twice as high as the dose absorbable in an average human (4 µM). The results of our work might be helpful in the construction of electrochemical sensors for testing the content of polyphenols and would allow determining their genoprotective functionality.

Review of Electrochemical DNA Biosensors for Detecting Food Borne Pathogens

The vital importance of rapid and accurate detection of food borne pathogens has driven the development of biosensor to prevent food borne illness outbreaks. Electrochemical DNA biosensors offer such merits as rapid response, high sensitivity, low cost, and ease of use. This review covers the following three aspects: food borne pathogens and conventional detection methods, the design and fabrication of electrochemical DNA biosensors and several techniques for improving sensitivity of biosensors. We highlight the main bioreceptors and immobilizing methods on sensing interface, electrochemical techniques, electrochemical indicators, nanotechnology, and nucleic acid-based amplification. Finally, in view of the existing shortcomings of electrochemical DNA biosensors in the field of food borne pathogen detection, we also predict and prospect future research focuses from the following five aspects: specific bioreceptors (improving specificity), nanomaterials (enhancing sensitivity), microfluidic chip technology (realizing automate operation), paper-based biosensors (reducing detection cost), and smartphones or other mobile devices (simplifying signal reading devices).

Microfluidic-Based Approaches for Foodborne Pathogen Detection

Food safety is of obvious importance, but there are frequent problems caused by foodborne pathogens that threaten the safety and health of human beings worldwide. Although the most classic method for detecting bacteria is the plate counting method, it takes almost three to seven days to get the bacterial results for the detection. Additionally, there are many existing technologies for accurate determination of pathogens, such as polymerase chain reaction (PCR), enzyme linked immunosorbent assay (ELISA), or loop-mediated isothermal amplification (LAMP), but they are not suitable for timely and rapid on-site detection due to time-consuming pretreatment, complex operations and false positive results. Therefore, an urgent goal remains to determine how to quickly and effectively prevent and control the occurrence of foodborne diseases that are harmful to humans. As an alternative, microfluidic devices with miniaturization, portability and low cost have been introduced for pathogen detection. In particular, the use of microfluidic technologies is a promising direction of research for this purpose. Herein, this article systematically reviews the use of microfluidic technology for the rapid and sensitive detection of foodborne pathogens. First, microfluidic technology is introduced, including the basic concepts, background, and the pros and cons of different starting materials for specific applications. Next, the applications and problems of microfluidics for the detection of pathogens are discussed. The current status and different applications of microfluidic-based technologies to distinguish and identify foodborne pathogens are described in detail. Finally, future trends of microfluidics in food safety are discussed to provide the necessary foundation for future research efforts.

Nitrogen doped chiral carbonaceous nanotube for ultrasensitive DNA direct electrochemistry, DNA hybridization and damage study

In the interest of developing novel electrocatalyst for high performance DNA biosensing, with distinctive chiral double helix nanostructure, nitrogen doped chiral carbonaceous nanotube (Chiral-CNT) was employed for ultrasensitive label-free DNA biosensing research. Chiral-CNT can quantitative detection of four DNA bases with high sensitivity and selectivity. Without any prehydrolysis and labeling process, direct electrochemistry of single-stranded DNA and double-stranded DNA, qualitative and quantitative detection of DNA hybridization (low detection limit: 0.0268 g L^-1) were realized. Moreover, sensitive detection of DNA damage induced by fenton reagent was also realized with low detection limit of 0.0350 mg mL^-1 and high sensitivity of 7.42 μA mg^-1 mL. The high biosensing performance attributes to the unique chiral structure of Chiral-CNT, leads to efficient interreaction between Chiral-CNT and DNA molecule.

Food Safety Analysis Using Electrochemical Biosensors

Rapid and precise analytical tools are essential for monitoring food safety and screening of any undesirable contaminants, allergens, or pathogens, which may cause significant health risks upon consumption. Substantial developments in analytical techniques have empowered the analyses and quantitation of these contaminants. However, conventional techniques are limited by delayed analysis times, expensive and laborious sample preparation, and the necessity for highly-trained workers. Therefore, prompt advances in electrochemical biosensors have supported significant gains in quantitative detection and screening of food contaminants and showed incredible potential as a means of defying such limitations. Apart from indicating high specificity towards the target analytes, these biosensors have also addressed the challenge of food industry by providing high analytical accuracy within complex food matrices. Here, we discuss some of the recent advances in this area and analyze the role and contributions made by electrochemical biosensors in the food industry. This article also reviews the key challenges we believe biosensors need to overcome to become the industry standard.

Photoelectrochemical Strategy for Discrimination of Microbial Pathogens Using Conjugated Polymers

A photoelectrochemical (PEC) biosensor for facile and sensitive identification of pathogenic microorganisms was developed. Cationic poly(phenylene vinylene) derivative (PPV) as photoelectrochemical active species was modified on the electrode. Under light irradiation, PPV could be excited and generate efficient photocurrent. PPV also had the ability to bind with negatively charged membrane of pathogenic microorganisms, which hindered the electron transfer between electrode and electrolyte. As a result, the photocurrent would decrease obviously. For E. coli, B. subtilis and C. albicans, the photocurrent density was reduced by 18, 33 and 59 %, respectively. Based on the reduction degree of the photocurrent after capturing different types of species of pathogenic microorganisms, a PEC sensor for discrimination of pathogenic microorganisms was realized.

Reduced graphene oxide nanoribbon immobilized gold nanoparticle based electrochemical DNA biosensor for the detection of Mycobacterium tuberculosis

Tuberculosis is one of the most dreadful diseases caused by Mycobacterium tuberculosis with more than 9 million individuals suffering from it in 2014. Traditional methods of detection are not efficient enough for its quick and reliable detection; therefore, it is imperative to develop methods of its detection in the early stages. Consequently, we report a highly sensitive and selective biosensor for detection of Mycobacterium tuberculosis. In this work, gold nanoparticles (AuNPs, dia. ∼6 nm, 1.81 wt% loading) are immobilized over reduced graphene oxide nanoribbons (RGONRs). An ssDNA/Au/RGONR electrode is prepared by immobilizing Au nanoparticles followed by covalent modification of Au nanoparticles with 5'SH-ssDNA. As per the best knowledge of the authors, the target DNA of Mycobacterium tuberculosis is detected using a ssDNA/Au/RGONR bioelectrode by cyclic voltammetry and chronoamperometric methods for the first time. With high detection efficiency (0.1 fM), the ssDNA/Au/RGONR bioelectrode exhibited better signal amplification and electrochemical response as compared to bare Au and RGONR electrodes. Additionally, the ssDNA/Au/RGONR bioelectrode displayed good linear response to different concentrations of target M. tuberculosis DNA. The ssDNA/Au/RGONR has shown excellent specificity (92%) to Mycobacterium tuberculosis target DNA as compared with non-complementary DNA. The Au/RGONR matrix has the potential to be used as an immobilization platform for single-stranded probe DNAs of different diseases other than tuberculosis reported here.

Electrochemical Methodologies for the Detection of Pathogens

Bacterial infections remain one of the principal causes of morbidity and mortality worldwide. The number of deaths due to infections is declining every year by only 1% with a forecast of 13 million deaths in 2050. Among the 1400 recognized human pathogens, the majority of infectious diseases is caused by just a few, about 20 pathogens only. While the development of vaccinations and novel antibacterial drugs and treatments are at the forefront of research, and strongly financially supported by policy makers, another manner to limit and control infectious outbreaks is targeting the development and implementation of early warning systems, which indicate qualitatively and quantitatively the presence of a pathogen. As toxin contaminated food and drink are a potential threat to human health and consequently have a significant socioeconomic impact worldwide, the detection of pathogenic bacteria remains not only a big scientific challenge but also a practical problem of enormous significance. Numerous analytical methods, including conventional culturing and staining techniques as well as molecular methods based on polymerase chain reaction amplification and immunological assays, have emerged over the years and are used to identify and quantify pathogenic agents. While being highly sensitive in most cases, these approaches are highly time, labor, and cost consuming, requiring trained personnel to perform the frequently complex assays. A great challenge in this field is therefore to develop rapid, sensitive, specific, and if possible miniaturized devices to validate the presence of pathogens in cost and time efficient manners. Electrochemical sensors are well accepted powerful tools for the detection of disease-related biomarkers and environmental and organic hazards. They have also found widespread interest in the last years for the detection of waterborne and foodborne pathogens due to their label free character and high sensitivity. This Review is focused on the current electrochemical-based microorganism recognition approaches and putting them into context of other sensing devices for pathogens such as culturing the microorganism on agar plates and the polymer chain reaction (PCR) method, able to identify the DNA of the microorganism. Recent breakthroughs will be highlighted, including the utilization of microfluidic devices and immunomagnetic separation for multiple pathogen analysis in a single device. We will conclude with some perspectives and outlooks to better understand shortcomings. Indeed, there is currently no adequate solution that allows the selective and sensitive binding to a specific microorganism, that is fast in detection and screening, cheap to implement, and able to be conceptualized for a wide range of biologically relevant targets.

Electrochemical Aptasensors for Food and Environmental Safeguarding: A Review

Food and environmental monitoring is one of the most important aspects of dealing with recent threats to human well-being and ecosystems. In this framework, electrochemical aptamer-based sensors are resilient due to their ability to resolve food and environmental contamination. An aptamer-based sensor is a compact analytical device combining an aptamer as the bio-sensing element integrated on the transducer surface. Aptamers display many advantages as biorecognition elements in sensor development when compared to affinity-based (antibodies) sensors. Aptasensors are small, chemically unchanging, and inexpensive. Moreover, they offer extraordinary elasticity and expediency in the design of their assemblies, which has led to innovative sensors that show tremendous sensitivity and selectivity. This review will emphasize recent food and environmental safeguarding using aptasensors; there are good prospects for their performance as a supplement to classical techniques.

The Use of Electrochemical Biosensors in Food Analysis

Rapid and accurate analysis of food produce is essential to screen for species that may cause significant health risks like bacteria, pesticides and other toxins. Considerable developments in analytical techniques and instrumentation, for example chromatography, have enabled the analyses and quantitation of these contaminants. However, these traditional technologies are constrained by high cost, delayed analysis times, expensive and laborious sample preparation stages and the need for highly-trained personnel. Therefore, emerging, alternative technologies, for example biosensors may provide viable alternatives. Rapid advances in electrochemical biosensors have enabled significant gains in quantitative detection and screening and show incredible potential as a means of countering such limitations. Apart from demonstrating high specificity towards the analyte, these biosensors also address the challenge of the multifactorial food industry of providing high analytical accuracy amidst complex food matrices, while also overcoming differing densities, pH and temperatures. This (public and Industry) demand for faster, reliable and cost-efficient analysis of food samples, has driven investment into biosensor design. Here, we discuss some of the recent work in this area and critique the role and contributions biosensors play in the food industry. We also appraise the challenges we believe biosensors need to overcome to become the industry standard.

The molecular characterizations of Cu/ZnSOD and MnSOD and its responses of mRNA expression and enzyme activity to Aeromonas hydrophila or lipopolysaccharide challenge in Qihe crucian carp Carassius auratus

Superoxide dismutases (SODs), as the prime antioxidant enzymes, present the first line of defense against oxidative stress caused by excessive reactive oxygen species (ROS) in organism. In the study, two distinct members of SOD family were cloned and analyzed in Qihe crucian carp Carassius auratus (designated as CaCu/ZnSOD and CaMnSOD, respectively). The full-length cDNA of CaCu/ZnSOD is 759 bp, containing a 5' -untranslated region (UTR) of 39 bp, a ORF (including stop codon, TAG) of 465 bp and a 3'-UTR of 255 bp. The ORF of CaCu/ZnSOD encodes a protein of 154 amino acids (aa), in which, two Cu/ZnSOD signature (⁴⁵GFHVHAFGDNT⁵⁵ and ¹³⁹GNAGGRLACGVI¹⁵⁰) and four conserved amino acids for Cu/Zn²⁺-binding sites (H64, H72, H81 and D84) were observed. The full-length CaMnSOD cDNA (960 bp) consists of a 5'-UTR of 114 bp, a ORF of 675 bp and a 3'-UTR of 231 bp, the ORF of CaMnSOD encodes a 224 aa protein with a 26 aa mitochondrial-targeting sequence (MTS) in the N-terminus, and four conserved amino acids for manganese binding (H52, H100, D185 and H189) were observed. Multiple alignment and the structural analysis revealed two Cu/ZnSOD signature motifs and a MnSOD signature motif as well as the invariant binding sites for Cu²⁺/Zn²⁺ in CaCu/ZnSOD and Mn²⁺ in CaMnSOD. The phylogenetic analysis indicated that CaCu/ZnSOD was homologous to cytosolic Cu/ZnSODs, and CaMnSOD was high similarity with mitochondrial MnSODs from other fish. The tissue distribution analysis demonstrated that CaCu/ZnSOD and CaMnSOD were highly expressed in liver, heart and muscle. The dynamic expressions of CaCu/ZnSOD and CaMnSOD were observed after the challenges with Aeromonas hydrophila or LPS, which generally increased in liver, gill, kidney and spleen, while, the mRNA expressions were down-regulated at some time points in head kidney. The enzyme activities increased after A. hydrophila or LPS challenge, compared to the control. In this study, the molecular structures and functional motifs of CaCu/ZnSOD and CaMnSOD were determined, and it is crucial for us to understand the biological functions of SODs. The highest level in liver showed that the function of liver to remove ROS is much more important. The obvious responses of mRNA expression levels and enzyme activities to pathogens indicate the important roles of CaCu/ZnSOD and CaMnSOD in antioxidant defense in C. auratus.

Electrochemical Genosensor To Detect Pathogenic Bacteria (Escherichia coli O157:H7) As Applied in Real Food Samples (Fresh Beef) To Improve Food Safety and Quality Control

The electrochemical genosensor is one of the most promising methods for the rapid and reliable detection of pathogenic bacteria. In a previous work, we performed an efficient electrochemical genosensor detection of Staphylococcus aureus by using lead sulfide nanoparticles (PbSNPs). As a continuation of this study, in the present work, the electrochemical genosensor was used to detect Escherichia coli O157:H7. The primer and probes were designed using NCBI database and Sigma-Aldrich primer and probe software. The capture and signalizing probes were modified by thiol (SH) and amine (NH2), respectively. Then, the signalizing probe was connected using cadmium sulfide nanoparticles (CdSNPs), which showed well-defined peaks after electrochemical detection. The genosensor was prepared by immobilization of complementary DNA on the gold electrode surface, which hybridizes with a specific fragment gene from pathogenic to make a sandwich structure. The conductivity and sensitivity of the sensor were increased by using multiwalled carbon nanotubes (MWCNT) that had been modified using chitosan deposited as a thin layer on the glass carbon electrode (GCE) surface, followed by a deposit of bismuth. The peak currents of E. coli O157:H7 correlated in a linear fashion with the concentration of tDNA. The detection limit was 1.97 × 10(-14) M, and the correlation coefficient was 0.989. A poorly defined current response was observed as the negative control and baseline. Our results showed high sensitivity and selectivity of the electrochemical DNA biosensor to the pathogenic bacteria E. coli O157:H7. The biosensor was also used to evaluate the detection of pathogen in real beef samples contaminated artificially. Compared with other electrochemical DNA biosensors, we conclude that this genosensor provides for very efficient detection of pathogenic bacteria. Therefore, this method may have potential application in food safety and related fields.

Electrochemical DNA Biosensor Based on a Tetrahedral Nanostructure Probe for the Detection of Avian Influenza A (H7N9) Virus

A DNA tetrahedral nanostructure-based electrochemical biosensor was developed to detect avian influenza A (H7N9) virus through recognizing a fragment of the hemagglutinin gene sequence. The DNA tetrahedral probe was immobilized onto a gold electrode surface based on self-assembly between three thiolated nucleotide sequences and a longer nucleotide sequence containing complementary DNA to hybridize with the target single-stranded (ss)DNA. The captured target sequence was hybridized with a biotinylated-ssDNA oligonucleotide as a detection probe, and then avidin-horseradish peroxidase was introduced to produce an amperometric signal through the interaction with 3,3',5,5'-tetramethylbenzidine substrate. The target ssDNA was obtained by asymmetric polymerase chain reaction (PCR) of the cDNA template, reversely transcribed from the viral lysate of influenza A (H7N9) virus in throat swabs. The results showed that this electrochemical biosensor could specifically recognize the target DNA fragment of influenza A (H7N9) virus from other types of influenza viruses, such as influenza A (H1N1) and (H3N2) viruses, and even from single-base mismatches of oligonucleotides. Its detection limit could reach a magnitude of 100 fM for target nucleotide sequences. Moreover, the cycle number of the asymmetric PCR could be reduced below three with the electrochemical biosensor still distinguishing the target sequence from the negative control. To the best of our knowledge, this is the first report of the detection of target DNA from clinical samples using a tetrahedral DNA probe functionalized electrochemical biosensor. It displays that the DNA tetrahedra has a great potential application as a probe of the electrochemical biosensor to detect avian influenza A (H7N9) virus and other pathogens at the gene level, which will potentially aid the prevention and control of the disease caused by such pathogens.