GPCR–drug interactions prediction using random forest with drug-association-matrix-based post-processing procedure

G-protein-coupled receptors (GPCRs) are important targets of modern medicinal drugs. The accurate identification of interactions between GPCRs and drugs is of significant importance for both protein function annotations and drug discovery. In this paper, a new sequence-based predictor called TargetGDrug is designed and implemented for predicting GPCR–drug interactions. In TargetGDrug, the evolutionary feature of GPCR sequence and the wavelet-based molecular fingerprint feature of drug are integrated to form the combined feature of a GPCR–drug pair; then, the combined feature is fed to a trained random forest (RF) classifier to perform initial prediction; finally, a novel drug-association-matrix-based post-processing procedure is applied to reduce potential false positive or false negative of the initial prediction. Experimental results on benchmark datasets demonstrate the efficacy of the proposed method, and an improvement of 15% in the Matthews correlation coefficient (MCC) was observed over independent validation tests when compared with the most recently released sequence-based GPCR–drug interactions predictor. The implemented webserver, together with the datasets used in this study, is freely available for academic use at http://csbio.njust.edu.cn/bioinf/TargetGDrug.     

Computational identification of circular RNAs based on conformational and thermodynamic properties in the flanking introns

Circular RNAs (circRNAs) were found more than 30 years ago, but have been treated as molecular flukes in a long time. Combining deep sequencing studies with bioinformatics technique, thousands of endogenous circRNAs have been found in mammalian cells, and some researchers have proved that several circRNAs act as competing endogenous RNAs (ceRNAs) to regulate gene expression. However, the mechanism by which the precursor mRNA to be transformed into a circular RNA or a linear mRNA is largely unknown. In this paper, we attempted to bioinformatically identify shared genomic features that might further elucidate the mechanism of formation and proposed a SVM-based model to distinguish circRNAs from non-circularized, expressed exons. Firstly, conformational and thermodynamic dinucleotide properties in the flanking introns were extracted as potential features. Secondly, two feature selection methods were applied to gain the optimal feature subset. Our 10-fold cross-validation results showed that the model can be used to distinguish circRNAs from non-circularized, expressed exons with an Sn of 0.884, Sp of 0.900, ACC of 0.892, MCC of 0.784, respectively. The identification results suggest that conformational and thermodynamic properties in the flanking introns are closely related to the formation of circRNAs. Datasets and the tool involved in this paper are all available at https://sourceforge.net/projects/predicircrnatool/files/.     

A computational method for prediction of rSNPs in human genome

Regulatory single nucleotide polymorphisms (rSNPs) in human genomes are thought to be responsible for phenotypic differences, including susceptibility to diseases and treatment outcomes, even they do not change any gene product. However, a genome-wide search for rSNPs has not been properly addressed so far. In this work, a computational method for rSNP identification is proposed. As background SNPs far outnumber rSNPs, an ensemble method is applied to handle imbalanced data, which firstly converts an unbalanced dataset into several balanced ones and then models for every balanced dataset. Two major types of features are extracted, that are sequence based features and allele-specific based features. Then random forest is applied to build the recognition model for each balanced dataset. Finally, ensemble strategies are adopted to combine the result of each model together. We have tested our method on a set of experimentally verified rSNPs, and leave-one-out cross-validation results showed that our method can achieve accuracy with sensitivity of 73.8%, specificity of 71.8% and the area under ROC curve (AUC) is 0.756. In addition, our method is threshold free and doesn’t rely on data of regulatory elements, thus it will have better adaptability when facing different data scenarios. The original data and the source matlab codes involved are available at https://sourceforge.net/projects/rsnpdect/.     

Electrocatalytic Properties and Voltammetric Determination of Melatonin at a Nanostructured Film Electrode

A multi-wall carbon nanotube (MWNT) film coated glassy carbon electrode (GCE) was fabricated, and the electrochemical behavior of melatonin on the MWNT film coated GCE was investigated. The oxidation peak current of melatonin increases significantly and the oxidation peak position shifts positively at the MWNT film modified GCE compared to that at a bare GCE. This indicates that MWNTs feature highly effective catalysis to the electrochemical oxidation of melatonin. A simple and sensitive electroanalytical method was developed for the determination of melatonin. The oxidation peak current is proportional to the concentration of melatonin from 8×10^–8 to 1×10^–5molL^–1. The detection limit is about 2×10^–8molL^–1 for 3min accumulation. The proposed method was demonstrated to work satisfactorily with commercial capsules.     

DEEPAligner: Deep encoding of pathways to align epigenetic signatures

Background and objectiveRecently, differential DNA Methylation is known to affect the regulatory mechanism of biological pathways. A pathway encompasses a set of interacting genes or gene products that altogether perform a given biological function. Pathways often encode strong methylation signatures that are capable of distinguishing biologically distinct subtypes. Even though Next Generation Sequencing techniques such as MeDIP-seq and MBD-isolated genome sequencing (MiGS) allow for genome-wide identification of clinical and biological subtypes, there is a pressing need for computational methods to compare epigenetic signatures across pathways.MethodsA novel alignment method, called DEEPAligner (Deep Encoded Epigenetic Pathway Aligner), is proposed in this paper that finds functionally consistent and topologically sound alignments of epigenetic signatures from pathway networks. A deep embedding framework is used to obtain epigenetic signatures from pathways which are then aligned for functional consistency and local topological similarity.ResultsExperiments on four benchmark cancer datasets reveal epigenetic signatures that are conserved in cancer-specific and across-cancer subtypes.ConclusionThe proposed deep embedding framework obtains highly coherent signatures that are aligned for biological as well as structural orthology. Comparison with state-of-the-art network alignment methods clearly suggest that the proposed method obtains topologically and functionally more consistent alignments.Availabilityhttp://bdbl.nitc.ac.in/DEEPAligner     

Encapsulation of Bovine Serum Albumin in Temperature‐Programmed “Shell‐in‐Shell” Structures

A novel approach to load a hydrophilic bovine serum albumin into drug carriers was proposed in terms of temperature‐programmed “shell‐in‐shell” structures, which were fabricated with poly(N‐isopropylacrylamide), poly(lactide), poly(ethylene glycol), and Au nanoparticles. Spherically well‐defined “shell‐in‐shell” structures were constructed by a modified‐double‐emulsion method (MDEM). The lower critical solubility temperature of the structures was manipulated to 36.4 °C which was confirmed by UV/Vis spectroscopy and DSC (Differential Scanning Calorimetry).

TEM image of the Au@PLLA‐PEG@PNIPAAm‐PDLA structure.     

A Solution‐Processable (Tetraaniline‐b‐Polyethylene Glycol)3 Star‐Shaped Rod‐Coil Block Copolymer with Enhanced Electrochromic Properties

A novel electroactive star‐shaped rod‐coil copolymer composed of a benzene core and three symmetrically positioned tetraaniline‐b‐poly(ethylene glycol) arms, (TAni‐b‐PEG)₃ rod‐coil block copolymer, is synthesized successfully and characterized using Fourier transform infrared spectroscopy (FTIR), UV–vis, ¹H NMR, and matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry. Uniform and high‐quality (TAni‐b‐PEG)₃ thin films onto indium tin oxide‐coated glass surface are fabricated simply from its DMF solution. Resulting (TAni‐b‐PEG)₃ copolymer thin films possess excellent electrochromic properties with a high optical contrast of 73.3%, superb coloration efficiency of 318.5 cm² C⁻¹ at 750 nm. Very short switching times, that is, 2.11 s and 2.14 s for coloring and bleaching times, respectively, are observed as well. The mechanism of these impressive electrochromic properties of (TAni‐b‐PEG)₃ thin films possessed is proposed based on the atomic force microscopy investigation, star‐shaped molecular geometry, synergetic electronic and ionic conductivity and amphiphilic self‐assembly feature of (TAni‐b‐PEG)₃ copolymer, which can self‐assemble to form cylinder pattern consisting of quick pathways for electronic charges and ionic species, respectively.

     

Novel C60‐Anchored Two‐Armed Poly(tert‐butyl acrylate): Synthesis and Characterization

Summary: A multistep synthetic procedure for preparing novel C₆₀‐anchored two‐armed poly(tert‐butyl acrylate) was developed. First, two‐armed poly(tert‐butyl acrylate) bearing a malonate ester core with well‐controlled molecular weight was synthesized through atom transfer radical polymerization. The effective Bingel reaction between C₆₀ and the well‐defined polymer was then carried out to yield C₆₀‐anchored polymer. GPC, ¹H NMR, and UV‐vis spectroscopy indicated that the C₆₀‐anchored polymer was a monosubstituted and ‘closed’ 6,6‐ring‐bridged methanofullerene derivative.

Schematic of a novel C₆₀‐anchored two‐armed polymer.     

Highly Efficient and Facile Photocatalytic Recycling System Suitable for ICAR ATRP of Hydrophilic Monomers

Photoinduced initiators for continuous activator regeneration atom transfer radical polymerization (ATRP) of hydrophilic monomers in heptane/ethanol latent‐biphasic system for copper catalyst separation and recycling have been realized for the first time at room temperature with different wavelengths of visible light LED (green, blue, purple, and white LED) as external stimulus, using 2‐bromophenylacetate as the ATRP initiator and camphorquinone/triethylamine as the photoinitiator. In this system, hybrid catalyst complex (HCc) is synthesized as a novel nonpolar catalyst, which is preferentially dissolved in heptane. The hydrophilic polymers obtained catalyzed by HCc in heptane/ethanol mixture solvent show typical “living” features, for example, the values of M_n,GPC increase linearly with monomer conversion up to quantitative level (>96%) and the molecular weight distributions were kept narrow (M_w/M_n < 1.20) throughout the polymerization process. It should be noted that the excellent controllability of this novel polymerization system can be achieved even after 5 catalyst recycling experiments under LED irradiation.

     

Assessing the similarity of ligand binding conformations with the Contact Mode Score

Structural and computational biologists often need to measure the similarity of ligand binding conformations. The commonly used root-mean-square deviation (RMSD) is not only ligand-size dependent, but also may fail to capture biologically meaningful binding features. To address these issues, we developed the Contact Mode Score (CMS), a new metric to assess the conformational similarity based on intermolecular protein-ligand contacts. The CMS is less dependent on the ligand size and has the ability to include flexible receptors. In order to effectively compare binding poses of non-identical ligands bound to different proteins, we further developed the eXtended Contact Mode Score (XCMS). We believe that CMS and XCMS provide a meaningful assessment of the similarity of ligand binding conformations. CMS and XCMS are freely available at http://brylinski.cct.lsu.edu/content/contact-mode-score and http://geaux-computational-bio.github.io/contact-mode-score/.     

Substrate‐Induced Controllable Wrinkling for Facile Nanofabrication

In this work, we report a facile and effective strategy to generate patterned wrinkles. This strategy includes first adhering a thin poly(dimethylsiloxane) (PDMS) film (<82 µm) on porous conductive adhesive tape (CAT), followed by sputter coating of Au onto PDMS under vacuum condition, which results in formation of patterned wrinkles on the Au‐PDMS bilayer. CAT was found to induce local stretching of PDMS thin film, which was the key for controlled wrinkle formation. Compared with previous wrinkling methods, our strategy is simpler and gives smaller feature sizes (down to 300 nm).

     

A Facile Strategy for Preparation of α‐Heterobifunctional Polystyrenes with Well‐Defined Molecular Weight

A facile strategy for synthesis of α‐heterobifunctional polystyrenes is reported. The novel functional polystyrenes have been successfully synthesized via a combination of atom transfer radical polymerization (ATRP) and chemical modification of end‐functional groups. First, ε‐caprolactone end‐capped polystyrenes with controlled molecular weight and low polydispersity were prepared by ATRP of styrene using α‐bromo‐ε‐caprolactone (αBrCL) as an initiator. Then, removal of the terminal bromine atom was performed with iso‐propylbenzene in the presence of CuBr/PMDETA. Finally, ring‐opening modifications of the caprolactone group were carried out with amines, n‐butanol and H₂O to produce novel polystyrenes containing two different functional groups at one end.

     

Contributions to the Experimental Investigation of the Nascent Polymerisation of Ethylene on Supported Catalysts, 1

A detailed investigation of the kinetics, morphology and polymer properties observed during the polymerisation of ethylene on a Ziegler‐Natta catalyst at very short times (t ≥ 40 ms) in a novel, quenched‐flow reactor is presented. It was found that for times shorter than a tenth of a second, the observed rate of polymerisation was significantly higher than expected, and that the crystallinity of the nascent ethylene homopolymer was of the order of 25 to 30% – much lower than expected. Evidence is presented that shows that fragmentation is essentially complete in a small fraction of a second.

     

A novel fuzzy set based multifactor dimensionality reduction method for detecting gene–gene interaction

BackgroundGene-gene interaction (GGI) is one of the most popular approaches for finding the missing heritability of common complex traits in genetic association studies. The multifactor dimensionality reduction (MDR) method has been widely studied for detecting GGIs. In order to identify the best interaction model associated with disease susceptibility, MDR compares all possible genotype combinations in terms of their predictability of disease status from a simple binary high(H) and low(L) risk classification. However, this simple binary classification does not reflect the uncertainty of H/L classification.MethodsWe regard classifying H/L as equivalent to defining the degree of membership of two risk groups H/L. By adopting the fuzzy set theory, we propose Fuzzy MDR which takes into account the uncertainty of H/L classification. Fuzzy MDR allows the possibility of partial membership of H/L through a membership function which transforms the degree of uncertainty into a [0,1] scale. The best genotype combinations can be selected which maximizes a new fuzzy set based accuracy measure.ResultsTwo simulation studies are conducted to compare the power of the proposed Fuzzy MDR with that of MDR. Our results show that Fuzzy MDR has higher power than MDR. We illustrate the proposed Fuzzy MDR by analysing bipolar disorder (BD) trait of the WTCCC dataset to detect GGI associated with BD.ConclusionsWe propose a novel Fuzzy MDR method to detect gene–gene interaction by taking into account the uncertainly of H/L classification and show that it has higher power than MDR. Fuzzy MDR can be easily extended to handle continuous phenotypes as well. The program written in R for the proposed Fuzzy MDR is available at https://statgen.snu.ac.kr/software/FuzzyMDR.     

Metal‐Free Organic Dyes for Dye‐Sensitized Solar Cells: From Structure: Property Relationships to Design Rules

Works without ruthenium as well : Dye‐sensitized solar cells (DSSCs) incorporating metal‐free organic dyes have been considerably improved in recent years. Various design strategies have been established and are employed successfully in the synthesis of novel sensitizers. In this Review, structure–property–efficiency correlations are deduced from a vast number of dyes, which should help to design new and highly efficient sensitizers.

     

Atomic Force Microscopy Characterization and Interpretation of Thin‐Film Poly(butylene adipate) Spherulites with Ring Bands

Atomic force microscopy characterization has been conducted to reveal the morphological difference between single‐ring bands in poly(butylene adipate) (PBA). Furthermore, morphological features of the ring‐less Maltese‐cross spherulites are compared to the ring‐band spherulites. Periodic changes in height seem to be common for either the ring‐band or ring‐less (Maltese‐cross) crystal domains; however, the steepness in height change is greater for the ring‐band crystal, while height change in the ring‐less crystal exhibits a terrace‐like layer pattern. In the ring‐band crystal region, the lamellar stalks, which taper off to pointed needle‐like stalks, monotonously protrude out of the layers of softer materials, with no signs of twisting, bending, or turning. In contrast, all lamellae in the ring‐less (Maltese‐cross) crystal region are uniform platelets arranged like flower petals in a layered pattern.

     

Fluorescence enhancement method for measuring anionic surfactants with a hydrophobic cyanine dye

A novel fluorimetric method based on use of a hydrophobic cationic cyanine dye has been developed for determination of the anionic surfactant sodium dodecylbenzenesulfonate (DBS). The method is based on the enhancement effect of DBS on the fluorescence of the hydrophobic cyanine dye 2-[-4-chloro-7-(1-ethyl-3,3-dimethylindolin-2-ylidene)-3,5-(propane-1,3-diyl)-1,3,5-heptatrien-1-yl]-1-ethyl-3,3-dimethyl-3H-indolium iodide. Under the optimum conditions the extent of fluorescence enhancement is proportional to the concentration of DBS in the range 0.05–5.0 mg L^–1; the detection limit is 0.014mg L^–1. The relative standard deviation for 0.35 mg L^–1 DBS was 1.1% (n=10). The proposed method, which avoided use of toxic solvents and tedious solvent-extraction, and was applied to the determination of DBS in natural water with recoveries between 99.9 and 107%. Preliminary research shows that the fluorescence enhancement is due to the formation of a dye aggregate facilitated by DBS.     

Connecting Linear Polymers Molecular Structure to Viscoelastic Properties and Melt Flow Index

A modeling pathway and software tool for linking entangled linear polymer molecular properties to linear viscoelasticity and melt index (MI) values is presented. A reptation model links molecular properties to the flow curve, and then, an ANSYS Polyflow model calculates MI values based on the flow curve predicted. The method is thoroughly tested and validated for uni‐ and bimodal, low‐ and high‐density polyethylene grades. An overall accuracy level in the range of 90% on average is exhibited, considering both model prediction steps: (i) molecular weight distribution to flow curve and (ii) flow curve to MI.

     

Folate‐Conjugated PEG on Single Walled Carbon Nanotubes for Targeting Delivery of Doxorubicin to Cancer Cells

A highly effective drug carrier is constructed by coating folic acid‐terminated poly(ethylene glycol) (PEG‐FA) on single walled carbon nanotubes (SWNTs) in a facile non‐covalent method. The anti‐cancer drug, doxorubicin (DOX), is further loaded on the surface of SWNTs at a very high loading efficiency, 149.3 ± 4.1%. The drug system (DOX/PEG‐FA/SWNTs) exhibits excellent stability under neutral pH conditions such as serum, but dramatically releases DOX at reduced pH typical of the tumour environment and intracellular lysosomes and endosomes. With the help of FA, DOX/PEG‐FA/SWNTs tend to selectively attach onto cancer cells and enter the lysosomes or endosomes by clathrin‐mediated endocytosis. This can greatly improve the pharmaceutical efficiency and reduce potential side effects.