No abstract

The development of simple, rapid-response sensors for water detection in organic solvents is highly desirable in the chemical industry. Here we demonstrate a unique luminescence water sensor based on a dual-emitting europium-organic framework (Eu-MOF), which is assembled from a purposely selected 2-aminoterephthalic acid ligand with responsive fluorescence inherent in its intramolecular charge transfer (ICT) process. This ICT process can be rapidly switched-on in the presence of water owing to its ability to boost and stabilize the ICT state. In contrast, the Eu3+ emission within the framework is insensitive to water and can serve as a reference, thus enabling highly sensitive water detection in a turn-on and ratiometric way. In addition, the significant ratiometric luminescence response induced by water makes Eu-MOF undergo a distinct change of emitting color from red to blue, which is favorable for visual analysis with the naked eye. Sensitive determination of water content (0.05–10% v/v) in various organic solvents is achieved in multiple readouts including ratiometric emission intensity, emission color, or the Commission Internationale de l’Eclairage (CIE) chromaticity coordinate. The present Eu-MOF sensor featuring high sensitivity and reusability, self-calibration, simple fabrication and operation, and capability for real-time and in situ detection is expected to have practical applications in water analysis for industrial processes.

No abstract

Background: The analysis of cancer diversity based on a logical framework of hallmarks has greatly improved our understanding of the occurrence, development and metastasis of various cancers. Methods: We designed Cancer Hallmark Genes (CHG) database which focuses on integrating hallmark genes in a systematic, standard way and annotates the potential roles of the hallmark genes in cancer processes. Following the conceptual criteria description of hallmark function the keywords for each hallmark were manually selected from the literature. Candidate hallmark genes collected were derived from 301 pathways of KEGG database by Lucene and manually corrected. Results: Based on the variation data, we finally identified the hallmark genes of various types of cancer and constructed CHG. And we also analyzed the relationships among hallmarks and potential characteristics and relationships of hallmark genes based on the topological structures of their networks. We manually confirm the hallmark gene identified by CHG based on literature and database. We also predicted the prognosis of breast cancer, glioblastoma multiforme and kidney papillary cell carcinoma patients based on CHG data. Conclusions: In summary, CHG, which was constructed based on a hallmark feature set, provides a new perspective for analyzing the diversity and development of cancers.

BackgroundConstructing and modeling the gene regulatory network is one of the central themes of systems biology. With the growing understanding of the mechanism of microRNA biogenesis and its biological function, establishing a microRNA-mediated gene regulatory network is not only desirable but also achievable.MethodologyIn this study, we propose a bioinformatics strategy to construct the microRNA-mediated regulatory network using genome-wide binding patterns of transcription factor(s) and RNA polymerase II (RPol II), derived using chromatin immunoprecipitation following next generation sequencing (ChIP-seq) technology. Our strategy includes three key steps, identification of transcription start sites and promoter regions of primary microRNA transcripts using RPol II binding patterns, selection of cooperating transcription factors that collaboratively function with the transcription factors targeted by ChIP-seq assay, and construction of the network that contains regulatory cascades of both transcription factors and microRNAs.Principal FindingsUsing CAMDA (Critical Assessment of Massive Data Analysis) 2009 data set that includes ChIP-seq data on RPol II and STAT1 (signal transducers and activators of transcription 1) in HeLa S3 cells in control condition and with interferon γ stimulation, we first identified promoter regions of 83 microRNAs in HeLa cells. We then identified two potential STAT1 collaborating factors, AP-1 and C/EBP (CCAAT enhancer-binding proteins), and further established eight feedback network elements that may regulate cellular response during interferon γ stimulation.ConclusionsThis study offers a bioinformatics strategy to provide testable hypotheses on the mechanisms of microRNA-mediated transcriptional regulation, based upon genome-wide protein-DNA interaction data derived from ChIP-seq experiments.