Evolutionary dynamics of RNA-like replicator systems: A bioinformatic approach to the origin of life

We review computational studies on prebiotic evolution, focusing on informatic processes in RNA-like replicator systems. In particular, we consider the following processes: the maintenance of information by replicators with and without interactions, the acquisition of information by replicators having a complex genotype–phenotype map, the generation of information by replicators having a complex genotype–phenotype–interaction map, and the storage of information by replicators serving as dedicated templates. Focusing on these informatic aspects, we review studies on quasi-species, error threshold, RNA-folding genotype–phenotype map, hypercycle, multilevel selection (including spatial self-organization, classical group selection, and compartmentalization), and the origin of DNA-like replicators. In conclusion, we pose a future question for theoretical studies on the origin of life.     

Measurement of diameter of cylindrical openings using a disk beam probe

The diameter of cylindrical openings is conventionally measured with the mechanical and contact method. In this paper, we propose a contactless optical approach to measure dimensions of inner profile by a disk beam probe. The measurement is carried out illuminating the inner cylindrical opening with a light sheet generated by the disk beam probe, acquiring the light-section image of the object with an image sensor through a widefield lens, then numerically extracting the diameter. During measurement, the probe is aligned inside the openings with high freedom, which causes the optical section to manifest a variety of ellipses besides a circle accordingly. The measurement method copes with extracting the diameter of openings from various ellipse optical sections. The high freedom of probe alignment allows optical diameter measurement to be flexible and simple. The dimensions of cylindrical openings of manufactured parts were practically measured with the disk beam probe, and the results were confirmed with those measured with the vernier caliper.     

Counter‐Anion‐Regulated Mixed‐Valency of Cobalt(II/III) Centers in a Metallosupramolecular Framework

A diamagnetic Au^I₄Co^III₂ hexanuclear complex, [Au₄Co₂(dppe)₂(l ‐nmc)₄]²⁺ ([ 1_{L ‐ nmc} ]²⁺; dppe=1,2‐bis(diphenylphosphino)ethane, l ‐H₂nmc=N‐methyl‐l ‐cysteine), was newly synthesized by the reaction of [Co(l ‐nmc)₂]^? with [Au₂Cl₂(dppe)] and crystallized with different inorganic anions (X=ClO₄^?, NO₃^?, Cl^?, SO₄^2?) to produce ionic solids ([ 1_{L ‐ nmc} ]X_n). Single‐crystal X‐ray analysis revealed that all the solids crystallize in the chiral space group F432 with a face‐centered‐cubic lattice structure consisting of supramolecular octahedra of complex cations. The paramagnetic nature of all the solids was evidenced by magnetic susceptibility measurements, showing the variation of the oxidation states of two cobalt centers in [ 1_{L ‐ nmc} ]ⁿ⁺ from Co^II_1.00Co^III_1.00 for X=ClO₄^? or NO₃^? to Co^II_0.67Co^III_1.33 for X=Cl^?, via Co^II_0.83Co^III_1.17 for X=SO₄^2?. The difference in the Co^II/III mixed‐valences was explained by the difference in sizes and charges of counter anions accommodated in lattice interstices with a fixed volume.     

Racemic Tartrate/Malate Anions Combine with Racemic Complex Cations to Form Optically Active Ionic Crystals

Spontaneous resolution has attracted continuing attention in various research fields since Pasteur's work on the crystallization behavior of racemic tartrate. Here, a unique example of this phenomenon is reported, involving ionic crystals generated from racemic RR/SS- tartrate or R/S-malate and racemic ΔΔ/ΛΛ-[Ag₃Rh₂(2-aminoethanethiolato)₆]³⁺ (ΔΔ/ΛΛ-[ 1 ]³⁺) in water. RR- and SS-tartrate selectively recognize the ΛΛ and ΔΔ isomers of [ 1 ]³⁺ to produce ionic crystals of (ΛΛ-[ 1 ])₂(RR-tartrate)₃ and (ΔΔ-[ 1 ])₂(SS-tartrate)₃, respectively, which can undergo spontaneous resolution. While spontaneous resolution also occurs when using R/S-malate, R- and S-malate select the opposite isomers of [ 1 ]³⁺ to give ionic crystals of (ΔΔ-[ 1 ])₂(R-malate)₃ and (ΛΛ-[ 1 ])₂(S-malate)₃, respectively. In the presence of S-aspartate, (ΛΛ-[ 1 ])₂(R-tartrate)₃ and (ΔΔ-[ 1 ])₂(S-tartrate)₃ are preferentially crystallized from ΔΔ/ΛΛ-[ 1 ]³⁺ and RR/SS-tartrate at solution pH values of 6 and 10, respectively. This finding provides significant insight into the optical resolution of chemical species by spontaneous resolution and the origin of homochirality in nature.     

Improvement of in vitro-transcribed amber suppressor tRNAs toward higher suppression efficiency in wheat germ extract

In vitro-transcribed, unmodified, and non-aminoacylated amber suppressor tRNAs that are recognized by natural aminoacyl-tRNA synthetase were improved toward higher suppression efficiency in batch-mode cell-free translation in wheat germ extract. The suppression efficiency of the suppressor obtained through four sequence optimization steps (anticodon alteration of natural tRNAs (the first generation); chimerization of the efficient suppressors in the first generation; investigation and optimization of the effective parts in the second generation; combination of the optimized parts in the third generation) and by the terminal tuning was approximately 60%, which was 2.4-fold higher than that of the best suppressor in the first generation. In addition, an eRF1 aptamer further increased the efficiency up to 85%. This highly efficient suppression system also functioned well in a dialysis-based large-scale protein synthesis.     

PHOTODYNAMIC INACTIVATION OF RUBELLA VIRUS ENHANCES RECOMBINATION WITH A LATENT VIRUS OF A BABY HAMSTER KIDNEY CELL LINE BHK21*

Rubella virus is very sensitive to photodynamic action. When tested with 1.2 X 10(-5) M toluidine blue and 8 W fluorescent lamp at a fluence of 11 W/m2, inactivation kinetics showed a linear single hit curve with a k value of 1.48 min-1. Photodynamic inactivation of rubella virus greatly enhanced recombination with a latent virus (R-virus) of baby hamster kidney BHK21 cells. In contrast, no hybrids were detected in lysates of the cells infected with either UV-treated or untreated rubella virus. Therefore, hybrid viruses were readily detected only in lysates of BHK21 cells infected with photodynamically treated rubella virus. Photodynamic damage of rubella virus genomes generated a new hybrid type (hybrid type 3) in addition to a previously described type 2 hybrid (formerly designated as HPV-RV variant). Although both of these hybrid types carry the CF antigens of rubella virus, plaque forming ability of type 3 hybrid is neutralized neither by anti-rubella serum nor by anti-latent virus serum while type 2 hybrid is neutralized by anti-latent virus serum.     

Heterometallation of Photoluminescent Silver(I) Sulfide Nanoclusters Protected by Octahedral Iridium(III) Thiolates

The recently-increasing interest in coinage metal clusters stems from their photophysical properties, which are controlled via heterometallation. Herein, we report homometallic Ag^I₄₆S₁₃ clusters protected by octahedral fac-[Ir(aet)₃] (aet=2-aminoethanethiolate) molecules and their conversion to heterometallic Ag^I₄₃M^I₃S₁₃ (M=Cu, Au) clusters. The reactions of fac-[Ir(aet)₃] with Ag⁺ and penicillamine produced [Ag₄₆S₁₃{Ir(aet)₃}₁₄]²⁰⁺ ([ 1 ]²⁰⁺), where a spherical Ag^I₄₆S₁₃ cluster is covered by fac-[Ir(aet)₃] octahedra through thiolato bridges. [ 1 ]²⁰⁺ was converted to [Ag₄₃M₃S₁₃{Ir(aet)₃}₁₄]²⁰⁺ ([ 1^M ]²⁰⁺) with an Ag^I₄₃M^I₃S₁₃ cluster by treatment with M⁺, retaining its overall structure. [ 1 ]²⁰⁺ was photoluminescent and had an emission band ca. 690 nm that originated from an S-to-Ag charge transfer. While [ 1^Cu ]²⁰⁺ showed an emission band with a slightly higher energy of ca. 650 nm and a lower quantum yield, the emission band for [ 1^Au ]²⁰⁺ shifted to a much higher energy of ca. 590 nm with an enhanced quantum yield.     

Synthesis of two water-soluble polysaccharides by Acetobacter sp. NCI 1005

A new polysaccharide was isolated from the culture of Acetobacter aceti subsp. xylinum (A. xylinum) NCI 1005 grown on sucrose. The structure of the polymer was analyzed by nuclear magnetic resonance (NMR) spectroscopy. The water-soluble polysaccharide (WSP) was determined to be β(2, 6) linked polyfructan, which was structurally different from the polymer synthesized from glucose instead of sucrose by the same strain. The discovery of the new polysaccharide has elucidated that the bacterium has the ability to synthesize two different kinds of water-soluble polysaccharides.