Phage-mediated counting by the naked eye of miRNA molecules at attomolar concentrations in a Petri dish

Biomimetic Plasmonic Nanophages by Head/Tail Self-Assembling: Gold Nanoparticle/Virus Interactions

Gold nanoparticles (AuNPs), because of their dual plasmonic and catalytic functionalities, are among the most promising nanomaterials for the development of therapeutic and diagnostic tools for severe diseases such as cancer and neurodegeneration. Bacteriophages, massively present in human biofluids, are emerging as revolutionary biotechnological tools as they can be engineered to display multiple specific binding moieties, providing effective targeting ability, high stability, low cost, and sustainable production. Coupling AuNPs with phages can lead to an advanced generation of nanotools with great potential for biomedical applications. In the present study, we analyzed the interactions between differently sized AuNPs and filamentous M13 phages, establishing an advanced characterization platform that combines analytical techniques and computational models for an in-depth understanding of these hybrid self-assembling systems. A precise and structurally specific interaction of the AuNP-M13 hybrid complexes was observed, leading to a peculiar head/tail "tadpole-like" configuration. In silico simulations allowed explaining the mechanisms underlying the preferential assembly route and providing information about AuNPs' size-dependent interplay with specific M13 capsid proteins. The AuNP-M13 structures were proven to be biomimetic, eluding the formation of biomolecular corona. By keeping the biological identity of the virion, hybrid nanostructures maintained their natural recognition/targeting ability even in the presence of biomolecular crowding. In addition, we were able to tune the hybrid nanostructures' tropism toward E. coli based on the AuNP size. Overall, our results set the fundamental basis and a standard workflow for the development of phage-based targeting nanotools, valuable for a wide spectrum of nanotechnology applications.

Bacteriophage-Based Bioanalysis

Bacteriophages, which are viral predators of bacteria, have evolved to efficiently recognize, bind, infect, and lyse their host, resulting in the release of tens to hundreds of propagated viruses. These abilities have attracted biosensor developers who have developed new methods to detect bacteria. Recently, several comprehensive reviews have covered many of the advances made regarding the performance of phage-based biosensors. Therefore, in this review, we first describe the landscape of phage-based biosensors and then cover advances in other aspects of phage biology and engineering that can be used to make high-impact contributions to biosensor development. Many of these advances are in fields adjacent to analytical chemistry such as synthetic biology, machine learning, and genetic engineering and will allow those looking to develop phage-based biosensors to start taking alternative approaches, such as a bottom-up design and synthesis of custom phages with the singular task of detecting their host.

Phage-based delivery systems: engineering, applications, and challenges in nanomedicines

Bacteriophages (phages) represent a unique category of viruses with a remarkable ability to selectively infect host bacteria, characterized by their assembly from proteins and nucleic acids. Leveraging their exceptional biological properties and modifiable characteristics, phages emerge as innovative, safe, and efficient delivery vectors. The potential drawbacks associated with conventional nanocarriers in the realms of drug and gene delivery include a lack of cell-specific targeting, cytotoxicity, and diminished in vivo transfection efficiency. In contrast, engineered phages, when employed as cargo delivery vectors, hold the promise to surmount these limitations and attain enhanced delivery efficacy. This review comprehensively outlines current strategies for the engineering of phages, delineates the principal types of phages utilized as nanocarriers in drug and gene delivery, and explores the application of phage-based delivery systems in disease therapy. Additionally, an incisive analysis is provided, critically examining the challenges confronted by phage-based delivery systems within the domain of nanotechnology. The primary objective of this article is to furnish a theoretical reference that contributes to the reasoned design and development of potent phage-based delivery systems.

Nanotechnology's frontier in combatting infectious and inflammatory diseases: prevention and treatment

Inflammation-associated diseases encompass a range of infectious diseases and non-infectious inflammatory diseases, which continuously pose one of the most serious threats to human health, attributed to factors such as the emergence of new pathogens, increasing drug resistance, changes in living environments and lifestyles, and the aging population. Despite rapid advancements in mechanistic research and drug development for these diseases, current treatments often have limited efficacy and notable side effects, necessitating the development of more effective and targeted anti-inflammatory therapies. In recent years, the rapid development of nanotechnology has provided crucial technological support for the prevention, treatment, and detection of inflammation-associated diseases. Various types of nanoparticles (NPs) play significant roles, serving as vaccine vehicles to enhance immunogenicity and as drug carriers to improve targeting and bioavailability. NPs can also directly combat pathogens and inflammation. In addition, nanotechnology has facilitated the development of biosensors for pathogen detection and imaging techniques for inflammatory diseases. This review categorizes and characterizes different types of NPs, summarizes their applications in the prevention, treatment, and detection of infectious and inflammatory diseases. It also discusses the challenges associated with clinical translation in this field and explores the latest developments and prospects. In conclusion, nanotechnology opens up new possibilities for the comprehensive management of infectious and inflammatory diseases.

Living virus-based nanohybrids for biomedical applications

Living viruses characterized by distinctive biological functions including specific targeting, gene invasion, immune modulation, and so forth have been receiving intensive attention from researchers worldwide owing to their promising potential for producing numerous theranostic modalities against diverse pathological conditions. Nevertheless, concerns during applications, such as rapid immune clearance, altering immune activation modes, insufficient gene transduction efficiency, and so forth, highlight the crucial issues of excessive therapeutic doses and the associated biosafety risks. To address these concerns, synthetic nanomaterials featuring unique physical/chemical properties are frequently exploited as efficient drug delivery vehicles or treatments in biomedical domains. By constant endeavor, researchers nowadays can create adaptable living virus-based nanohybrids (LVN) that not only overcome the limitations of virotherapy, but also combine the benefits of natural substances and nanotechnology to produce novel and promising therapeutic and diagnostic agents. In this review, we discuss the fundamental physiochemical properties of the viruses, and briefly outline the basic construction methodologies of LVN. We then emphasize their distinct diagnostic and therapeutic performances for various diseases. Furthermore, we survey the foreseeable challenges and future perspectives in this interdisciplinary area to offer insights. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Therapeutic Approaches and Drug Discovery > Emerging Technologies.

Rapid and reliable ultrasensitive detection of pathogenic H9N2 viruses through virus-binding phage nanofibers decorated with gold nanoparticles

The rapid and sensitive detection of pathogenic viruses is important for controlling pandemics. Herein, a rapid, ultrasensitive, optical biosensing scheme was developed to detect avian influenza virus H9N2 using a genetically engineered filamentous M13 phage probe. The M13 phage was genetically engineered to bear an H9N2-binding peptide (H9N2BP) at the tip and a gold nanoparticle (AuNP)-binding peptide (AuBP) on the sidewall to form an engineered phage nanofiber, M13@H9N2BP@AuBP. Simulated modelling showed that M13@H9N2BP@AuBP enabled a 40-fold enhancement of the electric field enhancement in surface plasmon resonance (SPR) compared to conventional AuNPs. Experimentally, this signal enhancement scheme was employed for detecting H9N2 particles with a sensitivity down to 6.3 copies/mL (1.04 × 10-5 fM). The phage-based SPR scheme can detect H9N2 viruses in real allantoic samples within 10 min, even at very low concentrations beyond the detection limit of quantitative polymerase chain reaction (qPCR). Moreover, after capturing the H9N2 viruses on the sensor chip, the H9N2-binding phage nanofibers can be quantitatively converted into plaques that are visible to the naked eye for further quantification, thereby allowing us to enumerate the H9N2 virus particles through a second mode to cross-validate the SPR results. This novel phage-based biosensing strategy can be employed to detect other pathogens because the H9N2-binding peptides can be easily switched with other pathogen-binding peptides using phage display technology.

Genetic Engineering and Biosynthesis Technology: Keys to Unlocking the Chains of Phage Therapy

Phages possess the ability to selectively eliminate pathogenic bacteria by recognizing bacterial surface receptors. Since their discovery, phages have been recognized for their potent bactericidal properties, making them a promising alternative to antibiotics in the context of rising antibiotic resistance. However, the rapid emergence of phage-resistant strains (generally involving temperature phage) and the limited host range of most phage strains have hindered their antibacterial efficacy, impeding their full potential. In recent years, advancements in genetic engineering and biosynthesis technology have facilitated the precise engineering of phages, thereby unleashing their potential as a novel source of antibacterial agents. In this review, we present a comprehensive overview of the diverse strategies employed for phage genetic engineering, as well as discuss their benefits and drawbacks in terms of bactericidal effect.

Quantitative analysis of miRNAs using SplintR ligase-mediated ligation of complementary-pairing probes enhanced by RNase H (SPLICER)-qPCR

Here, a method using SplintR ligase-mediated ligation of complementary-pairing probes enhanced by RNase H (SPLICER) for miRNAs quantification was established. The strategy has two steps: (1) ligation of two DNA probes specifically hybridize to target miRNA and (2) qPCR amplifying the ligated probe. The miRNA-binding regions of the probes are stem-looped, a motif significantly reduces nonspecific ligation at high ligation temperature (65°C). The ends of the probes are designed complementary to form a paired probe, facilitating the recognition of target miRNAs with low concentrations. RNase H proved to be able to stabilize the heteroduplex formed by the probe and target miRNA, contributing to enhanced sensitivity (limit of detection = 60 copies). High specificity (discriminating homology miRNAs differing only one nucleotide), wide dynamic range (seven orders of magnitude) and ability to accurately detect plant miRNAs (immune to hindrance of 2'-O-methyl moiety) enable SPLICER comparable with the commercially available TaqMan and miRCURY assays. SYBR green I, rather than expensive hydrolysis or locked nucleic acid probes indispensable to TaqMan and miRCURY assays, is adequate for SPLICER. The method was efficient (<1 h), economical ($7 per sample), and robust (able to detect xeno-miRNAs in mammalian bodies), making it a powerful tool for molecular diagnosis and corresponding therapy.

Gires-Tournois Immunoassay Platform for Label-Free Bright-Field Imaging and Facile Quantification of Bioparticles

Bright-field imaging of nanoscale bioparticles is a challenging task for optical microscopy because the light-matter interactions of bioparticles are weak on conventional surfaces due to their low refractive index and small size. Alternatively, advanced imaging techniques, including near-field microscopy and phase microscopy, have enabled visualization and quantification of the bioparticles, but they require assistance of sophisticated/customized systems and post-processing with complex established algorithms. Here, a simple and fast immunoassay device, Gires-Tournois immunoassay platform (GTIP) is presented, which provides unique color dynamics in response to optical environment changes and thus enables the label-free bright-field imaging and facile quantification of bioparticles using conventional optical microscopy. Bioparticles on GTIP slow down the velocity of reflected light, leading to vivid color change according to the local particle density and maximizing chromatic contrast for high spatial distinguishability. The particle distribution and density on the surface of the resonator are readily analyzed through 2D raster-scanning-based chromaticity analysis. GTIP offers multiscale sensing capability for target analytes that possess different refractive indices and sizes.

Accelerated Digital Biodetection Using Magneto-plasmonic Nanoparticle-Coupled Photonic Resonator Absorption Microscopy

Rapid, ultrasensitive, and selective quantification of circulating microRNA (miRNA) biomarkers in body fluids is increasingly deployed in early cancer diagnosis, prognosis, and therapy monitoring. While nanoparticle tags enable detection of nucleic acid or protein biomarkers with digital resolution and subfemtomolar detection limits without enzymatic amplification, the response time of these assays is typically dominated by diffusion-limited transport of the analytes or nanotags to the biosensor surface. Here, we present a magnetic activate capture and digital counting (mAC+DC) approach that utilizes magneto-plasmonic nanoparticles (MPNPs) to accelerate single-molecule sensing, demonstrated by miRNA detection via toehold-mediated strand displacement. Spiky Fe₃O₄@Au MPNPs with immobilized target-specific probes are "activated" by binding with miRNA targets, followed by magnetically driven transport through the bulk fluid toward nanoparticle capture probes on a photonic crystal (PC). By spectrally matching the localized surface plasmon resonance of the MPNPs to the PC-guided resonance, each captured MPNP locally quenches the PC reflection efficiency, thus enabling captured MPNPs to be individually visualized with high contrast for counting. We demonstrate quantification of the miR-375 cancer biomarker directly from unprocessed human serum with a 1 min response time, a detection limit of 61.9 aM, a broad dynamic range (100 aM to 10 pM), and a single-base mismatch selectivity. The approach is well-suited for minimally invasive biomarker quantification, enabling potential applications in point-of-care testing with short sample-to-answer time.

T7 Phage as an Emerging Nanobiomaterial with Genetically Tunable Target Specificity

Bacteriophages, also known as phages, are specific antagonists against bacteria. T7 phage has drawn massive attention in precision medicine owing to its distinctive advantages, such as short replication cycle, ease in displaying peptides and proteins, high stability and cloning efficiency, facile manipulation, and convenient storage. By introducing foreign gene into phage DNA, T7 phage can present foreign peptides or proteins site-specifically on its capsid, enabling it to become a nanoparticle that can be genetically engineered to screen and display a peptide or protein capable of recognizing a specific target with high affinity. This review critically introduces the biomedical use of T7 phage, ranging from the detection of serological biomarkers and bacterial pathogens, recognition of cells or tissues with high affinity, design of gene vectors or vaccines, to targeted therapy of different challenging diseases (e.g., bacterial infection, cancer, neurodegenerative disease, inflammatory disease, and foot-mouth disease). It also discusses perspectives and challenges in exploring T7 phage, including the understanding of its interactions with human body, assembly into scaffolds for tissue regeneration, integration with genome editing, and theranostic use in clinics. As a genetically modifiable biological nanoparticle, T7 phage holds promise as biomedical imaging probes, therapeutic agents, drug and gene carriers, and detection tools.

Advances in the Development of Phage-Based Probes for Detection of Bio-Species

Bacteriophages, abbreviated as "phages", have been developed as emerging nanoprobes for the detection of a wide variety of biological species, such as biomarker molecules and pathogens. Nanosized phages can display a certain length of exogenous peptides of arbitrary sequence or single-chain variable fragments (scFv) of antibodies that specifically bind to the targets of interest, such as animal cells, bacteria, viruses, and protein molecules. Metal nanoparticles generally have unique plasmon resonance effects. Metal nanoparticles such as gold, silver, and magnetism are widely used in the field of visual detection. A phage can be assembled with metal nanoparticles to form an organic-inorganic hybrid probe due to its nanometer-scale size and excellent modifiability. Due to the unique plasmon resonance effect of this composite probe, this technology can be used to visually detect objects of interest under a dark-field microscope. In summary, this review summarizes the recent advances in the development of phage-based probes for ultra-sensitive detection of various bio-species, outlining the advantages and limitations of detection technology of phage-based assays, and highlighting the commonly used editing technologies of phage genomes such as homologous recombination and clustered regularly interspaced palindromic repeats/CRISPR-associated proteins system (CRISPR-Cas). Finally, we discuss the possible scenarios for clinical application of phage-probe-based detection methods.

Advanced graphene oxide-based paper sensor for colorimetric detection of miRNA

MicroRNAs (miRNAs), found in blood and body fluids, have emerged as potential non-invasive biomarkers for disease and injury. miRNAs are quantitatively evaluated using typical RNA analysis methods such as the quantitative reverse transcription polymerase chain reaction, microarrays, and Northern blot, all of which require complex procedures and expensive reagents. To utilize miRNAs as practical biomarkers, it will be helpful to develop simple and user-friendly sensors. In this study, a paper-based miRNA sensor was developed by combining two methods: (1) target-recycled DNAzyme (Dz) amplification and (2) graphene oxide-assisted Dz blotting on paper. The Dz spots on paper caused a miRNA-dependent color change in presence of colorimetric reagents and facilitated the quantification of absolute amount of the target miRNA, irrespective of the volume, with high reproducibility. This approach is technologically straightforward and enables quantification of as low as 7.75 fmol miRNA using a portable smartphone.

Attomolar analyte sensing techniques (AttoSens): a review on a decade of progress on chemical and biosensing nanoplatforms

Detecting the ultra-low abundance of analytes in real-life samples, such as biological fluids, water, soil, and food, requires the design and development of high-performance biosensing modalities. The breakthrough efforts from the scientific community have led to the realization of sensing technologies that measure the analyte's ultra-trace level, with relevant sensitivity, selectivity, response time, and sampling efficiency, referred to as Attomolar Analyte Sensing Techniques (AttoSens) in this review. In an AttoSens platform, 1 aM detection corresponds to the quantification of 60 target analyte molecules in 100 μL of sample volume. Herein, we review the approaches listed for various sensor probe design, and their sensing strategies that paved the way for the detection of attomolar (aM: 10^-18 M) concentration of analytes. A summary of the technological advances made by the diverse AttoSens trends from the past decade is presented.

Digital Counting of Biomolecules Using Engineered Functional DNA Superstructures

There is currently a great need for developing a simple and effective biosensing platform for the detection of single biomolecules (e.g., DNAs, RNAs, or proteins) in the biological, medical, and environmental fields. Here, we show a versatile and sensitive fluorescence counting strategy for quantifying proteins and microRNAs by employing functional DNA superstructures (denoted as 3D DNA). A 3D DNA biolabel was first engineered to become highly fluorescent and carry recognition elements for the target of interest. The presence of a target cross-links the resultant of the 3D DNA biolabel and a surface-bound capturing antibody or DNA oligonucleotide, thus forming a sandwich complex that can be easily resolved using traditional fluorescence microscopy. The broad utility of this platform is illustrated by engineering two different 3D DNA biolabels that enable the quantification of β-lactamase (one secreted bacterial hydrolase) and miR-21 (one overexpressed microRNA in cancer cells) with detection limits of 100 aM and 1 fM, respectively. We envision that the approach described herein will find useful applications in chemical biology, medical diagnostics, and biosensing.

The immuno-reactivity of polypseudorotaxane functionalized magnetic CDMNP-PEG-CD nanoparticles

pH‐magnetic dual‐responsive nanocomposites have been widely used in drug delivery and gene therapy. Recently, a polypseudorotaxane functionalized magnetic nanoparticle (MNP) was developed by synthesizing the magnetic nanoparticles with cyclodextrin (CD) molecules (CDMNP) via polyethylene glycol (PEG) (CDMNP‐PEG‐CD). The purpose of this study was to explore the antigenicity and immunogenicity of the nanoparticles in vivo prior to their further application explorations. Here, nanoparticles were assessed in vivo for retention, bio‐distribution and immuno‐reactivity. The results showed that, once administered intravenously, CDMNP‐PEG‐CD induced a temporary blood monocyte response and was cleared effectively from the body through the urine system in mice. The introduction of β‐CD and PEG/β‐CD polypseudorotaxane on SiO₂ magnetic nanoparticles (SOMNP) limited particle intramuscular dispersion after being injected into mouse gastrocnemius muscle (GN), which led to the prolonged local inflammation and muscle toxicity by CDMNP and CDMNP‐PEG‐CD. In addition, T cells were found to be more susceptible for β‐CD–modified CDMNP; however, polypseudorotaxane modification partially attenuated β‐CD–induced T cell response in the implanted muscle. Our results suggested that CDMNP‐PEG‐CD nanoparticles or the decomposition components have potential to prime antigen‐presenting cells and to break the muscle autoimmune tolerance.

Phage engineering and the evolutionary arms race

Phages are versatile agents for delivering a variety of cargo, including nanomaterials, nucleic acids, and small molecules. A potentially important application is treatment of antibiotic-resistant infections. All of these applications require molecular engineering of the phages, including chemical modification and genetic engineering. Phages are remarkably amenable to such engineering. We review some examples, including for controlled phage therapy. We suggest that the ability of phages to support extensive engineering may have evolutionary origins in the billions-year-old 'arms race' between bacteria and phages, which selects for sequences and structures that are robust in the face of rapid evolutionary change. This leads to high tolerance of both naturally evolved mutations and synthetic molecular engineering.

Label-free fluorometric detection of microRNA using isothermal rolling circle amplification generating tandem G-quadruplex

MicroRNAs (miRNAs) play an important role in various biological processes and have been regarded as promising diagnostic biomarkers for solid tumors in the field of clinical diagnostics. In this study, we developed a simple label/quencher-free fluorometric system for sensitive and selective miRNA detection using isothermal gene amplification such as rolling circle amplification generating tandem G-quadruplex DNA structures (GQ-RCA). The closed-circular dumbbell-shaped padlock DNA was designed to be complementary to its corresponding target miRNA. In the presence of the target miRNA, a long stretch of ssDNA with tandem G-quadruplex sequence repeats was readily generated by RCA, initiated by phi29 DNA polymerase through DNA synthesis priming at the 3'-OH of the target miRNA annealed to the padlock DNA. The RCA product harboring tandem G-quadruplex was monitored with fluorophore Thioflavin T (ThT) that emits strong fluorescence only when it intercalates into the G-quadruplex. The GQ-RCA assay enabled us to detect miRNA as low as 4.9 fM with a linear range from 25.6 fM to 80 pM within 0.5 h. In addition, our system was applied to the miRNA samples present in human plasma, showing its potential use in the clinical diagnosis of cancer.

Quantification of silk protein using phage nanofibers with high binding specificity

Silk sericin (SS) has emerged as an important silk protein for use in medicine and textiles. However, no sensitive method is available for detecting it. Here, we employed phage nanofibers (∼7 nm wide) as a probe to quantify SS from a dilute aqueous solution by exploiting two properties of the bacteria-infecting phage nanofibers, its use as a platform for discovering SS-binding peptide and its ultrasensitive quantification by a simple titering assay (where the number of phage nanofibers displaying the SS-binding peptide is equal to the number of countable millimeter-sized plaques derived from the phage nanofibers by infecting bacteria through plating). We first discovered a SS-binding peptide and the phage nanofibers (SS-phage) displaying this peptide at the tip. We found that this peptide can even differentiate SS from another silk protein (silk fibroin), showing its high specificity. We then employed SS-phage nanofibers as a probe to bind the SS casted from the aqueous solution. Because SS-phage nanofibers bound to the SS and the SS in the original SS solution were numerically correlated and the number of SS-phage nanofibers can be determined by counting the plaques in a Petri dish by the titering assay, determining the number of phage-derived plaques with the naked eye led to the rapid quantification of SS concentration with a detection limit of 19.50 ng ml^-1. This phage-based counting strategy can be potentially applied to the facile detection of other proteins.

Structure Engineering of a Lanthanide-Based Metal-Organic Framework for the Regulation of Dynamic Ranges and Sensitivities for Pheochromocytoma Diagnosis

Exploring innovative technologies to precisely quantify biomolecules is crucial but remains a great challenge for disease diagnosis. Unfortunately, the humoral concentrations of most biotargets generally vary within rather limited scopes between normal and pathological states, while most literature-reported biosensors can detect large spans of targets concentrations, but are less sensitive to small concentration changes, which consequently make them mostly unsatisfactory or even unreliable in distinguishing positives from negatives. Herein, a novel strategy of precisely quantifying the small concentration changes of a certain biotarget by editing the dynamic ranges and sensitivities of a lanthanide-based metal-organic framework (Eu-ZnMOF) biosensor is reported. By elaborately tailoring the biosensor's structure and surface areas, the tunable Eu-ZnMOF is developed with remarkably enhanced response slope within the "optimized useful detection window," enabling it to serve as a powerful signal amplifier (87.2-fold increase) for discriminating the small concentration variation of urinary vanillylmandelic acid (an early pathological signature of pheochromocytoma) within only three times between healthy and diseased subjects. This study provides a facile approach to edit the biosensors' performances through structure engineering, and exhibits promising perspectives for future clinical application in the non-invasive and accurate diagnosis of severe diseases.

Phage nanofibers in nanomedicine: Biopanning for early diagnosis, targeted therapy, and proteomics analysis

Display of a peptide or protein of interest on the filamentous phage (also known as bacteriophage), a biological nanofiber, has opened a new route for disease diagnosis and therapy as well as proteomics. Earlier phage display was widely used in protein-protein or antigen-antibody studies. In recent years, its application in nanomedicine is becoming increasingly popular and encouraging. We aim to review the current status in this research direction. For better understanding, we start with a brief introduction of basic biology and structure of the filamentous phage. We present the principle of phage display and library construction method on the basis of the filamentous phage. We summarize the use of the phage displayed peptide library for selecting peptides with high affinity against cells or tissues. We then review the recent applications of the selected cell or tissue targeting peptides in developing new targeting probes and therapeutics to advance the early diagnosis and targeted therapy of different diseases in nanomedicine. We also discuss the integration of antibody phage display and modern proteomics in discovering new biomarkers or target proteins for disease diagnosis and therapy. Finally, we propose an outlook for further advancing the potential impact of phage display on future nanomedicine. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.

Fluorescent-Magnetic-Catalytic Nanospheres for Dual-Modality Detection of H9N2 Avian Influenza Virus

The outbreak of H9N2 avian influenza virus (H9N2 AIV) brings high mortality and huge economic losses every year. Sensitive and reliable detection methods are essential to timely diagnosis and treatment. Herein, a dual-modality immunoassay is proposed for H9N2 AIV detection by employing fluorescent-magnetic-catalytic nanospheres (FMCNs) as labels and alkaline phosphatase (ALP)-induced metallization as a signal amplification strategy. The excellent magnetic properties of FMCNs endow the assay a potential application in complex samples. Also, the excellent fluorescence properties of FMCNs enable fluorescence modality readout. The antibodies on the FMCN surface can achieve efficient capture and separation of targets. Amplified electrochemical modality readout can be obtained through ALP-catalyzed silver deposition. Dual-modality immunoassay combined the advantages of electrochemical assay with fluorescence assay and provides accurate detection results to meet different testing needs. With two quantitative analysis forms, H9N2 AIV can be detected by electrochemical signals with a quantitation range of 0.1 to 1000 ng/mL and a detection limit of 10 pg/mL. The linear range is 300 to 1000 ng/mL with a detection limit of 69.8 ng/mL by the fluorescence signal readout. Moreover, the specificity, anti-interference ability, accuracy, and diversity of the proposal have unlimited potential for early diagnosis of suspect infections.

Enhancement of Photodynamic Cancer Therapy by Physical and Chemical Factors

The viable use of photodynamic therapy (PDT) in cancer therapy has never been fully realized because of its undesirable effects on healthy tissues. Herein we summarize some physicochemical factors that can make PDT a more viable and effective option to provide future oncological patients with better-quality treatment options. These physicochemical factors include light sources, photosensitizer (PS) carriers, microwaves, electric fields, magnetic fields, and ultrasound. This Review is meant to provide current information pertaining to PDT use, including a discussion of in vitro and in vivo studies. Emphasis is placed on the physicochemical factors and their potential benefits in overcoming the difficulty in transitioning PDT into the medical field. Many advanced techniques, such as employing X-rays as a light source, using nanoparticle-loaded stem cells and bacteriophage bio-nanowires as a photosensitizer carrier, as well as integration with immunotherapy, are among the future directions.

Delivery of Liver-Specific miRNA-122 Using a Targeted Macromolecular Prodrug toward Synergistic Therapy for Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) poses a great threat to human health. The elegant combination of gene therapy and chemotherapy by nanocarriers has been repeatedly highlighted to realize enhanced therapeutic efficacy relative to monotreatment. However, the leading strategy to achieve the efficient codelivery of the gene and drug remains the electrostatic condensation with the nucleic acid and the hydrophobic encapsulation of drug molecules by the nanocarriers, which suffers substantially from premature drug leakage during circulation and severe off-target-associated side effects. To address these issues, we reported in this study the codelivery of liver-specific miRNA-122 and anti-cancer drug 5-fluorouracil (5-Fu) using a macromolecular prodrug approach, that is, electrostatic condensation with miRNA-122 using galactosylated-chitosan-5-fluorouracil (GC-FU). The delivery efficacy was evaluated comprehensively in vitro and in vivo. Specifically, the biocompatibility of GC-FU/miR-122 nanoparticles (NPs) was assessed by hemolysis activity analysis, BSA adsorption test, and cell viability assay in both normal liver cells (L02 cells) and endothelial cells. The resulting codelivery systems showed enhanced blood and salt stability, efficient proliferation inhibition of HCC cells, and further induction apoptosis of HCC cells, as well as downregulated expression of ADAM17 and Bcl-2. The strategy developed herein is thus a highly promising platform for an effective codelivery of miRNA-122 and 5-Fu with facile fabrication and great potential for the clinical translation toward HCC synergistic therapy.

Gold Nanoparticle Probe-Assisted Antigen-Counting Chip Using SEM

Currently, it remains challenging to count protein-biomarker molecules present in a small droplet of biological samples. Herein, we propose a gold nanoparticle (GNP) probe-assisted sandwich-counting strategy that relies on a GNP probe, an antibody-functionalized chip to "count" antigen molecules using a scanning electron microscope. Both standard carcinoembryonic antigen (CEA) and two real CEA-related tumor samples (tumor tissues and serum) were assayed to demonstrate the proof-of-concept of the counting strategy. Results show that our method is excellently correlative with enzyme-linked immuno-sorbent assay (ELISA) that is widely used in clinics for antigen or antibody detection and the limit of detection of our enumeration strategy reaches down to 0.045 ng/mL, which is ∼40 times more sensitive than the conventional ELISA. Therefore, our GNP probe-assisted sandwich-counting strategy has the potential to be used for quantification of protein biomarkers at ultralow concentrations in early tumor specimens and detection of target proteins in much diluted concentrations.

Paper-Supported Self-Powered System Based on a Glucose/O2 Biofuel Cell for Visual MicroRNA-21 Sensing

The exploitation of self-powered devices that get rid of the power source restriction represents the development tendency of sensing systems. Herein, a paper-supported glucose/O₂ biofuel cell (BFC)-based self-powered sensing platform for visual analysis was developed. The BFC device utilized gold nanoparticle-modified paper fibers as the electrode to wire glucose oxidase (GOx) and bilirubin oxidase for the fabrication of bioanodes and biocathodes. To implement an assay protocol, a target-responsive cargo release system based on mesoporous silica nanocarriers controlled by microRNA-21 (miRNA-21) was designed. During the BFC operation, undesired H₂O₂, the side product of glucose oxidation which would be deleterious for GOx, was generated, leading to inevitable degeneration of BFC performance. On the basis of the H₂O₂-mediated iodide oxidation reaction to form iodine that further modulated the starch chromogenic reaction, undesired H₂O₂ could be effectively removed, resulting in remarkably improved BFC performance as well as providing a means for visual signal readout. Thanks to the dual output signals (maximum power output density or length of blue bar), enhanced analysis reliability and sensitive detection of miRNA-21 over a range of 5 fM to 100 pM were achieved. Moreover, this study demonstrates a proof of concept in visualized BFC-based self-powered systems for sensing applications and provides a blueprint to advance future sensors and analysis devices powered by BFCs in a wide variety of in vitro applications.

Polypseudorotaxane functionalized magnetic nanoparticles as a dual responsive carrier for roxithromycin delivery

A magnetic-pH dual responsive drug delivery system was prepared for antibacterial therapy to reduce the side effects on nonpathological cells or tissues. Iron oxide (Fe₃O₄) core was surface-functionalized with silane coupling agents to link β‑cyclodextrin (β-CD) (CDMNP), and a polypseudorotaxanes shell where polyethyleneglycol chains threaded much CD molecules was further prepared on the magnetic Fe₃O₄ core (CDMNP-PEG-CD) to enhance loading capacity of roxithromycin (ROX). CDMNP-PEG-CD with a hydrodynamic diameter of ~168 nm was cytocompatible, superparamagnetic, magnetic-responsive and stable for 180 min of storage. No significant interaction with serum albumin was shown for the nanocomposites. The in vitro release from ROX-loaded CDMNP-PEG-CD nanocomposites was about 76% of total drug within 30 min at pH 1.0, 1.6-fold of that at pH 7.4 and 2-fold of that at pH 8.0, presenting pH-responsive drug release behaviors. The nanocomposites showed positive antibacterial activity against both E. coli and S. aureus based on an agar diffusion method. The antibacterial activity of the nanocomposites was more sensitive against E. coli than S. aureus, and the inhibition halo against E. coli was 85% more than that of Fe₃O₄. CDMNP-PEG-CD nanocomposites allowed for the localization and fast concentration of hydrophobic drugs, providing a broad potential range of therapeutic applications.

Intermolecular distance measurement with TNT suppressor on the M13 bacteriophage-based Förster resonance energy transfer system

An M13 bacteriophage-based Förster resonance energy transfer (FRET) system is developed to estimate intermolecular distance at the nanoscale using a complex of CdSSe/ZnS nanocrystal quantum dots, genetically engineered M13 bacteriophages labeled with fluorescein isothiocyanate and trinitrotoluene (TNT) as an inhibitor. In the absence of trinitrotoluene, it is observed that a significant spectral shift from blue to green occur, which represents efficient energy transfer through dipole-dipole coupling between donor and acceptor, or FRET-on mode. On the other hand, in the presence of trinitrotoluene, the energy transfer is suppressed, since the donor-to-acceptor intermolecular distance is detuned by the specific capturing of TNT by the M13 bacteriophage, denoted as FRET-off mode. These noble features are confirmed by changes in the fluorescence intensity and the fluorescence decay curve. TNT addition to our system results in reducing the total energy transfer efficiency considerably from 16.1% to 7.6% compared to that in the non-TNT condition, while the exciton decay rate is significantly enhanced. In particular, we confirm that the energy transfer efficiency satisfies the original intermolecular distance dependence of FRET. The relative donor-to-acceptor distance is changed from 70.03 Å to 80.61 Å by inclusion of TNT.

Non-Cross-Linking Aggregation of DNA-Carrying Polymer Micelles Triggered by Duplex Formation

Colloidal behaviors of particles functionalized with biomolecules are generally complicated. This study describes that colloidal behaviors of double-stranded (ds) DNA-carrying polymer micelles are well controlled by altering the molar ratio of single-stranded (ss) DNA moiety in the dsDNA shell. ssDNA-carrying micelles composed of a poly( N-isopropylacrylamide) (PNIPAAm) core surrounded by a dense shell of ssDNAs were prepared through self-assembly of PNIPAAm grafted with ssDNA by incubating its solution above the lower critical solution temperature. Spontaneous, non-cross-linking aggregation of the micelles was triggered by DNA duplex formation on the surface. Comparison of the critical coagulation concentration of NaCl among a series of the DNA-carrying micelles revealed the relationship between the helical structure of the surface-bound DNA and the colloidal stability of the micelles. The electrophoretic mobility analysis of the micelles indicated that the duplex formation reduced the structural flexibility of the surface-bound DNA, thereby decreasing the interparticle entropic repulsion. It is also suggested that the augmented rigidity of the surface-bound DNA increases the number of terminal base pairs facing the solvent, which could lead to multiple blunt-end stacking interaction among the micelles. Therefore, small DNA molecules could be considered unique surface-modifiers capable of controlling interactions between the surfaces of materials.

Peptide-based nanoprobes for molecular imaging and disease diagnostics

Pathological changes in a diseased site are often accompanied by abnormal activities of various biomolecules in and around the involved cells. Identifying the location and expression levels of these biomolecules could enable early-stage diagnosis of the related disease, the design of an appropriate treatment strategy, and the accurate assessment of the treatment outcomes. Over the past two decades, a great diversity of peptide-based nanoprobes (PBNs) have been developed, aiming to improve the in vitro and in vivo performances of water-soluble molecular probes through engineering of their primary chemical structures as well as the physicochemical properties of their resultant assemblies. In this review, we introduce strategies and approaches adopted for the identification of functional peptides in the context of molecular imaging and disease diagnostics, and then focus our discussion on the design and construction of PBNs capable of navigating through physiological barriers for targeted delivery and improved specificity and sensitivity in recognizing target biomolecules. We highlight the biological and structural roles that low-molecular-weight peptides play in PBN design and provide our perspectives on the future development of PBNs for clinical translation.

Encoding activities of non-coding RNAs

The universal expression of various non-coding RNAs (ncRNAs) is now considered the main feature of organisms' genomes. Many regions in the genome are transcribed but not annotated to encode proteins, yet contain small open reading frames (smORFs). A widely accepted opinion is that a vast majority of ncRNAs are not further translated. However, increasing evidence underlines a series of intriguing translational events from the ncRNAs, which were previously considered to lack coding potential. Recent studies also suggest that products derived from such novel translational events display important regulatory functions in many fundamental biological and pathological processes. Here we give a critical review on the potential coding capacity of ncRNAs, in particular, about what is known and unknown in this emerging area. We also discuss the possible underlying coding mechanisms of these extraordinary ncRNAs and possible roles of peptides or proteins derived from the ncRNAs in disease development and theranostics. Our review offers an extensive resource for studying the biology of ncRNAs and sheds light into the use of ncRNAs and their corresponding peptides or proteins for disease diagnosis and therapy.

Viral-based nanomaterials for plasmonic and photonic materials and devices

Over the last decade, viruses have established themselves as a powerful tool in nanotechnology. Their proteinaceous capsids benefit from biocompatibility, chemical addressability, and a variety of sizes and geometries, while their ability to encapsulate, scaffold, and self-assemble enables their use for a wide array of purposes. Moreover, the scaling up of viral-based nanotechnologies is facilitated by high capsid production yield and speed, which is particularly advantageous when compared with slower and costlier lithographic techniques. These features enable the bottom-up fabrication of photonic and plasmonic materials, which relies on the precise arrangement of photoactive material at the nanoscale to control phenomena such as electromagnetic wave propagation and energy transfer. The interdisciplinary approach required for the fabrication of such materials combines techniques from the life sciences and device engineering, thus promoting innovative research. Materials with applications spanning the fields of sensing (biological, chemical, and physical sensors), nanomedicine (cellular imaging, drug delivery, phototherapy), energy transfer and conversion (solar cells, light harvesting, photocatalysis), metamaterials (negative refraction, artificial magnetism, near-field amplification), and nanoparticle synthesis are considered with exclusive emphasis on viral capsids and protein cages. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.

Recent advances in microRNA detection

Recent advances in miRNA detection methods and new applications.

Bioinspired structural transition of synthetic polymers through biomolecular ligand binding

The bioinspired structural transition of thermoresponsive poly(N-isopropylacrylamide) was demonstrated by specific ligand binding of artificially evolved peptides to the polymer.

Advances in the T7 phage display system (Review)

The present review describes the advantages and updated applications of the T7 phage display system in bioscience and medical science. Current phage display systems are based on various bacteriophage vectors, including M13, T7, T4 and f1. Of these, the M13 phage display is the most frequently used, however, the present review highlights the advantages of the T7 system. As a phage display platform, M13 contains single‑stranded DNA, while the T7 phage consists of double‑stranded DNA, which exhibits increased stability and is less prone to mutation during replication. Additional characteristics of the T7 phage include the following: The T7 phage does not depend on a protein secretion pathway in the lytic cycle; expressed peptides and proteins are usually located on the C‑terminal region of capsid protein gp10B, which avoids problems associated with steric hindrance; and T7 phage particles exhibit high stability under various extreme conditions, including high temperature and low pH, which facilitates effective high‑throughput affinity elutriation. Recent applications of the T7 phage display system have been instrumental in uncovering mechanisms of molecular interaction, particularly in the fields of antigen discovery, vaccine development, protein interaction, and cancer diagnosis and treatment.

Virus-Derived Peptides for Clinical Applications

Novel affinity agents with high specificity are needed to make progress in disease diagnosis and therapy. Over the last several years, peptides have been considered to have fundamental benefits over other affinity agents, such as antibodies, due to their fast blood clearance, low immunogenicity, rapid tissue penetration, and reproducible chemical synthesis. These features make peptides ideal affinity agents for applications in disease diagnostics and therapeutics for a wide variety of afflictions. Virus-derived peptide techniques provide a rapid, robust, and high-throughput way to identify organism-targeting peptides with high affinity and selectivity. Here, we will review viral peptide display techniques, how these techniques have been utilized to select new organism-targeting peptides, and their numerous biomedical applications with an emphasis on targeted imaging, diagnosis, and therapeutic techniques. In the future, these virus-derived peptides may be used as common diagnosis and therapeutics tools in local clinics.

Bacteriophages in the human gut: Our fellow travelers throughout life and potential biomarkers of heath or disease

The gastrointestinal (GI) tract is populated by a huge variety of viruses. Bacterial viruses (bacteriophages) constitute the largest and the most unrecognized part of virome. The total bacteriophage community of the human gut is called phageome. Phages colonize the gut from the earliest moments of life and become our fellow travelers throughout life. Phageome seems to be unique to each individual and shows a high degree of interpersonal variation. In the healthy gut, a vast majority of phages have a lysogenic lifestyle. These prophages serve as a major respository of mobile genetic elements in the gut and play key roles in the exchange of genetic material between bacterial species via horizontal gene transfer (HGT). But, imbalance in the gut microbial community during dysbiosis, caused by diseases or environmental stresses such as antibiotics, is accompanied by induction of prophages leading to a decreased ratio of symbionts to pathobionts. Based on this, a diseased gut is transformed from an environment predominantly occupied by prophages to an ecosystem mostly inhabited by lytic phages. A growing body of evidence has provided support for the notion that phageome structure and composition change dependent on the physiological or pathological status of the body. This has been demonstrated by pronounced quantitative and qualitative differences between the phageome of healthy individuals and patients. Although many aspects of the contribution made by phages to human biology remain to be understood, recent findings favor the suggestion that phageome might represent potential to serve as a biomarker of health or disease.

A novel serum microRNA-based identification and classification biomarker of human glioma

Malignant glioma is one of the most common primary brain tumors that develop via multiple pathways and gene deregulation. MicroRNAs are involved in human cancer development and progression, and their serum expression profiles of glioma patients may be useful for classifying cancers. However, the profile and molecular mechanism of serum microRNAs for human glioma are poorly understood. Thus, it is crucial to analyze microRNA expression in human glioma serum to identify molecular subclasses and early stage of glioma. In this study, we performed microRNA alteration that contributes to glioma profile via analysis of The Cancer Genome Atlas RNA sequencing data and other independent Gene Expression Omnibus microarray data. We identified the glioma-associated novel microRNA as a key regulator of human glioma development and progression. The putative novel miR-1825 was validated by real-time polymerase chain reaction and its expression was significantly decreased in the serum of glioma patients compared with healthy controls. Patients with high miR-1825 expression had a longer survival rate. Interestingly, we found that miR-1825 expression levels were dependent on tumor size and pathological grading in glioma patients, but not associated with other factors including age and T classification. MicroRNA-Gene Ontology network indicated that miR-1825 may play an important role in the development of human glioma including apoptosis, cell proliferation, and invasion. In vitro assays of miR-1825 inhibit U87 cell proliferation and invasion and induce apoptosis. Furthermore, we provide evidence that the tumor-suppressive microRNA miR-1825 controls KLF2 expression. Reporter gene analyses revealed that both microRNAs directly targeted the 3'-untranslated region of KLF2 messenger RNA. These data demonstrated that miR-1825 expression in serum of human glioma was associated with tumorigenesis and miR-1825 may be used as a biomarker for identification of the pathological grade of glioma.

Development of Engineered Bacteriophages for Escherichia coli Detection and High-Throughput Antibiotic Resistance Determination

T7 bacteriophages (phages) have been genetically engineered to carry the lacZ operon, enabling the overexpression of beta-galactosidase (β-gal) during phage infection and allowing for the enhanced colorimetric detection of Escherichia coli (E. coli). Following the phage infection of E. coli, the enzymatic activity of the released β-gal was monitored using a colorimetric substrate. Compared with a control T7 phage, our T7_lacZ phage generated significantly higher levels of β-gal expression following phage infection, enabling a lower limit of detection for E. coli cells. Using this engineered T7_lacZ phage, we were able to detect E. coli cells at 10 CFU·mL^-1 within 7 h. Furthermore, we demonstrated the potential for phage-based sensing of bacteria antibiotic resistance profiling using our T7_lacZ phage, and subsequent β-gal expression to detect antibiotic resistant profile of E. coli strains.