Principles of microRNA regulation of a human cellular signaling network

MicroRNAs (miRNAs) are endogenous 22-nucleotide RNAs, which suppress gene expression by selectively binding to the 3-noncoding region of specific message RNAs through base-pairing. Given the diversity and abundance of miRNA targets, miRNAs appear to functionally interact with various components of many cellular networks. By analyzing the interactions between miRNAs and a human cellular signaling network, we found that miRNAs predominantly target positive regulatory motifs, highly connected scaffolds and most downstream network components such as signaling transcription factors, but less frequently target negative regulatory motifs, common components of basic cellular machines and most upstream network components such as ligands. In addition, when an adaptor has potential to recruit more downstream components, these components are more frequently targeted by miRNAs. This work uncovers the principles of miRNA regulation of signal transduction networks and implies a potential function of miRNAs for facilitating robust transitions of cellular response to extracellular signals and maintaining cellular homeostasis

SHP-1 Associates with Both Platelet-derived Growth Factor Receptor and the p85 Subunit of Phosphatidylinositol 3-Kinase*

The Src homology 2 (SH2)-containing protein tyrosine phosphatase 1, SHP-1, is highly expressed in all hematopoietic cells as well as in many non-hematopoietic cells, particularly in some malignant epithelial cell lines. In hematopoietic cells, SHP-1 negatively regulates multiple cytokine receptor pathways. The precise function and the targets of SHP-1 in non-hematopoietic cells, however, are largely unknown. Here we demonstrate that SHP-1 associates with both the tyrosine-phosphorylated platelet-derived growth factor (PDGF) receptor and the p85 subunit of phosphatidylinositol 3-kinase in MCF-7 and TRMP cells. Through the use of mutant PDGF receptors and performing peptide competition for immunoprecipitation, it was determined that SHP-1 independently associates with the PDGF receptor and p85 and that its N-terminal SH2 domain is directly responsible for the interactions. Overexpression of SHP-1 in TRMP cells transfected with the PDGF receptor markedly inhibited PDGF-induced c-fos promoter activation, whereas the expression of three catalytically inactive SHP-1 mutants increased the c-fos promoter activation in response to PDGF stimulation. These results indicate that SHP-1 might negatively regulate PDGF receptor-mediated signaling in these cells. Identification of the association of SHP-1 with the PDGF receptor and p85 in MCF-7 and TRMP cells furthers our understanding of the function of SHP-1 in non-hematopoietic cells

Fluorescent sensors using DNA-functionalized graphene oxide

The final publication is available at Springer via http://dx.doi.org/10.1007/s00216-014-7888-3In the past few years, graphene oxide (GO) has emerged as a unique platform for developing DNA-based biosensors, given the DNA adsorption and fluorescence-quenching properties of GO. Adsorbed DNA probes can be desorbed from the GO surface in the presence of target analytes, producing a fluorescence signal. In addition to this initial design, many other strategies have been reported, including the use of aptamers, molecular beacons, and DNAzymes as probes, label-free detection, utilization of the intrinsic fluorescence of GO, and the application of covalently linked DNA probes. The potential applications of DNA-functionalized GO range from environmental monitoring and cell imaging to biomedical diagnosis. In this review, we first summarize the fundamental surface interactions between DNA and GO and the related fluorescence-quenching mechanism. Following that, the various sensor design strategies are critically compared. Problems that must be overcome before this technology can reach its full potential are described, and a few future directions are also discussed.University of Waterloo || Natural Sciences and Engineering Research Council || Ontario Ministry of Research and Innovation || Foundation for Shenghua Scholar || National Natural Science Foundation of China || Grant No. 81301258, 21301195 Postdoctoral Science Foundation of Central South University and Hunan province ||Grant No. 124896 China Postdoctoral Science Foundation || Grant No. 2013M540644 Hunan Provincial Natural Science Foundation of China || Grant No. 13JJ4029 Specialized Research Fund for the Doctoral Program of Higher Education of China || Grant No. 2013016212007

Crack Risk Evaluation of Early Age Concrete Based on the Distributed Optical Fiber Temperature Sensing

Cracks often appear in concrete arch dams, due to the thermal stress and low tensile strength of early age concrete. There are three commonly used temperature controlling measures: controlling the casting temperature, burying cooling pipe, and protecting the surface. However, because of the difficulty to obtain accurate temperature and thermal stress field of the concrete, the rationality and economy of these measures are not assessed validly before and after construction. In this paper, a crack risk evaluation system for early age concrete is established, including distributed optical fiber temperature sensing (DTS), prediction of temperature and stress fields, and crack risk evaluation. Based on the DTS temperature data, the back-analysis method is applied to retrieve the thermal parameters of concrete. Then, the temperature and thermal stress of early age concrete are predicted using the reversed thermal parameters, as well as the laboratory test parameters. Finally, under the proposed cracking risk evaluation principle, the cracking risk level of each concrete block is given; the preliminary and later temperature controlling measures were recommended, respectively. The application of the proposed system in Xiluodu super high arch dam shows that this system works effectively for preventing cracks of early age concrete

Effective and efficient midlevel visual elements-oriented land-use classification using VHR remote sensing images

Land-use classification using remote sensing images covers a wide range of applications. With more detailed spatial and textural information provided in very high resolution (VHR) remote sensing images, a greater range of objects and spatial patterns can be observed than ever before. This offers us a new opportunity for advancing the performance of land-use classification. In this paper, we first introduce an effective midlevel visual elements-oriented land-use classification method based on “partlets,” which are a library of pretrained part detectors used for midlevel visual elements discovery. Taking advantage of midlevel visual elements rather than low-level image features, a partlets-based method represents images by computing their responses to a large number of part detectors. As the number of part detectors grows, a main obstacle to the broader application of this method is its computational cost. To address this problem, we next propose a novel framework to train coarse-to-fine shared intermediate representations, which are termed “sparselets,” from a large number of pretrained part detectors. This is achieved by building a single-hidden-layer autoencoder and a single-hidden-layer neural network with an L0-norm sparsity constraint, respectively. Comprehensive evaluations on a publicly available 21-class VHR land-use data set and comparisons with state-of-the-art approaches demonstrate the effectiveness and superiority of this paper

Protein-tyrosine phosphatase SHP2 is positively linked to proteinase-activated receptor 2-mediated mitogenic pathway.

Proteinase-activated receptor-2 (PAR2), a new member of family of the G protein-coupled receptors, is activated by proteolytic cleavage of its extracellular amino terminus, a mechanism similar to that used by the thrombin receptor. It has been suggested that PAR2 has a potential role in the late phases of the acute inflammatory response and in tissue repair and/or skin-related disorders. Here we demonstrate that the agonist peptide (SLIGRL) stimulated c-fos-mediated mitogenic activation and tyrosine phosphorylation of cellular proteins. One of the tyrosine-phosphorylated proteins was identified as an Src homology-2 domain-containing protein-tyrosine phosphatase, SHP2. The stimulatory effect of the agonist peptide on early gene transcription was markedly blocked by pertussis toxin treatment whereas the induced tyrosine phosphorylation of SHP2 was completely abolished by the drug. More importantly, while expression of wild-type SHP2 enhanced the agonist-stimulatory mitogenic activity, overexpression of a catalytically inactive mutant of SHP2 strongly suppressed the stimulatory effect of the agonist peptide on both early gene transcription and DNA synthesis. These results suggest that SHP2 acts as a positive regulator linked to the PAR2-mediated mitogenic pathway coupled to a pertussis toxin-sensitive heterotrimeric G protein. Demonstration of SHP2 as a positive mediator in a G protein-coupled, receptor-mediated signaling adds to our understanding of the function of both SHP2 and PAR2 in the signaling pathway

Arginine methylation by PRMT1 regulates muscle stem cell fate

Quiescent muscle stem cells (MSCs) become activated in response to skeletal muscle injury to initiate regeneration. Activated MSCs proliferate and differentiate to repair damaged fibers or self-renew to maintain the pool and ensure future regeneration. The balance between self-renewal, proliferation, and differentiation is a tightly regulated process controlled by a genetic cascade involving determinant transcription factors such as Pax7, Myf5, MyoD, and MyoG. Recently, there have been several reports about the role of arginine methylation as a requirement for epigenetically mediated control of muscle regeneration. Here we report that the protein arginine methyltransferase 1 (PRMT1) is expressed in MSCs and that conditional ablation of PRMT1 in MSCs using Pax7CreERT2 causes impairment of muscle regeneration. Importantly, PRMT1-deficient MSCs have enhanced cell proliferation after injury but are unable to terminate the myogenic differentiation program, leading to regeneration failure. We identify the coactivator of Six1, Eya1, as a substrate of PRMT1. We show that PRMT1 methylates Eya1 in vitro and that loss of PRMT1 function in vivo prevents Eya1 methylation. Moreover, we observe that PRMT1- deficient MSCs have reduced expression of Eya1/Six1 target MyoD due to disruption of Eya1 recruitment at the MyoD promoter and subsequent Eya1-mediated coactivation. These findings suggest that arginine methylation by PRMT1 regulates muscle stem cell fate through the Eya1/Six1/MyoD axis

Intracellular Detection of ATP Using an Aptamer Beacon Covalently Linked to Graphene Oxide Resisting Nonspecific Probe Displacement

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Analytical Chemistry copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see Liu, Z., Chen, S., Liu, B., Wu, J., Zhou, Y., He, L., … Liu, J. (2014). Intracellular Detection of ATP Using an Aptamer Beacon Covalently Linked to Graphene Oxide Resisting Nonspecific Probe Displacement. Analytical Chemistry, 86(24), 12229–12235. https://doi.org/10.1021/ac503358mFluorescent aptamer probes physisorbed on graphene oxide (GO) have recently emerged as a useful sensing platform. A signal is generated by analyte-induced probe desorption. To address nonspecific probe displacement and the false positive signal, we herein report a covalently linked aptamer probe for adenosine triphosphate (ATP) detection. A fluorophore and amino dual modified aptamer was linked to the carboxyl group on GO with a coupling efficiency of ∼50%. The linearity, specificity, stability, and regeneration of the covalent sensor were systematically studied and compared to the physisorbed probe. Both sensors have similar sensitivity, but the covalent one is more resistant to nonspecific probe displacement by proteins. The covalent sensor has a dynamic range from 0.125 to 2 mM ATP in buffer at room temperature and is resistance to DNase I. Intracellular ATP imaging was demonstrated using the covalent sensor, which generated a higher fluorescence signal than the physisorbed sensor. After the cells were stimulated with 5 mM Ca2+ for ATP production, the intracellular signal enhanced by 31.8%. This work highlights the advantages of covalent aptamer sensors using GO as both a quencher and a delivery vehicle for intracellular metabolite detection.National Natural Science Foundation of China || Grant No. 81301258, 21301195 Hunan Provincial Natural Science Foundation of China || Grant No. 13JJ4029 Specialized Research Fund for the Doctoral Program of Higher Education of China || Grant No. 20130162120078 Postdoctoral Science Foundation of Central South University and China || Grant No. 124896 China Postdoctoral Science Foundation || Grant No. 2013M540644 International Postdoctoral Exchange Fellowship Program ||Grant No. 20140014 Shenghua Scholar Foundation || Natural Sciences and Engineering Research Council |

Shear Resistance Capacity of Interface of Plate-Studs Connection between CFST Column and RC Beam

The combination of a concrete-filled steel tube (CFST) column and reinforced concrete (RC) beam produces a composite structural system that affords good structural performance, functionality, and workability. The effective transmission of moments and shear forces from the beam to the column is key to the full exploitation of the structural performance. The studs of the composite beam transfer the interfacial shear force between the steel beam and the concrete slab, with the web bearing most of the vertical shear force of the steel beam. In this study, the studs and vertical steel plate were welded to facilitate the transfer of the interfacial shear force between the RC beam and CFST column. Six groups of a total of 18 specimens were used to investigate the shear transfer mechanism and failure mode of the plate-studs connection, which was confirmed to effectively transmit the shear forces between the beam and column. The results of theoretical calculations were also observed to be in good agreement with the experimental measurements