Nanopore Blockade Sensors for Quantitative Analysis Using an Optical Nanopore Assay.

Nanopore sensing is a popular biosensing strategy that is being explored for the quantitative analysis of biomarkers. With low concentrations of analytes, nanopore sensors face challenges related to slow response times and selectivity. Here, we demonstrate an approach to rapidly detect species at ultralow concentrations using an optical nanopore blockade sensor for quantitative detection of the protein vascular endothelial growth factor (VEGF). This sensor relies on monitoring fluorescent polystyrene nanoparticles blocking nanopores in a nanopore array of 676 nanopores. The fluorescent signal is read out using a wide-field fluorescence microscope. Nonspecific blockade events are then distinguished from specific blockade events based on the ability to pull the particles out of the pore using an applied electric field. This allows the detection of VEGF at sub-picomolar concentration in less than 15 min.

Skeletal CH3OH/NOx Kinetic Model for Simulating Spark-Ignition and Turbulent Jet Ignition Engines.

Methanol is a promising renewable fuel for achieving a better engine combustion efficiency and lower exhaust emissions. Under exhaust gas recirculation conditions, trace amounts of nitrogen oxides have been shown to participate in fuel oxidation and impact the ignition characteristics significantly. Despite numerous studies that analyzed the methanol/NOx interaction, no reliable skeletal kinetic mechanism is available for computational fluid dynamics (CFD) modeling. This work focuses on developing a skeletal CH3OH/NOx kinetic model consisting of 25 species and 55 irreversible and 27 reversible reactions, used for full-cycle engine combustion simulations. New experiments of methanol with the presence of 200 ppmv NO/NO2 were conducted in a rapid compression machine (RCM) at engine-relevant conditions (20-30 bar, 850-950 K). Experimental results indicate notable enhancement effects of the presence of NO/NO2 on methanol ignition under the conditions tested, which highlights the importance of including the CH3OH/NOx interactions in predicting combustion performance. The proposed skeletal mechanism was validated against the literature and new methanol and methanol/NOx experiments over a wide range of operating conditions. Furthermore, the skeletal mechanism was applied in three-dimensional (3D) CFD full-cycle simulations of spark-ignition (SI) and turbulent jet ignition (TJI) engine combustion using methanol. Simulation results demonstrate good agreement with experimental measurements of pressure traces and engine metrics, proving that the proposed skeletal mechanism is suitable and sufficient for CFD simulations.

Understanding and modelling the magnitude of the change in current of nanopore sensors.

Nanopores are promising sensing devices that can be used for the detection of analytes at the single molecule level. It is of importance to understand and model the current response of a nanopore sensor for improving the sensitivity of the sensor, a better interpretation of the behaviours of different analytes in confined nanoscale spaces, and quantitative analysis of the properties of the targets. The current response of a nanopore sensor, usually called a resistive pulse, results from the change in nanopore resistance when an analyte translocates through the nanopore. This article reviews the theoretical models used for the calculation of the resistance of the nanopore, and the corresponding change in nanopore resistance due to a translocation event. Models focus on the resistance of the pore cavity region and the access region of the nanopore. The influence of the sizes, shapes and surface charges of the translocating species and the nanopore, as well as the trajectory that the analyte follows are also discussed. This review aims to give a general guidance to the audience for understanding the current response of a nanopore sensor and the application of this class of sensor to a broad range of species with the theoretical models.

A Transparent Semiconducting Surface for Capturing and Releasing Single Cells from a Complex Cell Mixture.

Selective isolation of individual target cells from a heterogeneous population is technically challenging; however, the ability to retrieve single cells can have high significance in various aspects of biological research. Here, we present a new photoelectrochemical surface based on a transparent electrode that is compatible with high-resolution fluorescence microscopy for isolating individual rare cells from complex biological samples. This is underpinned by two important factors: (i) careful design of the electrode by patterning discrete Au disks of micron dimension on amorphous silicon-indium tin oxide films and (ii) orthogonal surface chemistry, which modifies the patterned electrode with self-assembly layers of different functionalities, to selectively capture target cells on the Au disks and resist cell binding to the amorphous silicon surface. The co-stimulation of the surface using light from a microscope and an electric potential triggers the reductive desorption of the alkanethiol monolayer from the Au disks to release the single cells of interest from the illuminated regions only. Using circulating tumor cells as a model, we demonstrate the capture of cancer cells on an antibody-coated surface and selective release of single cancer cells with low expression of epithelial cell adhesion molecules.

Key Parameters That Determine the Magnitude of the Decrease in Current in Nanopore Blockade Sensors.

Nanopore blockade sensors were developed to address the challenges of sensitivity and selectivity for conventional nanopore sensors. To date, the parameters affecting the current of the sensor have not been elucidated. Herein, the impacts of nanopore size and charge and the shape, size, surface charge, and aggregation state of magnetic nanoparticles were assessed. The sensor was tolerant to all parameters contrary to predictions from electronic or geometric arguments on the current change. Theoretical models showed the greater importance of the polymers around nanoparticles and the access resistance of nanopores to the current, when compared with translocation-based nanopore sensors. The signal magnitude was dominated by the change in access resistance of ∼4.25 MΩ for all parameters, resulting in a robust system. The findings provide understandings of changes in current when nanopores are blocked, like in RNA trapping or nanopore blockade sensors, and are important for designing sensors based on nanopore blockades.

High-resolution light-activated electrochemistry on amorphous silicon-based photoelectrodes.

Light-activated electrochemistry (LAE) consists of employing a focused light beam to illuminate a semiconducting area and make it electrochemically active. Here, we show how to reduce the electrochemical spatial resolution to submicron by exploiting the short lateral diffusion of charge carriers in amorphous silicon to improve the resolution of LAE by 60 times.

Patterned Molecular Films of Alkanethiol and PLL-PEG on Gold-Silicate Interfaces: How to Add Functionalities while Retaining Effective Antifouling.

Spatial control of surface functionalization and interactions is essential for microarray-based analysis. This study reports the fabrication of two-dimensional molecular films with site-specific functionalities, forming microarrays at discrete locations. Arrays of microsized gold disks were produced on a silicate membrane using microfabrication. On these arrays, orthogonal self-assembly of molecules was performed that can specifically bind to gold or silicate. The gold array elements were functionalized with a range of alkanethiols and the silicate with polymeric poly-l-lysine-grafted-poly(ethylene glycol) (PLL-PEG). The surface functionalization on the gold disk array and the surrounding substrate was characterized at each step using X-ray photoelectron spectroscopy (XPS) to show that alkanethiols are specifically attached to the gold. PLL-PEG was used to provide resistance against nonspecific protein and cell adsorption and attached exclusively to the silicate. The effectiveness of the surface chemistry was validated by the selective self-assembly of a gold nanoparticle monolayer array on the gold regions. In a more sophisticated example, selective adhesion of MCF-7 cells to anti-EpCAM antibody modified gold areas of the gold-silicate surface was demonstrated to give a cell microarray. This study provides a general approach to fabricate chemical patterns on silicon-based devices with the convergence of microfabrication and material-specific surface modification, which may be useful to expand the functionalities and potential applications for patterned biomolecular films. Importantly, the ability to pattern surfaces with different surface chemistries is not limited to planar surfaces using this orthogonal surface-coupling approach.

Dual-valve parallel prediction control for an electro-hydraulic servo system.

To improve the dynamic response performance of a high-flow electro-hydraulic servo system, scholars have conducted considerable research on the synchronous and time-sharing controls of multiple valves. However, most scholars have used offline optimization to improve control performance. Thus, control performance cannot be dynamically adjusted or optimized. To repeatedly optimize the performance of multiple valves online, this study proposes a method for connecting a high-flow proportional valve in parallel with a low-flow servo valve. Moreover, this study proposes an algorithm in which a proportional-integral-derivative system and multivariable predictive control system are used as an inner loop and outer loop, respectively. The simulation and experimental results revealed that dual-valve parallel control could effectively improve the control accuracy and dynamic response performance of an electro-hydraulic servo system and that the proportional-integral-derivative-multivariable predictive control controller could further dynamically improve the control accuracy.

Inhibitory effect of tranilast on the myofibroblast differentiation of rat mesenchymal stem cells induced by transforming growth factor­ß1 in vitro.

Mesenchymal stem cell (MSC) transplantation is able to attenuate organ fibrosis; however, increasing evidence has indicated that MSCs may be an important cell source of myofibroblasts, which are vital pathogenic cells in fibrotic diseases. The results of the present study revealed that co­culturing with exogenous transforming growth factor (TGF)­ß1 can induce the transdifferentiation of cultured rat MSCs into myofibroblasts in vitro. Treatment of the MSCs with tranilast [N­(3',4'­dimethoxycinnamoyl)­anthranilic acid] attenuated this fibrotic process. Immunocytochemical staining, western blot analysis, reverse transcription­quantitative polymerase chain reaction analysis and cell viability assays were performed in order to evaluate the molecular mechanisms underlying the effects of tranilast on TGF­ß1­mediated MSC­to­myofibroblast activation. The results demonstrated that TGF­ß1 upregulated the expression of α­smooth muscle actin (α­SMA) and collagen type I, and increased the phosphorylation of mothers against decapentaplegic homolog 3 (Smad3) and extracellular signal­regulated kinase 1/2 (ERK1/2) in the rat MSCs; by contrast, tranilast pretreatment downregulated their expression. Furthermore, the proliferation of MSCs induced by TGF­ß1 was decreased by pretreatment with tranilast. In conclusion, the results of the present study demonstrated that tranilast treatment markedly suppressed the TGF­ß1­induced differentiation of cultured rat MSCs into myofibroblasts, potentially by inhibiting the Smad3 and ERK1/2 signaling pathways. Therefore, this may be a potential antifibrotic therapeutic strategy, serving as an adjuvant treatment following transplantation of MSCs.

Hypoxic culture enhances the expansion of rat bone marrow-derived mesenchymal stem cells via the regulatory pathways of cell division and apoptosis.

This study aimed to examine the proliferative behavior and molecular mechanisms of rat bone marrow-derived MSCs (rBMSCs) cultured under three different oxygen concentrations. Passaged rBMSCs exhibited significantly greater proliferation rates at 1% O2 and 5% O2 than those at 18% O2 and the cells exposed to 1% O2 showed the highest proliferative potential, which was evidenced by the growth curves, colony-forming efficiencies, and CCK-8 absorbance values. The rBMSCs grown under hypoxic culture conditions (1% O2 and 5% O2) had the increased percentage of cells in S + G2/M-phase and the decreased apoptotic index, compared with normoxia (18% O2). It was revealed for the first time that there were more phosphohistone H3 (PHH3)-positive cells and higher expressions of proliferating cell nuclear antigen (PCNA) in the hypoxic cultures of rBMSCs than in the normoxic culture. Hypoxia upregulated the anti-apoptotic protein Bcl-2 and downregulated the pro-apoptotic proteins Bax and the cleaved caspase-3 in cultured rBMSCs. The levels of hypoxia-inducible factor-1α (HIF-1α) and phosphorylated extracellular signal-regulated kinase 1/2 (p-ERK1/2) were increased in the hypoxic-cultured rBMSCs. Nevertheless, no significant difference was observed in p53 level of rBMSCs between different oxygen concentrations. In conclusion, the hypoxia exerts a promoting effect on the in vitro expansion of rBMSCs via several signaling and molecular pathways involved in the control of cell cycle and apoptosis.

Identification and validation of microRNAs as endogenous controls for quantitative polymerase chain reaction in plasma for stable coronary artery disease.

BACKGROUND: Circulating microRNAs (miRNAs) have been proved to serve as biomarkers for diagnosis and assessment of prognosis of coronary artery disease (CAD). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a widely-used technique to estimate expression levels of circulating miRNAs. Selection of optimal endogenous control (EC) remains critical to obtain reliable qPCR data of miRNAs expression. However, reference controls for normalization of circulating miRNA in CAD are still lacking. The purpose of this study was to identify stably expressed miRNAs to normalize RT-qPCR data derived from plasma in stable CAD. METHODS: We identified 10 stably expressed candidate ECs by combining miRNA microarray screening and literature screening. These 10 candidate ECs were estimated by RT-qPCR and the data were analyzed by NormFinder and BestKeeper algorithm. RESULTS: Two most stable ECs were identified as EC candidates and they were subsequently validated in another larger cohort. The 2 candidates were also validated by normalizing the expression levels of miR-21. In general, they were superior to the commonly used reference gene RNU6 in quantification cycle (Cq) value, stability value and normalization effect. CONCLUSIONS: Our results demonstrated that miR-6090 and miR-4516 can be used as reference genes for plasma miRNA analysis in stable CAD.

[Preliminary efficacy of video-assisted anal fistula treatment for complex anal fistula].

OBJECTIVE: To evaluate the preliminary efficacy of video-assisted anal fistula treatment (VAAFT) for complex anal fistula. METHODS: Clinical data of 11 consecutive patients with complex anal fistula undergoing VAAFT in our department from May to July 2015 were reviewed. VAAFT was performed to manage the fistula under endoscope without cutting or resection. RESULTS: VAAFT was successfully performed in all the 11 patients. The internal ostium was closed using mattress suture in 10 cases, and Endo-GIA stapler in 1 case. The mean operative time was (42.0±12.4) min, mean hospital stay was (4.1±1.5) d. Complication included bleeding and perianal infection in 1 case respectively. After 1 to 3.2 months follow-up, success rate was 72.7%(8/11), and no fecal incontinence was observed. CONCLUSION: Video-assisted anal fistula treatment is an effective, safe and minimally invasive surgical procedure for complex anal fistula with preservation of anal sphincter function.

Rapid analysis of polysaccharides contents in Glycyrrhiza by near infrared spectroscopy and chemometrics.

A method for quantitative analysis of the polysaccharides contents in Glycyrrhiza was developed based on near infrared (NIR) spectroscopy, and by adopting the phenol-sulphuric acid method as the reference method. This is the first time to use this method for predicting polysaccharides contents in Glycyrrhiza. To improve the predictive ability (or robustness) of the model, the competitive adaptive reweighted sampling (CARS) mathematical strategy was used for selecting relevance wavelengths. By using the restricted relevance wavelengths, the PLS model was more efficient and parsimonious. The coefficient of determination of prediction (Rp(2)) and the root mean square error of prediction (RMSEP) of the obtained optimum models were 0.9119 and 0.4350 for polysaccharides. The selected relevance wavelengths were also interpreted. It proved that all the wavelengths selected by CARS were related to functional groups of polysaccharide. The overall results show that NIR spectroscopy combined with chemometrics can be efficiently utilised for analysis of polysaccharides contents in Glycyrrhiza.

High-throughput RNAi screening of human kinases identifies predictors of clinical outcome in colorectal cancer patients treated with oxaliplatin.

The purpose of this study is to identify protein kinase genes that modulate oxaliplatin cytotoxicity in vitro and evaluate the roles of these genes in predicting clinical outcomes in CRC patients receiving oxaliplatin-based adjuvant chemotherapy. A high-throughput RNAi screening targeting 626 human kinase genes was performed to identify kinase genes whose inhibition potentiates oxaliplatin sensitivity in CRC cells. The associations between copy numbers of the candidate genes and recurrence-free survival and overall survival were analyzed in 142 stage III CRC patients receiving first-line oxaliplatin-based adjuvant chemotherapy who were enrolled from two independent hospitals. HT-RNAi screening identified 40 kinase genes whose inhibition potentiated oxaliplatin cytotoxicity in DLD1 cells. The relative copy number (RCN) of MAP4K1 and CDKL4 were associated with increased risks of both recurrence and death. Moreover, significant genes-based risk score and the ratios of RCN of different genes can further categorize patients into subgroups with distinctly differing outcomes. The estimated AUC for the prediction models including clinical variables plus kinase biomarkers was 0.77 for the recurrence and 0.82 for the survival models. The copy numbers of MAP4K1 and CDKL4 can predict clinical outcomes in CRC patients treated with oxaliplatin-based chemotherapy.

Role of svp in Drosophila pericardial cell growth.

The Drosophila dorsal vessel is a segmentally repeated linear organ, in which seven-up (svp) is expressed in two pairs of cardioblasts and two pairs of pericardial cells in each segment. Under the control of hedgehog (hh) signaling from the dorsal ectoderm, svp participates in diversifying cardioblast identities within each segment. In this experiment, the homozygous embryos of svp mutants exhibited an increase in cell size of Eve positive pericardial cells (EPCs) and a disarranged expression pattern, while the cardioblasts pattern of svp-lacZ expression was normal. In the meantime, the DAI muscle founders were absent in some segments in svp mutant embryos, and the dorsal somatic muscle patterning was also severely damaged in the late stage mutant embryos, suggesting that svp is required for the differentiation of Eve-positive pericardial cells and DA1 muscle founders and may have a role in EPC cell growth.

A novel human KRAB-containing zinc-finger gene ZNF446 inhibits transcriptional activities of SRE and AP-1.

Kruppel-related zinc-finger proteins constitute the largest individual family of transcription factors in mammals [C. Looman, L. Hellman, M. Abrink, A novel Kruppel-associated box identified in a panel of mammalian zinc-finger proteins, Mammalian Genome 15 (1) (2004) 35-40.[1]]. Here we identified and characterized a novel zinc-finger gene named ZNF446. The predicted protein contains a KRAB and three C(2)H(2) zinc fingers. Northern blot analysis shows that ZNF446 is expressed in a variety of human adult tissues with the highest expression level in muscle. ZNF446 is a transcription repressor when fused to GAL4 DNA-binding domain and co-transfected with VP-16. Overexpression of ZNF446 in COS-7 cells inhibits the transcriptional activities of SRE and AP-1, in which the KRAB motif represents the basal transcriptional repressive activity, suggesting that the ZNF446 protein may act as a transcriptional repressor in mitogen-activated protein kinase (MAPK) signaling pathway to mediate cellular functions.