Integration of the Transcriptome and Genome-Wide Landscape of BRD2 and BRD4 Binding Motifs Identifies Key Superenhancer Genes and Reveals the Mechanism of Bet Inhibitor Action in Rheumatoid Arthritis Synovial Fibroblasts.

Fibroblast-like synoviocytes (FLS), one of the main cell types of the rheumatoid arthritis (RA) synovium, possess phenotypic and molecular characteristics of transformed cells. JQ1, an inhibitor of the bromodomain and extra terminal domain family that includes BRD2, BRD3, BRD4, and BRDt, has shown efficacy in models of arthritis. We demonstrate that the active isomer of JQ1 but not its inactive isomer inhibits IL-1ß-induced RA-FLS activation and proliferation. To understand the mechanism of JQ1 action, we subjected JQ1-treated RA-FLS to transcriptional profiling and determined BRD2 and BRD4 cistromes by identifying their global chromatin binding sites. In addition, assay for transposable accessible chromatin by high throughput sequencing was employed to identify open and closed regions of chromatin in JQ1-treated RA-FLS. Through an integrated analysis of expression profiling, Brd2/Brd4 cistrome data, and changes in chromatin accessibility, we found that JQ1 inhibited key BRD2/BRD4 superenhancer genes, downregulated multiple crucial inflammatory pathways, and altered the genome-wide occupancy of critical transcription factors involved in inflammatory signaling. Our results suggest a pleiotropic effect of JQ1 on pathways that have shown to be individually efficacious in RA (in vitro, in vivo, and/or in humans) and provide a strong rationale for targeting BRD2/BRD4 for disease treatment and interception.

Application of life cycle assessment for municipal solid waste management options in Hohhot, People's Republic of China.

With increasing population and urbanization levels in the People's Republic of China, environmental problems related to the management of municipal solid waste (MSW) are inevitable. This study aimed to determine the environmental impact of the current MSW management system in Hohhot City and to establish an optimum future strategy for it by applying life cycle assessment (LCA) methodology. Four scenarios were compared using the CML-IA impact characterization method, which took into account their potential contribution to global warming, ozone depletion, human toxicity, photochemical ozone creation, acidification, and eutrophication potentials. The system boundaries included the collection and recycling, transfer and transportation of MSW, and its disposal by incineration, landfilling, and carbon dioxide (CO2) capture methods. The results showed that the scenario involving landfill and incineration in a ratio of 1:5 was the optimal waste management option; however, increasing the proportion of waste incinerated led to a significant increase in global warming potential. Additional technologies are thus required to overcome this problem, and it was found that the use of CO2 capture technology resulted in a 30% reduction in the total environmental impact potential. This study's results indicate that LCA is a valuable and practical tool to support decision-making that can be used to suggest problematic areas in current waste management strategies and to determine an optimal alternative to the solid waste management option.

The small protein MgtS and small RNA MgrR modulate the PitA phosphate symporter to boost intracellular magnesium levels.

In response to low levels of magnesium (Mg2+ ), the PhoQP two component system induces the transcription of two convergent genes, one encoding a 31-amino acid protein denoted MgtS and the second encoding a small, regulatory RNA (sRNA) denoted MgrR. Previous studies showed that the MgtS protein interacts with and stabilizes the MgtA Mg2+ importer to increase intracellular Mg2+ levels, while the MgrR sRNA base pairs with the eptB mRNA thus affecting lipopolysaccharide modification. Surprisingly, we found overexpression of the MgtS protein also leads to induction of the PhoRB regulon. Studies to understand this activation showed that MgtS forms a complex with a second protein, PitA, a cation-phosphate symporter. Given that the additive effect of ∆mgtA and ∆mgtS mutations on intracellular Mg2+ concentrations seen previously is lost in the ∆pitA mutant, we suggest that MgtS binds to and prevents Mg2+ leakage through PitA under Mg2+ -limiting conditions. Consistent with a detrimental role of PitA in low Mg2+ , we also observe MgrR sRNA repression of PitA synthesis. Thus, PhoQP induces the expression of two convergent small genes in response to Mg2+ limitation whose products act to modulate PitA at different levels to increase intracellular Mg2+ .

Salt-assisted acetonitrile extraction and HPLC-QTOF-MS/MS detection for residues of multiple classes of pesticides in human serum samples.

Detecting pesticide residues in human serum is a challenging process. In this study we developed and validated a method for the extraction and recovery of residues of multiple classes of pesticides from serum using one reagent. Salt-assisted acetonitrile extraction and high-performance liquid chromatography with quadrupole time of flight tandem mass spectrometry were used to quantitate 34 pesticides classified in nine groups of chemicals in human serum samples, which are frequently detected in food. The recoveries for 33 of analyzed pesticides ranged from 86 to 112% with relative standard deviations below 15%. The limits of quantitation and linearity of 31 of the pesticides were 1 µg/L and >0.990, respectively. The lower limit of quantitation has been reported in the literature particularly for multi-classes pesticide mixtures in human serum. The salt-acetonitrile reagent was allowed to achieve good recoveries and detection limits, which could be attributed to salt altering the solvent polarity, preferentially collecting the organic phase in the solution, and promoting the extraction. The developed method was applied for two organophosphate pesticide metabolites, diethylphosphate and 3,5,6-trichloro-2-pyridinol, in serum from rats that were fed a nonlethal quantity of chlorpyrifos. The concentrations of these two were 252.18 ± 15.47 and 0.63 ± 0.23 µg/L, respectively.

Increasing intracellular magnesium levels with the 31-amino acid MgtS protein.

Synthesis of the 31-amino acid, inner membrane protein MgtS (formerly denoted YneM) is induced by very low Mg2+ in a PhoPQ-dependent manner in Escherichia coli Here we report that MgtS acts to increase intracellular Mg2+ levels and maintain cell integrity upon Mg2+ depletion. Upon development of a functional tagged derivative of MgtS, we found that MgtS interacts with MgtA to increase the levels of this P-type ATPase Mg2+ transporter under Mg2+-limiting conditions. Correspondingly, the effects of MgtS upon Mg2+ limitation are lost in a ∆mgtA mutant, and MgtA overexpression can suppress the ∆mgtS phenotype. MgtS stabilization of MgtA provides an additional layer of regulation of this tightly controlled Mg2+ transporter and adds to the list of small proteins that regulate inner membrane transporters.

A Novel Experiment-free Site-specific TDoA Localization Performance-Evaluation Approach.

Time difference of arrival (TDoA) technology is widely utilized for source localization, which stimulates many studies on performance-evaluation approaches for TDoA localization systems. Some approaches using simulations are designed merely for a simple Line-of-Sight (LoS) scenario while some other ones using experiments show high cost and inefficiency. This paper proposes an integrated approach to evaluate a TDoA localization system in an area with a complicated environment. Radio propagation graph is applied through a simulation to obtain channel impulse responses (CIRs) between a source to be located and the TDoA sensors for the area. Realistic signals received by the sensors in baseband are emulated combining the source transmitted signal and the CIRs. A hardware unit takes charge of sending the radio emulated received signals to the system under test, which is consistent with real experimental measurements. Statistical analysis of the system is allowed based on localization errors obtained comparing the system's estimates with the ground truth of the source location. Verified results for LoS and non-LoS scenarios with variable transmitted signal bandwidths and signal-to-noise ratios, as well as for three variations of the sensor locations in an automobile circuit, show the usability of the proposed experiment-free performance-evaluation approach.

CD40L-Dependent Pathway Is Active at Various Stages of Rheumatoid Arthritis Disease Progression.

The inflammatory CD40-CD40L pathway is implicated in various autoimmune diseases, but the activity status of this pathway in various stages of rheumatoid arthritis (RA) progression is unknown. In this study, we used gene signatures of CD40L stimulation derived from human immature dendritic cells and naive B cells to assess the expression of CD40-downstream genes in synovial tissues from anti-citrullinated protein Ab-positive arthralgia, undifferentiated arthritis (UA), early RA, and established RA cohorts in comparison with healthy donors. Interestingly, the expression of CD40LG and active full-length CD40 was increased in the disease tissues, whereas that of a dominant-negative CD40 isoform was decreased. Gene set variation analysis revealed that CD40L-responsive genes in immature dendritic cells and naive B cells were significantly enriched in synovial tissues from UA, early RA, and established RA patients. Additionally, CD40L-induced naive B cell genes were also significantly enriched in synovial tissues from arthralgia patients. In our efforts to characterize downstream mediators of CD40L signaling, we have identified GPR120 and KDM6B as novel components of the pathway. In conclusion, our data suggest that therapeutic CD40-CD40L blocking agents may prove efficacious not only in early and established RA, but also in inhibiting the progression of the disease from arthralgia or UA to RA.

Platelet-derived growth factor subunit B is required for tendon-bone healing using bone marrow-derived mesenchymal stem cells after rotator cuff repair in rats.

As a common cause of shoulder pain and disability, rotator cuff injury (RCI) represents a debilitating condition affecting an individual's quality of life. Although surgical repair has been shown to be somewhat effective, many patients may still suffer from reduced shoulder function. The aim of the current study was to identify a more effective mode of RCI treatment by investigating the effect of platelet-derived growth factor subunit B (PDGF-B) on tendon-bone healing after RCI repair by modifying bone marrow-derived mesenchymal stem cells (BMSCs). Surface markers of BMSCs were initially detected by means of flow cytometry, followed by establishment of the rat models and construction of the lentiviral vector. 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide, Thiazolyl Blue Tetrazolium Bromide (MTT) assay, alizarin red staining, and oil red O staining were used to provide verification that PDGF-B was indeed capable of promoting BMSC viability, osteogenic and adipogenic differentiation capability. Furthermore, biomechanical assessment results indicated that PDGF-B could increase the ultimate load and stiffness of the tendon tissue. Real-time reverse-transcription quantitative polymerase chain reaction and Western blot analysis methods provided evidence suggesting that PDGF-B facilitated the expression of tendon-bone healing-related genes and proteins, while contrasting results were obtained after PDGF-B silencing. Taken together, the key findings of the current study provided evidence suggesting that overexpressed PDGF-B could act to enhance tendon-bone healing after RCI repair, thus highlighting the potential of the functional promotion of PDGF-B as a future RCI therapeutic approach.

Isolation and purification of two antioxidant isomers of resveratrol dimer from the wine grape by counter-current chromatography.

Resveratrol dimers belong to a group of compounds called stilbenes, which along with proanthocyanidins, anthocyanins, catechins, and flavonols are natural phenolic compounds found in grapes and red wine. Stilbenes have a variety of structural isomers, all of which exhibit various biological properties. Counter-current chromatography with a two-phase solvent system composed of n-hexane/ethyl acetate/methanol/water (2:5:4:5, v/v/v/v) was applied to isolate and purify stilbene from the stems of wine grape. Two isomers of resveratrol dimers trans-ε-viniferin and trans-δ-viniferin were obtained from the crude sample in a one-step separation, with purities of 93.2 and 97.5%, respectively, as determined by high-performance liquid chromatography. The structures of these two compounds were identified by (1) H and (13) C NMR spectroscopy. In addition, their antioxidant activities were assessed by 1,1-diphenyl-2-picrylhydrazyl (DPPH) assay. The antioxidant activities of trans-δ-viniferin were higher than that of trans-ε-viniferin in this model. This work demonstrated that counter-current chromatography is a powerful and effective method for the isolation and purification of polyphenols from wine grape. Additionally, the DPPH radical assay showed that the isolated component trans-δ-viniferin exhibited stronger antioxidant activities than trans-ε-viniferin and a little bit weaker than vitamin E at the same concentration.

Conserved small protein associates with the multidrug efflux pump AcrB and differentially affects antibiotic resistance.

The AcrAB-TolC multidrug efflux pump confers resistance to a wide variety of antibiotics and other compounds in Escherichia coli. Here we show that AcrZ (formerly named YbhT), a 49-amino-acid inner membrane protein, associates with the AcrAB-TolC complex. Co-purification of AcrZ with AcrB, in the absence of both AcrA and TolC, two-hybrid assays and suppressor mutations indicate that this interaction occurs through the inner membrane protein AcrB. The highly conserved acrZ gene is coregulated with acrAB through induction by the MarA, Rob, and SoxS transcription regulators. In addition, mutants lacking AcrZ are sensitive to many, but not all, of the antibiotics transported by AcrAB-TolC. This differential antibiotic sensitivity suggests that AcrZ may enhance the ability of the AcrAB-TolC pump to export certain classes of substrates.

Gene expression analysis in biomarker research and early drug development using function tested reverse transcription quantitative real-time PCR assays.

The identification of new biomarkers is essential in the implementation of personalized health care strategies that offer new therapeutic approaches with optimized and individualized treatment. In support of hypothesis generation and testing in the course of our biomarker research an online portal and respective function-tested reverse transcription quantitative real-time PCR assays (RT-qPCR) facilitated the selection of relevant biomarker genes. We have established workflows applicable for convenient high throughput gene expression analysis in biomarker research with cell lines (in vitro studies) and xenograft mouse models (in vivo studies) as well as formalin-fixed paraffin-embedded tissue (FFPET) sections from various human research and clinical tumor samples. Out of 92 putative biomarker candidate genes selected in silico, 35 were shown to exhibit differential expression in various tumor cell lines. These were further analysed by in vivo xenograft mouse models, which identified 13 candidate genes including potential response prediction biomarkers and a potential pharmacodynamic biomarker. Six of these candidate genes were selected for further evaluation in FFPET samples, where optimized RNA isolation, reverse transcription and qPCR assays provided reliable determination of relative expression levels as precondition for differential gene expression analysis of FFPET samples derived from projected clinical studies. Thus, we successfully applied function tested RT-qPCR assays in our biomarker research for hypothesis generation with in vitro and in vivo models as well as for hypothesis testing with human FFPET samples. Hence, appropriate function-tested RT-qPCR assays are available in biomarker research accompanying the different stages of drug development, starting from target identification up to early clinical development. The workflow presented here supports the identification and validation of new biomarkers and may lead to advances in efforts to achieve the goal of personalized health care.

Enhanced homogeneity and flexibility in a humidity sensor using cellulose nanocrystal-based composite film with circular shear flow.

Cellulose nanocrystal (CNC) film is known to be one kind of dynamic color-sensing material, capable of reversible color changes in response to varying humidity levels. However, the brittleness, low hygroscopicity and poor homogeneity of these films have hindered their development. To address this limitation, we present a novel approach where we combine natural deep eutectic solvents (NADES) with sorbitol under the influence of circular shear flow to craft a CNC humidity-sensitive film with enhanced flexibility, hygroscopicity and homogeneity. The inclusion of sorbitol and NADES enhances hygroscopicity and improves the flexibility. Surprisingly, the introduction of circular shear flow was found not only to improve homogeneity, macroscopically and microscopically, but also to further enhance flexibility, toughness, and water absorption capability. The resulting composite films demonstrated highly reversible color changes across the whole visible spectrum depending on the relative humidity, showing their capability to be reliable humidity-sensing materials. Thanks to the improved homogeneity and flexibility, the obtained humidity-sensing composite film can be employed in its entirety without the need for cutting, making it a promising candidate for various applications.

Preparation of sea buckthorn (Hippophae rhamnoides L.) seed meal peptide by mixed fermentation and its effect on volatile compounds and hypoglycemia.

This study employed mixed bacterial strains to ferment seabuckthorn seed meal into peptides, and conducted a comprehensive evaluation of the growth adaptive conditions, molecular weight distribution, volatile compounds, and in vitro hypoglycemic activity required for fermentation. Results showed that when the amount of maltose was 1.1% and MgSO4·7H2O was added at 0.15 g/L, the peptide yield reached 43.85% with a mixed fermentation of Lactobacillus fermentum, Bacillus subtilis, Lactobacillus casei, Lactobacillus rhamnosus, and Lactobacillus acidophilus. Components with a molecular weight below 1 kDa were found to be more effective in inhibiting the activity of α-amylase and α-glucosidase, with the identified sequence being FYLPKM. Finally, SPME/GC-MS results showed that 86 volatile components were detected during the fermentation of seabuckthorn seed meal, including 22 alcohols, 9 acids, 7 ketones, 14 alkanes, 20 esters, and 14 other compounds. With prolonged fermentation time, the content of acids and esters increased significantly.

A study on the system of nonaqueous microchip electrophoresis with on-line peroxyoxalate chemiluminescence detection.

This article describes a further development of our previously reported miniaturized analysis system of microchip electrophoresis with on-line chemiluminescence detection. The system, developed first time for nonaqueous microchip electrophoresis with peroxyoxalate chemiluminescence detection, consists of a suction pressure device for sample or reagent introduction, a constant voltage supplied for electrophoretic separation, an either hydrophilic or hydrophobic porous polymer plug for preventing chemiluminescence reagent flowing upstream and a spiral detection channel for enhancement of both detection sensitivity and reproducibility. Especially, by using organic solvent as BGE medium, the developed system avoided the interface problem between aqueous running buffer and low-water-content chemiluminescence solvent in previous reports. The influencing factors on chemiluminescence signal were optimized using rhodamine 6G as model molecule. The system performance was further investigated in the experiment of separation of hydrophilic rhodamine dyes and analysis of hydrophobic polycyclic aromatic hydrocarbon, providing the detection limit (S/N = 3) of 3.5 nmol/L for rhodamine 123, 6.8 nmol/L for rhodamine 6G, and 60 nmol/L for 1-aminopyrene, respectively. The experimental results showed the system offered a number of benefits, including compact structure, high sensitivity, good reproducibility, and a wide range of application prospect.

Microflow-injection chemiluminescence of luminol and hypochlorite enhanced by phloxine B.

We report for the first time that the sensitivity of the luminol-hypochlorite chemiluminescence (CL) reaction was enhanced approximately 10 times by the addition of phloxine B. The maximum wavelength of CL emission shifted from 431 to 595 nm in the absence and presence, respectively, of phloxine B, suggesting that an efficient chemiluminescence resonance energy transfer occurred between a luminol donor and a phloxine B acceptor in the luminol-hypochlorite-phloxine B system. Based on this observation, a simple, rapid and sensitive microflow injection CL method, using a microchip with spiral channel configurations, was developed for the determination of hypochlorite. Under optimized conditions, a linear calibration curve (R(2) = 0.9944) over the range 0.1-10.0 µmol/L was obtained, with a detection limit of 0.025 µmol/L (S:N = 3). The relative standard deviation (RSD) was found to be 4.2% (n = 10) for 2.5 µmol/L hypochlorite. The sample consumption was only 2 µL, with a sample throughput of 90/h. The method has been used for determining trace amounts of hypochlorite in water samples with satisfactory results.

Research on deep eutectic solvents for the construction of humidity-responsive cellulose nanocrystal composite films.

Photonic crystal materials based on cellulose nanocrystals (CNC), which are environmentally responsive and green, have attracted widespread attention. To overcome the brittleness of CNC films, many researchers have explored functional additives to improve their performance. In this study, a new green deep eutectic solvents (DESs) and an amino acid-based natural deep eutectic solvents (NADESs) were introduced into CNC suspensions for the first time, and hydroxyl-rich small molecules (glycerol, sorbitol) and polymers (polyvinyl alcohol, polyethylene glycol) were coassembled with the DESs and NADESs to form three-component composite films. The CNC/G/NADESs-Arg three-component film reversibly changed color from blue to crimson as the relative humidity rose from 35 % to 100 %; additionally, the elongation at break increased to 3.05 %, and the Young's modulus decreased to 4.52 GPa. The hydrogen bond network structure provided by trace amounts of the DESs or NADESs not only improved the mechanical properties of the composite films but also increased their water absorption capacities without destroying their optical activities. This allows for the development of more stable CNC films and creates potential for biological applications in the future.

Effects of adding milk to fermented black mulberry (Morus nigra L.) juice on its antioxidant activity in C2C12 cells and changes in volatile flavor compounds during storage.

This study assessed the impact of milk on the bioactive compounds, physicochemical properties, antioxidant activity, ROS inhibition, and volatile flavor compounds of fermented black mulberry juice (FBMJ). Firstly, the results showed that 25% concentration of milk was the most suitable for preparing FBMJ-Milk. Compared to the control group, the addition of milk significantly increased the SOD activity and antioxidant capacity, as well as enhanced the total phenolic content (TPC) and SOD storage stability. Secondly, HS-SPME-GC-MS combined with OPLS-DA analysis identified 49 compounds in FBMJM, including 12 esters, 6 acids, 1 ketone, 2 aldehydes, 19 alcohols and 9 other compounds. During the storage, the levels of ethyl ester compounds decreased significantly, while the degradation of ester produced some acid and alcohol compounds. The findings revealed that the addition of milk was beneficial for maintaining the antioxidant stability of FBMJM during storage and enhancing the richness of product flavor.

Shape deformation and recovery of multilayer microcapsules after being squeezed through a microchannel.

The deformation and recovery behaviors of multilayer microcapsules were investigated after being forced to flow through a microchannel. The microchannel device with a constriction (5.7 µm in depth) in the middle was designed, and the multilayer microcapsules with different size and layer thickness (and thereby different mechanical strength) were used. Deformation in the microchannel was observed for all the capsules with a size larger than the constriction height, and its extent was mainly governed by the difference between capsule size and constriction height. The squeezed microcapsules could recover their original spherical shape when the deformation extent was smaller than 16%, whereas permanent physical deformation took place when the deformation extent was larger than 34%. The capsules filled with polyelectrolytes could greatly enhance their shape recovery ability due to the higher osmotic pressure in the capsule interior and could well maintain the preloaded low-molecular-weight dyes regardless of the squeezing.

Elimination of suction effect in interfacing microchip electrophoresis with inductively coupled plasma mass spectrometry using porous monolithic plugs.

A suction-free interfacing method was developed for microchip electrophoresis hyphenated with inductively coupled plasma mass spectrometry (MCE-ICP-MS). The hyphenated system was composed of a microchip, a demountable capillary microflow nebulizer (d-CMN) combined with a heated single pass spray chamber, a negative pressure sampling device, a high voltage power supply, a syringe pump and an ICP-MS. To eliminate the nebulizer suction generated by the pneumatic nebulizer and to ensure that the makeup solution flowed into the nebulizer, two porous polymer plugs were fabricated in the microchip. As a result, reasonably true electropherograms were obtained when compared to the CE separation performed in the traditional MCE-ICP-MS mode without porous polymer plugs. Electrophoretic separation of I(-) and IO(3)(-) was achieved within 25 s in a microchip with an effective separation length of only 15 mm at an electric field of 857 V cm(-1) using 10 mmol L(-1) borate (pH 9.2) as the running buffer. A resolution of 1.3 was obtained and the absolute detection limits for I(-) and IO(3)(-) were 0.12 and 0.13 fg, respectively. The precisions (RSD, n = 10) of the migration time and peak height for I(-) and IO(3)(-) were in the range of 1.1-1.6% and 2.5-2.8%, respectively. Two table salt samples were analyzed by an external calibration method. The iodate contents were in accordance with their labeled values. The recoveries of I(-) and IO(3)(-) in the table salt samples were in the range of 92-105%.

Efficiency and mechanism of C18-functionalized magnetic nanoparticles for extracting weakly polar pesticides from human serum determined by UHPLC-QTOF-MS and molecular dynamics simulations.

Detecting pesticide residues in human serum is a challenging process due to trace-level chronic exposure. Several methods using magnetic adsorbents have been developed for analyzing pesticide residue levels in human serum, but it is still difficult to achieve lower quantitative levels, and the adsorption mechanism for extracting pesticides is unclear. Herein, we propose a feasibility concept of using C18-functionalized magnetic nanoparticles for the adsorption of target pesticides, focusing on the extensively used weakly polar pesticides based on molecular dynamics (MD) simulations. To support this, the facilitated target nanoparticles of Fe3O4@SiO2-C18 were synthesized at a size of 12-13 nm with a magnetic saturation of 40 emu/g. After optimizing and establishing the extraction conditions (1.8 mL C18 modifier, 10 mg sorbents, 3 min adsorption time, 1000 µL ACN for desorption eluent at pH 3.8 and 5 min desorption time), which exhibited recovery = 72.3%-118.3% with RSDs = 0.03-6.57, linearity at 0.01-10 ng/mL with R2 = 0.9561-0.9993, and LODs = 0.01-0.30 ng/mL for the 11 weakly polar pesticides in human serum. Furthermore, the mechanism by which the C18 group selectively extracts weakly polar pesticides was confirmed by binding van der Waals and electrostatic interactions under stable and strong binding energy. The extraction process of efficient adsorption and desorption with C18 functional magnetite nanoparticles suggests a simple method for detecting weakly polar pesticides. The concept may lead to a general approach to analyzing multiple pesticide residues in human serum at trace levels.