Mail-in data collection at SPring-8 protein crystallography beamlines

A mail-in data collection system at SPring-8, which is a web application with automated beamline operation, has been developed

Optimized protocol for the extraction of RNA and DNA from frozen whole blood sample stored in a single EDTA tube

Cryopreservation of whole blood is useful for DNA collection, and clinical and basic research. Blood samples in ethylenediaminetetraacetic acid disodium salt (EDTA) tubes stored at − 80 °C are suitable for DNA extraction, but not for high-quality RNA extraction. Herein, a new methodology for high-quality RNA extraction from human blood samples is described. Quickly thawing frozen whole blood on aluminum blocks at room temperature could minimize RNA degradation, and improve RNA yield and quality compared with thawing the samples in a 37 °C water bath. Furthermore, the use of the NucleoSpin RNA kit increased RNA yield by fivefold compared with the PAXgene Blood RNA Kit. Thawing blood samples on aluminum blocks significantly increased the DNA yield by ~ 20% compared with thawing in a 37 °C water bath or on ice. Moreover, by thawing on aluminum blocks and using the NucleoSpin RNA and QIAamp DNA Blood kits, the extraction of RNA and DNA of sufficient quality and quantity was achieved from frozen EDTA whole blood samples that were stored for up to 8.5 years. Thus, extracting RNA from frozen whole blood in EDTA tubes after long-term storage is feasible. These findings may help advance gene expression analysis, as well as biomarker research for various diseases

In Situ Measurements of Stress Evolution in Silicon Thin Films During Electrochemical Lithiation and Delithiation

We report in situ measurements of stress evolution in a silicon thin-film electrode during electrochemical lithiation and delithiation by using the Multi-beam Optical Sensor (MOS) technique. Upon lithiation, due to substrate constraint, the silicon electrode initially undergoes elastic deformation, resulting in rapid rise of compressive stress. The electrode begins to deform plastically at a compressive stress of ca. -1.75 GPa; subsequent lithiation results in continued plastic strain, dissipating mechanical energy. Upon delithiation, the electrode first undergoes elastic straining in the opposite direction, leading to a tensile stress of ca. 1 GPa; subsequently, it deforms plastically during the rest of delithiation. The plastic flow stress evolves continuously with lithium concentration. Thus, mechanical energy is dissipated in plastic deformation during both lithiation and delithiation, and it can be calculated from the stress measurements; we show that it is comparable to the polarization loss. Upon current interrupt, both the film stress and the electrode potential relax with similar time-constants, suggesting that stress contributes significantly to the chemical potential of lithiated-silicon.Comment: 12 pages, 3 figure

An oxyl/oxo mechanism for dioxygen bond formation in PSII revealed by X-ray free electron lasers

Photosynthetic water oxidation is catalyzed by the Mn4CaO5 cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S0 to S4). To reveal the mechanism of water oxidation, we analyzed structures of PSII in the S1, S2, and S3 states by x-ray free-electron laser serial crystallography. No insertion of water was found in S2, but flipping of D1 Glu189 upon transition to S3 leads to the opening of a water channel and provides a space for incorporation of an additional oxygen ligand, resulting in an open cubane Mn4CaO6 cluster with an oxyl/oxo bridge. Structural changes of PSII between the different S states reveal cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation

Interferon signaling and hypercytokinemia-related gene expression in the blood of antidepressant non-responders

Only 50% of patients with depression respond to the first antidepressant drug administered. Thus, biomarkers for prediction of antidepressant responses are needed, as predicting which patients will not respond to antidepressants can optimize selection of alternative therapies. We aimed to identify biomarkers that could predict antidepressant responsiveness using a novel data-driven approach based on statistical pattern recognition. We retrospectively divided patients with major depressive disorder into antidepressant responder and non-responder groups. Comprehensive gene expression analysis was performed using peripheral blood without narrowing the genes. We designed a classifier according to our own discrete Bayes decision rule that can handle categorical data. Nineteen genes showed differential expression in the antidepressant non-responder group (n = 15) compared to the antidepressant responder group (n = 15). In the training sample of 30 individuals, eight candidate genes had significantly altered expression according to quantitative real-time polymerase chain reaction. The expression of these genes was examined in an independent test sample of antidepressant responders (n = 22) and non-responders (n = 12). Using the discrete Bayes classifier with the HERC5, IFI6, and IFI44 genes identified in the training set yielded 85% discrimination accuracy for antidepressant responsiveness in the 34 test samples. Pathway analysis of the RNA sequencing data for antidepressant responsiveness identified that hypercytokinemia- and interferon-related genes were increased in non-responders. Disease and biofunction analysis identified changes in genes related to inflammatory and infectious diseases, including coronavirus disease. These results strongly suggest an association between antidepressant responsiveness and inflammation, which may be useful for future treatment strategies for depression

Study of J/psi to p pbar, Lambda Lambdabar and observation of eta_c to Lambda Lambdabar at Belle

We study the baryonic charmonium decays of B mesons, B+ to etac K+ and B+ to J/psi K+, where the etac and J/psi subsequently decay into a p pbar or Lambda Lambdabar pair. We measure the J/psi to p pbar, Lambda Lambdabar anisotropy parameters, alpha_B = -0.60 +- 0.13 +-0.14 (p pbar), -0.44 +- 0.51 +- 0.31 (Lambda Lambdabar) and compare to results from e+e- to J/psi formation experiments. We also report the first observation of etac to Lambda Lambdabar. The measured branching fraction is B(etac to Lambda Lambdabar) = (0.87 +0.24 -0.21(stat) +0.09 -0.14(syst) +- 0.27 (PDG)) x 10^-3. This study is based on a 357 fb^-1 data sample recorded on the Upsilon(4S) resonance with the Belle detector at the KEKB asymmetric-energy e+e- collider.Comment: 8 pages, two figures (4 figure files), an update of hep-ex/0509020 for journal submissio

Genetic and Phenotypic Landscape of PRPH2-Associated Retinal Dystrophy in Japan

Peripherin-2 (PRPH2) is one of the causative genes of inherited retinal dystrophy. While the gene is relatively common in Caucasians, reports from Asian ethnicities are limited. In the present study, we report 40 Japanese patients from 30 families with PRPH2-associated retinal dystrophy. We identified 17 distinct pathogenic or likely pathogenic variants using next-generation sequencing. Variants p.R142W and p.V200E were relatively common in the cohort. The age of onset was generally in the 40’s; however, some patients had earlier onset (age: 5 years). Visual acuity of the patients ranged from hand motion to 1.5 (Snellen equivalent 20/13). The patients showed variable phenotypes such as retinitis pigmentosa, cone-rod dystrophy, and macular dystrophy. Additionally, intrafamilial phenotypic variability was observed. Choroidal neovascularization was observed in three eyes of two patients with retinitis pigmentosa. The results demonstrate the genotypic and phenotypic variations of the disease in the Asian cohort

Observation of Two Resonant Structures in e+e- to pi+ pi- psi(2S) via Initial State Radiation at Belle

The cross section for e+e- to pi+ pi- psi(2S) between threshold and \sqrt{s}=5.5 GeV is measured using 673 fb^{-1} of data on and off the \Upsilon(4S) resonance collected with the Belle detector at KEKB. Two resonant structures are observed in the pi+ pi- psi(2S) invariant mass distribution, one at 4361\pm 9\pm 9 MeV/c2 with a width of 74\pm 15\pm 10 MeV/c2, and another at 4664\pm 11\pm 5 MeV/c2 with a width of 48\pm 15\pm 3 MeV/c2, if the mass spectrum is parameterized with the coherent sum of two Breit-Wigner functions. These values do not match those of any of the known charmonium states.Comment: 10 pages, 5 figures, 2 tables, version to appear in Phys. Rev. Let