Diffusive hydrogenation reactions of CO embedded in amorphous solid water at elevated temperatures ~70 K

The surface processes on interstellar dust grains have an important role in the chemical evolution in molecular clouds. Hydrogenation reactions on ice surfaces have been extensively investigated and are known to proceed at low temperatures mostly below 20 K. In contrast, information about the chemical processes of molecules within an ice mantle is lacking. In this work, we investigated diffusive hydrogenation reactions of carbon monoxide (CO) embedded in amorphous solid water (ASW) as a model case and discovered that the hydrogenation of CO efficiently proceeds to yield H2CO and CH3OH even above 20 K when CO is buried beneath ASW. The experimental results suggest that hydrogen atoms diffuse through the cracks of ASW and have a sufficient residence time to react with embedded CO. The hydrogenation reactions occurred even at temperatures up to ~70 K. Cracks collapse at elevated temperatures but the occurrence of hydrogenation reactions means that the cracks would not completely disappear and remain large enough for penetration by hydrogen atoms. Considering the hydrogen-atom fluence in the laboratory and molecular clouds, we suggest that the penetration of hydrogen and its reactions within the ice mantle occur in astrophysical environments. Unified Astronom

Divergence of Evolutionary Ways Among Common sym Genes: CASTOR and CCaMK Show Functional Conservation Between Two Symbiosis Systems and Constitute the Root of a Common Signaling Pathway

In recent years a number of legume genes involved in root nodule (RN) symbiosis have been identified in the model legumes, Lotus japonicus (Lotus) and Medicago truncatula. Among them, a distinct set of genes has been categorized as a common symbiosis pathway (CSP), because they are also essential for another mutual interaction, the arbuscular mycorrhiza (AM) symbiosis, which is evolutionarily older than the RN symbiosis and is widely distributed in the plant kingdom. Based on the concept that the legume RN symbiosis has evolved from the ancient AM symbiosis, one issue is whether the CSP is functionally conserved between non-nodulating plants, such as rice, and nodulating legumes. We identified three rice CSP gene orthologs, OsCASTOR, OsPOLLUX and OsCCaMK, and demonstrated the indispensable roles of OsPOLLUX and OsCCaMK in rice AM symbiosis. Interestingly, molecular transfection of either OsCASTOR or OsCCaMK could fully complement symbiosis defects in the corresponding Lotus mutant lines for both the AM and RN symbioses. Our results not only provide a conserved genetic basis for the AM symbiosis between rice and Lotus, but also indicate that the core of the CSP has been well conserved during the evolution of RN symbiosis. Through evolution, CASTOR and CCaMK have remained as the molecular basis for the maintenance of CSP functions in the two symbiosis system

Low-Temperature Crystallization of Amorphous Silicate in Astrophysical Environments

We construct a theoretical model for low-temperature crystallization of amorphous silicate grains induced by exothermic chemical reactions. As a first step, the model is applied to the annealing experiments, in which the samples are (1) amorphous silicate grains and (2) amorphous silicate grains covered with an amorphous carbon layer. We derive the activation energies of crystallization for amorphous silicate and amorphous carbon from the analysis of the experiments. Furthermore, we apply the model to the experiment of low-temperature crystallization of amorphous silicate core covered with an amorphous carbon layer containing reactive molecules. We clarify the conditions of low-temperature crystallization due to exothermic chemical reactions. Next, we formulate the crystallization conditions so as to be applicable to astrophysical environments. We show that the present crystallization mechanism is characterized by two quantities: the stored energy density Q in a grain and the duration of the chemical reactions \tau . The crystallization conditions are given by Q > Q_{min} and \tau < \tau _{cool} regardless of details of the reactions and grain structure, where \tau _{cool} is the cooling timescale of the grains heated by exothermic reactions, and Q_{min} is minimum stored energy density determined by the activation energy of crystallization. Our results suggest that silicate crystallization occurs in wider astrophysical conditions than hitherto considered.Comment: 9 figures, accepted for publication in Astrophysical

Simulations and spectra of water in CO matrices.

Models for the inclusion of water molecules in carbon monoxide matrices are developed using density functional theory applied to amorphous solid systems. The models cover a large range of systems for smaller or larger CO matrices with different water content, consisting of either individual H2O molecules or small clusters linked by H-bonds. The vibrational spectra of the samples are predicted at the minimum of their potential energy surface. The spectra allow instances where the water molecules remain isolated or form aggregates to be discerned, and they also provide an indication of the strength of the H-bonding, when present. The calculations support recent experimental observations that linked IR bands at 3707 cm-1 and 3617 cm-1 to the presence of unbound water molecules in water-poor CO/H2O mixed ices. Assignment of some observed bands to water dimers or trimers is suggested as well. The residual static pressure in fixed-volume simulation cells is also calculated

Wavelet analysis of transonic buffet on a two-dimensional airfoil with vortex generators

We visualized the shock buffets on a two-dimensional transonic airfoil with and without vortex generators (VGs) by using a fast-framing focusing schlieren imaging. The focusing schlieren visualization showed that the flow three-dimensionality around the airfoil became remarkable with installing the VGs. This implies that narrow depth of focus of imaging systems was a key to accurately capture the characteristics of the shock oscillation due to the buffet for the cases with VGs. The time-resolved imaging also revealed that non-periodic components were included in the shock oscillation due to the buffet for the cases with VGs. This prevented Fourier analysis from being applied. We used wavelet analysis to extract the characteristic of the shock oscillation for the cases with VGs. The wavelet spectrograms revealed that the low-frequency oscillation having the buffet frequency was still included intermittently in the shock oscillation even when VG controlled the buffet. The rate of appearing the low-frequency oscillation increased with increasing both the interval between VGs and the angle of attack

Transcriptome Profiling of Lotus japonicus Roots During Arbuscular Mycorrhiza Development and Comparison with that of Nodulation

To better understand the molecular responses of plants to arbuscular mycorrhizal (AM) fungi, we analyzed the differential gene expression patterns of Lotus japonicus, a model legume, with the aid of a large-scale cDNA macroarray. Experiments were carried out considering the effects of contaminating microorganisms in the soil inoculants. When the colonization by AM fungi, i.e. Glomus mosseae and Gigaspora margarita, was well established, four cysteine protease genes were induced. In situ hybridization revealed that these cysteine protease genes were specifically expressed in arbuscule-containing inner cortical cells of AM roots. On the other hand, phenylpropanoid biosynthesis-related genes for phenylalanine ammonia-lyase (PAL), chalcone synthase, etc. were repressed in the later stage, although they were moderately up-regulated on the initial association with the AM fungus. Real-time RT–PCR experiments supported the array experiments. To further confirm the characteristic expression, a PAL promoter was fused with a reporter gene and introduced into L. japonicus, and then the transformants were grown with a commercial inoculum of G. mosseae. The reporter activity was augmented throughout the roots due to the presence of contaminating microorganisms in the inoculum. Interestingly, G. mosseae only colonized where the reporter activity was low. Comparison of the transcriptome profiles of AM roots and nitrogen-fixing root nodules formed with Mesorhizobium loti indicated that the PAL genes and other phenylpropanoid biosynthesis-related genes were similarly repressed in the two organs

Divergence of evolutionary ways among common sym genes: CASTOR and CCaMK show functional conservation between two symbiosis systems and constitute the root of a common signaling pathway

In recent years a number of legume genes involved in root nodule (RN) symbiosis have been identified in the model legumes, Lotus japonicus (Lotus) and Medicago truncatula. Among them, a distinct set of genes has been categorized as a common symbiosis pathway (CSP), because they are also essential for another mutual interaction, the arbuscular mycorrhiza (AM) symbiosis, which is evolutionarily older than the RN symbiosis and is widely distributed in the plant kingdom. Based on the concept that the legume RN symbiosis has evolved from the ancient AM symbiosis, one issue is whether the CSP is functionally conserved between non-nodulating plants, such as rice, and nodulating legumes. We identified three rice CSP gene orthologs, OsCASTOR, OsPOLLUX and OsCCaMK, and demonstrated the indispensable roles of OsPOLLUX and OsCCaMK in rice AM symbiosis. Interestingly, molecular transfection of either OsCASTOR or OsCCaMK could fully complement symbiosis defects in the corresponding Lotus mutant lines for both the AM and RN symbioses. Our results not only provide a conserved genetic basis for the AM symbiosis between rice and Lotus, but also indicate that the core of the CSP has been well conserved during the evolution of RN symbiosis. Through evolution, CASTOR and CCaMK have remained as the molecular basis for the maintenance of CSP functions in the two symbiosis systems

Derepression of the Plant Chromovirus LORE1 Induces Germline Transposition in Regenerated Plants

Transposable elements represent a large proportion of the eukaryotic genomes. Long Terminal Repeat (LTR) retrotransposons are very abundant and constitute the predominant family of transposable elements in plants. Recent studies have identified chromoviruses to be a widely distributed lineage of Gypsy elements. These elements contain chromodomains in their integrases, which suggests a preference for insertion into heterochromatin. In turn, this preference might have contributed to the patterning of heterochromatin observed in host genomes. Despite their potential importance for our understanding of plant genome dynamics and evolution, the regulatory mechanisms governing the behavior of chromoviruses and their activities remain largely uncharacterized. Here, we report a detailed analysis of the spatio-temporal activity of a plant chromovirus in the endogenous host. We examined LORE1a, a member of the endogenous chromovirus LORE1 family from the model legume Lotus japonicus. We found that this chromovirus is stochastically de-repressed in plant populations regenerated from de-differentiated cells and that LORE1a transposes in the male germline. Bisulfite sequencing of the 5′ LTR and its surrounding region suggests that tissue culture induces a loss of epigenetic silencing of LORE1a. Since LTR promoter activity is pollen specific, as shown by the analysis of transgenic plants containing an LTR::GUS fusion, we conclude that male germline-specific LORE1a transposition in pollen grains is controlled transcriptionally by its own cis-elements. New insertion sites of LORE1a copies were frequently found in genic regions and show no strong insertional preferences. These distinctive novel features of LORE1 indicate that this chromovirus has considerable potential for generating genetic and epigenetic diversity in the host plant population. Our results also define conditions for the use of LORE1a as a genetic tool