Engineering the Protein Corona Structure on Gold Nanoclusters Enables Red-Shifted Emissions in the Second Near-infrared Window for Gastrointestinal Imaging.

The application of NIR-II emitters for gastrointestinal (GI) tract imaging remains challenging due to fluorescence quenching in the digestive microenvironment. Herein, we report that red-shifting of the fluorescence emission of Au nanoclusters (AuNCs) into NIR-II region with improved quantum yields (QY) could be achieved by engineering a protein corona structure consisting of a ribonuclease-A (RNase-A) on the particle surfaces. RNase-A-encapsulated AuNCs (RNase-A@AuNCs) displayed emissions at 1050 nm with a 1.9 % QY. Compared to rare earth and silver-based NIR-II emitters, RNase-A@AuNCs had excellent biocompatibility, showing >50-fold higher sensitivity in GI tract, and migrated homogenously during gastrointestinal peristalsis to allow visualization of the detailed structures of the GI tract. RNase-A@AuNCs could successfully examine intestinal tumor mice from healthy mice, indicating a potential utility for early diagnosis of intestinal tumors.

Correction: Fluorescence detection of three types of pollutants based on fluorescence resonance energy transfer and its comparison with colorimetric detection.

[This corrects the article DOI: 10.1039/D3RA02647G.].

Effects of short-term florfenicol exposure on the gene expression pattern, midgut microbiota, and metabolome in the lepidopteran model silkworm (Bombyx mori).

Florfenicol (FF), an alternative veterinary antibiotic for chloramphenicol, has been widely utilized in livestock breeding to prevent and treat bacterial diseases. However, the toxicological effects of FF have yet to be fully disclosed. The domesticated silkworm (Bombyx mori), a lepidopteran model, was selected to assess the toxicological effects of FF dietary exposure with multi-omics. The findings showed that high-dose (250 µg/L) FF exposure increased the whole cocoon weight. High-dose FF exposure affected the species richness and community diversity of the microbiota in the silkworm midgut. Biochemical processes and innate immunity were impacted by FF exposure. The KEGG pathways impacted by the midgut microbiota and their metabolites were compared, and several pathways were found to be related to the two ecosystems. In addition, the innate immunity and lipid metabolism pathways were impacted, and some of the differentially expressed genes were enriched in these pathways. These related pathways may involve crosstalk between the midgut microbiota shift, midgut biological functions, and global gene expression. Therefore, our study also advances the application of the silkworm larval model in assessing antibiotic metabolic toxicity and provides novel insights into the potential risks of FF.

Fluorescence detection of three types of pollutants based on fluorescence resonance energy transfer and its comparison with colorimetric detection.

This study aimed at three representative pollutants, benzidine, cyromazine, and streptomycin, which were commonly used and posed a great threat to both environment and human health, mainly to explore a fast, simple, sensitive, visible naked-eye detection method. Colorimetric detection by gold nanoparticles (AuNPs) was first attempted. The cross-linking reaction occurred owing to the strong forces between the targets and AuNPs, leading to aggregation and color change. However, large-scale aggregation was easily formed and settled, which failed to achieve accurate quantification. Thus, AuNPs are considered to be used in fluorescence detection as reaction bridges. The introduction of AuNPs could effectively quench the fluorescence of Rhodamine B based on fluorescence resonance energy transfer (FRET). Moreover, a classical "on-off-on" fluorescence detection system was constructed based on nanomaterials. When AuNPs were added, the red fluorescence of the Rhodamine B solution could be effectively quenched (the "off" reaction). However, the tight cross-linking reaction between the three targets and AuNPs occurred through the strong affinity, causing Rhodamine B to dissociate in the solution. The fluorescence was rapidly restored, accompanied by a significant enhancement of fluorescence intensity (the "on" reaction). The fluorescent responses toward the three targets were established, resulting in good linearity in a wide range with low detection limits. Moreover, through the investigation of specificity, the fluorescence sensor exhibited satisfying selectivity and high binding affinity to the detected targets among the same types of inferences, indicating great potential for practical application. This simple, fast and sensitive fluorescence detection system was first used for simultaneously detecting three types of pollutants and finally successfully applied to real samples.

The effects of short-term dietary exposure to SiO2 nanoparticle on the domesticated lepidopteran insect model silkworm (Bombyx mori): Evidence from the perspective of multi-omics.

Silicon dioxide nanoparticles (nSiO2) are one of the widely utilized nanoparticle (NPSs) materials, and exposure to nSiO2 is ubiquitous. With the increasing commercialization of nSiO2, the potential risk of nSiO2 release to the health and the ecological environment have been attracted more attention. In this study, the domesticated lepidopteran insect model silkworm (Bombyx mori) was utilized to evaluate the biological effects of dietary exposure to nSiO2. Histological investigations showed that nSiO2 exposure resulted in midgut tissue injury in a dose-dependent manner. Larval body mass and cocoon production were reduced by nSiO2 exposure. ROS burst was not triggered, and the activities of antioxidant enzymes were induced in the midgut of silkworm exposure to nSiO2. RNA-sequencing revealed that the differentially expressed genes induced by nSiO2 exposure were predominantly enriched into xenobiotics biodegradation and metabolism, lipid, and amino acid metabolism pathways. 16 S rDNA sequencing revealed that nSiO2 exposure altered the microbial diversity in the gut of the silkworm. Metabolomics analysis showed that the combined uni- and multivariate analysis identified 28 significant differential metabolites from the OPLS-DA model. These significant differential metabolites were predominantly enriched into the metabolic pathways, including purine metabolism and tyrosine metabolism and so. Spearman correlation analysis and the Sankey diagram established the relationship between microbe and metabolites, and some genera may play crucial and pleiotropic functions in the interaction between microbiome and host. These findings indicated that nSiO2 exposure could impact the dysregulation of genes related to xenobiotics metabolism, gut dysbiosis, and metabolic pathways and provided a valuable reference for assessing nSiO2 toxicity from a multi-dimensional perspective.

Bacterial glyphosate resistance conferred by overexpression of an E. coli membrane efflux transporter.

Glyphosate herbicide-resistant crop plants, introduced commercially in 1994, now represent approximately 85% of the land area devoted to transgenic crops. Herbicide resistance in commercial glyphosate-resistant crops is due to expression of a variant form of a bacterial 5-enolpyruvylshikimate-3-phosphate synthase with a significantly decreased binding affinity for glyphosate at the target site of the enzyme. As a result of widespread and recurrent glyphosate use, often as the only herbicide used for weed management, increasing numbers of weedy species have evolved resistance to glyphosate. Weed resistance is most often due to changes in herbicide translocation patterns, presumed to be through the activity of an as yet unidentified membrane transporter in plants. To provide insight into glyphosate resistance mechanisms and identify a potential glyphosate transporter, we screened Escherichia coli genomic DNA for alternate sources of glyphosate resistance genes. Our search identified a single non-target gene that, when overexpressed in E. coli and Pseudomonas, confers high-level glyphosate resistance. The gene, yhhS, encodes a predicted membrane transporter of the major facilitator superfamily involved in drug efflux. We report here that an alternative mode of glyphosate resistance in E. coli is due to reduced accumulation of glyphosate in cells that overexpress this membrane transporter and discuss the implications for potential alternative resistance mechanisms in other organisms such as plants.

BRCAA1 monoclonal antibody conjugated fluorescent magnetic nanoparticles for in vivo targeted magnetofluorescent imaging of gastric cancer.

BACKGROUND: Gastric cancer is 2th most common cancer in China, and is still the second most common cause of cancer-related death in the world. How to recognize early gastric cancer cells is still a great challenge for early diagnosis and therapy of patients with gastric cancer. This study is aimed to develop one kind of multifunctional nanoprobes for in vivo targeted magnetofluorescent imaging of gastric cancer. METHODS: BRCAA1 monoclonal antibody was prepared, was used as first antibody to stain 50 pairs of specimens of gastric cancer and control normal gastric mucous tissues, and conjugated with fluorescent magnetic nanoparticles with 50 nm in diameter, the resultant BRCAA1-conjugated fluorescent magnetic nanoprobes were characterized by transmission electron microscopy and photoluminescence spectrometry, as-prepared nanoprobes were incubated with gastric cancer MGC803 cells, and were injected into mice model loaded with gastric cancer of 5 mm in diameter via tail vein, and then were imaged by fluorescence optical imaging and magnetic resonance imaging, their biodistribution was investigated. The tissue slices were observed by fluorescent microscopy, and the important organs such as heart, lung, kidney, brain and liver were analyzed by hematoxylin and eosin (HE) stain method. RESULTS: BRCAA1 monoclonal antibody was successfully prepared, BRCAA1 protein exhibited over-expression in 64% gastric cancer tissues, no expression in control normal gastric mucous tissues, there exists statistical difference between two groups (P < 0.01). The BRCAA1-conjugated fluorescent magnetic nanoprobes exhibit very low-toxicity, lower magnetic intensity and lower fluorescent intensity with peak-blue-shift than pure FMNPs, could be endocytosed by gastric cancer MGC803 cells, could target in vivo gastric cancer tissues loaded by mice, and could be used to image gastric cancer tissues by fluorescent imaging and magnetic resonance imaging, and mainly distributed in local gastric cancer tissues within 12 h post-injection. HE stain analysis showed that no obvious damages were observed in important organs. CONCLUSIONS: The high-performance BRCAA1 monoclonal antibody-conjugated fluorescent magnetic nanoparticles can target in vivo gastric cancer cells, can be used for simultaneous magnetofluorescent imaging, and may have great potential in applications such as dual-model imaging and local thermal therapy of early gastric cancer in near future.

Innovative Systems to Deliver Allergen Powder for Epicutaneous Immunotherapy.

Allergy is a disorder owing to hyperimmune responses to a particular kind of substance like food and the disease remains a serious healthcare burden worldwide. This unpleasant and sometimes fatal allergic disease has been tackled vigorously by allergen-specific immunotherapy over a century, but the progress made so far is far from satisfactory for some allergies. Herein, we introduce innovative, allergen powder-based epicutaneous immunotherapies (EPIT), which could potentially serve to generate a new stream of technological possibilities that embrace the features of super safety and efficacious immunotherapy by manipulating the plasticity of the skin immune system via sufficient delivery of not only allergens but also tolerogenic adjuvants. We attempt to lay a framework to help understand immune physiology of the skin, epicutaneous delivery of powdered allergy, and potentials for tolerogenic adjuvants. Preclinical and clinical data are reviewed showing that deposition of allergen powder into an array of micropores in the epidermis can confer significant advantages over intradermal or subcutaneous injection of aqueous allergens or other epicutaneous delivery systems to induce immunological responses toward tolerance at little risk of anaphylaxis. Finally, the safety, cost-effectiveness, and acceptability of these novel EPITs are discussed, which offers the perspective of future immunotherapies with all desirable features.

Thermosensitive and Conductive Hybrid Polymer for Real-Time Monitoring of Spheroid Growth and Drug Responses.

Three-dimensional (3D) cell culture based on polymer scaffold provides a promising tool to mimic a physiological microenvironment for drug testing; however, the next-generation cell activity monitoring technology for 3D cell culture is still challenging. Conventionally, drug efficacy evaluation and cell growth heavily rely on cell staining assays, using optical devices or flow cytometry. Here, we report a dual-function polymer scaffold (DFPS) composed of thermosensitive, silver flake- and gold nanoparticle-decorated polymers, enabling conductance change upon cell proliferation or death for in situ cell activity monitoring and drug screening. The cell activity can be quantitatively monitored via measuring the conductance change induced by polymeric network swelling or shrinkage. This novel dual-function system (1) provides a 3D microenvironment to enable the formation and growth of tumor spheroid in vitro and streamlines the harvesting of tumor spheroids through the thermosensitive scaffold and (2) offers a simple and direct quantitative method to monitor 3D cell culture in situ for drug responses. As a proof of concept, we demonstrated that a breast cancer stem cell line MDA-MB-436 was able to form cell spheroids in the scaffold, and the conductance change of the sensor exhibited a linear relationship with cell concentration. To examine its potential in drug screening, cancer spheroids in the cell sensor were treated with paclitaxel (PTX) and docetaxel (DTX), and predicted quantitative evaluation of the cytotoxic effect of drugs was established. Our results indicated that this cell sensing system may hold promising potential in expanding into an array device for high-throughput drug screening.

Bacteria-specific phototoxic reactions triggered by blue light and phytochemical carvacrol.

Development of alternatives to antibiotics is one of the top priorities in the battle against multidrug-resistant (MDR) bacterial infections. Here, we report that two naturally occurring nonantibiotic modalities, blue light and phytochemical carvacrol, synergistically kill an array of bacteria including their planktonic forms, mature biofilms, and persisters, irrespective of their antibiotic susceptibility. Combination but not single treatment completely or substantially cured acute and established biofilm-associated Acinetobacter baumannii and methicillin-resistant Staphylococcus aureus infections of full thickness murine third-degree burn wounds and rescued mice from lethal Pseudomonas aeruginosa skin wound infections. The combined therapy diminished bacterial colony-forming units as high as 7.5 log10 within 30 min and introduced few adverse events in the survival of cocultured mammalian cells, wound healing, or host DNA. Mechanistic studies revealed that carvacrol was photocatalytically oxidized into a series of photoreactive substrates that underwent photolysis or additional photosensitization reactions in response to the same blue light, forming two autoxidation cycles that interacted with each other resulting in robust generation of cytotoxic reactive oxygen species. This phototoxic reaction took place exclusively in bacteria, initiated by blue light excitation of endogenous porphyrin-like molecules abundantly produced in bacteria compared with mammalian cells. Moreover, no bacterial resistance developed to the combined treatment after 20 successive passages. This highly selective phototoxic reaction confers a unique strategy to combat the growing threat of MDR bacteria.

Microneedles for transdermal diagnostics: Recent advances and new horizons.

Point-of-care testing (POCT), defined as the test performed at or near a patient, has been evolving into a complement to conventional laboratory diagnosis by continually providing portable, cost-effective, and easy-to-use measurement tools. Among them, microneedle-based POCT devices have gained increasing attention from researchers due to the glorious potential for detecting various analytes in a minimally invasive manner. More recently, a novel synergism between microneedle and wearable technologies is expanding their detection capabilities. Herein, we provide an overview on the progress in microneedle-based transdermal biosensors. It covers all the main aspects of the field, including design philosophy, material selection, and working mechanisms as well as the utility of the devices. We also discuss lessons from the past, challenges of the present, and visions for the future on translation of these state-of-the-art technologies from the bench to the bedside.

Photon induced quantum yield regeneration of cap-exchanged CdSe/CdS quantum rods for ratiometric biosensing and cellular imaging.

Full water-dispersion of commercial hydrophobic CdSe/CdS core/shell quantum rods (QRs) was achieved by cap-exchange using a dihydrolipoic acid zwitterion ligand at a low ligand:QR molar ratio (LQMR) of 1000. However, this process almost completely quenched the QR fluorescence, greatly limiting its potential in downstream fluorescence based applications. Fortunately, we found that the QR fluorescence could be recovered by exposure to near ultra-violet to blue light radiation (e.g. 300-450 nm). These "reborn" QRs were found to be compact, bright, and stable, and were resistant to non-specific adsorption, which make them powerful fluorescent probes in broad biomedical applications. We demonstrated their potential in two model applications: first, the QRs were conjugated with His8-tagged small antibody mimetic proteins (also known as Affimers) for the sensitive detection of target proteins via a Förster resonance energy transfer (FRET) readout strategy and second, the QR surface was functionalized with biotins for targeted imaging of cancer cells.

Ultrasonically Patterning Silver Nanowire-Acrylate Composite for Highly Sensitive and Transparent Strain Sensors Based on Parallel Cracks.

It has long been a challenge to develop strain sensors with large gauge factor (GF) and high transparency for a broad strain range, to which field silver nanowires (AgNWs) have recently been applied. A dense nanowire (NW) network benefits achieving large stretchability, while a sparse NW network favors realizing high transparency and sensitive response to small strains. Herein, a patterned AgNW-acrylate composite-based strain sensor is developed to circumvent the above trade-off issue via a novel ultrasonication-based patterning technique, where a water-soluble, UV-curable acrylate composite was blended with AgNWs as both a tackifier and a photoresist for finely patterning dense AgNWs to achieve high transparency, while maintaining good stretchability. Moreover, the UV-cured AgNW-acrylate patterns are brittle and capable of forming parallel cracks which effectively evade the Poisson effect and thus increase the GF by more than 200-fold compared to that of the bulk AgNW film-based strain sensor. As a result, the AgNW-based strain sensor possesses a GF of ∼10,486 at a large strain (8%), a high transparency of 90.3%, and a maximum stretchability of 20% strain. The precise monitoring of human radial pulse and throat movements proves the great potential of this sensor as a measurement module for wearable healthcare systems.

Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis.

PDZ domains are found in many signaling proteins. One of their functions is to provide scaffolds for forming membrane-associated protein complexes by binding to the carboxyl termini of their partners. PDZ domains are thought also to play a signal transduction role by propagating the information that binding has occurred to remote sites. In this study, a molecular dynamics (MD) simulation-based approach, referred to as an interaction correlation analysis, is applied to the PDZ2 domain to identify the possible signal transduction pathways. A residue correlation matrix is constructed from the interaction energy correlations between all residue pairs obtained from the MD simulations. Two continuous interaction pathways, starting at the ligand binding pocket, are identified by a hierarchical clustering analysis of the residue correlation matrix. One pathway is mainly localized at the N-terminal side of helix alpha1 and the adjacent C-terminus of loop beta1-beta2. The other pathway is perpendicular to the central beta-sheet and extends toward the side of PDZ2 domain opposite to the ligand binding pocket. The results complement previous studies based on multiple sequence analysis, NMR, and MD simulations. Importantly, they reveal the energetic origin of the long-range coupling. The PDZ2 results, as well as the earlier rhodopsin analysis, show that the interaction correlation analysis is a robust approach for determining pathways of intramolecular signal transduction.

The signaling pathway of rhodopsin.

The signal-transduction mechanism of rhodopsin was studied by molecular dynamics (MD) simulations of the high-resolution, inactive structure in an explicit membrane environment. The simulations were employed to calculate equal-time correlations of the fluctuating interaction energy of residue pairs. The resulting interaction-correlation matrix was used to determine a network that couples retinal to the cytoplasmic interface, where transducin binds. Two highly conserved motifs, D(E)RY and NPxxY, were found to have strong interaction correlation with retinal. MD simulations with restraints on each transmembrane helix indicated that the major signal-transduction pathway involves the interdigitating side chains of helices VI and VII. The functional roles of specific residues were elucidated by the calculated effect of retinal isomerization from 11-cis to all-trans on the residue-residue interaction pattern. It is suggested that Glu134 may act as a "signal amplifier" and that Asp83 may introduce a threshold to prevent background noise from activating rhodopsin.

Comprehensive Stability Improvement of Silver Nanowire Networks via Self-Assembled Mercapto Inhibitors.

Instability of silver nanowire (AgNW) has been regarded as a major obstacle to its practical applications in optoelectrical devices as transparent electrodes. Physical barrier layers such as polymer, metal, and graphene have been generally employed to improve the stability of AgNW in previous study. Herein, we first report self-assembled organothiols as an inhibitor for AgNW to achieve an overall enhancement in antioxidation, antisulfidation, thermal stability, and anti-electromigration. The self-assembled monolayers (SAMs) of phenyl azoles, methoxy silane, and methyl alkane were formed on the surface of AgNW via Ag-S covalent bond as barrier layers which provided protective effects against corrosives (e.g., O2, H2S). In particular, the decoration of 2-mercaptobenzimidazole (MBI) offered the best resistance to H2S and excellent stability under a high-temperature and high-humidity environment (85 °C and 85 RH %) for 4 months. Moreover, different SAMs exhibited a stabilizing or destabilizing effect on Plateau-Rayleigh instability of AgNW, which realized the tunability of degradation temperature of AgNWs, for example, increasing by ≥100 °C with MBI SAM or decreasing by ∼50 °C with octadecanethiol SAM compared with pristine AgNWs. Notably, the MBI-decorated AgNWs could survive at 400 °C which is by far the highest bearing temperature for solution-processed AgNW film. As a result, a transparent heater made of the MBI-AgNWs exhibited superior heating characteristics (higher working temperature and durability), as compared with the pristine AgNW-based heater. Our findings on the organothiols decoration not only provide a new paradigm in overall stability improvement of NW of noble metals but also show the potential in morphology controllability of metal NW.

The allosteric mechanism of yeast chorismate mutase: a dynamic analysis.

The effector-regulated allosteric mechanism of yeast chorismate mutase (YCM) was studied by normal mode analysis and targeted molecular dynamics. The normal mode analysis shows that the conformational change between YCM in the R state and in the T state can be represented by a relatively small number of low-frequency modes. This suggests that the transition is coded in the structure and is likely to have a low energetic barrier. Quantitative comparisons (i.e. frequencies) between the low-frequency modes of YCM with and without effectors (modeled structures) reveal that the binding of Trp increases the global flexibility, whereas Tyr decreases global flexibility. The targeted molecular dynamics simulation of substrate analog release from the YCM active site suggests that a series of residues are critical for orienting and "recruiting" the substrate. The simulation led to the switching of a series of substrate-release-coupled salt-bridge partners in the ligand-binding domain; similar changes occur in the transition between YCM R-state and T-state crystal structures. Thus, the normal mode analysis and targeted molecular dynamics results provide evidence that the effectors regulate YCM activity by influencing the global flexibility. The change in flexibility is coupled to the binding of substrate to the T state and release of the product from the R state, respectively.

Ultraefficient Cap-Exchange Protocol To Compact Biofunctional Quantum Dots for Sensitive Ratiometric Biosensing and Cell Imaging.

An ultraefficient cap-exchange protocol (UCEP) that can convert hydrophobic quantum dots (QDs) into stable, biocompatible, and aggregation-free water-dispersed ones at a ligand:QD molar ratio (LQMR) as low as 500, some 20-200-fold less than most literature methods, has been developed. The UCEP works conveniently with air-stable lipoic acid (LA)-based ligands by exploiting tris(2-carboxylethyl phosphine)-based rapid in situ reduction. The resulting QDs are compact (hydrodynamic radius, Rh, < 4.5 nm) and bright (retaining > 90% of original fluorescence), resist nonspecific adsorption of proteins, and display good stability in biological buffers even with high salt content (e.g., 2 M NaCl). These advantageous properties make them well suited for cellular imaging and ratiometric biosensing applications. The QDs prepared by UCEP using dihydrolipoic acid (DHLA)-zwitterion ligand can be readily conjugated with octa-histidine (His8)-tagged antibody mimetic proteins (known as Affimers). These QDs allow rapid, ratiometric detection of the Affimer target protein down to 10 pM via a QD-sensitized Förster resonance energy transfer (FRET) readout signal. Moreover, compact biotinylated QDs can be readily prepared by UCEP in a facile, one-step process. The resulting QDs have been further employed for ratiometric detection of protein, exemplified by neutravidin, down to 5 pM, as well as for fluorescence imaging of target cancer cells.

Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis.

Fatty acid synthase (FAS) is a 550 kDa homodimeric enzyme with multiple functional and structural domains. Normal mode analysis of a previously determined 19 A structure of FAS suggested that this enzyme might assume different conformational states with several distinct hinge movements. We have used a simultaneous multiple-model refinement method to search for the presence of the structural conformers from the electron images of FAS. We have demonstrated that the resulting models observed in the electron images are consistent with the predicted conformational changes. This technique demonstrates the potential of the combination of normal mode analysis with multiple model refinement to elucidate the multiple conformations of flexible proteins. Since each of these structures is based on a more homogeneous particle set, this technique has the potential, provided that sufficient references are used, to improve the resolution of the final reconstructions of single particles from electron cryomicroscopy.

Facile synthesis of ß-lactoglobulin capped Ag2S quantum dots for in vivo imaging in the second near-infrared biological window.

Effective in vivo fluorescence imaging for cancer screening and diagnostics requires bright and biocompatible fluorophores whose emission can effectively penetrate biological tissues. Recent studies have confirmed that the second near-infrared window (NIR-II, 1000-1400 nm) is the most sensitive spectral range for in vivo imaging due to ultralow tissue absorption and autofluorescence. We report herein a facile synthesis of Ag2S quantum dots (QDs) that emit at ∼1100 nm using ß-lactoglobulin (ß-LG) as a biological template. The ß-LG protein coating improves water-solubility, faciliates rapid biodistribution and reduces in vivo toxicity of the QDs. Compared to other currently used NIR emitters, ß-LG capped Ag2S QDs exhibit superior photostability and biocompatibility, making them promising probes for in vivo NIR-II imaging.