Organic Fluorophores with Large Stokes Shift for the Visualization of Rapid Protein and Nucleic Acid Assays.

Organic small-molecule fluorophores, characterized by flexible chemical structure and adjustable optical performance, have shown tremendous potential in biosensing. However, classical organic fluorophore motifs feature large overlap between excitation and emission spectra, leading to the requirement of advanced optical set up to filter desired signal, which limits their application in scenarios with simple settings. Here, a series of wavelength-tunable small-molecule fluorescent dyes (PTs) bearing simple organic moieties have been developed, which exhibit Stokes shift up to 262 nm, molar extinction coefficients ranged 30,000-100,000 M-1 cm-1, with quantum yields up to 54.8 %. Furthermore, these dyes were formulated into fluorescent nanoparticles (PT-NPs), and applied in lateral flow assay (LFA). Consequently, limit of detection for SARS-CoV-2 nucleocapsid protein reached 20 fM with naked eye, a 100-fold improvement in sensitivity compared to the pM detection level for colloidal gold-based LFA. Besides, combined with loop-mediated isothermal amplification (LAMP), the LFA system achieved the visualization of single copy level nucleic acid detection for monkeypox (Mpox).

A Novel Cell Membrane-Associated RNA Extraction Method and Its Application in the Discovery of Breast Cancer Markers.

Cell membrane-associated RNA (mem-RNA) has been demonstrated to be cell-specific and disease-related and are considered as potential biomarkers for disease diagnostics, drug delivery, and cell screening. However, there is still a lack of methods specifically designed to extract mem-RNA from cells, limiting the discovery and applications of mem-RNA. In this study, we propose the first all-in-one solution for high-purity mem-RNA isolation based on two types of magnetic nanoparticles, named MREMB (Membrane-associated RNA Extraction based on Magnetic Beads), which achieved ten times enrichment of cell membrane components and over 90% recovery rate of RNA extraction. To demonstrate MREMB's potential in clinical research, we extracted and sequenced mem-RNA of typical breast cancer MCF-7, MDA-MB-231, and SKBR-3 cell lines and non-neoplastic breast epithelial cell MCF-10A. Compared to total RNA, sequencing results revealed that membrane/secreted protein-encoding mRNAs and long noncoding RNAs (lncRNAs) were enriched in the mem-RNA, some of which were significantly overexpressed in the three cancer cell lines, including extracellular matrix-related genes COL5A1 and lncRNA TALAM1. The results indicated that MREMB could enrich membrane/secreted protein-coding RNA and amplify the expression differences of related RNAs between cancer and non-neoplastic cells, promising for cancer biomarker discovery.

Secrecy performance analysis in the FSO communication system considering different eavesdropping scenarios.

In this paper, we numerically study the secrecy performance of the free-space optical (FSO) system by considering different eavesdropping scenarios. More precisely, we considered three possible eavesdropping scenarios for Eve: 1) Eve is between Alice and Bob; 2) Eve and Bob are in the same receiving plane; 3) Eve is behind Bob. We adopt the Málaga (M)-distribution channel to model atmospheric turbulence due to the presence of link blockage while considering the non-zero boresight pointing error and path loss. To do so, we obtain a novel probability density function (PDF) and cumulative distribution function (CDF) under different eavesdropping scenarios, based on which we derived the secrecy outage probability (SOP) analytical expressions as well as their asymptotic expressions at a high SNR regime. We verified the results using Monte Carlo simulations, which showed that the parameters related to atmospheric turbulence and pointing errors, as well as the location of the eavesdropper, have different effects on different eavesdropping scenarios.

Amplification-free microRNA profiling with femtomolar sensitivity on a plasmonic enhanced fluorescence nano-chip.

MicroRNAs (miRNAs) are a class of small, non-coding RNA molecules involved in the regulation of gene expression, thus considered as promising biomarkers for cancer, cardiovascular diseases, neurodegenerative diseases, etc. However, quantitative analysis of miRNAs faces challenges owing to their high homology, small size & ultra-low abundance, and disease occurrence is often related to abnormal expression of multiple miRNAs where method for parallel miRNAs analysis is required. In this work, multiplexed analysis of miRNAs was established on a plasmonic nano-chip capable of fluorescence enhancement in the near-infrared region. Combined with polyadenylation at the hydroxyl terminate of target miRNA to afford abundant sites for fluorophore labeling, our assay achieved amplification-free detection of miRNAs from nM to fM with the limit of detection down to ca. 5 fM. A miRNA panel was constructed to detect 10 miRNAs differentially expressed in MCF-7 and A549 cell lines and validated with qRT-PCR, demonstrating the practical application of this method. This scalable platform can be customized for different miRNA panels, facilitating multiple miRNA profiling for various diseases.

Multiplexed discrimination of SARS-CoV-2 variants via plasmonic-enhanced fluorescence in a portable and automated device.

Portable assays for the rapid identification of lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to aid large-scale efforts in monitoring the evolution of the virus. Here we report a multiplexed assay in a microarray format for the detection, via isothermal amplification and plasmonic-gold-enhanced near-infrared fluorescence, of variants of SARS-CoV-2. The assay, which has single-nucleotide specificity for variant discrimination, single-RNA-copy sensitivity and does not require RNA extraction, discriminated 12 lineages of SARS-CoV-2 (in three mutational hotspots of the Spike protein) and detected the virus in nasopharyngeal swabs from 1,034 individuals at 98.8% sensitivity and 100% specificity, with 97.6% concordance with genome sequencing in variant discrimination. We also report a compact, portable and fully automated device integrating the entire swab-to-result workflow and amenable to the point-of-care detection of SARS-CoV-2 variants. Portable, rapid, accurate and multiplexed assays for the detection of SARS-CoV-2 variants and lineages may facilitate variant-surveillance efforts.

A nano-magnetic size selective cfDNA extraction platform for liquid biopsy with enhanced precision.

As an emerging biomarker, cell-free DNA (cfDNA) carries crucial genetic information for the diagnosis of hereditary disease and cancer. However, test accuracy was severely compromised by the low abundance of cell-free DNA in peripheral blood, frequently diluted by genomic DNA released from white blood cells, resulting in sample rejection, test inaccuracy, and restricted clinical utility. Herein we report a novel strategy for the efficient recovery of cfDNA with significant removal of genomic DNA contamination during the cfDNA extraction process, based on a nano-magnetic size selective cfDNA extraction platform. With this platform, over 90% cfDNA recovery rate was achieved with minimal genomic DNA contamination. For non-invasive prenatal testing, an increase of fetal fraction from 10.10% to 29.94% medially was observed in 11 maternal plasma samples, with two false-negative samples identified by the proposed workflow. Enrichment of cfDNA in plasma sample of cancer patient demonstrated âˆ¼ 100% increase of circulating tumor DNA (ctDNA) percentage by panel sequencing of specific mutation sites. The approach is simple, automatable and cost-efficient, can improve liquid biopsy precision and reduce sequencing depth through significant enrichment of target abundance. The nano-magnetic platform demonstrated its potential application in liquid biopsy, since it exhibited numerous advantages in avoiding false negative results, reducing sequencing cost, improving data quality, and rescuing contaminated samples.

Structural and electronic properties of SnO2 doped with non-metal elements.

Crystal structure and electronic properties of SnO2 doped with non-metal elements (F, S, C, B, and N) were studied using first-principles calculations. The theoretical results show that doping of non-metal elements cannot change the structure of SnO2 but result in a slight expansion of the lattice volume. The most obvious finding from the analysis is that F-doped SnO2 has the lowest defect binding energy. The doping with B and S introduced additional defect energy levels within the forbidden bandgap, which improved the crystal conductivity. The Fermi level shifts up due to the doping with B, F, and S, while the Fermi level of SnO2 doped with C or N has crossed the impurity level. The Fermi level of F-doped SnO2 is inside the conduction band, and the doped crystal possesses metallicity. The optical properties of SnO2 crystals doped with non-metal elements were analyzed and calculated. The SnO2 crystal doped with F had the highest reflectivity in the infrared region, and the reflectance of the crystals doped with N, C, S, and B decreased sequentially. Based on this theoretical calculations, F-doped SnO2 is found to be the best photoelectric material for preparing low-emissivity coatings.

Stable isotopes reveal the formation diversity of humic substances derived from different cotton straw-based materials.

Humic substances (HS) are essential in environment processes and carbon (C) sequestration in soils. In this study, organic materials such as cotton straw and its derived compost and biochar were added to the soil on a C-equivalent basis and incubated for 30 and 180 days in order to investigate the different forms of plant biomass derived C sequestration in HS. The C distribution in humic acid (HA), fulvic acid (FA), and humin (Hu) derived from organic materials was investigated using the 13C isotope method, while the catalase, sucrose, and ß-glucosidase activities were also determined. The results showed that C3 distribution of Hu derived from straw, compost and biochar increased from 40.94% to 67.12%, 74.47% and 80.75%, respectively. In addition, the increase of C3 distribution of HA or FA derived from straw, compost and biochar were 4.69%, 10.09% and 1.49%, respectively. There were significantly positive correlations between catalase, sucrase and ß-glucosidase activities and C3 derived HA and FA. The principal component analysis showed that catalase, sucrase and ß-glucosidase were explained mainly by the first principal component indicating a significant correlation. These findings suggest that straw, compost and biochar are mainly sequestrated in Hu. Comparatively, the straw and compost are more likely to contribute to the formation of HA and FA in soil, but biochar favors the Hu, which helps in soil C sequestration. The formation of HA and FA derived from organic materials was supported by catalase, sucrase and ß-glucosidase activities.

Mutual Effects of Fluorine Dopant and Oxygen Vacancies on Structural and Luminescence Characteristics of F Doped SnO2 Nanoparticles.

SnO2 and F doped SnO2 (FTO) nanoparticles (NPs) have been synthesized by the hydrothermal method with subsequent annealing at 500 °C. The microstructure and photoluminescence (PL) property of SnO2 and FTO NPs have been investigated, and an assumption model about the luminescence process of FTO NPs has been proposed. All of the SnO2 and FTO NPs possess polycrystalline tetragonal rutile structures, and the average size in the range of 16.5-20.2 nm decreases with the increasing of F doping content. The doping element F is shown a uniformly distribution by electron energy loss spectroscopy (EELS) mapping. The oxygen vacancy concentration becomes higher as is verified by Raman and X-ray photoelectron spectra (XPS). There are three kinds of oxygen chemical states in SnO2 and FTO NPs, in which Oα corresponds to oxygen vacancies. The room temperature PL position is observed to be independent of F doping content. F- may substitute O2- into the SnO2 lattice by generating F O + and one extra e-, which can combine with V O + or V O + + to generate V O 0 or V O + to ensure charge balance.