Diversity of transactivation regions of DMRT1 in vertebrates.

BACKGROUND: Doublesex and mab-3 related transcription factor (DMRT) 1, commonly found in all vertebrates, regulates the transcription of genes involved in the masculinization and maintenance of gonadal somatic cells and/or germline cell development. DMRT1 has a DNA-binding domain called the DM domain and a transcription regulatory region. Unlike the former, there is little knowledge about the latter transcription regulatory region. This study aimed to identify the transcription activation regions of DMRT1 from four species: humans and mice (mammals), leopard geckos (reptiles), and medaka (teleost fish), adding perspectives on evolutionary conservation and diversity. METHODS AND RESULTS: For each species, several expression plasmids of deletion mutants were constructed, and the resultant plasmid and a DMRT1-driven luciferase reporter were co-transfected into cultured cells to measure transactivation ability. The key point of this analysis is that the transactivation ability was normalized by quantifying the expression levels of DMRT1 variants using the HiBiT tag. As a result, two to three transactivation regions were suggested to exist in the C-terminal region of the DM domain in all four species. Among seven regions in DMRT1, the fourth region from the N-terminus contributed to transactivation common to the four species, and the sixth and seventh regions on the C-terminal side differed depending on the species. CONCLUSIONS: These findings indicated that the regions involved in the transactivation ability of DMRT1 could subtly change during evolution, indicating diversity in transactivation domains.

Correlation Between Subgenome-biased DNA Loss and DNA Transposon Activation Following Hybridization in the Allotetraploid Xenopus Frogs.

In certain tetraploid species resulting from interspecific hybridization, one parent's subgenome is known to selectively undergo DNA loss. The molecular mechanisms behind this remain unclear. In our study, we compared the genomes of a standard diploid species with two allotetraploid species from the Xenopus genus, both possessing L (longer) and S (shorter) homoeologous subgenomes. We observed substantial gene losses and intergenic DNA deletions in both the S and L subgenomes of the tetraploid species. Gene losses were around 1,000 to 3,000 for L and 4,000 to 6,000 for S, with especially prominent losses in the S subgenome. Many of these losses likely occurred shortly after interspecific hybridization in both L/S subgenomes. We also deduced frequent large inversions in the S subgenome. Upon reassessing transposon dynamics using updated genome databases, we reaffirmed heightened DNA transposon activity during the hybridization, as previously reported. We next investigated whether S subgenome-biased DNA loss could be correlated with the activation of DNA transposons following hybridization. Notably, distinct patterns were observed in the dynamics of DNA transposons between the L and S subgenomes. Several DNA transposon subfamilies correlated positively with DNA deletions in the S subgenome and negatively in the L subgenome. Based on these results, we propose a model that, upon and after hybridization between two related diploid Xenopus species, the mixture of their genomes resulted in the derepression of DNA transposons, especially in the S subgenome, leading to selective DNA loss in the S subgenome.

Sex chromosome cycle as a mechanism of stable sex determination.

Recent advances in DNA sequencing technology have enabled the precise decoding of genomes in non-model organisms, providing a basis for unraveling the patterns and mechanisms of sex chromosome evolution. Studies of different species have yielded conflicting results regarding the traditional theory that sex chromosomes evolve from autosomes via the accumulation of deleterious mutations and degeneration of the Y (or W) chromosome. The concept of the 'sex chromosome cycle,' emerging from this context, posits that at any stage of the cycle (i.e., differentiation, degeneration, or loss), sex chromosome turnover can occur while maintaining stable sex determination. Thus, understanding the mechanisms that drive both the persistence and turnover of sex chromosomes at each stage of the cycle is crucial. In this review, we integrate recent findings on the mechanisms underlying maintenance and turnover, with a special focus on several organisms having unique sex chromosomes. Our review suggests that the diversity of sex chromosomes in the maintenance of stable sex determination is underappreciated and emphasizes the need for more research on the sex chromosome cycle.

Prediction of combination effect of quinidine on the pharmacokinetics of tipepidine using a physiologically based pharmacokinetic model.

Tipepidine, an antitussive drug, has been reported to have central pharmacological effects and can be expected to be safely repositioned as treatment for psychiatric disorders. Since tipepidine requires three doses per day, development of a once-daily medication would be highly beneficial. Previously, we reported that combination use with quinidine, a CYP2D6 inhibitor, prolongs the half-life of tipepidine in chimeric mice with humanised liver.In this study, to predict this combination effect in humans, a physiologically based pharmacokinetic (PBPK) model was developed, and quantitative simulation was conducted. The simulation results indicated that concomitant administration of tipepidine with quinidine increased the predicted Cmax, AUC, and t1/2 of tipepidine in the Japanese population by 3.4-, 6.6-, and 2.4-fold, respectively.Furthermore, to compare with another approach that aims to prolong the half-life, the PK profile of tipepidine administered in hypothetical extended-release form was simulated. Extended-release form was predicted to be more influenced by CYP2D6 genotype than combination with quinidine, and the predicted plasma exposure was markedly increased in poor metabolizers, potentially leading to adverse effects.In conclusion, quantitative simulation using the PBPK model suggests the feasibility of the safe repositioning of tipepidine as a once-daily medication in combination with quinidine.

Highly Active and Durable Rh-Mo-Based Catalyst for the NO-CO-C3H6-O2 Reaction Prepared by Using Hybrid Clustering.

We developed a method for preparing catalysts by using hybrid clustering to form a high density of metal/oxide interfacial active sites. A Rh-Mo hybrid clustering catalyst was prepared by using a hybrid cluster, [(RhCp*)4Mo4O16] (Cp* = η5-C5Me5), as the precursor. The activities of the Rh-Mo catalysts toward the NO-CO-C3H6-O2 reaction depended on the mixing method (hybrid clustering > coimpregnation ≈ pristine Rh). The hybrid clustering catalyst also exhibited high durability against thermal aging at 1273 K in air. The activity and durability were attributed to the formation of a high-density of Rh/MoOx interfacial sites. The NO reduction mechanism on the hybrid clustering catalyst was different from that on typical Rh catalysts, where the key step is the N-O cleavage of adsorbed NO. The reducibility of the Rh/MoOx interfacial sites contributed to the partial oxidation of C3H6 to form acetate species, which reacted with NO+O2 to form N2 via the adsorbed NCO species. The formation of reduced Rh on Rh4Mo4/Al2O3 was not as essential as that on typical Rh catalysts; this explained the improvement in durability.

High-Density Formation of Ir/MoOx Interface through Hybrid Clustering for Chemoselective Nitrostyrene Hydrogenation.

To form high-density metal/oxide interfacial active sites, we developed a catalyst preparation method based on hybrid clustering. An iridium-molybdenum (Ir-Mo) hybrid clustering catalyst was prepared by using the hybrid cluster [(IrCp*)4Mo4O16] (Cp* = η5-C5Me5) as the precursor. The Ir-Mo hybrid clustering catalyst selectively reduced the nitro group in the hydrogenation of 4-nitrostyrene, whereas the coimpregnated Ir-Mo catalyst reduced both the nitro and vinyl groups nonselectively. The hybrid clustering catalyst also exhibited high selectivity, even at a high Ir loading (5 wt %), in contrast to Ir/MoO3, which exhibited high selectivity only at low Ir loadings (<0.3 wt %). In situ X-ray absorption spectroscopy analysis revealed that oxygen vacancies were formed at the Ir/MoOx interface in the presence of H2. We concluded that a high-density Ir/MoOx interface contributes to the preferential adsorption of nitro groups on vacant sites, promoting the selective hydrogenation of nitro groups.

Estimation of contribution of CYP2D6 to tipepidine metabolism in humans and prolongation of the half-life of tipepidine by combination use with a CYP2D6 inhibitor in chimeric mice with humanised liver.

Recently, it has been reported that tipepidine has various central pharmacological effects and can be expected to be safely repositioned as a treatment for psychiatric disorders. Since tipepidine has a very short half-life and requires three doses per day, the development of a once-daily medication would be highly beneficial to improve adherence and quality of life in patients with chronic psychiatric disorders. The aim of this study was to identify the enzymes involved in tipepidine metabolism and to verify that combination use with an enzyme inhibitor prolongs the half-life of tipepidine.Metabolism studies using recombinant human cytochrome P450 (P450, CYP) isoforms and inhibition studies using various selective P450 inhibitors and human liver microsomes revealed that CYP2D6 is the main enzyme catalysing tipepidine metabolism, with a metabolic contribution ratio of 85.4%.Furthermore, a pharmacokinetic study using chimeric mice with humanised liver showed that oral coadministration of a CYP2D6 inhibitor, quinidine, increased the Cmax, AUC0-t, and t1/2 of tipepidine by 1.5-, 3.2-, and 3.0-fold, respectively.These results indicated that coadministration of a CYP2D6 inhibitor is effective in increasing plasma exposure and prolonging the half-life of tipepidine and is useful for repositioning tipepidine as a treatment for psychiatric disorders.

Promoter generation for the chimeric sex-determining gene dm-W in Xenopus frogs.

Many sex-determining genes (SDGs) were generated as neofunctionalized genes through duplication and/or mutation of gonadal formation-related genes. We previously identified dm-W as an SDG in the African clawed frog Xenopus laevis and found that a partial duplication of the masculinization gene dmrt1 created the neofunctionalized dm-W after allotetraploidization by interspecific hybridization. The allotetraploid Xenopus species have two dmrt1 genes, dmrt1.L and dmrt1.S. Xenopus laevis dm-W has four exons: two dmrt1.S-derived exons (exons 2 and 3) and two other exons (noncoding exon 1 and exon 4). Our recent work revealed that exon 4 originated from a DNA transposon, hAT-10. Here, to clarify when and how the noncoding exon 1 and its coexisting promoter evolved during the establishment of dm-W after allotetraploidization, we newly determined nucleotide sequences of the dm-W promoter region from two other allotetraploid species, X. largeni and X. petersii, and performed an evolutionary analysis. We found that dm-W acquired a new exon 1 and TATA-type promoter in the common ancestor of the three allotetraploid Xenopus species, resulting in the deletion of the dmrt1.S-derived TATA-less promoter. In addition, we demonstrated that the TATA box contributes to dm-W promoter activity in cultured cells. Collectively, these findings suggest that this novel TATA-type promoter was important for the establishment of dm-W as a sex-determining gene, followed by the degeneration of the preexisting promoter.

Prediction of Oral Drug Absorption in Rats from In Vitro Data.

PURPOSE: In drug discovery, rats are widely used for pharmacological and toxicological studies. We previously reported that a mechanism-based oral absorption model, the gastrointestinal unified theoretical framework (GUT framework), can appropriately predict the fraction of a dose absorbed (Fa) in humans and dogs. However, there are large species differences between humans and rats. The purpose of the present study was to evaluate the predictability of the GUT framework for rat Fa. METHOD: The Fa values of 20 model drugs (a total of 39 Fa data) were predicted in a bottom-up manner. Based on the literature survey, the bile acid concentration (Cbile) and the intestinal fluid volume were set to 15 mM and 4 mL/kg, respectively, five and two times higher than in humans. LogP, pKa, molecular weight, intrinsic solubility, bile micelle partition coefficients, and Caco-2 permeability were used as input data. RESULTS: The Fa values were appropriately predicted for highly soluble drugs (absolute average fold error (AAFE) = 1.65, 18 Fa data) and poorly soluble drugs (AAFE = 1.57, 21 Fa data). When the species difference in Cbile was ignored, Fa was over- and under-predicted for permeability and solubility limited cases, respectively. High Cbile in rats reduces the free fraction of drug molecules available for epithelial membrane permeation while increasing the solubility of poorly soluble drugs. CONCLUSION: The Fa values in rats were appropriately predicted by the GUT framework. This result would be of great help for a better understanding of species differences and model-informed preclinical formulation development.

Neofunctionalization of a Noncoding Portion of a DNA Transposon in the Coding Region of the Chimerical Sex-Determining Gene dm-W in Xenopus Frogs.

Most vertebrate sex-determining genes (SDGs) emerge as neofunctionalized genes through duplication and/or mutation of ancestral genes that are involved with sexual differentiation. We previously demonstrated dm-W to be the SDG in the African clawed frog Xenopus laevis and found that a portion of this gene emerged from the masculinization gene dmrt1 after allotetraploidization by interspecific hybridization between two ancestral species around 17-18 Ma. dm-W has four exons consisting of a noncoding exon 1, dmrt1-derived exons 2 and 3, and an orphan exon 4 (Ex4) of unknown origin that includes coding sequence (CDS). In this study, we searched for the origin of Ex4 and investigated the function of the CDS of this exon. We found that the Ex4-CDS is derived from a noncoding portion of the hAT-10 family of DNA transposon. Evolutionary analysis of transposons and determination of the Ex4 sequences from three other species indicated that Ex4 was generated before the diversification of most or all extant allotetraploid species in subgenus Xenopus, during which time we hypothesize that transposase activity of this hAT superfamily was active. Using DNA-protein binding and transfection assays, we further demonstrate that the Ex4-encoded amino acid sequence increases the DNA-binding ability and transrepression activity of DM-W. These findings suggest that the conversion of the noncoding transposon sequence to the CDS of dm-W contributed to neofunctionalization of a new chimeric SDG in the ancestor of the allotetraploid Xenopus species, offering new insights into de novo origin and functional evolution of chimerical genes.

Activation of DNA Transposons and Evolution of piRNA Genes Through Interspecific Hybridization in Xenopus Frogs.

Interspecific hybridization between two closely related species sometimes resulted in a new species with allotetraploid genomes. Many clawed frog species belonging to the Xenopus genus have diverged from the allotetraploid ancestor created by the hybridization of two closely related species with the predicted L and S genomes. There are species-specific repeated sequences including transposable elements in each genome of organisms that reproduce sexually. To understand what happened on and after the hybridization of the two distinct systems consisting of repeated sequences and their corresponding piRNAs, we isolated small RNAs from ovaries and testes of three Xenopus species consisting of allotetraploid X. laevis and X. borealis and diploid X. tropicalis as controls. After a comprehensive sequencing and selection of piRNAs, comparison of their sequences showed that most piRNA sequences were different between the ovaries and testes in all three species. We compared piRNA and genome sequences and specified gene clusters for piRNA expression in each genome. The synteny and homology analyses showed many distinct piRNA clusters among the three species and even between the two L and/or S subgenomes, indicating that most clusters of the two allotetraploid species changed after hybridization. Moreover, evolutionary analysis showed that DNA transposons including Kolobok superfamily might get activated just after hybridization and then gradually inactivated. These findings suggest that some DNA transposons and their piRNAs might greatly influence allotetraploid genome evolution after hybridization.

High-Density Formation of Metal/Oxide Interfacial Catalytic Active Sites through Hybrid Clustering.

We developed a method for preparing catalysts based on hybrid clusters that formed high-density metal/oxide interfacial active sites. A Ru-V hybrid cluster, [{Ru(cym)}4V6O19] (cym = p-cymene), was used as a precursor to prepare Ru-V catalysts. Transmission electron microscopy and X-ray absorption spectroscopy (XAS) analyses revealed that composite nanoparticles of Ru and V were formed through hybrid clustering, while conventional coimpregnation of Ru and V afforded separate nanoparticles. The activity of the Ru-V catalysts toward N-alkylation of amines with alcohols depended on the mixing method (hybrid clustering > coimpregnation > physical mixing ≈ pristine Ru). The formation mechanism of the composite nanoparticles from the hybrid cluster was revealed using in situ XAS analysis. Finally, we proposed a simple but efficient catalyst preparation method, based on in situ formation of hybrid cluster precursors combined with a conventional coimpregnation method.

Prediction Characteristics of Oral Absorption Simulation Software Evaluated Using Structurally Diverse Low-Solubility Drugs.

The purpose of the present study was to characterize current biopharmaceutics modeling and simulation software regarding the prediction of the fraction of a dose absorbed (Fa) in humans. As commercial software products, GastroPlus™ and Simcyp® were used. In addition, the gastrointestinal unified theoretical framework, a simple and publicly accessible model, was used as a benchmark. The Fa prediction characteristics for a total of 96 clinical Fa data of 27 model drugs were systematically evaluated using the default settings of each software product. The molecular weight, dissociation constant, octanol-water partition coefficient, solubility in biorelevant media, dose, and particle size of model drugs were used as input data. Although the same input parameters were used, GastroPlus™, Simcyp®, and the gastrointestinal unified theoretical framework showed different Fa prediction characteristics depending on the rate-limiting steps of oral drug absorption. The results of the present study would be of great help for the overall progression of physiologically based absorption models.

Elucidating the Doping Effect on the Electronic Structure of Thiolate-Protected Silver Superatoms by Photoelectron Spectroscopy.

Gas-phase photoelectron spectroscopy (PES) was conducted on [XAg24 (SPhMe2 )18 ]- (X=Ag, Au) and [YAg24 (SPhMe2 )18 ]2- (Y=Pd, Pt), which have a formal superatomic core (X@Ag12 )5+ or (Y@Ag12 )4+ with icosahedral symmetry. PES results show that superatomic orbitals in the (Au@Ag12 )5+ core remain unshifted with respect to those in the (Ag@Ag12 )5+ core, whereas the orbitals in the (Y@Ag12 )4+ (Y = Pd, Pt) core shift up in energy by about 1.4 eV. The remarkable doping effect of a single Y atom (Y=Pd, Pt) on the electronic structure of the chemically modified (Ag@Ag12 )5+ superatom was reproduced by theoretical calculations on simplified model systems and was ascribed to 1) the weaker binding of valence electrons in Y@(Ag+ )12 compared to Ag+ @(Ag+ )12 due to the reduction in formal charge of the core potential, and 2) the upward shift of the apparent vacuum level due to the presence of a repulsive Coulomb barrier between [YAg24 (SPhMe2 )18 ]- and electron.

Harmonizing solubility measurement to lower inter-laboratory variance - progress of consortium of biopharmaceutical tools (CoBiTo) in Japan.

The purpose of the present study was to harmonize the protocol of equilibrium solubility measurements for poorly water-soluble drugs to lower inter-laboratory variance. The "mandatory" and "recommended" procedures for the shake-flask method were harmonized based on the knowledge and experiences of each company and information from the literature. The solubility of model drugs was measured by the harmonized protocol (HP) and the non-harmonized proprietary protocol of each company (nonHP). Albendazole, griseofulvin, dipyridamole, and glibenclamide were used as model drugs. When using the nonHP, the solubility values showed large inter-laboratory variance. In contrast, inter-laboratory variance was markedly reduced when using the HP.

Determination of Fluorine Chemical Structure in Slag by Thermal Hydrolysis He-MIP-OES.

A novel microwave-induced helium plasma optical emission spectrometry (He-MIP-OES) combined with a thermal hydrolysis sample introduction system was newly established for the determination of fluorine (F) compounds in slags. The MIP maintained through an Okamoto cavity was adopted, which was quite stable and provided a higher detection capability of F by helium plasma. The basic analytical performance of He-MIP-OES combined with an ultrasonic nebulizer for F analysis was also examined, and expected results could be obtained. The thermal hydrolysis behavior of CaF2, Ca4(Si2O7)(F,OH)2 and Ca5(PO4)3F, as known F chemical structures in slag, was also examined by thermal hydrolysis He-MIP-OES; F compounds in actual slag could be successfully identified and determined by this developed system.

Synthesis and optimization of 4,5,6,7-tetrahydrooxazolo[4,5-c]pyridines as potent and orally-active metabotropic glutamate receptor 5 negative allosteric modulators.

We describe here the design, synthesis and characterization of a series of 4,5,6,7-tetrahydrooxazolo[4,5-c]pyridines as metabotropic glutamate receptor (mGluR) 5 negative allosteric modulators (NAMs). Optimization of the substituents led to the identification of several compounds with good pharmacokinetic profiles, including long half life and high oral bioavailability, in both rats and monkeys. The receptor occupancy test in the rat cortex revealed favorable brain penetration of these compounds. The reprsentative compound 13 produced oral antidepressant-like effect in the rat forced swimming test (MED: 0.3mg/kg, q.d.).

Lewis Base Catalytic Properties of [Nb10 O28 ]6- for CO2 Fixation to Epoxide: Kinetic and Theoretical Studies.

The decaniobate cluster (TBA)6 [Nb10 O28 ] (TBA+ =tetrabutylammonium cation) was found to act as a Lewis base catalyst for fixation of carbon dioxide (CO2 ) to styrene oxide (SO). A kinetic study showed that the cycloaddition of CO2 adsorbed on [Nb10 O28 ]6- with SO corresponds to the rate-determining step in the Eley-Rideal mechanism. Density functional theory calculation predicted that CO2 on the corner and edge O atoms of [Nb10 O28 ]6- is negatively charged and thus activated for nucleophilic attack on SO.

Hydrogen-Mediated Electron Doping of Gold Clusters As Revealed by In Situ X-ray and UV-vis Absorption Spectroscopy.

We previously reported that small (∼1.2 nm) gold clusters stabilized by poly(N-vinyl-2-pyrrolidone) (Au:PVP) exhibited a localized surface plasmon resonance (LSPR) band at ∼520 nm in the presence of NaBH4. To reveal the mechanism of this phenomenon, the electronic structure of Au:PVP during the reaction with NaBH4 in air was examined by means of in situ X-ray absorption spectroscopy at Au L3-edge and UV-vis spectroscopy. These measurements indicated that the appearance of the LSPR band is not associated with the growth in size but is ascribed to electron doping to the Au sp band by the adsorbed H atoms.

Synthesis, structure-activity relationships and biological evaluation of 4,5,6,7-tetrahydropyrazolopyrazines as metabotropic glutamate receptor 5 negative allosteric modulators.

The design, synthesis and SAR studies of novel 4,5,6,7-tetrahydropyrazolopyrazines as metabotropic glutamate receptor 5 (mGluR5) negative allosteric modulators (NAMs) are presented in this letter. Starting from a HTS hit compound (1, IC50=477nM), optimization of various groups led to the synthesis of a potent mGluR5 NAM (32, IC50=75nM) with excellent rat PK profile and good brain penetration. This compound produced oral antidepressant-like effect in a mouse tale suspension model (MED: 30mg/kg).