Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome

精子形成に重要なヒストンによるDNAの新たな折りたたみを解明. 京都大学プレスリリース. 2021-02-22.H2A.B is an evolutionarily distant histone H2A variant that accumulates on DNA repair sites, DNA replication sites, and actively transcribing regions in genomes. In cells, H2A.B exchanges rapidly in chromatin, but the mechanism has remained enigmatic. In the present study, we found that the H2A.B-H2B dimer incorporated within the nucleosome exchanges with the canonical H2A-H2B dimer without assistance from additional factors, such as histone chaperones and nucleosome remodelers. High-speed atomic force microscopy revealed that the H2A.B nucleosome, but not the canonical H2A nucleosome, transiently forms an intermediate “open conformation”, in which two H2A.B-H2B dimers may be detached from the H3-H4 tetramer and bind to the DNA regions near the entry/exit sites. Mutational analyses revealed that the H2A.B C-terminal region is responsible for the adoption of the open conformation and the H2A.B-H2B exchange in the nucleosome. These findings provide mechanistic insights into the histone exchange of the H2A.B nucleosome

High-resolution seismic reflection survey across the Western Boundary Fault Zone of the Nagano Basin, Central Japan: Data acquisition and processing

The Western Boundary Fault Zone of the Nagano Basin borders the eastern margin of Northern Fossa Magna, which has undergone strong horizontal shortening since Pliocene. The Western Boundary Fault Zone of the Nagano Basin is considered to be a back thrust that developed on the hanging wall side of the Itoigawa-Shizuoka Tectonic Line. To reveal the subsurface structure of the Western Boundary Fault Zone of the Nagano Basin, we carried out a high-resolution seismic reflection survey along the Saigawa River, southern Nagano City. The source used in this survey was a mini-vibrator (T-15000). Source and receiver spacing was 10 m. 180 channels of geophone arrays were used to record each shot. The seismic section obtained after careful data processing shows fairly flat Quaternary basin fillings in the eastern part of the seismic line. The Quaternary basin fillings are interpreted to be in west-dipping fault contact with west-dipping Neogene strata underlying the Saigawa Hills

Integral approach to biomacromolecular structure by analytical-ultracentrifugation and small-angle scattering

溶液中の蛋白質構造を正確に評価するための新規解析法を開発 --構造評価の妨げとなる凝集の影響を実験データから除去--. 京都大学プレスリリース. 2020-06-09.Currently, a sample for small-angle scattering (SAS) is usually highly purified and looks monodispersed: The Guinier plot of its SAS intensity shows a fine straight line. However, it could include the slight aggregates which make the experimental SAS profile different from the monodispersed one. A concerted method with analytical-ultracentrifugation (AUC) and SAS, named as AUC-SAS, offers the precise scattering intensity of a concerned biomacromolecule in solution even with aggregates as well that of a complex under an association-dissociation equilibrium. AUC-SAS overcomes an aggregation problem which has been an obstacle for SAS analysis and, furthermore, has a potential to lead to a structural analysis for a general multi-component system

Canna Starch Improves Intestinal Barrier Function, Inhibits Allergen Uptake, and Suppresses Anaphylactic Symptoms in Ovalbumin-Induced Food Allergy in Mice

Edible canna rhizomes contain extremely high levels of resistant starch among cereals and potatoes. We previously showed that feeding canna rhizome starch to mice may increase intestinal barrier function and improve the intestinal environment. Here, we investigated the effects of canna starch intake in a murine food allergy model. Five-week-old female BALB/c mice were divided into four groups: Control and OVA groups fed on the control diet (AIN-93G) ad libitum and Canna and OVA-Canna groups fed on the canna diet (AIN-93G with 10% replaced with canna starch). The OVA and OVA-Canna groups were sensitized to ovalbumin (OVA), and the anaphylactic response was assessed by measuring body temperature. Body temperature was significantly lower in the OVA group than in the non-sensitized group, but no decrease was observed in the OVA-Canna group. Fecal weight, fecal mucin content, and goblet cells of colorectal tissue were significantly increased in the Canna and OVA-Canna groups compared with those in the Control and OVA groups. Allergen uptake into the liver was also increased in the OVA group and decreased in the OVA-Canna group to the same level as in the non-sensitized group. These results indicate that canna starch supplementation in a murine food allergy model suppresses anaphylactic symptoms by improving the intestinal environment and reducing allergen uptake by increasing intestinal barrier function

Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach

巨大タンパク質複合体による概日リズム制御 --小角散乱と計算科学の統合アプローチ--. 京都大学プレスリリース. 2022-03-11.A-B-C is not as easy as 1-2-3 but assembles like clockwork. 京都大学プレスリリース. 2022-03-11.In the cyanobacterial circadian clock system, KaiA, KaiB and KaiC periodically assemble into a large complex. Here we determined the overall structure of their fully assembled complex by integrating experimental and computational approaches. Small-angle X-ray and inverse contrast matching small-angle neutron scatterings coupled with size-exclusion chromatography provided constraints to highlight the spatial arrangements of the N-terminal domains of KaiA, which were not resolved in the previous structural analyses. Computationally built 20 million structural models of the complex were screened out utilizing the constrains and then subjected to molecular dynamics simulations to examine their stabilities. The final model suggests that, despite large fluctuation of the KaiA N-terminal domains, their preferential positionings mask the hydrophobic surface of the KaiA C-terminal domains, hindering additional KaiA-KaiC interactions. Thus, our integrative approach provides a useful tool to resolve large complex structures harboring dynamically fluctuating domains

Deformation Process and Mechanism of the Frontal Megathrust at the Nankai Subduction Zone

Abstract The frontal megathrust of the Nankai Trough subduction zone is recognized as a seismogenic fault based on a record of frictional heating, but the underlying micromechanical processes that act on the fault surface are poorly known. Here we present a layer of fault gouge ∼2 mm thick within a core drilled across the megathrust, in which smectite‐rich siltstone has been transformed into a preferentially oriented illite aggregate. The nearly complete breakdown of smectite is consistent with fast frictional heating on this fault; however, the microtextures of the gouge and its surroundings are asserted one produced experimentally by slow slip. We suggest that slow slip with small shear strain has overprinted the textures produced by the previous faster and larger slip. This interpretation based on microtectonic evidence suggests a slow slip around the frontal megathrust took place during slow down, afterslip, or interseismic as observed now going in subduction zone. We suggest that the illite‐dominated gouge is conditionally stable, likely to shift from rapid to slow slip at different times

Newly developed Laboratory-based Size exclusion chromatography Small-angle x-ray scattering System (La-SSS)

To understand a biological system, it is important to observe structures of biomolecules in the solution where the system is functionalized. Small-Angle X-ray Scattering coupled with Size Exclusion Chromatography (SEC-SAXS) is one of techniques to selectively observe the target molecules in the multi-component system. However, this technique is believed to be available only with a synchrotron-based SAXS instrument due to requirement of high beam intensity and, therefore, the limitation of the beam time was obstacle to satisfy demands from many bio-researchers. We newly developed Laboratory-based Size exclusion chromatography SAXS System (La-SSS) by utilizing a latest laboratory-based SAXS instrument and finely optimization of the balance between flow rate, cell volume, irradiation time and so on. La-SSS succeeded not only decoupling of target protein(s) from non-specific aggregates but also measurement of each concerned component in a multi-component system. In addition, an option: “stopping mode”, which is designed for improving statistics of SAXS profile, realized a high S/N data acquisition for the most interesting protein in a multi-component system. Furthermore, by utilizing a column having small bed volume, the small-scale SEC-SAXS study makes available. Through optimization of instrumental parameters and environments, La-SSS is highly applicable for experimental requirements from various biological samples. It is strongly expected that a La-SSS concept must be a normal option for laboratory-based SAXS in the near future

Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach

In the cyanobacterial circadian clock system, KaiA, KaiB and KaiC periodically assemble into a large complex. Here we determined the overall structure of their fully assembled complex by integrating experimental and computational approaches. Small-angle X-ray and inverse contrast matching small-angle neutron scatterings coupled with size-exclusion chromatography provided constraints to highlight the spatial arrangements of the N-terminal domains of KaiA, which were not resolved in the previous structural analyses. Computationally built 20 million structural models of the complex were screened out utilizing the constrains and then subjected to molecular dynamics simulations to examine their stabilities. The final model suggests that, despite large fluctuation of the KaiA N-terminal domains, their preferential positionings mask the hydrophobic surface of the KaiA C-terminal domain, hindering additional KaiA-KaiC interactions. Thus, our integrative approach provides a useful tool to resolve large complex structures harboring dynamically fluctuating domains