Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion

The SMC complex cohesin mediates interphase chromatin structural formation in eukaryotic cells through DNA loop extrusion. Here, we sought to investigate its mechanism using molecular dynamics simulations. To achieve this, we first constructed the amino-acid-residue-resolution structural models of the cohesin subunits, SMC1, SMC3, STAG1, and NIPBL. By simulating these subunits with double-stranded DNA molecules, we predicted DNA binding patches on each subunit and quantified the affinities of these patches to DNA using their dissociation rate constants as a proxy. Then, we constructed the structural model of the whole cohesin complex and mapped the predicted high-affinity DNA binding patches on the structure. From the spatial relations of the predicted patches, we identified that multiple patches on the SMC1, SMC3, STAG1, and NIPBL subunits form a DNA clamping patch group. The simulations of the whole complex with double-stranded DNA molecules suggest that this patch group facilitates DNA bending and helps capture a DNA segment in the cohesin ring formed by the SMC1 and SMC3 subunits. In previous studies, these have been identified as critical steps in DNA loop extrusion. Therefore, this study provides experimentally testable predictions of DNA binding sites implicated in previously proposed DNA loop extrusion mechanisms and highlights the essential roles of the accessory subunits STAG1 and NIPBL in the mechanism

Assignment of IR spectra of nucleobases in solution

令和6年度 京都大学化学研究所 スーパーコンピュータシステム 利用報告

The comparison of miR-222-3p expression levels between BHA patients with tumors and those without tumors (Supplemental Figure 6)

For BHA patients with tumors (n = 6), the relative expression level of miR-222-3p in the adrenal vein on the tumor side was quantified. For BHA patients without tumors (n = 8), the relative expression level of miR-222-3p in the adrenal vein on the aldosterone-higher side was quantified. Relative expression level of miR-222-3p was quantified by qPCR. miR-191-5p was used as internal control. Data are presented as the mean ± SEM from six patients with tumors and eight patients without tumors, respectively

Theoretical calculation of photo-, electro-, and magneto-functional organic systems

令和6年度 京都大学化学研究所 スーパーコンピュータシステム 利用報告

Oxygen isotope fractionation during anaerobic ammonium oxidation by the marine representative Candidatus Scalindua sp.

海洋の窒素循環を解明する新たな研究 --アナモックスの酸素同位体分別測定に初めて成功-- . 京都大学プレスリリース. 2025-06-20.Analysing the nitrogen (¹⁵ε) and oxygen (¹⁸ε) isotope effects of anaerobic ammonium oxidation (anammox) is essential for accurately assessing its potential contribution to fixed-N losses in the ocean, yet the ¹⁸ε of anammox remains unexplored. Here, we determined the previously unexplored ¹⁸ε of anammox using a highly enriched culture of the marine anammox species “Ca. Scalindua sp”. Because Scalindua significantly accelerated oxygen isotope exchange between NO₂⁻ and H₂O, we introduced a new rate constant for anammox-mediated oxygen isotope exchange (k[eq], [AMX] = 8.44 ~ 13.56 × 10⁻² h⁻¹), which is substantially faster than abiotic oxygen isotope exchange (k[eq], [abio] = 1.13 × 10⁻² h⁻¹), into a numerical model to estimate the ¹⁸ε during anammox. Based on our experimental results, we successfully determined the ¹⁸ε associated with: (1) conversion of NO₂⁻ to N₂ (¹⁸ε[NO]₂₋ → [N]₂ = 10.6 ~ 16.1‰), (2) NO₂⁻ oxidation to NO₃⁻ (18ε[NO]₂₋ → [NO]₃₋ = −2.9 ~ −11.0‰, inverse fractionation), (3) incorporation of oxygen from water during NO₂⁻ oxidation to NO₃⁻ (¹⁸ε[H₂O] = 16.4 ~ 19.2‰). Our study underscores the possibility that unique anammox oxygen isotope signals may be masked due to substantial anammox-mediated oxygen isotope exchange between NO₂⁻ and H₂O. Therefore, careful consideration is required when utilizing δ¹⁸O[NO]₃₋ and δ¹⁸O[NO]₂₋ as geochemical markers to assess the potential contribution of anammox to fixed-N losses in the ocean

Softening and Recovery of Near‐Surface Layers During the 2024 M7.6 Noto Earthquake

On 1 January 2024, a devastating MJ 7.6 earthquake occurred on the Noto Peninsula in Japan. When such a strong earthquake occurs, affected near-surface soil layers behave nonlinearly and may undergo some structural changes driven by Flow Liquefaction, Cyclic Mobility, or Slow Dynamics phenomena. The structural changes can be manifested by short-lasting coseismic and long-lasting postseismic site-response changes that are related to variations in near-surface shear-wave velocity. To examine this behavior, we perform a systematic analysis of Horizontal-to-Vertical (H/V) spectral ratios from regional earthquake waveforms recorded at 160 sites in the years 1996–2024. We identify significant H/V peaks and their directionality in the frequency range of 0.1–25 Hz separately for periods before and after the MJ 7.6 earthquake. This allows us to measure long-lasting relative changes in predominant frequency caused by the strong shaking, with maximum drops of −21% and a dependence on experienced ground motion levels. Next, the short-lasting changes during the MJ 7.6 earthquake reveal strongly nonstationary behavior. The frequency of spectral peaks decreases simultaneously and omnidirectionally with the strong shaking and then logarithmically recovers. The observed extreme short-lasting predominant frequency drops reach −93% relative to the initial value, and their occurrence time divides the nonstationary behavior into elastic softening and recovery phases. This behavior is physically related to temporal changes in near-surface shear-wave velocity as a consequence of changes in shear moduli. The introduced phenomenon of elastic softening and recovery may have a significant impact on a broad scale of geophysical research topics

NinjaSat monitoring of Type I X-ray bursts from the clocked burster SRGA J144459.2-604207

キューブサットX線衛星NinjaSatによる宇宙観測の革新 --決まった時間間隔で爆発を起こす奇妙な中性子星の長期観測-- . 京都大学プレスリリース. 2025-05-29.The CubeSat X-ray observatory NinjaSat was launched on 2023 November 11 and has provided opportunities for agile and flexible monitoring of bright X-ray sources. On 2024 February 23, the NinjaSat team started long-term observation of the new X-ray source SRGA J144459.2-604207 as the first scientific target, which was discovered on 2024 February 21 and recognized as the sixth clocked X-ray burster. Our 25-day observation covered almost the entire decay of this outburst from two days after the peak at ∼100 mCrab on February 23 until March 18 at a few mCrab level. The Gas Multiplier Counter on board NinjaSat successfully detected 12 Type I X-ray bursts with a typical burst duration of ∼20 s, shorter than other clocked burster systems. As the persistent X-ray emission declined by a factor of five, X-ray bursts showed a notable change in its morphology: the rise time became shorter from 4.4(7) s to 0.3(3) s (1σ errors), and the peak amplitude increased by 44%. The burst recurrence time Δt[rec] also became longer, from 2 to 10 hr, following the relation of Δt[rec] ∝ [−0.84]F[per] , where F[per] is the persistent X-ray flux, by applying a Markov chain Monte Carlo method. The short duration of bursts is explained by the He-enhanced composition of accretion matter and the relation between Δt[rec] and F[per] by a massive neutron star. This study demonstrated that CubeSat pointing observations can provide valuable astronomical X-ray data

各施設年次報告

芦生研究林年次報告 [3]北海道研究林年次報告 [6]和歌山研究林年次報告 [10]上賀茂試験地年次報告 [13]徳山試験地年次報告 [16]北白川試験地年次報告 [19

Comparison of DWI techniques in patients with epidermoid cyst: TGSE-BLADE DWI vs. SS-EPI DWI

[Purpose]To compare quantitative values and image quality between single-shot echo-planar imaging (SS-EPI) diffusion-weighted imaging (DWI) and two-dimensional turbo gradient- and spin-echo DWI with non-Cartesian BLADE trajectory (TGSE-BLADE DWI) in patients with epidermoid cyst. [Methods]Patients with epidermoid cyst who underwent both SS-EPI DWI and TGSE-BLADE DWI were included in this study. Two raters placed ROIs encircling the entire epidermoid cyst on SS-EPI DWI, and then on TGSE-BLADE DWI. Apparent diffusion coefficient (ADC) of the epidermoid cyst was measured within each ROI, then the intraclass correlation coefficient (ICC) between raters was obtained for each DWI. The areas of ROIs placed by the two raters were measured and compared using the Dice coefficient. In the selected slice analysis, one rater selected the most appropriate slice and carefully placed the ROIs slightly smaller than the epidermoid outline to avoid artifacts. Image quality analysis was assessed qualitatively for geometric distortion, susceptibility artifacts, lesion conspicuity, and diagnostic confidence. ADCs for both DWI techniques were compared with theoretical values derived from the diffusion phantom. [Results]Twenty patients with epidermoid cyst were included in this study. The ICC of ADC measured by the two raters for TGSE-BLADE (0.80) was higher than that for SS-EPI (0.59). Dice coefficient of ROI areas was significantly higher with TGSE-BLADE (0.78) than with SS-EPI (0.71, P = 0.007). Selected slice analysis showed that the ADC of epidermoid cyst was significantly higher with TGSE-BLADE DWI than with SS-EPI DWI (P < 0.001). ADCs measured from carefully selected ROIs avoiding artifacts with the two techniques correlated positively (r = 0.87, P < 0.001; ICC 0.75). TGSE-BLADE DWI rated better for image quality than SS-EPI DWI according to all raters. ICCs of measured ADC and theoretical ADCs exceeded 0.99 for both techniques. [Conclusions]TGSE-BLADE DWI appears more suitable than SS-EPI DWI for evaluating epidermoid cyst

1920年代上海会审公廨债权回收机能的衰退 --以美中商事纷争为中心

第一部 経済編Part I Economy第一部 经济