Fluorophore‐Promoted RNA Folding and Photostability Enables Imaging of Single Broccoli‐Tagged mRNAs in Live Mammalian Cells

Spinach and Broccoli are fluorogenic RNA aptamers that bind DFHBI, a mimic of the chromophore in green fluorescent protein, and activate its fluorescence. Spinach/Broccoli‐DFHBI complexes exhibit high fluorescence in vitro, but they exhibit lower fluorescence in mammalian cells. Here, computational screening was used to identify BI, a DFHBI derivative that binds Broccoli with higher affinity and leads to markedly higher fluorescence in cells compared to previous ligands. BI prevents thermal unfolding of Broccoli at 37 °C, leading to more folded Broccoli and thus more fluorescent Broccoli‐BI complexes in cells. Broccoli‐BI complexes are more photostable owing to impaired photoisomerization and rapid unbinding of photoisomerized cis‐BI. These properties enable single mRNA containing 24 Broccoli aptamers to be imaged in live mammalian cells treated with BI. Small molecule ligands can thus promote RNA folding in cells, and thus allow single mRNA imaging with fluorogenic aptamers.     

Optimization of Biocompatibility for a Hydrophilic Biological Molecule Encapsulation System

Despite considerable advances in recent years, challenges in delivery and storage of biological drugs persist and may delay or prohibit their clinical application. Though nanoparticle-based approaches for small molecule drug encapsulation are mature, encapsulation of proteins remains problematic due to destabilization of the protein. Reverse micelles composed of decylmonoacyl glycerol (10MAG) and lauryldimethylamino-N-oxide (LDAO) in low-viscosity alkanes have been shown to preserve the structure and stability of a wide range of biological macromolecules. Here, we present a first step on developing this system as a future platform for storage and delivery of biological drugs by replacing the non-biocompatible alkane solvent with solvents currently used in small molecule delivery systems. Using a novel screening approach, we performed a comprehensive evaluation of the 10MAG/LDAO system using two preparation methods across seven biocompatible solvents with analysis of toxicity and encapsulation efficiency for each solvent. By using an inexpensive hydrophilic small molecule to test a wide range of conditions, we identify optimal solvent properties for further development. We validate the predictions from this screen with preliminary protein encapsulation tests. The insight provided lays the foundation for further development of this system toward long-term room-temperature storage of biologics or toward water-in-oil-in-water biologic delivery systems.     

Recognition of Dimethylarginine Analogues by Tandem Tudor Domain Protein Spindlin1

Epigenetic readout of the combinatorial posttranslational modification comprised of trimethyllysine and asymmetric dimethylarginine (H3K4me3R8me2a) takes place via biomolecular recognition of tandem Tudor-domain-containing protein Spindlin1. Through comparative thermodynamic data and molecular dynamics simulations, we sought to explore the binding scope of asymmetric dimethylarginine mimics by Spindlin1. Herein, we provide evidence that the biomolecular recognition of H3K4me2R8me2a is not significantly affected when R8me2a is replaced by dimethylarginine analogues, implying that the binding of K4me3 provides the major binding contribution. High-energy water molecules inside both aromatic cages of the ligand binding sites contribute to the reader–histone association upon displacement by histone peptide, with the K4me3 hydration site being lower in free energy due to a flip of Trp151.     

Use of FTIR spectroscopy coupled with ATR for the determination of atmospheric compounds

Attenuated total reflection Fourier transformed infrared spectroscopy (ATR-FTIR) can be successfully used for the quantitative determination of small amounts of pollutants like the organic fraction of aerosols. The relation between sample concentration and reflectance is described by the Kubelka-Munk equation and was found to be linearly proportional to the absorption band of some functional group. Several parameters like the matter of solid matrix, the cleaning of the sampling support, the treatment of reflectance spectra and the base line correction considerably influenced the reflectance spectra and facilitated data interpretations. The feasibility of the ATR-FTIR was evaluated by the monitoring of specific organic group bands on filters collected in the French cities of Grenoble and Clermont-Ferrand. We have obtained for hydroxyl group a calibration curve by plotting the relative intensity of reflectance versus the concentration. The linearity was obtained for OH from 1 × 10⁻¹ to 1 × 10⁰ mol L⁻¹ with r² = 0.9959. We can consider that for a direct measurement of the intensity of reflectance, it is possible to perform quantitative ATR-FTIR organic group analysis.     

Formation and emission of tetraalkylammonium salt molecular ions sputtered from a gelatin matrix

A gelatin matrix was simultaneously doped with nine equimolar, homologous, tetraalkylammonium salts ranging in mass from 210 to 700 Da. Bombardment of the sample with kiloelectronvolt ions resulted in a nonidentical distribution of relative cation intensities with a maximum at m/z 242 for samples with a total salt concentration of 0.004 g of salt/g of gelatin. A rapid increase in relative intensities with increasing mass is observed for the low mass salts and is believed to be linked to changes in the ionization efficiencies. The changes in ionization efficiencies are likely related to decreasing coulombic attractive forces between the organic cation and the counterion. Disappearance cross-sections, determined from decay curves, indicate that sputter-induced damage increases with increasing mass of the cation. Fragment-to-intact cation ratios also suggest that damage accumulates fastest in the heaviest salts. These observations indicate that desorption yields of the organic salts in a gelatin matrix decrease with increasing mass. In addition, suppression of lower mass tetraalkylammonium salt intact cation intensities was observed for salt-in-gelatin concentrations greater than 10⁻³ g/g.     

Best cooperative partner selection and input resource reallocation using DEA

Reallocation of input resources (RIR) is a process by which certain decision making units (DMUs) reallocate resources among themselves; a process that occurs frequently in many enterprises. In this paper, a new data envelopment analysis (DEA) approach is developed to select the best cooperative partner DMU. Context-dependent DEA is used to identify the different levels of best-practice frontiers. Two DEA-based models are established for two cooperative scenarios, namely, resources pooling only and best-practice sharing. A cooperative method is applied to determine how to reallocate the input resources, and Shapley value is used to estimate the revenue changes that the various DMUs should expect after RIR. Two different situations with different objectives are considered. One objective is to maximize total revenue for the partnership, while the other is to maximize the Shapley value. The proposed approaches are illustrated with two examples.     

Reactivity of tetrahydrochromeno[2,3‐b]indoles: chromic indicators of cyanide

The synthesis and reactivity of a tetrahydrochromeno[2,3‐b]indoles are reported. Evidence for reversible ring‐opening is based on H/D exchange and trapping experiments. These compounds readily undergo reaction with tetra‐n‐butylammonium cyanide. The cyanide reaction is 10–100× faster when the solution is irradiated with 350 nm light. Reaction with trimethylsilyl cyanide occurs only with UV irradiation demonstrating photoreactivity. The rate of tetrahydrochromeno[2,3‐b]indole ring‐opening is greater for (i) Me substitution at the hemiaminal carbon (compared to Ph), and (ii) substitution of fluorine at the 9‐position of the indole. Under acidic conditions, the ring‐opened indolium ion is observed. Copyright © 2013 John Wiley & Sons, Ltd.     

Reactive ligand influence on initiation in phenylene catalyst‐transfer polymerization

Synthesizing conjugated polymers via catalyst‐transfer polymerization (CTP) has led to unprecedented control over polymer sequence and molecular weight. Yet many challenges remain, including broadening the monomer scope and narrowing the molecular weight dispersities. Broad polymer dispersities can arise from nonliving pathways as well as slow initiation. Previously, slow initiation was observed in Ni‐mediated CTP of phenylene monomers. Although precatalysts with faster initiation rates have been reported, the rates still do not exceed propagation. Herein a second‐ and third‐generation of reactive ligands are described, along with a simple method for measuring initiation rates. A precatalyst with an initiation rate that exceeds propagation is now reported, however, the resulting polymer samples still exhibit broad dispersities, suggesting that slow initiation is not the most significant contributing factor in Ni‐mediated phenylene polymerizations. In addition, initiation rates measured under authentic polymerization conditions revealed that both exogenous triphenylphosphine and an ortho‐trifluoroethoxy substituent on the reactive ligand have a strong influence. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 1530–1535     

Superdense coding with single-particle entanglement

Recent work has explored the idea that nonlocality or entanglement involving a single particle should be taken seriously and has real measurable consequences. Theoretical and experimental schemes have shown, for example, that single-particle states can violate Bell’s inequalities. Here we discuss the possibility of using single-particle entanglement for implementing a superdense coding protocol. Particle-number superselection rules restrict this scheme to being able to transmit log₂(3) bits of information. While this falls short of the two-particle limit of two bits, it still exceeds what can be achieved without entanglement.