G-Clamp Heterocycle Modification Containing Interstrand Photo-Cross-Linker to Capture Intracellular MicroRNA Targets.

MicroRNAs (miRNAs) play indispensable roles in post-transcriptional gene regulation. The identification of target mRNAs is essential for dissecting the recognition basis, dynamics, and regulatory mechanism of miRNA-mRNA interactions. However, the lack of an unbiased method for detecting weak miRNA-mRNA interactions remains a long-standing obstacle for miRNA research. Here, we develop and provide proof-of-concept evidence demonstrating a chemical G-clamp-enhanced photo-cross-linking strategy for covalent capture of intracellular miRNA targets in different cell lines. This approach relies on an aryl-diazirine-G-clamp-modified-nucleoside (ARAGON) miRNA probe containing an alkynyl group that improves the thermal stability of miRNA-target mRNA duplex molecules and can rapidly cross-link with the complementary strand upon UV 365 nm activation, enhancing the transient capture of mRNA targets. After validating the accuracy and binding properties of ARAGON-based miRNA probes through the successful enrichment for the known targets of miR-106a, miR-21, and miR-101, we then extend ARAGON's application to screen for previously unknown targets of different miRNAs in various cell lines. Ultimately, results in this study uncover GAB1 as a target of miR-101 in H1299 lung cancer cells and show that miR-101 silencing of GAB1 can promote apoptosis in H1299 cells, suggesting an oncogenic mechanism of GAB1. This study thus provides a powerful and versatile tool for enhanced screening of global miRNA targets in cells to facilitate investigations of miRNA functions in fundamental cellular processes and disease pathogenesis.

GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution.

N6-methyladenosine (m6A) is the most abundant posttranscriptional chemical modification in mRNA, involved in regulating various physiological and pathological processes throughout mRNA metabolism. Recently, we developed GLORI, a sequencing method that enables the production of a globally absolute-quantitative m6A map at single-base resolution. Our technique utilizes the glyoxal- and nitrite-based chemical reaction, which selectively deaminates unmethylated adenosines while leaving m6A intact. The RNA library can then be prepared using a modified library construction protocol from enhanced UV crosslinking and immunoprecipitation (eCLIP) or commercial kits. Here we provide a detailed protocol for proper RNA sample handling and provide further guidelines for the use of a tailored bioinformatics pipeline (GLORI-tools) for subsequent data analysis. Compared with current methods, this new method is both exceptionally sensitive and robust, capable of identifying ~80,000 m6A sites with 50 Gb sequencing data in mammalian cells. It also provides a quantitative readout for m6A sites at single-base resolution. We hope the technique will provide a precise and unbiased tool for investigating m6A biology across various fields. Basic expertise in molecular biology and knowledge of bioinformatics are required for the protocol. The entire procedure can be completed within a week, with the library construction process taking ~4 d.

Absolute quantification of single-base m6A methylation in the mammalian transcriptome using GLORI.

N6-methyladenosine (m6A) is the most abundant RNA modification in mammalian cells and the best-studied epitranscriptomic mark. Despite the development of various tools to map m6A, a transcriptome-wide method that enables absolute quantification of m6A at single-base resolution is lacking. Here we use glyoxal and nitrite-mediated deamination of unmethylated adenosines (GLORI) to develop an absolute m6A quantification method that is conceptually similar to bisulfite-sequencing-based quantification of DNA 5-methylcytosine. We apply GLORI to quantify the m6A methylomes of mouse and human cells and reveal clustered m6A modifications with differential distribution and stoichiometry. In addition, we characterize m6A dynamics under stress and examine the quantitative landscape of m6A modification in gene expression regulation. GLORI is an unbiased, convenient method for the absolute quantification of the m6A methylome.

Liquid-liquid phase equilibrium and the effect of a water-soluble polymer on the interaction between droplets in water-in-oil microemulsions.

The liquid-liquid phase equilibria of {water/PEG200/sodium bis(2-ethylhexyl)sulfosuccinate (AOT)/n-decane} with the molar ratio of water to AOT being 37.9 and various concentrations cPEG of PEG in water were measured in this study. The critical exponent ß corresponding to the width of the coexistence curve was determined, which showed good agreement with the 3D-Ising value and supported the proposal of the pseudo binary droplet solution for these multiple microemulsions. A previously developed thermodynamic approach based on the Carnahan-Starling-van der Waals type equation was improved and used to analyze the coexistence curve data of {water/PEG200/AOT/n-decane} microemulsions to deduce the interaction properties between droplets and further to investigate the effect of the additive PEG200 on these interactions. It was found that the addition of PEG200 into the {water/AOT/n-decane} microemulsion resulted in the decrease in the critical temperature and the interaction enthalpy and entropy. Both the interaction enthalpy and entropy decreased first, then increased with an increase of cPEG and had minimum values at cPEG = 25 g L-1, which showed the same tendency as the isothermal titration microcalorimetric results for the {water/PEG200/AOT/isooctane} microemulsion we reported very recently. The effects of the interaction enthalpy and the entropy on the phase separation and their dependences on cPEG were discussed and related to the effects of the additive on the rigidity of the interface layer of the microemulion droplet.

Liquid-Liquid Phase Equilibria and Interactions between Droplets in Water-in-Oil Microemulsions.

The liquid-liquid phase equilibria of [water/sodium bis(2-ethylhexyl)sulfosuccinate (AOT)/n-decane] with the molar ratio w0 of water to AOT being 37.9 and [water/AOT/ethoxylated-2,5,8,11-tetramethyl-6-dodecyne-5,8-diol(Dynol-604)/n-decane] with w0 = 37.9 and the mole fraction α of Dynol-604 in the total surfactants being 0.158 were measured in this study. From the data collected in the critical region, the critical exponent ß corresponding to the width of the coexistence curve was determined, which showed good agreement with the 3D-Ising value. A thermodynamic approach based on the Carnahan-Starling-van der Waals type equation was proposed to describe the coexistence curves and to deduce the interaction properties between droplets in the microemulsions. The interaction enthalpies were found to be positive for the studied systems, which evidenced that the entropy effect dominated the phase separations as the temperature increased. The addition of Dynol-604 into the (water/AOT/n-decane) microemulsion resulted in the decrease in the critical temperature and the interaction enthalpy. Combining the liquid-liquid equilibrium data for (water/AOT/n-decane) microemulsions with various w0 values determined previously, it was shown that the interaction enthalpy decreased with w0 and tended to change its sign at low w0, which coincided with the results from the isothermal titration calorimetry investigation. All of these behaviors were interpreted by the effects of entropy and enthalpy and their competition, which resulted from the release of solvent molecules entrapped in the interface of microemulsion droplets and were dependent on the rigidity of the surfactant layers and the size of the droplet.

Polypyrrole and graphene quantum dots @ Prussian Blue hybrid film on graphite felt electrodes: Application for amperometric determination of l-cysteine.

A novel polypyrrole (PPy) and graphene quantum dots (GQDs) @ Prussian Blue (PB) nanocomposite has been grafted on a graphite felt (GF) substrate (PPy/GQDs@PB/GF), and has been proven to be an efficient electrochemical sensor for the determination of l-cysteine (l-cys). GQDs, which were fabricated by carbonization of citric acid and adsorbed on GF surface ultrasonically, played an important role for promoting the synthesis process of PB via a spontaneous redox reaction between Fe(3+) and [Fe(CN)6](3-). The PPy film has been electro-polymerized to improve the electrochemical stability of the PPy/GQDs@PB/GF electrode. The as-prepared electrode was characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), infrared spectroscopy (IR), X-ray diffraction (XRD) and electrochemical methods. It exhibited an excellent activity for the electrocatalytic oxidation of l-cys, with a detection sensitivity equal to 0.41 Amol(-1) L for a concentration range of 0.2-50 µmolL(-1), and equal to 0.15 Amol(-1) L for a concentration range of 50-1000 µmolL(-1). A low detection limit of 0.15 µmolL(-1), as well as a remarkable long-time stability and a negligible sensitivity to interfering analytes, were also ascertained.

Solvent dependent interactions between droplets in water-in-oil microemulsions.

In this paper, we investigated the dilution enthalpies of the droplets in water/AOT/oil microemulsions with oil being isooctane, decane, or cyclohexane by isothermal titration microcalorimetry (ITC). Combining with the results obtained from the study of the water/AOT/toluene system in our previous work, it was found that the enthalpy interactions between droplets for isooctane and decane systems were repulsive, while the enthalpy interactions were attractive for cyclohexane and toluene systems. The repulsive droplet interaction for the isooctane system was also confirmed by static light scattering. The solvents appear to play important roles in varying the droplet enthalpy interactions from positive to negative, and the entropy contribution seems to be dominant for the stability of these microemulsion droplet systems.

Rhodamine 6G conjugated-quantum dots used for highly sensitive and selective ratiometric fluorescence sensor of glutathione.

Rhodamine 6G (R6G) and 3-mercaptopropionic acid (MPA) capped-CdTe quantum dots (QDs) were conjugated by electrostatic interactions in aqueous solution. The R6G-QDs conjugate was utilized as a photoluminescence (PL) ratiometric sensor for the detection of glutathione (GSH). In this method, intentional introduction of GSH destroyed the conjugation of R6G and QDs, and induced regular PL change of R6G-QDs conjugates due to the competitive chelation between GSH and MPA ligand on the surface of QDs. The ratio of PL intensity of R6G (I(R6G)) to that of QDs (I(QDs)) in this conjugate was near linear toward the concentration of GSH in the range from 0.05 to 80 µM, and corresponding regression equation showed a good linear coefficient of 0.9954. The limit of detection of 15 nM in this proposed method was about 40-fold lower than that of other QDs-based PL sensors. Interferential experiments testified that R6G-QDs conjugates-based ratiometric PL sensor of GSH showed high selectivity over other related thiols and amino acids. Real sample assays further verified perfect analysis performance of the PL sensor of GSH. In comparison with conventional analytical techniques for the measurement of GSH, this ratiometric PL sensor was facile, economic, highly sensitive and selective.

Atmospheric concentrations, sources and gas-particle partitioning of PAHs in Beijing after the 29th Olympic Games.

A comprehensive sampling campaign was carried out to study atmospheric concentration of polycyclic aromatic hydrocarbons (PAHs) in Beijing and to evaluate the effectiveness of source control strategies in reducing PAHs pollution after the 29th Olympic Games. The sub-cooled liquid vapor pressure (logP(L)(o))-based model and octanol-air partition coefficient (K(oa))-based model were applied based on each seasonal dateset. Regression analysis among log K(P), logP(L)(o) and log K(oa) exhibited high significant correlations for four seasons. Source factors were identified by principle component analysis and contributions were further estimated by multiple linear regression. Pyrogenic sources and coke oven emission were identified as major sources for both the non-heating and heating seasons. As compared with literatures, the mean PAH concentrations before and after the 29th Olympic Games were reduced by more than 60%, indicating that the source control measures were effective for reducing PAHs pollution in Beijing.

Investigation on the application of steel slag-fly ash-phosphogypsum solidified material as road base material.

The aim of the present work is to prepare a new type of steel slag-fly ash-phosphogypsum solidified material totally composed with solid wastes to be utilized as road base material. The mix formula of this material was optimized, the solidified material with optimal mix formula (fly ash/steel slag=1:1, phosphogypsum dosage=2.5%) results in highest strength. The strength development, resilience modulus and splitting strength of this material were studied comparing with some typical road base materials, the 28- and 360-day strength of this material can reach 8MPa and 12MPa, respectively, its resilience modulus reaches 1987MPa and splitting strength reaches 0.82MPa, it has higher early strength than lime-fly ash and lime-soil road base material, its long-term strength is much higher than cement stabilized granular materials, the solidified material has best water stability among those road base materials, it can be engineered as road base material with competitive properties. The strength formation mechanism of this solidified material is discussed also.