Phylogenetic analysis of endogenous viral elements in the rice genome reveals local chromosomal evolution in Oryza AA-genome species.

Introduction: Rice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family Caulimoviridae. These viral elements, known as endogenous RTBV-like sequences (eRTBVLs), comprise five subfamilies, eRTBVL-A, -B, -C, -D, and -X. Four subfamilies (A, B, C, and X) are present to a limited degree in the genomes of the Asian cultivated rice Oryza sativa (spp. japonica and indica) and the closely related wild species Oryza rufipogon. Methods: The eRTBVL-D sequences are widely distributed within these and other Oryza AA-genome species. Fifteen eRTBVL-D segments identified in the japonica (Nipponbare) genome occur mostly at orthologous chromosomal positions in other AA-genome species. The eRTBVL-D sequences were inserted into the genomes just before speciation of the AA-genome species. Results and discussion: Ten eRTBVL-D segments are located at six loci, which were used for our evolutionary analyses during the speciation of the AA-genome species. The degree of genetic differentiation varied among the eRTBVL-D segments. Of the six loci, three showed phylogenetic trees consistent with the standard speciation pattern (SSP) of the AA-genome species (Type A), and the other three represented phylogenies different from the SSP (Type B). The atypical phylogenetic trees for the Type B loci revealed chromosome region-specific evolution among the AA-genome species that is associated with phylogenetic incongruences: complex genome rearrangements between eRTBVL-D segments, an introgression between the distant species, and low genetic diversity of a shared eRTBVL-D segment. Using eRTBVL-D as an indicator, this study revealed the phylogenetic incongruence of local chromosomal regions with different topologies that developed during speciation.

A Photoredox/Sulfide Dual Catalysis System That Uses Sulfide Radical Cations to Promote Alkene Chlorotrifluoromethylation.

Sulfides and their derivatives are among the most important class of reagent in synthetic chemistry. Despite the importance of such compounds, the use of sulfide radical cations in synthetic chemistry is underdeveloped. To address this issue, herein, we describe alkene chlorotrifluoromethylation reactions promoted by photoredox/sulfide dual catalysis systems, which involves sulfide radical cations generated through the oxidation of sulfides by a photoredox catalyst. The high functional group tolerance of this chemistry was demonstrated using natural products and drug molecules as substrate alkenes.

Synthesis of N-(acyloxy)-N-alkynylamides via generation of "C2" from hypervalent alkynyliodane and a weak base.

The first synthesis of N-(acyloxy)ynamides was realized through the coupling of N-(acyloxy)amides and hypervalent alkynyliodane under mild conditions. This reaction probably involves biradical species ("C2") generation and radical processes. Furthermore, we also demonstrated that N-(acyloxy)ynamide could be transformed into a N-sulfonylimidate derivative by a copper catalyst. This study provides new building blocks for synthetic organic chemistry reactions and improves understanding of the chemical reactivity of "C2".

Prolonged infective SARS-CoV-2 omicron variant shedding in a patient with diffuse large B cell lymphoma successfully cleared after three courses of remdesivir.

We report a case of prolonged shedding of the infective SARS-CoV-2 omicron variant BA.1.1.2 in a 79-year-old male patient with diffuse large B-cell lymphoma, after receiving chemotherapy with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisolone (R-CHOP). The patient was admitted to our hospital in late March 2022 for the sixth course of R-CHOP chemotherapy. Initially, the patient tested negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using an in-hospital loop-mediated amplification assay with a nasopharyngeal swab, both on the day of admission and three days later. However, the patient developed fever and was diagnosed with coronavirus disease (COVID-19) six days after admission and was suspected to have contracted the infection in the ward. Viral shedding continued for more than three months, with confirmed viral infectivity. As compared to the original Wuhan-Hu-1/2019 strain, amino acid substitutions including S36 N in non-structural protein (NSP)2, S148P, S1265del and L1266I in NSP3, G105D in NSP4, G496S, A831V, or V987F in spike protein, and I45T in open-reading frame (ORF)9b were randomly detected in isolated viruses. Although the patient had received two doses of the BNT162b2 vaccine approximately six months earlier and the third dose on day 127 after the infection, both serum anti-spike and anti-nuclear protein IgG and IgM tests were negative at day 92, 114, and 149 after the infection. The patient finally cleared the virus after the third course of remdesivir and did not have further recurrence.

Order-order transitions in poly(N-octadecyl acrylamide-co-hydroxyethyl acrylamide) statistical copolymer films.

This study demonstrates that a simple statistical copolymer can form self-assembled lamellae, whose structures depend on both the comonomer composition and the annealing temperature. Statistical copolymers of octadecyl acrylamide and hydroxyethyl acrylamide [p(ODA/HEAm)] were prepared via free-radical copolymerization, and their thermal properties were studied by differential scanning calorimetry. Thin films of p(ODA/HEAm) were prepared via spin-coating, and their structures were analyzed using X-ray diffraction. It was found that copolymers with HEAm contents between 28 and 50% formed self-assembled lamellae upon annealing at a temperature ∼10 °C above the glass-transition temperature. The self-assembled form was found to possess a "side-chain-mixed" lamellar structure, in which the ODA and HEAm side chains are oriented perpendicular to the lamellar plane composed of the polymer main chain. Interestingly, a copolymer with a HEAm content between 36 and 50% transformed from the side-chain-mixed lamellar structure to generate a "side-chain-segregated" lamellar structure upon annealing at a significantly higher temperature (∼50 °C above Tg). In this structure, the ODA and HEAm side chains were found to be oriented in opposite directions but perpendicular to the lamellar plane. The packing of the side chains in the lamellar structures was studied using Fourier-transform infrared spectroscopy. It was concluded that the structures of the self-assembled lamellae are determined by the strain forces generated during self-assembly, and by the segregation forces existing between the comonomers.

Does Selectivity of Molecular Catalysts Change with Time? Polymerization Imaged by Single-Molecule Spectroscopy.

The chemoselectivity of molecular catalysts underpins much of modern synthetic organic chemistry. However, little is known about the selectivity of individual catalysts because this single-catalyst-level behavior is hidden by the bulk catalytic behavior. Here, for the first time, the selectivity of individual molecular catalysts for two different reactions is imaged in real time at the single-catalyst level. This imaging is achieved through fluorescence microscopy paired with spectral probes that produce a snapshot of the instantaneous chemoselectivity of a single catalyst for either a single-chain-elongation or a single-chain-termination event during ruthenium-catalyzed polymerization. Superresolution imaging of multiple selectivity events, each at a different single-molecular ruthenium catalyst, indicates that catalyst selectivity may be unexpectedly spatially and time-variable.

Proximate stochastic chiral symmetry breaking is mechanically tunable: formation of enantiomeric hetero-double-helices and aggregates from racemic oxymethylenehelicene oligomers.

A mixture of oxymethylenehelicene (P)-hexamer and (M)-hexamer in solution exhibited chiral symmetry breaking, which was induced by mechanical stirring, during the formation of enantiomeric hetero-double-helices and their aggregates. A racemic 50 : 50 mixture was heated to 90 °C to form a dissociated state, and then cooled to 25 °C. Mechanical stirring with a magnetic stirrer at 2000 rpm for 100 h resulted in the exhibition of a strong negative Cotton effect at 322 nm. Repeated experiments provided negative Cotton effects, which is due to the deterministic chiral symmetry breaking. No change in the Cotton effect occurred in the absence of stirring. The (P)-hexamer to (M)-hexamer mixing molar fraction was varied, and a positive Cotton effect appeared at molar fractions between 40 : 60 and 46 : 54 and a negative Cotton effect at molar fractions between 48 : 52 and 60 : 40, which was reversed at 47 : 53. The slight deviation of symmetry from that at 50 : 50 was termed proximate stochastic chiral symmetry breaking. The process of chiral symmetry breaking could be tuned by varying the procedures of mechanical stirring and mixing procedures for solutions of (P)-hexamer and/or (M)-hexamer.

Chemical Systems Involving Two Competitive Self-Catalytic Reactions.

Self-catalytic reactions are chemical phenomena, in which a product catalyzes the reactions of substrates further to yield products. A significant amplification of product concentration occurs during the reactions in a dilute solution, which exhibit notable properties such as sigmoidal kinetics, seeding effects, and thermal hysteresis. Chemical systems involving two competitive self-catalytic reactions can be considered, in which the competitive formation of two products occurs, which is affected by environmental changes, subtle perturbations, and fluctuations, and notable chemical phenomena appear such as formation of different structures in response to slow/fast temperature changes, chiral symmetry breaking, shortcut in reaction time, homogeneous-heterogeneous transitions, and mechanical responses. Studies on such chemical systems provide understanding on biological systems and can also be extended to the development of novel functional materials.

Chemical CD oscillation and chemical resonance phenomena in a competitive self-catalytic reaction system: a single temperature oscillation induces CD oscillations twice.

Chemical CD oscillation and chemical resonance phenomena appear in a competitive chemical reaction system involving amplification. A pseudoenantiomeric mixture of an aminomethylenehelicene (P)-tetramer and an (M)-hexamer in toluene forms three states, namely hetero-double-helix B, hetero-double-helix C, and dissociated random-coil 2A. When the temperature of the solution is oscillated between -5 and 38 °C at a rate of 2 K min-1, Δε reaches maxima twice during a single temperature oscillation, which is called a chemical CD oscillation phenomenon. The phenomenon arises from the sharp competition between the two self-catalytic 2A + C-to-2C and 2A + B-to-2B reactions. In addition, the chemical CD oscillation appears, when temperature oscillation occurs at a rate of 2 K min-1, and higher and lower rates provide a single maximum, a process referred to as the chemical resonance phenomenon. The changes in concentration induced by temperature oscillation repeatedly crossed equilibrium.

Ferroelectric Alkylamide-Substituted Helicene Derivative with Two-Dimensional Hydrogen-Bonding Lamellar Phase.

Alkylamide (-CONHC nH2 n+1)-substituted benzene and its pyrene derivatives have shown a discotic hexagonal columnar liquid-crystalline phase through a one-dimensional (1D) intermolecular N-H···O═ hydrogen-bonding interaction, the direction of which is inverted through the application of an alternate current voltage. The polar hydrogen-bonding chains and dipole inversion reveal a ferroelectric polarization-electric field ( P- E) hysteresis curve. Non-π-planar helicene derivatives bearing two -CONHC14H29 chains also indicate a ferroelectric response. The racemic helicene derivative shows a bilayer lamellar liquid-crystal phase within a temperature range of 330-420 K, whereas there is no liquid crystallinity for the optically active derivative because of the different molecular assembly structure. The racemic phase is constructed through a two-dimensional (2D) N-H···O═ hydrogen-bonding network, which shows ferroelectric P- E hysteresis curves at above 340 K. The collective dipole inversion in the 2D layer contributes to the ferroelectricity in the lamellar phase. The remanent polarization ( Pr) of 11.1 µC cm-2 is about 6 times higher than those of the π-planar benzene- and pyrene-based 1D ferroelectrics. Both the density of the hydrogen-bonding site and the domain orientation in the 2D system are higher than those of the 1D columnar system.

Formation and dissociation of synthetic hetero-double-helix complex in aqueous solutions: significant effect of water content on dynamics of structural change.

A 1 : 1 mixture of the ethynylhelicene pseudoenantiomers (M)-tetramer and (P)-pentamer, which possess hydrophilic terminal tri(ethyleneglycol) (TEG) groups, changes their structures in the water-THF (10 µM) solvent system between dissociated random-coils and an associated hetero-double-helix upon heating and cooling. A small change in water content between 30 and 33% significantly affects the dynamics of structural changes. At 30% water content, heating to 60 °C causes rapid formation of random-coil and cooling to 10 °C causes the rapid formation of hetero-double-helix, accompanied by repeated changes in Δε at 369 nm between 0 and -2000 cm-1 M-1. Heating and cooling experiments at constant rates between 60 and 10 °C resulted in sigmoidal curves in Δε/temperature profiles, which indicate rapid structural changes. Different phenomena occurred at 33% water content. Heating to 60 °C and cooling to 0 °C initially induced changes in Δε between 0 and -2000 cm-1 M-1, and repeated cycles gradually reduced the range between 0 and -500 cm-1 M-1. Heating and cooling experiments at constant rates between 60 and 10 °C caused small changes in Δε, and repeated cycles at 10 °C gradually increased Δε to -500 cm-1 M-1. These phenomena involved rapid changes in molecular structure and slow structural changes in the water-THF solvent system. The sharp switching of the dynamics of structural changes at water content between 30 and 33% indicated discontinuous structural changes in the hydration of TEG and/or in water clusters in the vicinity of oligomer molecules.

Long-Range Anisotropic Structural Films and Fibers Formed from Lyotropic Liquid Crystal Gels Containing Hetero-Double-Helices with C16 Terminal Groups.

Long-range anisotropic structural materials exhibit notable optical and mechanical properties, and an efficient method for synthesizing such materials involving self-assembly of well-defined monodispersed organic molecules is described here. Hetero-double-helices are formed in toluene using a pseudoenantiomeric mixture of an ethynylhelicene ( M)-tetramer with C16 terminal groups and a ( P)-pentamer. When the concentration of the mixture was increased, the hetero-double-helices self-assembled to form lyotropic liquid crystal gels. On evaporating the solvent by drop casting, a long-range anisotropic structural film with a single domain and a size of up to centimeter order was spontaneously formed. Kinetics analysis of the film formation indicated the generation of perpendicularly aligned liquid crystal domains at the interface of the liquid and solid phases. When the lyotropic liquid crystal gel was extruded into methanol, a long-range anisotropic structural fiber with a single domain was formed. Different shapes of long-range anisotropic structural materials were obtained by different mechanical treatments of lyotropic liquid crystal gels.

Optically active iodohelicene derivatives exhibit histamine N-methyl transferase inhibitory activity.

Optically active helicene derivatives inhibit the activity on histamine N-methyl transferase (HNMT). Specifically, methyl (P)-1,12-dimethylbenzo[c]phenanthrene-8-carboxylate with 6-iodo and 5-trifluoromethanesulfonyloxy groups inhibits HNMT activity on the µM order of IC50. Chirality is important, and (M)-isomers exhibits substantially reduced activity. The 6-iodo group is also essential, which suggests the involvement of halogen bonds in protein binding. Substituents on the sulfonate moiety also affect the inhibitory activity.

Ancient Endogenous Pararetroviruses in Oryza Genomes Provide Insights into the Heterogeneity of Viral Gene Macroevolution.

Endogenous viral sequences in eukaryotic genomes, such as those derived from plant pararetroviruses (PRVs), can serve as genomic fossils to study viral macroevolution. Many aspects of viral evolutionary rates are heterogeneous, including substitution rate differences between genes. However, the evolutionary dynamics of this viral gene rate heterogeneity (GRH) have been rarely examined. Characterizing such GRH may help to elucidate viral adaptive evolution. In this study, based on robust phylogenetic analysis, we determined an ancient endogenous PRV group in Oryza genomes in the range of being 2.41-15.00 Myr old. We subsequently used this ancient endogenous PRV group and three younger groups to estimate the GRH of PRVs. Long-term substitution rates for the most conserved gene and a divergent gene were 2.69 × 10-8 to 8.07 × 10-8 and 4.72 × 10-8 to 1.42 × 10-7 substitutions/site/year, respectively. On the basis of a direct comparison, a long-term GRH of 1.83-fold was identified between these two genes, which is unexpectedly low and lower than the short-term GRH (>3.40-fold) of PRVs calculated using published data. The lower long-term GRH of PRVs was due to the slightly faster rate decay of divergent genes than of conserved genes during evolution. To the best of our knowledge, we quantified for the first time the long-term GRH of viral genes using paleovirological analyses, and proposed that the GRH of PRVs might be heterogeneous on time scales (time-dependent GRH). Our findings provide special insights into viral gene macroevolution and should encourage a more detailed examination of the viral GRH.

Lineage-specific gene acquisition or loss is involved in interspecific hybrid sterility in rice.

Understanding the genetic basis of reproductive barriers between species has been a central issue in evolutionary biology. The S1 locus in rice causes hybrid sterility and is a major reproductive barrier between two rice species, Oryza sativa and Oryza glaberrima The O. glaberrima-derived allele (denoted S1g) on the S1 locus causes preferential abortion of gametes with its allelic alternative (denoted S1s) in S1g/S1s heterozygotes. Here, we used mutagenesis and screening of fertile hybrid plants to isolate a mutant with an allele, S1mut, which does not confer sterility in the S1mut/S1g and S1mut/S1s hybrids. We found that the causal mutation of the S1mut allele was a deletion in the peptidase-coding gene (denoted "SSP") in the S1 locus of O. glaberrima No orthologous genes of SSP were found in the O. sativa genome. Transformation experiments indicated that the introduction of SSP in carriers of the S1s allele did not induce sterility. In S1mut/S1s heterozygotes, the insertion of SSP led to sterility, suggesting that SSP complemented the loss of the functional phenotype of the mutant and that multiple factors are involved in the phenomenon. The polymorphisms caused by the lineage-specific acquisition or loss of the SSP gene were implicated in the generation of hybrid sterility. Our results demonstrated that artificial disruption of a single gene for the reproductive barrier creates a "neutral" allele, which facilitates interspecific hybridization for breeding programs.

Synthesis and Self-Assembly of Chiral Cylindrical Molecular Complexes: Functional Heterogeneous Liquid-Solid Materials Formed by Helicene Oligomers.

Chiral cylindrical molecular complexes of homo- and hetero-double-helices derived from helicene oligomers self-assemble in solution, providing functional heterogeneous liquid-solid materials. Gels and liotropic liquid crystals are formed by fibril self-assembly in solution; molecular monolayers and fibril films are formed by self-assembly on solid surfaces; gels containing gold nanoparticles emit light; silica nanoparticles aggregate and adsorb double-helices. Notable dynamics appears during self-assembly, including multistep self-assembly, solid surface catalyzed double-helix formation, sigmoidal and stairwise kinetics, molecular recognition of nanoparticles, discontinuous self-assembly, materials clocking, chiral symmetry breaking and homogeneous-heterogeneous transitions. These phenomena are derived from strong intercomplex interactions of chiral cylindrical molecular complexes.

Development of a highly sensitive in vitro system to detect and discriminate between vitamin D receptor agonists and antagonists based on split-luciferase technique.

Split-luciferase techniques are widely used to detect protein-protein interaction and bioactive small molecules including some hormones and vitamins. Previously, we successfully expressed chimeric proteins of luciferase and the ligand binding domain (LBD) of the vitamin D receptor (VDR), LucC-LBD-LucN in COS-7 cells. The LucC-LBD-LucN biosensor was named split-luciferase vitamin D biosensor (SLDB). This biosensor can detect and discriminate between VDR agonists and antagonists in mammalian cells. In this study, we established an in vitro screening system for VDR ligands using the SLDB proteins expressed in Escherichia coli (E. coli) cells. Our in vitro screening system using cell lysate of recombinant E. coli cells could be completed within 30min, and its activity was unchanged after 10 freeze-thaw cycles. This highly sensitive and convenient system would be quite useful to screen VDR ligands with therapeutic potential for various bone-related diseases, age-related cognitive disorders, cancer, and immune disorders. In addition, our system might be applicable to diagnostic measurement of serum concentrations of 25-hydroxyvitamin D3 and 1α,25-dihydroxyvitamin D3.

Total Synthesis of (+)-Gliocladin C Based on One-Pot Construction of a 3a-(3-Indolyl)pyrroloindoline Skeleton by Sulfonium-Mediated Cross-Coupling of Tryptophan and Indole.

Total synthesis of (+)-gliocladin C has been achieved on the basis of one-pot construction of the 3a-(3-indolyl)pyrroloindoline core structure by the cross-coupling of a tryptophan derivative and an indole promoted by a sulfonium species generated from dialkylsulfoxide and triflic anhydride.

[Synthesis, Aggregation, Self-assembly, and Dynamic Properties of Helicene Oligomers].

Biological systems exhibit dynamic phenomena at the macroscopic level as a result of the hierarchical integration of phenomena at the molecular level. For example, a number of amino acids compose actin proteins, which form three-dimensional structures determined by the sequence of amino acids. They form fibers by self-assembly, which then form ordered structures such as meshes, lyotropic liquid crystals (LCs), and bundles. The dynamic and reversible polymorphism between these nano- to centimeter-sized ordered structures is essential for biological functions such as cell division, contraction, and locomotion. To understand biological systems and create new functional materials, it is essential to develop a methodology to integrate phenomena at the molecular level into those at the macroscopic level using synthetic molecules. In this research, synthetic oligomers containing helicenes, which exhibit reversible structural transitions between cylindrical double helices and random coils in response to thermal stimuli, were employed as building blocks for the development of such a methodology. The properties of homo- and hetero-double helices at the molecular level were first controlled by taking advantage of the diversity of their molecular structures. Then, nano- to micrometer-sized structures were constructed by the self-assembly of hetero-double helices, which include fibers/gels, vesicles, and lyotropic LCs, and their dynamic properties were controlled by molecular design.

Pendant-Type Helicene Oligomers with p-Phenylene Ethynylene Main Chains: Synthesis, Reversible Formation of Ladderlike Bimolecular Aggregates, and Control of Intramolecular and Intermolecular Aggregation.

Pendant-type (P)-helicene oligomers with p-phenylene ethynylene main chains up to a tetramer were synthesized by a building block method. The (P)-tetramer reversibly formed a ladderlike bimolecular aggregate upon cooling and disaggregated upon heating in (trifluoromethyl)benzene. Two bis(tetramer)s, in which two (P)-tetramers were connected by hexadecamethylene linkers, were also synthesized. The head-to-tail bis(tetramer) formed an intramolecular aggregate, and the head-to-head bis(tetramer) formed an intermolecular aggregate in toluene. The results suggest the antiparallel aggregation structure of the pendant-type (P)-tetramers. The structure of the linker was proven to be effective in controlling intramolecular and intermolecular aggregations.