Differences in nature killer cell response and interference with mitochondrial DNA induced apoptosis in moxifloxacin environment.

OBJECTIVES: As antibiotics become more prevalent, accuracy and safety are critical. Moxifloxacin (MXF) have been reported to have immunomodulatory effects on a variety of immune cells and even anti-proliferative and pro-apoptotic effects, but the mechanism of action is not fully clear. METHODS: Peripheral blood mononuclear cells (PBMC) from experimental groups of healthy adults (n = 3) were treated with MXF (10ug/ml) in vitro for 24 h. Single-cell sequencing was performed to investigate differences in the response of each immune cell to MXF. Flow cytometry determined differential gene expression in subsets of most damaged NK cells. Pseudo-time analysis identified drivers that influence MXF-stimulated cell differentiation. Detection of mitochondrial DNA and its involvement in the mitochondrial respiratory chain pathway clarifies the origin of MXF-induced stress injury. RESULTS: Moxifloxacin-environmental NK cells are markedly reduced: a new subset of NK cells emerges, and immediate-early-response genes in this subset indicate the presence of an early activation response. The inhibitory receptor-dominant subset shows enhanced activation, leading to increased expression of cytokines and chemokines. The near-mature subset showed greater cytotoxicity and the most pronounced cellular damage. CD56bright cells responded by antagonizing the regulation of activation and inhibitory signals, demonstrating a strong cleavage capacity. The severe depletion of mitochondrial genes was focused on apoptosis induced by the mitochondrial respiratory chain complex. CONCLUSION: NK cells exhibit heightened sensitivity to the MXF environment. Different NK subsets upregulate the expression of cytokines and chemokines through different activation pathways. Concurrently, MXF induces impairment of the mitochondrial oxidative phosphorylation system, culminating in apoptosis.

Genetic and phenotypic profiling of single living circulating tumor cells from patients with microfluidics.

Accurate prediction of the efficacy of immunotherapy for cancer patients through the characterization of both genetic and phenotypic heterogeneity in individual patient cells holds great promise in informing targeted treatments, and ultimately in improving care pathways and clinical outcomes. Here, we describe the nanoplatform for interrogating living cell host-gene and (micro-)environment (NICHE) relationships, that integrates micro- and nanofluidics to enable highly efficient capture of circulating tumor cells (CTCs) from blood samples. The platform uses a unique nanopore-enhanced electrodelivery system that efficiently and rapidly integrates stable multichannel fluorescence probes into living CTCs for in situ quantification of target gene expression, while on-chip coculturing of CTCs with immune cells allows for the real-time correlative quantification of their phenotypic heterogeneities in response to immune checkpoint inhibitors (ICI). The NICHE microfluidic device provides a unique ability to perform both gene expression and phenotypic analysis on the same single cells in situ, allowing us to generate a predictive index for screening patients who could benefit from ICI. This index, which simultaneously integrates the heterogeneity of single cellular responses for both gene expression and phenotype, was validated by clinically tracing 80 non-small cell lung cancer patients, demonstrating significantly higher AUC (area under the curve) (0.906) than current clinical reference for immunotherapy prediction.

Rapid Cryptococcus electroporated-lysis and sensitive detection on a miniaturized platform.

Fast and accurate detection of Cryptococcus and precise differentiation of its subtypes is of great significance in protecting people from cryptococcal disease and preventing its spread in populations. However, traditional Cryptococcus identification and detection techniques still face significant challenges in achieving high analysis speed as well as high sensitivity. In this work, we report an electric microfluidic biochip. Compared to conventional methods that take several hours or even a day, this chip can detect Cryptococcus within 20 min, and achieve its maximum detection limit within 1 h, with the ability to differentiate between the Cryptococcus neoformans (NEO) and rare Cryptococcus gattii (GAT) efficiently, which accounts for nearly 100%. This device integrated two functional zones of an electroporation lysis (EL) zone for rapid cell lysis (<30 s) and an electrochemical detection (ED) zone for sensitive analysis of the released nucleic acids. The EL zone adopted a design of microelectrode arrays, which obtains a large electric field intensity at the constriction of the microchannel, addressing the safety concerns associated with high-voltage lysis. The device enables a limit of detection (LOD) of 60 pg/mL for NEO and 100 pg/mL for GAT through the modification of nanocomposites and specific probes. In terms of the detection time and sensitivity, the integrated microfluidic biochip demonstrates broad potential in Cryptococcus diagnosis and disease prevention.

Identification of lncRNA-based regulatory mechanisms of Takifugu rubripes growth traits in fast and slow-growing family lines.

Family selection is an important method in fish aquaculture because growth is the most important economic trait. Fast-and slow-growing families of tiger puffer fish (Takifugu rubripes) have been established through family selection. The development of teleost fish is primarily controlled by the growth hormone (GH)-insulin-like growth factor 1 (IGF-1) axis that includes the hypothalamus-pituitary-liver. In this study, the molecular mechanisms underlying T. rubripes growth were analyzed by comparing transcriptomes from fast- and slow-growing families. The expressions of 214 lncRNAs were upregulated, and those of 226 were downregulated in the brain tissues of the fast-growing T. rubripes family compared to those of the slow-growing family. Differentially expressed lncRNAs centrally regulate mitogen-activated protein kinase (MAPK) and forkhead box O (FoxO) signaling pathways. Based on the results of lncRNA-gene network construction, we found that lncRNA3133.13, lncRNA23169.1, lncRNA23145.1, and lncRNA23141.3 regulated all four genes (igf1, mdm2, flt3, and cwf19l1). In addition, lncRNA7184.10 may be a negative regulator of rasgrp2 and a positive regulator of gadd45ga, foxo3b, and dusp5. These target genes are associated with the growth and development of organisms through the PI3K/AKT and MAPK/ERK pathways. Overall, transcriptomic analyses of fast- and slow-growing families of T. rubripes provided insights into the molecular mechanisms of teleost fish growth rates. Further, these analyses provide evidence for key genes related to growth regulation and the lncRNA expression regulatory network that will provide a framework for improving puffer fish germplasm resources.

Sensitive, rapid detection of NCOA4-m6A towards precisely quantifying radiation dosage on a Cas13a-Microdroplet platform.

Precise quantification of low-dose ionizing radiation is of great significance in protecting people from damage caused by clinical radiotherapy or environmental radiation. Traditional techniques for detecting radiation, however, remain extreme challenges to achieve high sensitivity and speed in quantifying radiation dosage. In this work, we report a Cas13a-Microdroplet platform that enables sensitive detection of ultra-low doses of radiation (0.5 Gy vs. 1 Gy traditional) within 1 h. The micro-platform adopts an ideal, specific radiation-sensitive marker, m6A on NCOA4 gene (NCOA4-m6A) that was first reported in our recent work. Microfluidics of the platform generate uniform microdroplets that encapsulate a CRISPR/Cas13a detection system and NCOA4-m6A target from the whole RNA extraction, achieving 10-fold enhancement in sensitivity and significantly reduced limit of detection (LOD). Systematic mouse models and clinical patient samples demonstrated its superior sensitivity and LOD (0.5 Gy) than traditional qPCR, which show wide potentials in radiation tracking and damage protection.

Performance enhancement of nitrogen-polar GaN-based light-emitting diodes prepared by metalorganic chemical vapor deposition.

Nitrogen-polar (N-polar) III-nitride materials have great potential for application in long-wavelength light-emitting diodes (LEDs). However, the poor quality of N-polar nitride materials hinders the development of N-polar devices. In this work, we report the enhanced performance of N-polar GaN-based LEDs with an optimized InGaN/GaN double quantum well (DQW) structure grown by metalorganic chemical vapor deposition. We improved the quality of the N-polar InGaN/GaN DQWs by elevating the growth temperature and introducing hydrogen as the carrier gas during the growth of the quantum barrier layers. N-polar LEDs prepared based on the optimized InGaN/GaN DQWs show significantly enhanced (by over 90%) external quantum efficiency and a weakened droop effect compared with a reference LED. More importantly, the optimized N-polar DQWs show a significantly longer emission wavelength than Ga-polar DQWs grown at the same QW growth temperature. This work provides a feasible approach to improving the quality of the N-polar InGaN/GaN QW structure, and it will promote the development of N-polar GaN-based long-wavelength light-emitting devices for micro-LED displays.

Companion-Probe & Race platform for interrogating nuclear protein and migration of living cells.

Probing nuclear protein expression while correlating cellular behavior is crucial for deciphering underlying causes of cellular disorders, such as tumor metastasis. Despite efforts to access nuclear proteins by trafficking the double barriers of cell membrane and nuclear membrane, they mostly fall short of the capacity for analyzing various proteins in different cells. Herein, we introduce a Companion-Probe & Race (CPR) platform that enables interrogating nuclear proteins in living cells, while guiding and tracking cellular behaviors (e.g., migration) in real time. The Companion-Probe consists of two polypeptide complexes that were structured with nuclear localization signal (NLS) for entering nucleus, recognition polypeptide for targeting different sites of nuclear proteins, and fragments of green fluorescent protein (GFP) that can recover a whole fluorescent GFP once the two polypeptide complexes combine with a same target protein. The two polypeptide complexes were expressed by two plasmids (named "probe plasmids") that were uniformly and efficiently delivered into cells by nano-electroporation (NEP), a high-performance delivery method for cell focal-poration and accelerated intracellular delivery. To track cell migration, multiple radial microchannels were designed with micro-landmarks on the platform to serve as addressable runways for cells. The proof-of-concept of CPR platform was validated with clinical primary cells that indicated the positive-correlation between nuclear protein murine double minute 2 (MDM2) expression level and cell migration velocity. This platform shows great promises to interrogate nuclear proteins in live cells, and to decode their roles in determining cellular behaviors on a chip.

A One-Step Electropolymerized Biomimetic Polypyrrole Membrane-Based Electrochemical Sensor for Selective Detection of Valproate.

Bipolar disorder is a chronic mental disease with a heavy social and economic burden that causes extreme mood swings in patients. Valproate is a first-line drug for bipolar disorder patients to stabilize their daily mood. However, an excessive amount of valproate in the blood could induce severe adverse effects, which necessitates the monitoring of blood valproate levels for patients. Here, we developed an innovative electrochemical sensor for selective and simple detection of valproate based on a molecularly imprinted polymer membrane via one-step electropolymerization. Gold nanoparticles were electrochemically modified to the screen-printed electrode under the selective membrane to enhance its conductivity and stability. The successfully fabricated biosensor was characterized by scanning electron microscopy, cyclic voltammetry, and differential pulse voltammetry methods. The binding of the target molecules to the valproate-customized biomimetic polypyrrole membrane blocks cavities in the membrane and alters its electric properties, which can be detected as a decrease in the peak current by differential pulse voltammetry method. The peak current change presents a great log-linear response to the valproate concentration around the therapeutic window. The limit of detection of this method was 17.48 µM (LOD, S/N = 3) and the sensitivity was 31.86 µM µA-1. Furthermore, the biosensors exhibited both satisfying specificity with the interference of other psychological pharmaceutical drugs and uniformity among sensors, indicating their potential and reliability in translational application. This simple and reliable method of sensing valproate molecules primarily provides an exceptional solution to valproate point-of-care testing in clinical practice.

Dual-band polarization-insensitive toroidal dipole quasi-bound states in the continuum in a permittivity-asymmetric all-dielectric meta-surface.

Ultra-high quality (Q) factor resonances derived from the bound states in the continuum (BICs) have drawn much attention in optics and photonics. Especially in meta-surfaces, they can enable ultrasensitive sensors, spectral filtering, and lasers because of their enhanced light-matter interactions and rare superiority of scalability. In this paper, we propose a permittivity-asymmetric all-dielectric meta-surface, comprising high-index cuboid tetramer clusters with symmetric structural parameters and configuring periodically on a glass substrate. Simulation results offer dual-band quasi-BICs with high Q values of 4447 and 11391, respectively. Multipolar decomposition in cartesian and electromagnetic distributions are engaged to analyze the physical mechanism of dual quasi-BIC modes, which reveals that they are both governed by magnetic quadrupole (MQ) and in-plane toroidal dipole (TD). The polarization-insensitive and scalable characteristics are also investigated. Additionally, we appraise the sensing performances of the proposed structure. As an example, our work supports an uncommon route to design dual-band polarization-insensitive TD quasi-BICs resonators and facilitates their applications in optic and photonics, such as low-threshold lasers and sensing.

Single Living Cell Analysis Nanoplatform for High-Throughput Interrogation of Gene Mutation and Cellular Behavior.

The genetic heterogeneities in cancer cells pose challenges to achieving precise drug treatment in a widely applicable manner. Most single-cell gene analysis methods rely on cell lysis for gene extraction and identification, showing limited capacity to provide the correlation of genetic properties and real-time cellular behaviors. Here, we report a single living cell analysis nanoplatform that enables interrogating gene properties and drug resistance in millions of single cells. We designed a Domino-probe to identify intracellular target RNAs while releasing 10-fold amplified fluorescence signals. An on-chip addressable microwell-nanopore array was developed for enhanced electro-delivery of the Domino-probe and in situ observation of cell behaviors. The proof-of-concept of the system was validated in primary lung cancer cell samples, revealing the positive-correlation of the ratio of EGFR mutant cells with their drug susceptibilities. This platform provides a high-throughput yet precise tool for exploring the relationship between intracellular genes and cell behaviors at the single-cell level.

A lamin-like protein OsNMCP1 regulates drought resistance and root growth through chromatin accessibility modulation by interacting with a chromatin remodeller OsSWI3C in rice.

Lamin proteins in animals are implicated in important nuclear functions, including chromatin organization, signalling transduction, gene regulation and cell differentiation. Nuclear Matrix Constituent Proteins (NMCPs) are lamin analogues in plants, but their regulatory functions remain largely unknown. We report that OsNMCP1 is localized at the nuclear periphery in rice (Oryza sativa) and induced by drought stress. OsNMCP1 overexpression resulted in a deeper and thicker root system, and enhanced drought resistance compared to the wild-type control. An assay for transposase accessible chromatin with sequencing (ATAC-seq) analysis revealed that OsNMCP1-overexpression altered chromatin accessibility in hundreds of genes related to drought resistance and root growth, including OsNAC10, OsERF48, OsSGL, SNAC1 and OsbZIP23. OsNMCP1 can interact with SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodelling complex subunit OsSWI3C. The reported drought resistance or root growth-related genes that were positively regulated by OsNMCP1 were negatively regulated by OsSWI3C under drought stress conditions, and OsSWI3C overexpression led to decreased drought resistance. We propose that the interaction between OsNMCP1 and OsSWI3C under drought stress conditions may lead to the release of OsSWI3C from the SWI/SNF gene silencing complex, thus changing chromatin accessibility in the genes related to root growth and drought resistance.

Small-Sized Mg-Al LDH Nanosheets Supported on Silica Aerogel with Large Pore Channels: Textural Properties and Basic Catalytic Performance after Activation.

Layered double hydroxides (LDHs) have been widely used as an important subset of solid base catalysts. However, developing low-cost, small-sized LDH nanoparticles with enhanced surface catalytic sites remains a challenge. In this work, silica aerogel (SA)-supported, small-sized Mg-Al LDH nanosheets were successfully prepared by one-pot coprecipitation of Mg and Al ions in an alkaline suspension of crushed silica aerogel. The supported LDH nanosheets were uniformly dispersed in the SA substrate with the smallest average radial diameter of 19.2 nm and the thinnest average thickness of 3.2 nm, both dimensions being significantly less than those of the vast majority of LDH nanoparticles reported. The SA/LDH composites also showed large pore volume (up to 1.3 cm3·g) and pore diameter (>9 nm), and therefore allow efficient access of reactants to the edge catalytic sites of LDH nanosheets. In a base-catalyzed Henry reaction of benzaldehyde with nitromethane, the SA/LDH catalysts showed high reactant conversions and favorable stability in 6 successive cycles of reactions. The low cost of the SA carrier and LDH precursors, easy preparation method, and excellent catalytic properties make these SA/LDH composites a competitive example of solid-base catalysts.

Silica Aerogel-supported Hydrozincite and Carbonate-intercalated Hydrotalcite for High-efficiency Removal of Pb(II) Ions by Precipitation Transformation Reactions.

In this work, hydrozincite and Zn/Al-CO32- hydrotalcite supported on silica aerogel were prepared via a simple and economical process and used as adsorbents for Pb(II) removal. The supported hydrozincite and Zn/Al-CO32- hydrotalcite possess ultra-thin thickness, high surface area, and weak crystallinity. In the batch Pb(II) adsorption experiments, the adsorbents with higher Zn(II) contents showed higher Pb(II) adsorption capacities, and the adsorption data fitted well with the Langmuir isotherm model and pseudo-second-order kinetic model, indicating a mechanism of surface chemisorption. The adsorption capacities calculated based Langmuir isotherm model are 684.9 mg/g and 555.6 mg/g for the supported hydrozincite and Zn/Al-CO32- hydrotalcite, respectively, higher than the adsorption capacities of other hydrotalcite-based adsorbents and most of other inorganic adsorbents reported previously. The XRD diffraction peaks of hydrozincite and Zn/Al-CO32- hydrotalcite disappeared after the adsorption, and the Pb(II) species were uniformly dispersed in the adsorbents in form of Pb3(CO3)2(OH)2 proven by TEM, EDS mapping and XRD analysis, demonstrating the nature of the adsorption is the precipitation conversion of hydrozincite or Zn/Al-CO32- hydrotalcite into Pb3(CO3)2(OH)2. These results demonstrate the synergic Pb(II) removal effect of the CO32- and OH- derived from hydrozincite and Zn/Al-CO32- hydrotalcite together with their ultra-thin thickness and high surface area contribute the excellent properties of the adsorbents.

Synthesis and In Vitro Characterization of Fe3+-Doped Layered Double Hydroxide Nanorings as a Potential Imageable Drug Delivery System.

Highly dispersed Fe3+-doped layered double hydroxide (LDH-Fe) nanorings were obtained by a simple coprecipitation-acid etching approach. The morphology, structure, magnetic resonance imaging (MRI) performance in vitro, drug loading and releasing, Fe3+ leakage, and cytotoxicity of the as-prepared LDH-Fe nanorings were characterized. The LDH-Fe nanorings showed good water dispersity and a well-crystallized structure. The DLS average size of nanoparticles was measured to be 94.5 nm. Moreover, the MRI tests showed a favourable T1-weighted MRI performance of the LDH-Fe nanoring with r1 values of 0.54 and 1.68, and low r2/r1 ratios of 10.1 and 6.3, pre- and after calcination, respectively. The nanoparticles also showed high model drug (ibuprofen) loading capacities, low Fe3+ leakage, and negligible cytotoxicity. All these results demonstrate the potential of LDH-Fe nanorings as an imageable drug delivery system.

Combining NMR and X-ray crystallography in fragment-based drug discovery: discovery of highly potent and selective BACE-1 inhibitors.

Fragment-based drug discovery (FBDD) has become increasingly popular over the last decade. We review here how we have used highly structure-driven fragment-based approaches to complement more traditional lead discovery to tackle high priority targets and those struggling for leads. Combining biomolecular nuclear magnetic resonance (NMR), X-ray crystallography, and molecular modeling with structure-assisted chemistry and innovative biology as an integrated approach for FBDD can solve very difficult problems, as illustrated in this chapter. Here, a successful FBDD campaign is described that has allowed the development of a clinical candidate for BACE-1, a challenging CNS drug target. Crucial to this achievement were the initial identification of a ligand-efficient isothiourea fragment through target-based NMR screening and the determination of its X-ray crystal structure in complex with BACE-1, which revealed an extensive H-bond network with the two active site aspartate residues. This detailed 3D structural information then enabled the design and validation of novel, chemically stable and accessible heterocyclic acylguanidines as aspartic acid protease inhibitor cores. Structure-assisted fragment hit-to-lead optimization yielded iminoheterocyclic BACE-1 inhibitors that possess desirable molecular properties as potential therapeutic agents to test the amyloid hypothesis of Alzheimer's disease in a clinical setting.

Discovery of cyclic acylguanidines as highly potent and selective beta-site amyloid cleaving enzyme (BACE) inhibitors: Part I--inhibitor design and validation.

A number of novel amidine containing heterocycles were designed to reproduce the unique interaction pattern, revealed by X-ray crystallography, between the BACE-1 catalytic diad and a weak NMR screening hit (3), with special attention paid to maintaining the appropriate basicity and limiting the number of H-bonding donors of these scaffolds. The iminohydantoin cores (10 and 23) were examined first and found to interact with the catalytic diad in one of two binding modes (A and B), each with the iminohydantoin core flipped 180 degrees in relation to the other. The amidine structural motif within each core forms a bidentate interaction with a different aspartic acid of the catalytic diad. Both modes reproduced a highly conserved interaction pattern between the inhibitors and the catalytic aspartates, as revealed by 3. Potent iminohydantoin BACE-1 inhibitors have been obtained, validating the molecular design as aspartyl protease catalytic site inhibitors. Brain penetrant small molecule BACE inhibitors with high ligand efficiencies have been discovered, enabling multiple strategies for further development of these inhibitors into highly potent, selective and in vivo efficacious BACE inhibitors.

Application of fragment-based NMR screening, X-ray crystallography, structure-based design, and focused chemical library design to identify novel microM leads for the development of nM BACE-1 (beta-site APP cleaving enzyme 1) inhibitors.

Fragment-based NMR screening, X-ray crystallography, structure-based design, and focused chemical library design were used to identify novel inhibitors for BACE-1. A rapid optimization of an initial NMR hit was achieved by a combination of NMR and a functional assay, resulting in the identification of an isothiourea hit with a K(d) of 15 microM for BACE-1. NMR data and the crystal structure revealed that this hit makes H-bond interactions with the two catalytic aspartates, occupies the nonprime side region of the active site of BACE-1, and extends toward the S3 subpocket (S3sp). A focused NMR-based search for heterocyclic isothiourea isosteres resulted in several distinct classes of BACE-1 active site directed compounds with improved chemical stability and physicochemical properties. The strategy for optimization of the 2-aminopyridine lead series to potent inhibitors of BACE-1 was demonstrated. The structure-based design of a cyclic acylguanidine lead series and its optimization into nanomolar BACE-1 inhibitors are the subject of the companion paper

Pyridine Carboxamides: Potent Palm Site Inhibitors of HCV NS5B Polymerase.

Pyridine carboxamide-based inhibitors of the hepatitis C virus (HCV) NS5B polymerase were diversified and optimized to a variety of topologically related scaffolds. In particular, the 2-methyl nicotinic acid scaffold was developed into inhibitors with improved biochemical (IC50-GT1b = 0.014 µM) and cell-based HCV replicon potency (EC50-GT1b = 0.7 µM). Biophysical and biochemical characterization identified this novel series of compounds as palm site binders to HCV polymerase.

Characterization of autocatalytic conversion of precursor BACE1 by heteronuclear NMR spectroscopy.

Accumulation of the cytotoxic 40- to 42-residue beta-amyloid peptide represents the primary pathological process in Alzheimer's disease (AD). BACE1 (beta-site APP cleaving enzyme 1) is responsible for the initial required step in the neuronal amyloidogenic processing of beta-amyloid precursor protein and is a major drug target for the therapeutic intervention of AD. In the present study, BACE1 is initially synthesized as an immature precursor protein containing part of the pre domain and the entire pro domain, and undergoes autocatalytic conversion to yield the well-folded mature BACE1 enzyme. To understand the mechanism of the conversion and the role of the pro domain, we monitored the autocatalytic conversion of BACE1 by heteronuclear NMR spectroscopy and used chemical shift perturbations as a probe to study the structural changes accompanying the autocatalytic conversion. NMR data revealed local conformational changes from a partially disordered to a well-folded conformation associated with the conversion. The conformational changes are largely concentrated in the NH(2)-terminal lobe. Conversely, the active site conformations are conserved during the autocatalytic conversion. The precursor and mature BACE1 proteins were further characterized for their ability to interact with a substrate-based transition state BACE1 peptide inhibitor. The precursor BACE1 rapidly adopted the bound conformation in the presence of the inhibitor, which is identical to the bound conformation of the mature protein. The interaction of the inhibitor with both the precursor BACE1 and the fully processed BACE1 is in slow exchange on the NMR time scale, indicating a tight binding interaction. Overall, the NMR data demonstrated that the pro domain does not hinder inhibitor binding and may assist in the proper folding of the protein. The fully processed BACE1 represents a high quality well-folded protein which is highly stable over a long period of time, and is suitable for evaluation of inhibitor binding by NMR for drug intervention.