Recent advances in M13 bacteriophage-based optical sensing applications

Genetically engineered bacteriophages as novel nanomaterials: applications beyond antimicrobial agents

Bacteriophages, also known as phages, are viruses that replicate in bacteria and archaea. Phages were initially discovered as antimicrobial agents, and they have been used as therapeutic agents for bacterial infection in a process known as "phage therapy." Recently, phages have been investigated as functional nanomaterials in a variety of areas, as they can function not only as therapeutic agents but also as biosensors and tissue regenerative materials. Phages are nontoxic to humans, and they possess self-assembled nanostructures and functional properties. Additionally, phages can be easily genetically modified to display specific peptides or to screen for functional peptides via phage display. Here, we demonstrated the application of phage nanomaterials in the context of tissue engineering, sensing, and probing.

Shape complementarity processes for ultrashort-burst sensitive M13-PEG-WS2-powered MCF-7 cancer cell sensors

Biomarkers have the potential to be utilized in disease diagnosis, prediction and monitoring. The cancer cell type is a leading candidate for next-generation biomarkers. Although traditional digital biomolecular sensor (DBS) technology has shown to be effective in assessing cell-based interactions, low cell-population detection of cancer cell types is extremely challenging. Here, we controlled the electrical signature of a two-dimensional (2D) nanomaterial, tungsten disulfide (WS2), by utilizing a combination of the Phage-integrated Polymer and the Nanosheet (PPN), viz., the integration of the M13-conjugated polyethylene glycol (PEG) and the WS2, through shape-complementarity phenomena, and developed a sensor system, i.e., the Phage-based DBS (P-DBS), for the specific, rapid, sensitive detection of clinically-relevant MCF-7 cells. The P-DBS attains a detection limit of 12 cells per μL, as well as a contrast of 1.25 between the MCF-10A sample signal and the MCF-7 sample signal. A reading length of 200 μs was further achieved, along with a relative cell viability of ∼100% for both MCF-7 and MCF-10A cells and with the PNN. Atomistic simulations reveal the structural origin of the shape complementarity-facilitated decrease in the output impedance of the P-DBS. The combination of previously unreported exotic sensing materials and digital sensor design represents an approach to unlocking the ultra-sensitive detection of cancer cell types and provides a promising avenue for early cancer diagnosis, staging and monitoring.

Understanding the Role of M13 Bacteriophage Thin Films on a Metallic Nanostructure through a Standard and Dynamic Model

The dynamic and surface manipulation of the M13 bacteriophage via the meeting application demands the creation of a pathway to design efficient applications with high selectivity and responsivity rates. Here, we report the role of the M13 bacteriophage thin film layer that is deposited on an optical nanostructure involving gold nanoparticles/SiO₂/Si, as well as its influence on optical and geometrical properties. The thickness of the M13 bacteriophage layer was controlled by varying either the concentration or humidity exposure levels, and optical studies were conducted. We designed a standard and dynamic model based upon three-dimensional finite-difference time-domain (3D FDTD) simulations that distinguished the respective necessity of each model under variable conditions. As seen in the experiments, the origin of respective peak wavelength positions was addressed in detail with the help of simulations. The importance of the dynamic model was noted when humidity-based experiments were conducted. Upon introducing varied humidity levels, the dynamic model predicted changes in plasmonic properties as a function of changes in NP positioning, gap size, and effective index (this approach agreed with the experiments and simulated results). We believe that this work will provide fundamental insight into understanding and interpreting the geometrical and optical properties of the nanostructures that involve the M13 bacteriophage. By combining such significant plasmonic properties with the numerous benefits of M13 bacteriophage (like low-cost fabrication, multi-wavelength optical characteristics devised from a single structure, reproducibility, reversible characteristics, and surface modification to suit application requirements), it is possible to develop highly efficient integrated plasmonic biomaterial-based sensor nanostructures.

Recent Advances on Peptide-Based Biosensors and Electronic Noses for Foodborne Pathogen Detection

Foodborne pathogens present a serious issue around the world due to the remarkably high number of illnesses they cause every year. In an effort to narrow the gap between monitoring needs and currently implemented classical detection methodologies, the last decades have seen an increased development of highly accurate and reliable biosensors. Peptides as recognition biomolecules have been explored to develop biosensors that combine simple sample preparation and enhanced detection of bacterial pathogens in food. This review first focuses on the selection strategies for the design and screening of sensitive peptide bioreceptors, such as the isolation of natural antimicrobial peptides (AMPs) from living organisms, the screening of peptides by phage display and the use of in silico tools. Subsequently, an overview on the state-of-the-art techniques in the development of peptide-based biosensors for foodborne pathogen detection based on various transduction systems was given. Additionally, limitations in classical detection strategies have led to the development of innovative approaches for food monitoring, such as electronic noses, as promising alternatives. The use of peptide receptors in electronic noses is a growing field and the recent advances of such systems for foodborne pathogen detection are presented. All these biosensors and electronic noses are promising alternatives for the pathogen detection with high sensitivity, low cost and rapid response, and some of them are potential portable devices for on-site analyses.

The development progress of multi-array colourimetric sensors based on the M13 bacteriophage

Techniques for detecting chemicals dispersed at low concentrations in air continue to evolve. These techniques can be applied not only to manage the quality of agricultural products using a post-ripening process but also to establish a safety prevention system by detecting harmful gases and diagnosing diseases. Recently, techniques for rapid response to various chemicals and detection in complex and noisy environments have been developed using M13 bacteriophage-based sensors. In this review, M13 bacteriophage-based multi-array colourimetric sensors for the development of an electronic nose is discussed. The self-templating process was adapted to fabricate a colour band structure consisting of an M13 bacteriophage. To detect diverse target chemicals, the colour band was utilised with wild and genetically engineered M13 bacteriophages to enhance their sensing abilities. Multi-array colourimetric sensors were optimised for application in complex and noisy environments based on simulation and deep learning analysis. The development of a multi-array colourimetric sensor platform based on the M13 bacteriophage is likely to result in significant advances in the detection of various harmful gases and the diagnosis of various diseases based on exhaled gas in the future.

Success of nano-vaccines against COVID-19: a transformation in nanomedicine

INTRODUCTION

The vaccines being used against COVID-19 are composed of either non-viral or viral nanoparticles (NPs). Nanotechnology-based vaccine technology was studied for its potentially transformative advancement of medicine.

AREAS COVERED

NPs protect the encapsulated mRNA in vaccines, thereby enhancing the stability of the ribonucleic acids and facilitating their intact delivery to their specific targets. Compared to liposomes, lipid nanoparticles (LNPs) are unique and, through their rigid morphology and better cellular penetrability, render enhanced cargo stability. To explore nanotechnology-mediated vaccine delivery and its potential in future pandemics, we assessed articles from various databases, such as PubMed, Embase, and Scopus, including editorial/research notes, expert opinions, and collections of data from several clinical research trials. In the current review, we focus on the nanoparticulate approach of the different SARS-CoV-2 vaccines and explore their success against the pandemic.

EXPERT OPINION

The mRNA-based vaccines, with their tremendous efficacy of ~95% (under phase III-IV clinical trials) and distinct nanocarriers (LNPs), represent a new medical front alongside DNA and siRNA-based vaccines.

Review: Development of SARS-CoV-2 immuno-enhanced COVID-19 vaccines with nano-platform

Vaccination is the most effective way to prevent coronavirus disease 2019 (COVID-19). Vaccine development approaches consist of viral vector vaccines, DNA vaccine, RNA vaccine, live attenuated virus, and recombinant proteins, which elicit a specific immune response. The use of nanoparticles displaying antigen is one of the alternative approaches to conventional vaccines. This is due to the fact that nano-based vaccines are stable, able to target, form images, and offer an opportunity to enhance the immune responses. The diameters of ultrafine nanoparticles are in the range of 1-100 nm. The application of nanotechnology on vaccine design provides precise fabrication of nanomaterials with desirable properties and ability to eliminate undesirable features. To be successful, nanomaterials must be uptaken into the cell, especially into the target and able to modulate cellular functions at the subcellular levels. The advantages of nano-based vaccines are the ability to protect a cargo such as RNA, DNA, protein, or synthesis substance and have enhanced stability in a broad range of pH, ambient temperatures, and humidity for long-term storage. Moreover, nano-based vaccines can be engineered to overcome biological barriers such as nonspecific distribution in order to elicit functions in antigen presenting cells. In this review, we will summarize on the developing COVID-19 vaccine strategies and how the nanotechnology can enhance antigen presentation and strong immunogenicity using advanced technology in nanocarrier to deliver antigens. The discussion about their safe, effective, and affordable vaccines to immunize against COVID-19 will be highlighted.

Additively manufactured nano-mechanical energy harvesting systems: advancements, potential applications, challenges and future perspectives

Additively manufactured nano-MEH systems are widely used to harvest energy from renewable and sustainable energy sources such as wind, ocean, sunlight, raindrops, and ambient vibrations. A comprehensive study focusing on in-depth technology evolution, applications, problems, and future trends of specifically 3D printed nano-MEH systems with an energy point of view is rarely conducted. Therefore, this paper looks into the state-of-the-art technologies, energy harvesting sources/methods, performance, implementations, emerging applications, potential challenges, and future perspectives of additively manufactured nano-mechanical energy harvesting (3DP-NMEH) systems. The prevailing challenges concerning renewable energy harvesting capacities, optimal energy scavenging, power management, material functionalization, sustainable prototyping strategies, new materials, commercialization, and hybridization are discussed. A novel solution is proposed for renewable energy generation and medicinal purposes based on the sustainable utilization of recyclable municipal and medical waste generated during the COVID-19 pandemic. Finally, recommendations for future research are presented concerning the cutting-edge issues hurdling the optimal exploitation of renewable energy resources through NMEHs. China and the USA are the most significant leading forces in enhancing 3DP-NMEH technology, with more than 75% contributions collectively. The reported output energy capacities of additively manufactured nano-MEH systems were 0.5-32 mW, 0.0002-45.6 mW, and 0.3-4.67 mW for electromagnetic, piezoelectric, and triboelectric nanogenerators, respectively. The optimal strategies and techniques to enhance these energy capacities are compiled in this paper.

Eco-Friendly Fluorescent ELISA Based on Bifunctional Phage for Ultrasensitive Detection of Ochratoxin A in Corn

Conventional enzyme-linked immunosorbent assay (ELISA) is commonly used for Ochratoxin A (OTA) screening, but it is limited by low sensitivity and harmful competing antigens of enzyme-OTA conjugates. Herein, a bifunctional M13 bacteriophage with OTA mimotopes fused on the p3 protein and biotin modified on major p8 proteins was introduced as an eco-friendly competing antigen and enzyme container for enhanced sensitivity. Mercaptopropionic acid-modified quantum dots (MPA-QDs), which are extremely sensitive to hydrogen peroxide, were chosen as fluorescent signal transducers that could manifest glucose oxidase-induced fluorescence quenching in the presence of glucose. On these bases, a highly sensitive and eco-friendly fluorescent immunoassay for OTA sensing was developed. Under optimized conditions, the proposed method demonstrates a good linear detection of OTA from 4.8 to 625 pg/mL and a limit of detection (LOD) of 5.39 pg/mL. The LOD is approximately 26-fold lower than that of a conventional horse radish peroxidase (HRP) based ELISA and six-fold lower than that of a GOx-OTA conjugate-based fluorescent ELISA. The proposed method also shows great specificity and accepted accuracy for analyzing OTA in real corn samples. The detection results are highly consistent with those obtained using the ultra-performance liquid chromatography-fluorescence detection method, indicating the high reliability of the proposed method for OTA detection. In conclusion, the proposed method is an excellent OTA screening platform over a conventional ELISA and can be easily extended for sensing other analytes by altering specific mimic peptide sequences in phages.

Strategies for Surface Immobilization of Whole Bacteriophages: A Review

Bacteriophage immobilization is a key unit operation in emerging biotechnologies, enabling new possibilities for biodetection of pathogenic microbes at low concentration, production of materials with novel antimicrobial properties, and fundamental research on bacteriophages themselves. Wild type bacteriophages exhibit extreme binding specificity for a single species, and often for a particular subspecies, of bacteria. Since their specificity originates in epitope recognition by capsid proteins, which can be altered by chemical or genetic modification, their binding specificity may also be redirected toward arbitrary substrates and/or a variety of analytes in addition to bacteria. The immobilization of bacteriophages on planar and particulate substrates is thus an area of active and increasing scientific interest. This review assembles the knowledge gained so far in the immobilization of whole phage particles, summarizing the main chemistries, and presenting the current state-of-the-art both for an audience well-versed in bioconjugation methods as well as for those who are new to the field.

M13 phage-based nanoprobe for SERS detection and inactivation of Staphylococcus aureus

Rapid and sensitive diagnosis of bacterial infections at early stage is of great significance for food safety monitoring as well as clinical treatment. Herein, we construct a surface-enhanced Raman scattering (SERS) nanoprobe based on M13 phages for the selective detection and inactivation of Staphylococcus aureus (S. aureus). M13 phage with specific S. aureus-binding heptapeptide displayed on the N-terminal of pIII protein is selected from phage display peptide library. The S. aureus-specific SERS probe is thus constructed by in situ growth of gold nanoparticles (AuNPs) on M13 phage surface, followed by modification with 5,5-dithiobis-(2-nitrobenzoic acid) (DTNB) as SERS active molecule. Upon the addition of this SERS probe, M13 phage selectively binds with S. aureus to induce anchoring of AuNPs on S. aureus surface, and the SERS probe-labeled S. aureus cells are collected by centrifugation for SERS detection. For the quantification of S. aureus, a linear range of 10-10⁶ cfu mL^-1 is achieved in aqueous medium. It is further demonstrated by spiking recovery in soft drinks. Furthermore, this SERS probe exhibits bactericidal capabilities towards S. aureus, which shows promising potential to serve as a multifunctional platform for simultaneous detection and inactivation of S. aureus.

Phage-Based Sensors in Medicine: A Review

Bacteriophages are interesting entities on the border of biology and chemistry. In nature, they are bacteria parasites, while, after genetic manipulation, they gain new properties, e.g., selectively binding proteins. Owing to this, they may be applied as recognition elements in biosensors. Combining bacteriophages with different transducers can then result in the development of innovative sensor designs that may revolutionize bioanalytics and improve the quality of medical services. Therefore, here, we review the use of bacteriophages, or peptides from bacteriophages, as new sensing elements for the recognition of biomarkers and the construction of the highly effective diagnostics tools.

Phage Display in the Quest for New Selective Recognition Elements for Biosensors

Phages are bacterial viruses that have gained a significant role in biotechnology owing to their widely studied biology and many advantageous characteristics. Perhaps the best-known application of phages is phage display that refers to the expression of foreign peptides or proteins outside the phage virion as a fusion with one of the phage coat proteins. In 2018, one half of the Nobel prize in chemistry was awarded jointly to George P. Smith and Sir Gregory P. Winter "for the phage display of peptides and antibodies." The outstanding technology has evolved and developed considerably since its first description in 1985, and today phage display is commonly used in a wide variety of disciplines, including drug discovery, enzyme optimization, biomolecular interaction studies, as well as biosensor development. A cornerstone of all biosensors, regardless of the sensor platform or transduction scheme used, is a sensitive and selective bioreceptor, or a recognition element, that can provide specific binding to the target analyte. Many environmentally or pharmacologically interesting target analytes might not have naturally appropriate binding partners for biosensor development, but phage display can facilitate the production of novel receptors beyond known biomolecular interactions, or against toxic or nonimmunogenic targets, making the technology a valuable tool in the quest of new recognition elements for biosensor development.

Mass spectrometry enumeration of filamentous M13 bacteriophage

In the last decade, filamentous M13 bacteriophage has emerged into numerous biotechnological applications as a promising nontoxic and self-assembling biomaterial with specific binding properties. This raises a question about its upscale production that consequently requires an accurate phage enumeration during the various protocol developments. However, traditional methods of measuring phage concentration are mainly biological in nature and therefore time and labor intensive. These traditional methods also demonstrate poor reproducibility and are semi-quantitative at best. In the present work, we capitalized on mass spectrometry based absolute protein quantitation. We have optimized the quantitation conditions for a major coat protein, pVIII. Enumeration of M13 bacteriophage can be further performed using the determined molar concentration of pVIII, Avogadro's number, and known copy number of pVIII per phage. Since many different phages have well-defined copy number of capsid proteins, the proposed approach can be simply applied to any phage with known copy number of a specific capsid protein.

A non-spectroscopic optical biosensor for the detection of pathogenic Salmonella Typhimurium based on a stem-loop DNA probe and retro-reflective signaling

The detection of foodborne pathogenic microorganisms is an essential issue in molecular diagnostics. Fluorescence-based assays have been widely utilized in molecular diagnostics because of their ability to detect and measure low analyte concentrations. However, conventional fluorescence-based assays require sophisticated optics systems, such as a specific light source and light filter. To overcome these limitations, we developed an optical sensing system using a retroreflective Janus microparticle (RJP) as a signaling probe. Compared to fluorescent dyes, RJPs have the advantage of not requiring complicated optic systems because they can be observed using visible light without a filter. To confirm that RJPs can be used as a probe for molecular diagnostics, Salmonella was detected using a biotinylated stem-loop DNA probe to capture the target gene DNA and a streptavidin-conjugated RJP (SA-RJP) as the detection molecule. When the target gene DNA was present at the sensing surface where the stem-loop DNA probe was immobilized, the biotinylated stem-loop DNA probe was stretched, exposing biotin, which can react with SA-RJP. Since the amount of exposed biotin increased according to the concentration of the applied target gene DNA, the number of observed RJPs on the sensing surface increased with the concentration of the target gene DNA. Consequently, the concentration of Salmonella could be quantitated by counting the number of observed RJPs. Using this system, Salmonella at concentrations ranging from 0 to 100 nM could be analyzed, with high sensitivity and selectivity, with a limit of detection of 2.48 pM.

The Robust Self-Assembling Tubular Nanostructures Formed by gp053 from Phage vB_EcoM_FV3

The recombinant phage tail sheath protein, gp053, from Escherichia coli infecting myovirus vB_EcoM_FV3 (FV3) was able to self-assemble into long, ordered and extremely stable tubular structures (polysheaths) in the absence of other viral proteins. TEM observations revealed that those protein nanotubes varied in length (~10–1000 nm). Meanwhile, the width of the polysheaths (~28 nm) corresponded to the width of the contracted tail sheath of phage FV3. The formed protein nanotubes could withstand various extreme treatments including heating up to 100 °C and high concentrations of urea. To determine the shortest variant of gp053 capable of forming protein nanotubes, a set of N- or/and C-truncated as well as poly-His-tagged variants of gp053 were constructed. The TEM analysis of these mutants showed that up to 25 and 100 amino acid residues could be removed from the N and C termini, respectively, without disturbing the process of self-assembly. In addition, two to six copies of the gp053 encoding gene were fused into one open reading frame. All the constructed oligomers of gp053 self-assembled in vitro forming structures of different regularity. By using the modification of cysteines with biotin, the polysheaths were tested for exposed thiol groups. Polysheaths formed by the wild-type gp053 or its mutants possess physicochemical properties, which are very attractive for the construction of self-assembling nanostructures with potential applications in different fields of nanosciences.

Trends in Synthetic Biology Applications, Tools, Industry, and Oversight and Their Security Implications

Recent developments in synthetic biology tools and techniques are driving commercialization of a wide range of products for human health, agriculture, environmental stewardship, and other purposes. This article reviews some of the trends in synthetic biology applications as well as some of the tools enabling these and future advances. These tools and capabilities are being developed in the context of a rapidly changing industry, which may have an impact on the rate and direction of progress. Final products are subject to a regulatory framework that is being challenged by the pace, scale, and novelty of this new era of biotechnology. This article includes discussion of these factors and how they may affect product design and the types of applications that are most likely to be supported and pursued commercially. The final section provides perspective on the security implications of these advances, with a focus on US interests.

Dodecagonal plasmonic quasicrystals for phage-based biosensing

In this work, we fabricate and characterize a novel sensitive two-dimensional surface enhanced Raman spectroscopy (SERS) substrate made of plasmonic nanocavities in a photonic quasicrystal arrangement characterized by a 12-fold rotational symmetry. Our SERS device is capable of detecting chemisorbed bacteriophages at a femtomolar range. Most importantly, the paper presents for the first time a study on the procedure to functionalize the plasmonic quasicrystal with bacteriophages of the Podoviridae family. The immobilization of the phages on the plasmonic substrate has been studied and verified through SERS measurements. A new stable peak, visible in the SERS spectra at 1326 cm^-1 at a greater than 60 times amplification, confirms the immobilization of the phages on the substrate. This functionalization approach can be used also for other types of phages or plasmonic sensors and hence, our achievements could allow the development of novel systems for the specific detection of different species of bacteria.

Flexible nanopillar-based electrochemical sensors for genetic detection of foodborne pathogens

Flexible and highly ordered nanopillar arrayed electrodes have brought great interest for many electrochemical applications, especially to the biosensors, because of its unique mechanical and topological properties. Herein, we report an advanced method to fabricate highly ordered nanopillar electrodes produced by soft-/photo-lithography and metal evaporation. The highly ordered nanopillar array exhibited the superior electrochemical and mechanical properties in regard with the wide space to response with electrolytes, enabling the sensitive analysis. As-prepared gold and silver electrodes on nanopillar arrays exhibit great and stable electrochemical performance to detect the amplified gene from foodborne pathogen of Escherichia coli O157:H7. Additionally, lightweight, flexible, and USB-connectable nanopillar-based electrochemical sensor platform improves the connectivity, portability, and sensitivity. Moreover, we successfully confirm the performance of genetic analysis using real food, specially designed intercalator, and amplified gene from foodborne pathogens with high reproducibility (6% standard deviation) and sensitivity (10 × 1.01 CFU) within 25 s based on the square wave voltammetry principle. This study confirmed excellent mechanical and chemical characteristics of nanopillar electrodes have a great and considerable electrochemical activity to apply as genetic biosensor platform in the fields of point-of-care testing (POCT).