The three-dimensional structure of the colicin E3 immunity protein by distance geometry calculation

AbstractThe three-dimensional solution structure of the colicin E3 immunity protein (84 residues) was determined by distance geometry calculations. The hydrophilic side of a four-stranded antiparallel β-sheet constitutes a part of the surface of the protein, and two loops lie on the hydrophobic side of the sheet. All the three specificity-determining residues, which are included in the center of the β-sheet, display their side groups on the protein surface

Difficulties Facing Junior Physicians and Solutions Toward Delivering End-of-Life Care for Patients with Cancer: A Nationwide Survey in Japan

Background: Junior physicians' perceived difficulty in end-of-life care of patients with cancer has not been structurally investigated; therefore, current challenges and solutions in this area remain unknown. Objectives: To identify some difficulties junior physicians face in delivering end-of-life care for patients with cancer and to clarify the support required to reduce these difficulties. Design: A nationwide survey was conducted in over 300 institutions selected randomly from 1037 clinical training hospitals in Japan. Participants: From each of these institutions, two resident physicians of postgraduate year (PGY) 1 or 2, two clinical fellows of PGY 3–5, and an attending physician were requested to respond to the survey. Measurements: The survey investigated issues regarding end-of-life care using the palliative care difficulties scale with two additional domains (“discussion about end-of-life care” and “death pronouncement”). Items related to potential solutions for alleviating the difficulties as well were investigated. Results: A total of 198 resident physicians, 134 clinical fellows, and 96 attending physicians responded to the survey (response rate: 33.0%, 22.3%, and 32.0%). The results revealed that junior physicians face difficulties within specific domains of end-of-life care. The most challenging domain comprised communication and end-of-life discussion with patients and family members, symptom alleviation, and death pronouncement. The most favored supportive measure for alleviating these difficulties was mentorship, rather than educational opportunities or resources regarding end-of-life care. Conclusion: The findings of this study reveal the need for further effort to enrich the mentorship and support systems for junior physicians delivering end-of-life care

Proposal for measuring magnetism with patterned apertures

We propose a magnetic measurement method utilizing a patterned post-sample aperture in a transmission electron microscope. While utilizing electron magnetic circular dichroism, the method circumvents previous needs to shape the electron probe to an electron vortex beam or astigmatic beam. The method can be implemented in standard scanning transmission electron microscopes by replacing the spectrometer entrance aperture with a specially shaped aperture, hereafter called ventilator aperture. The proposed setup is expected to work across the whole range of beam sizes -- from wide parallel beams down to atomic resolution magnetic spectrum imaging.Comment: 6 pages, 4 figure

Interfacial fracture strength property of micro-scale SiN/Cu components

AbstractThe strength against fracture nucleation from an interface free-edge of silicon-nitride (SiN)/copper (Cu) micro-components is evaluated. A special technique that combines a nano-indenter specimen holder and an environmental transmission electron microscope (E-TEM) is employed. The critical load at the onset of fracture nucleation from a wedge-shaped free-edge (opening angle: 90°) is measured both in a vacuum and in a hydrogen (H2) environment, and the critical stress distribution is evaluated by the finite element method (FEM). It is found that the fracture nucleation is dominated by the near-edge elastic singular stress field that extends about a few tens of nanometers from the edge. The fracture nucleation strength expressed in terms of the stress intensity factor (K) is found to be eminently reduced in a H2 environment

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