Cosmic Galaxy-IGM HI Relation at z∼2−3{\it{z}}\sim 2-3 Probed in the COSMOS/UltraVISTA 1.61.6 deg2^2 Field

We present spatial correlations of galaxies and IGM HI in the COSMOS/UltraVISTA 1.62 deg$^2$ field. Our data consist of 13,415 photo-$z$ galaxies at $z\sim2-3$ with $K_s<23.4$ and the Ly$\alpha$ forest absorptions in the background quasar spectra selected from SDSS data with no signature of damped Ly$\alpha$ system contamination. We estimate a galaxy overdensity $\delta_{gal}$ in an impact parameter of 2.5 pMpc, and calculate the Ly$\alpha$ forest fluctuations $\delta_{\langle F\rangle}$ whose negative values correspond to the strong Ly$\alpha$ forest absorptions. We identify weak evidence of an anti-correlation between $\delta_{gal}$ and $\delta_{\langle F\rangle}$ with a Spearman's rank correlation coefficient of $-0.39$ suggesting that the galaxy overdensities and the Ly$\alpha$ forest absorptions positively correlate in space at the $\sim90\%$ confidence level. This positive correlation indicates that high-$z$ galaxies exist around an excess of HI gas in the Ly$\alpha$ forest. We find four cosmic volumes, dubbed $A_{obs}$-$D_{obs}$, that have extremely large (small) values of $\delta_{gal} \simeq0.8$ ($-1$) and $\delta_{\langle F\rangle}$ $\simeq0.1$ ($-0.4$), three out of which, $B_{obs}$-$D_{obs}$, significantly depart from the correlation, and weaken the correlation signal. We perform cosmological hydrodynamical simulations, and compare with our observational results. Our simulations reproduce the correlation, agreeing with the observational results. Moreover, our simulations have model counterparts of $A_{obs}$-$D_{obs}$, and suggest that the observations pinpoint, by chance, a galaxy overdensity like a proto-cluster, gas filaments lying on the sightline, a large void, and orthogonal low-density filaments. Our simulations indicate that the significant departures of $B_{obs}$-$D_{obs}$ are produced by the filamentary large-scale structures and the observation sightline effects.Comment: 14 pages, 12 figures. Accepted for publication in Ap

Mass Spectra-Based Framework for Automated Structural Elucidation of Metabolome Data to Explore Phytochemical Diversity

A novel framework for automated elucidation of metabolite structures in liquid chromatography–mass spectrometer metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method

Large-scale Filamentary Structure around the Protocluster at Redshift z=3.1

We report the discovery of a large-scale coherent filamentary structure of Lyman alpha emitters in a redshift space at z=3.1. We carried out spectroscopic observations to map the three dimensional structure of the belt-like feature of the Lyman alpha emitters discovered by our previous narrow-band imaging observations centered on the protocluster at z=3.1. The feature was found to consist of at least three physical filaments connecting with each other. The result is in qualitative agreement with the prediction of the 'biased' galaxy-formation theories that galaxies preferentially formed in large-scale filamentary or sheet-like mass overdensities in the early Universe. We also found that the two known giant Lyman alpha emission-line nebulae showing high star-formation activities are located near the intersection of these filaments, which presumably evolves into a massive cluster of galaxies in the local Universe. This may suggest that massive galaxy formation occurs at the characteristic place in the surrounding large-scale structure at high redshift.Comment: 11 pages, 3 figures, accepted for publication in ApJ Letter

MPP6 stimulates both RRP6 and DIS3 to degrade a specified subset of MTR4-sensitive substrates in the human nucleus

ヒト細胞内でRNA分解時に働く因子の役割を解明 --細胞内におけるRNA分解機構の全容解明に期待--. 京都大学プレスリリース. 2022-08-05.Recent in vitro reconstitution analyses have proven that the physical interaction between the exosome core and MTR4 helicase, which promotes the exosome activity, is maintained by either MPP6 or RRP6. However, knowledge regarding the function of MPP6 with respect to in vivo exosome activity remains scarce. Here, we demonstrate a facilitative function of MPP6 that composes a specific part of MTR4-dependent substrate decay by the human exosome. Using RNA polymerase II-transcribed poly(A)⁺ substrate accumulation as an indicator of a perturbed exosome, we found functional redundancy between RRP6 and MPP6 in the decay of these poly(A)⁺ transcripts. MTR4 binding to the exosome core via MPP6 was essential for MPP6 to exert its redundancy with RRP6. However, at least for the decay of our identified exosome substrates, MTR4 recruitment by MPP6 was not functionally equivalent to recruitment by RRP6. Genome-wide classification of substrates based on their sensitivity to each exosome component revealed that MPP6 deals with a specific range of substrates and highlights the importance of MTR4 for their decay. Considering recent findings of competitive binding to the exosome between auxiliary complexes, our results suggest that the MPP6-incorporated MTR4-exosome complex is one of the multiple alternative complexes rather than the prevailing one

Keck Spectroscopy of Lyman-break Galaxies and its Implications for the UV-continuum and Ly_alpha Luminosity Functions at z>6

We present Keck spectroscopic observations of z>6 Lyman-break galaxy (LBG) candidates in the Subaru Deep Field (SDF). The candidates were selected as i'-dropout objects down to z'=27 AB magnitudes from an ultra-deep SDF z'-band image. With the Keck spectroscopy we identified 19 LBGs with prominent Ly_alpha emission lines at 6< z < 6.4. The median value of the Ly_alpha rest-frame equivalent widths (EWs) is ~50 A, with four EWs >100 A. This well-defined spectroscopic sample spans a UV-continuum luminosity range of -21.8< M_{UV}<-19.5 (0.6~5 L*_{UV}) and a Ly_alpha luminosity range of (0.3~3) x 10^{43} erg s^{-1} (0.3~3 L*_ {Ly_alpha}). We derive the UV and Ly_alpha luminosity functions (LFs) from our sample at ~6.2 after we correct for sample incompleteness. We find that our measurement of the UV LF is consistent with the results of previous studies based on photometric LBG samples at 5<z<7. Our Ly_alpha LF is also generally in agreement with the results of Ly_alpha-emitter surveys at z~5.7 and 6.6. This study shows that deep spectroscopic observations of LBGs can provide unique constraints on both the UV and Ly_alpha LFs at z>6.Comment: 14 pages, 7 figures, accepted for publication in Ap

A nucleoside anticancer drug, 1-(3-C-ethynyl-β-D-ribo-pentofuranosyl)cytosine (TAS106), sensitizes cells to radiation by suppressing BRCA2 expression

<p>Abstract</p> <p>Background</p> <p>A novel anticancer drug 1-(3-C-ethynyl-β-D-ribo-pentofuranosyl)cytosine (ECyd, TAS106) has been shown to radiosensitize tumor cells and to improve the therapeutic efficiency of X-irradiation. However, the effect of TAS106 on cellular DNA repair capacity has not been elucidated. Our aim in this study was to examine whether TAS106 modified the repair capacity of DNA double-strand breaks (DSBs) in tumor cells.</p> <p>Methods</p> <p>Various cultured cell lines treated with TAS106 were irradiated and then survival fraction was examined by the clonogenic survival assays. Repair of sublethal damage (SLD), which indicates DSBs repair capacity, was measured as an increase of surviving cells after split dose irradiation with an interval of incubation. To assess the effect of TAS106 on the DSBs repair activity, the time courses of γ-H2AX and 53BP1 foci formation were examined by using immunocytochemistry. The expression of DNA-repair-related proteins was also examined by Western blot analysis and semi-quantitative RT-PCR analysis.</p> <p>Results</p> <p>In clonogenic survival assays, pretreatment of TAS106 showed radiosensitizing effects in various cell lines. TAS106 inhibited SLD repair and delayed the disappearance of γ-H2AX and 53BP1 foci, suggesting that DSB repair occurred in A549 cells. Western blot analysis demonstrated that TAS106 down-regulated the expression of BRCA2 and Rad51, which are known as keys among DNA repair proteins in the homologous recombination (HR) pathway. Although a significant radiosensitizing effect of TAS106 was observed in the parental V79 cells, pretreatment with TAS106 did not induce any radiosensitizing effects in BRCA2-deficient V-C8 cells.</p> <p>Conclusions</p> <p>Our results indicate that TAS106 induces the down-regulation of BRCA2 and the subsequent abrogation of the HR pathway, leading to a radiosensitizing effect. Therefore, this study suggests that inhibition of the HR pathway may be useful to improve the therapeutic efficiency of radiotherapy for solid tumors.</p

Rre37 stimulates accumulation of 2-oxoglutarate and glycogen under nitrogen starvation in Synechocystis sp. PCC 6803

AbstractRre37 (sll1330) in a cyanobacterium Synechocystis sp. PCC 6803 acts as a regulatory protein for sugar catabolic genes during nitrogen starvation. Low glycogen accumulation in Δrre37 was due to low expression of glycogen anabolic genes. In addition to low 2-oxoglutarate accumulation, normal upregulated expression of genes encoding glutamate synthases (gltD and gltB) as well as accumulation of metabolites in glycolysis (fructose-6-phosphate, fructose-1,6-bisphosphate, and glyceraldehyde-3-phosphate) and tricarboxylic acid (TCA) cycle (oxaloacetate, fumarate, succinate, and aconitate) were abolished by rre37 knockout. Rre37 regulates 2-oxoglutarate accumulation, glycogen accumulation through expression of glycogen anabolic genes, and TCA cycle metabolites accumulation

Large Population of ALMA Galaxies at z>6 with Very High [OIII]88um to [CII]158um Flux Ratios: Evidence of Extremely High Ionization Parameter or PDR Deficit?

We present our new ALMA observations targeting [OIII]88um, [CII]158um, [NII]122um, and dust continuum emission for three Lyman break galaxies at z=6.0293-6.2037 identified in the Subaru/Hyper Suprime-Cam survey. We clearly detect [OIII] and [CII] lines from all of the galaxies at 4.3-11.8sigma levels, and identify multi-band dust continuum emission in two of the three galaxies, allowing us to estimate infrared luminosities and dust temperatures simultaneously. In conjunction with previous ALMA observations for six galaxies at z>6, we confirm that all the nine z=6-9 galaxies have high [OIII]/[CII] ratios of L[OIII]/L[CII]~3-20, ~10 times higher than z~0 galaxies. We also find a positive correlation between the [OIII]/[CII] ratio and the Lya equivalent width (EW) at the ~90% confidence level. We carefully investigate physical origins of the high [OIII]/[CII] ratios at z=6-9 using Cloudy, and find that high density of the interstellar medium, low C/O abundance ratio, and the cosmic microwave background attenuation are responsible to only a part of the z=6-9 galaxies. Instead, the observed high [OIII]/[CII] ratios are explained by 10-100 times higher ionization parameters or low photodissociation region (PDR) covering fractions of 0-10%, both of which are consistent with our [NII] observations. The latter scenario can be reproduced with a density bounded nebula with PDR deficit, which would enhance the Lya, Lyman continuum, and C+ ionizing photons escape from galaxies, consistent with the [OIII]/[CII]-Lya EW correlation we find.Comment: 20 pages, 18 figures, Accepted for publication in Ap