Identification of both copy number variation-type and constant-type core elements in a large segmental duplication region of the mouse genome

BACKGROUND: Copy number variation (CNV), an important source of diversity in genomic structure, is frequently found in clusters called CNV regions (CNVRs). CNVRs are strongly associated with segmental duplications (SDs), but the composition of these complex repetitive structures remains unclear. RESULTS: We conducted self-comparative-plot analysis of all mouse chromosomes using the high-speed and large-scale-homology search algorithm SHEAP. For eight chromosomes, we identified various types of large SD as tartan-checked patterns within the self-comparative plots. A complex arrangement of diagonal split lines in the self-comparative-plots indicated the presence of large homologous repetitive sequences. We focused on one SD on chromosome 13 (SD13M), and developed SHEPHERD, a stepwise ab initio method, to extract longer repetitive elements and to characterize repetitive structures in this region. Analysis using SHEPHERD showed the existence of 60 core elements, which were expected to be the basic units that form SDs within the repetitive structure of SD13M. The demonstration that sequences homologous to the core elements (\u3e70% homology) covered approximately 90% of the SD13M region indicated that our method can characterize the repetitive structure of SD13M effectively. Core elements were composed largely of fragmented repeats of a previously identified type, such as long interspersed nuclear elements (LINEs), together with partial genic regions. Comparative genome hybridization array analysis showed that whereas 42 core elements were components of CNVR that varied among mouse strains, 8 did not vary among strains (constant type), and the status of the others could not be determined. The CNV-type core elements contained significantly larger proportions of long terminal repeat (LTR) types of retrotransposon than the constant-type core elements, which had no CNV. The higher divergence rates observed in the CNV-type core elements than in the constant type indicate that the CNV-type core elements have a longer evolutionary history than constant-type core elements in SD13M. CONCLUSIONS: Our methodology for the identification of repetitive core sequences simplifies characterization of the structures of large SDs and detailed analysis of CNV. The results of detailed structural and quantitative analyses in this study might help to elucidate the biological role of one of the SDs on chromosome 13

Metastable Structure of Photoexcited WO3 Determined by the Pump-probe Extended X-ray Absorption Fine Structure Spectroscopy and Constrained Thorough Search Analysis

The local structure of WO3 photocatalyst in the photoexcited metastable state created 150 ps after laser irradiation have been determined by the pump-probe L3-edge EXAFS and the constrained thorough search analysis. A highly distorted octahedral local structure was found where one of the shortest W-O bonds was further shortened to 1.66 Å while the other five bonds were rather elongated even though theoretical calculations predicted the reverse change. We discuss this contradiction and propose a possible structure for the metastable state

Photoinduced anisotropic distortion as the electron trapping site of tungsten trioxide by ultrafast W L 1 -edge X-ray absorption spectroscopy with full potential multiple scattering calculations

International audienceUnderstanding the excited state of photocatalysts is significant to improve their activity for water splitting reaction. X-ray absorption fine structure (XAFS) spectroscopy in X-ray free electron lasers (XFEL) is a powerful method to address dynamic changes in electronic states and structures of photocatalysts in the excited state in ultrafast short time scales. The ultrafast atomic-scale local structural change in photoexcited WO3 was observed by W L1 edge XAFS spectroscopy using an XFEL. An anisotropic local distortion around the W atom could reproduce well the spectral features at a delay time of 100 ps after photoexcitation based on full potential multiple scattering calculations. The distortion involved the movement of W to shrink the shortest W–O bonds and elongate the longest one. The movement of the W atom could be explained by the filling of the dxy and dzx orbitals, which were originally located at the bottom of the conduction band with photoexcited electrons

Anomalous depth dependency of the stress field in the 2007 Noto Hanto, Japan, earthquake: Potential involvement of a deep fluid reservoir

We have elucidated depth variations in the stress field associated with the 2007 Noto Hanto, Japan, earthquake by stress tensor inversion using high-quality aftershock data obtained by a dense seismic network. Aftershocks that occurred above 4 km in depth indicated a strike-slip stress regime. By contrast, aftershocks in deeper parts indicated a thrust faulting stress regime. This depth variation in the stress regime correlates well with that in the slip direction derived from a finite source model using geodetic data. Furthermore, the maximum principal stress (σ1) axis was stably oriented approximately W20°N down to the depth of the mainshock hypocenter, largely in agreement with the regional stress field, but, below that depth, the σ1 axis had no definite orientation, indicating horizontally isotropic stress. One likely cause of these drastic changes in the stress regime with depth is the buoyant force of a fluid reservoir localized beneath the seismogenic zone