Complete Genome Sequence of Pseudomonas amygdali pv. tabaci Strain 6605, a Causal Agent of Tobacco Wildfire Disease

Pseudomonas amygdali pv. tabaci strain 6605 is the bacterial pathogen causing tobacco wildfire disease that has been used as a model for elucidating virulence mechanisms. Here, we present the complete genome sequence of P. amygdali pv. tabaci 6605 as a circular chromosome from reads using a PacBio sequencer

Laser-driven multi-MeV high-purity proton acceleration via anisotropic ambipolar expansion of micron-scale hydrogen clusters

強力なレーザーを使ってエネルギーがそろった純度100％の陽子ビーム発生に成功 --レーザー駆動陽子ビーム加速器の実現へ向けて大きく前進--. 京都大学プレスリリース. 2022-10-13.Multi-MeV high-purity proton acceleration by using a hydrogen cluster target irradiated with repetitive, relativistic intensity laser pulses has been demonstrated. Statistical analysis of hundreds of data sets highlights the existence of markedly high energy protons produced from the laser-irradiated clusters with micron-scale diameters. The spatial distribution of the accelerated protons is found to be anisotropic, where the higher energy protons are preferentially accelerated along the laser propagation direction due to the relativistic effect. These features are supported by three-dimensional (3D) particle-in-cell (PIC) simulations, which show that directional, higher energy protons are generated via the anisotropic ambipolar expansion of the micron-scale clusters. The number of protons accelerating along the laser propagation direction is found to be as high as 1.6 ±0.3 × 10⁹/MeV/sr/shot with an energy of 2.8 ±1.9 MeV, indicating that laser-driven proton acceleration using the micron-scale hydrogen clusters is promising as a compact, repetitive, multi-MeV high-purity proton source for various applications

Discriminative detection of laser-accelerated multi-MeV carbon ions utilizing solid state nuclear track detectors

A new diagnosis method for the discriminative detection of laser‐accelerated multi‐MeV carbon ions from background oxygen ions utilizing solid‐state nuclear track detectors (SSNTDs) is proposed. The idea is to combine two kinds of SSNTDs having different track registration sensitivities: Bisphenol A polycarbonate detects carbon and the heavier ions, and polyethylene terephthalate detects oxygen and the heavier ions. The method is calibrated with mono‐energetic carbon and oxygen ion beams from the heavy ion accelerator. Based on the calibration data, the method is applied to identify carbon ions accelerated from multilayered graphene targets irradiated by a high‐power laser, where the generation of high‐energy high‐purity carbon ions is expected. It is found that 93 ± 1% of the accelerated heavy ions with energies larger than 14 MeV are carbons. The results thus obtained support that carbon‐rich heavy ion acceleration is achieved

Robustness of large‐area suspended graphene under interaction with intense laser

Graphene is known as an atomically thin, transparent, highly electrically and thermally conductive, light‐weight, and the strongest 2D material. We investigate disruptive application of graphene asa target of laser‐driven ion acceleration. We develop large‐area suspended graphene (LSG) and by transferring graphene layer by layer we control the thickness with precision down to a single atomic layer. Direct irradiations of the LSG targets generate MeV protons and carbons from sub‐relativistic to relativistic laser intensities from low contrast to high contrast conditions without plasma mirror, evidently showing the durability of graphene

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Correlated Mutation Analysis of C2H2 Zinc Finger Domains

Introduction Zinc finger proteins perform various functions in cellular processes, such as transcription, translation, metabolism and signaling, by binding to nucleic acids or proteins. In a zinc finger domain, a zinc ion forms four coordinate bonds for its stable fold. A C2H2 domain has approximately 25 to 30 amino acid residues, including paired cysteines and histidines as zinc coordinating residues and possessing two short #-strands followed by an #-helix. Most C2H2 zinc finger proteins bind to DNA. Many of the proteins also bind to RNA or proteins. The binding properties depend on the amino acid residues of the zinc finger loop, the arrangement of C2H2 domains in proteins and the higher order structure of proteins [2]. In this research, we analyze C2H2 domains using a method of correlated mutation analysis(CMA). There has been several CMA methods based on substitution matrices [1] or likelihood matrices derived from previously solved structures [3]. We present a CMA method usin