Forty years of in vitro evolution

It has been 40 years since Spiegelman and co-workers demonstrated how RNA molecules can be evolved in the test tube. This result established Darwinian evolution as a chemical process and paved the way for the many directed evolution experiments that followed. Chemists can benefit from reflecting on Spiegelman's studies and the subsequent advances, which have taken the field to the brink of the generation of life itself in the laboratory. This Review summarizes the concepts and methods for the directed evolution of RNA molecules in vitro.     

Determining the mechanical response of particle-laden fluid interfaces using surface pressure isotherms and bulk pressure measurements of droplets

The mechanical response of particle-laden fluid interfaces is determined by measuring the internal pressures of particle-coated drops as a function of the drop volume. The particle monolayers undergoing compression-expansion cycles exhibit three distinct states: fluid state, jammed state, and buckled state. The P-V curves are compared to the surface pressure isotherms Pi-A that are measured using a Langmuir trough and a Wilhelmy plate on a flat water-decane interface covered with the same particles. We find that in the fluid and jammed states, the water drop in decane can be described by the Young-Laplace equation. Therefore in these relatively low compression states, the bulk pressure measurements can be used to deduce the interfacial tension of the droplets and yield similar surface pressure isotherms to the ones measured with the Wilhelmy plate. In the buckled state, the internal pressure of the drop yields a zero value, which is consistent with the zero interfacial tension measured with the Wilhelmy plate. Moreover we find that the compressibility in the jammed state does not depend on the particle size.     

A simple non-invasive method to detect and monitor hypercapnia: the sodium [13C]bicarbonate breath test

Arterial partial pressure of carbon dioxide (paCO(2)) is commonly evaluated by an invasive test, the arterial blood gas analysis (ABG). The sodium [(13)C]bicarbonate breath test (SBT) can potentially estimate arterial paCO(2). We studied 55 subjects with respiratory disorders and performed the ABG and the SBT to determine if the SBT can predict hypercapnia. The percentage of (13)CO(2) recovered in exhaled breath at 30 minutes (PDR(30)) alone was able to discriminate clinically significant hypercapnia (>53 mmHg) with a sensitivity of 82 % and specificity of 93 % (p<0.001). To evaluate the clinical utility of the SBT as a non-invasive substitute to repeated ABG, we monitored the progress of seven chronic obstructive pulmonary disease (COPD) patients on therapy with both the ABG and the SBT. The PDR(30) values from the SBT were able to correctly predict improvement or worsening of paCO(2) with 100 % accuracy. In conclusion, the SBT is a simple test that can be used in clinical practice to detect clinically significant hypercapnia and monitor COPD patients before and after therapy.     

The ability to listen with independent ears

In three experiments, listeners identified speech processed into narrow bands and presented to the right ("target") ear. The ability of listeners to ignore (or even use) conflicting contralateral stimulation was examined by presenting various maskers to the target ear ("ipsilateral") and nontarget ear ("contralateral"). Theoretically, an absence of contralateral interference would imply selectively attending to only the target ear; the presence of interference from the contralateral stimulus would imply that listeners were unable to treat the stimuli at the two ears independently; and improved performance in the presence of informative contralateral stimulation would imply that listeners can process the signals at both ears and keep them separate rather than combining them. Experiments showed evidence of the ability to selectively process (or respond to) only the target ear in some, but not all, conditions. No evidence was found for improved performance due to contralateral stimulation. The pattern of interference found across experiments supports an interaction of stimulus-based factors (auditory grouping) and task-based factors (demand for processing resources) and suggests that listeners may not always be able to listen to the "better" ear even when it would be beneficial to do so.     

Evaluation of the Synthetic Potential of an AHBA Knockout Mutant of the Rifamycin Producer Amycolatopsis mediterranei

Supplementing an AHBA(?) mutant strain of Amycolatopsis mediterranei, the rifamycin producer, with a series of benzoic acid derivatives yielded new tetraketides containing different phenyl groups. These mutasynthetic studies revealed unique reductive properties of A. mediterranei towards nitro‐ and azidoarenes, leading to the corresponding anilines. In selected cases, the yields of mutaproducts (fermentation products isolated after feeding bacteria with chemically prepared analogs of natural building blocks) obtained are in a range (up to 118 mg L^?1) that renders them useful as chiral building blocks for further synthetic endeavors. The configuration of the stereogenic centers at C6 and C7 was determined to be 6R,7S for one representative tetraketide. Importantly, processing beyond the tetraketide stage is not always blocked when the formation of the bicyclic naphthalene precursor cannot occur. This was proven by formation of a bromo undecaketide, an observation that has implications regarding the evolutionary development of rifamycin biosynthesis.     

The Stabilizing Effects in Gold Carbene Complexes

Bonding and stabilizing effects in gold carbene complexes are investigated by using Kohn–Sham density functional theory (DFT) and the intrinsic bond orbital (IBO) approach. The π‐stabilizing effects of organic substituents at the carbene carbon atom coordinated to the gold atom are evaluated for a series of recently isolated and characterized complexes, as well as intermediates of prototypical 1,6‐enyne cyclization reactions. The results indicate that these effects are of particular importance for gold complexes especially because of the low π‐backbonding contribution from the gold atom.     

Self‐Assembly Mechanism of Nanoparticles of Ni‐Based Prussian Blue Analogues at the Air/Liquid Interface: A Synchrotron X‐ray Reflectivity Study

Prussian Blue analogue (PBA) nanoparticles can be self‐assembled at air/liquid interfaces to build novel materials with interesting magnetic features. Herein, we study the influence of the size of PBA Cs_0.4Ni[Cr(CN)₆]_0.9 and K_0.25Ni[Fe(CN)₆]_0.75 nanoparticles on the self‐assembly behavior by synchrotron X‐ray reflectivity. Both nanoparticles show similar Z‐potential values. The phospholipid dipalmitoylphosphatidylcholine and the amino surfactant dimethyldioctadecylammonium have been used as Langmuir monolayers to anchor the PBA nanoparticles and study the interplay of forces directing the self‐assembly of the nanoparticles at the surfactant/liquid interface. Whereas Cs_0.4Ni[Cr(CN)₆]_0.9 nanoparticles with a diameter of 8 nm form an incomplete layer at the surfactant/water interface, the larger K_0.25Ni[Fe(CN)₆]_0.75 nanoparticles with a diameter of 20 nm generate complete layers that can be stacked to one another. The size of the PBA nanoparticles is the main parameter determining the final arrangement at the air/liquid interface, due to the different extent of interparticle interaction. This study aims at the rationale design of PBA nanoparticles for an effective interfacial self‐assembly, ultimately leading to functional materials.     

Two π-Electrons Make the Difference: From BODIPY to BODIIM Switchable Fluorescent Dyes

(aza-)BODIPY dyes (boron dipyrromethene dyes) are well-established fluorophores due to their large quantum yields, stability, and diversity, which led to promising applications including imaging techniques, sensors, organic (opto)electronic materials, or biomedical applications. Although the control of the optical properties in (aza-)BODIPY dyes by peripheral functional groups is well studied, we herein present a novel approach to modify the 12 π-electron core of the dipyrromethene scaffold. The replacement of two carbon atoms in the β-position of a BODIPY dye by two nitrogen atoms afforded a 14 π-electron system, which was termed BODIIM (boron diimidazolylmethene) in systematic analogy to the BODIPY dyes. Remarkably, the BODIIM dye was obtained with a BH₂-rigidifying entity, which is currently elusive and highly sought after for the BODIPY dye class. DFT-Calculations confirm the [12+2] π-electron relationship between BODIPY and BODIIM and reveal a strong shape correlation between LUMO in the BODIPY and the HOMO of the BODIIM. The modification of the π-system leads to a dramatic shift of the optical properties, of which the fluorescent emission is most noteworthy and occurs at much larger Stokes shift, that is, ≈500 cm⁻¹ in BODIPY versus >4170 cm⁻¹ in BODIIM system in all solvents investigated. Nucleophilic reactivity was found at the meso-carbon atom in the formation of stable borane adducts with a significant shift of the fluorescent emission, and this behavior contrasts the reactivity of conventional BODIPY systems. In addition, the reverse decomplexation of the borane adducts was demonstrated in reactions with a representative N-heterocyclic carbene to retain the strongly fluorescent BODIIM compound, which suggests applications as fully reversible fluorescent switch.