An amine-reactive tetraphenylethylene derivative for protein detection in SDS-PAGE

A new aggregation-induced emission (AIE) compound 1,2-bis[4-(isothiocyanatomethyl)phenyl]-1,2-diphenylethene (2) was synthesized for use in SDS-PAGE. The molecule is practically nonemissive in solution but becomes highly emissive after reacting with the amine groups of the proteins by either the prestaining or poststaining method. The sensitivity of 2 achieved in the prestaining method is the same as that of Coomassie brilliant blue (CBB), while that observed in the poststaining method is higher than that of CBB. Excellent linear responses with the amount of protein were obtained in both cases. The detection of a mixture of proteins with different molecular weights was successfully achieved

Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework

The identification of transcription factor binding sites and cis-regulatory motifs is a frontier whereupon the rules governing protein-DNA binding are being revealed. Here, we developed a new method (DEep Sequence and Shape mOtif or DESSO) for cis-regulatory motif prediction using deep neural networks and the binomial distribution model. DESSO outperformed existing tools, including DeepBind, in predicting motifs in 690 human ENCODE ChIP-sequencing datasets. Furthermore, the deep-learning framework of DESSO expanded motif discovery beyond the state-of-the-art by allowing the identification of known and new protein-protein-DNA tethering interactions in human transcription factors (TFs). Specifically, 61 putative tethering interactions were identified among the 100 TFs expressed in the K562 cell line. In this work, the power of DESSO was further expanded by integrating the detection of DNA shape features. We found that shape information has strong predictive power for TF-DNA binding and provides new putative shape motif information for human TFs. Thus, DESSO improves in the identification and structural analysis of TF binding sites, by integrating the complexities of DNA binding into a deep-learning framework

Integration of aggregation-induced emission and delayed fluorescence into electronic donor–acceptor conjugates

A series of luminogens comprised electron donors and acceptors are found to possess two types of interesting photophysical processes of aggregation-induced emission (AIE) and delayed fluorescence. According to theory calculation, restriction of intramolecular motions accounts for their AIE characteristics. Moreover, a separated distribution of the HOMOs and the LUMOs of these luminogens leads to small DEST values and therefore delayed fluorescence

Ferrocene-Decorated Hyperbranched Poly(aroxycarbonylphenylene)s: Synthesis, Light Refraction, Photopatterning and Precursor to Magnetic Ceramics

Ferrocene-decorated hyperbranched poly[1,3,5-tri(aroycarbonyl)phenylene]s (hb-PTACPs) are prepared in moderate yields with high molecular weights by one-pot polycyclotrimerization of 4,4'-isopropylidenediphenyl bipropiolate with 4-(ferrocenylmethyl)phenyl propiolate in reflux dimethylformamide. All the polymers are soluble and film-forming. They enjoy high thermal stability and lost little of their weight when heated to 300 °C under nitrogen. Thin solid films of the organometallic polymers shows high refractive indices (RI = 1.7038–1.6295) in the wavelength region of 400–1,700 nm. Ceramization of the organometallic hb-PTACPs at high temperature under inert atmosphere gives iron nanoparticles with high magnetizabilities. The organometallic polymers are readily cross-linked under UV irradiation and pyrolysis of the patterned polymer films produces magnetic ceramic patterns with good shape retention

IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq

group of genes controlled as a unit, usually by the same repressor or activator gene, is known as a regulon. The ability to identify active regulons within a specific cell type, i.e., cell-type-specific regulons (CTSR), provides an extraordinary opportunity to pinpoint crucial regulators and target genes responsible for complex diseases. However, the identification of CTSRs from single-cell RNA-Seq (scRNA-Seq) data is computationally challenging. We introduce IRIS3, the first-of-its-kind web server for CTSR inference from scRNA-Seq data for human and mouse. IRIS3 is an easy-to-use server empowered by over 20 functionalities to support comprehensive interpretations and graphical visualizations of identified CTSRs. CTSR data can be used to reliably characterize and distinguish the corresponding cell type from others and can be combined with other computational or experimental analyses for biomedical studies. CTSRs can, therefore, aid in the discovery of major regulatory mechanisms and allow reliable constructions of global transcriptional regulation networks encoded in a specific cell type. The broader impact of IRIS3 includes, but is not limited to, investigation of complex diseases hierarchies and heterogeneity, causal gene regulatory network construction, and drug development

Concentration effects in solid-state CD spectra of chiral atropisomeric compounds

Atropisomerism is one of the basic concepts in stereochemistry. Chiral crystals of stereochemically labile atropisomers that originated from Mirror Symmetry Breaking (MSB) can only be characterized by solid-state chiroptical techniques. Herein, solid-state circular dichroism and UV-Vis spectra of six atropisomeric compounds (most of them were obtained from MSB) have been studied. A concentration effect including a wavelength shift and inverse concentration-dependence has been found and preliminarily explained by the absorption flattening effect, scattering effect and the torsion in the molecular structures.National Natural Science Foundation of China[20973136, 20974028, 20732004]; Natural Science Foundation of Fujian Province[2010J01048