Streptavidin 2D crystal substrates for visualizing biomolecular processes by atomic force microscopy

Flat substrate surfaces are a key to successful imaging of biological macromolecules by atomic force microscopy (AFM). Although usable substrate surfaces have been prepared for still imaging of immobilized molecules, surfaces that are more suitable have recently been required for dynamic imaging to accompany the progress of the scan speed of AFM. In fact, the stateof-the-art high-speed AFM has achieved temporal resolution of 30 ms, a capacity allowing us to trace molecular processes played by biological macromolecules. Here, we characterize three types of streptavidin two-dimensional crystals as substrates, concerning their qualities of surface roughness, uniformity, stability, and resistance to nonspecific protein adsorption. These crystal surfaces are commonly resistant to nonspecific protein adsorption, but exhibit differences in other properties to some extent. These differences must be taken into consideration, but these crystal surfaces are still useful for dynamic AFM imaging, as demonstrated by observation of calcium-induced changes in calmodulin, GroES binding to GroEL, and actin polymerization on the surfaces. © 2009 by the Biophysical Society

Subaru near infrared coronagraphic images of T Tauri

High angular resolution near-infrared (JHK) adaptive optics images of T Tau were obtained with the infrared camera Coronagraphic Imager with Adaptive Optics (CIAO) mounted on the 8.2m Subaru Telescope in 2002 and 2004. The images resolve a complex circumstellar structure around a multiple system. We resolved T Tau Sa and Sb as well as T Tau N and S. The estimated orbit of T Tau Sb indicates that it is probably bound to T Tau Sa. The K band flux of T Tau S decreased by ˜ 1.7 Jy in 2002 November compared with that in 2001 mainly because T Tau Sa became fainter. The arc-like ridge detected in our near-infrared images is consistent with what is seen at visible wavelengths, supporting the interpretation in previous studies that the arc is part of the cavity wall seen relatively pole-on. Halo emission is detected out to ˜2\u27\u27from T Tau N. This may be light scattered off the common envelope surrounding the T Tauri multiple system

A Young Brown Dwarf Companion to DH Tauri

We present the detection of a young brown dwarf companion DH Tau B associated with the classical T Tauri star DH Tau. Near-infrared coronagraphic observations with CIAO on the Subaru Telescope have revealed DH Tau B with H = \~15 mag located at 2.3" (330 AU) away from the primary DH Tau A. Comparing its position with a Hubble Space Telescope archive image, we confirmed that DH Tau A and B share the common proper motion, suggesting that they are physically associated with each other. The near-infrared color of DH Tau B is consistent with those of young stellar objects. The near-infrared spectra of DH Tau B show deep water absorption bands, a strong K I absorption line, and a moderate Na I absorption line. We derived its effective temperature and surface gravity of Teff = 2700 -- 2800 K and log g = 4.0--4.5, respectively, by comparing the observed spectra with synthesized spectra of low-mass objects. The location of DH Tau B on the HR diagram gives its mass of 30 -- 50 M_Jupiter.Comment: 10 pages, 14 figures, 1 table, accepted for publication in Ap

Current Performance and On-Going Improvements of the 8.2 m Subaru Telescope

An overview of the current status of the 8.2 m Subaru Telescope constructed and operated at Mauna Kea, Hawaii, by the National Astronomical Observatory of Japan is presented. The basic design concept and the verified performance of the telescope system are described. Also given are the status of the instrument package offered to the astronomical community, the status of operation, and some of the future plans. The status of the telescope reported in a number of SPIE papers as of the summer of 2002 are incorporated with some updates included as of 2004 February. However, readers are encouraged to check the most updated status of the telescope through the home page, http://subarutelescope.org/index.html, and/or the direct contact with the observatory staff.Comment: 18 pages (17 pages in published version), 29 figures (GIF format), This is the version before the galley proo

High-Contrast Imaging of Intermediate-Mass Giants with Long-Term Radial Velocity Trends

A radial velocity (RV) survey for intermediate-mass giants has been operated for over a decade at Okayama Astrophysical Observatory (OAO). The OAO survey has revealed that some giants show long-term linear RV accelerations (RV trends), indicating the presence of outer companions. Direct imaging observations can help clarify what objects generate these RV trends. We present the results of high-contrast imaging observations of six intermediate-mass giants with long-term RV trends using the Subaru Telescope and HiCIAO camera. We detected co-moving companions to gamma Hya B (0.61+0.12 0.14 Stellar Mass), HD 5608 B (0.10 +/- 0.01 Stellar Mass), and HD 109272 B (0.28 +/- 0.06 Stellar Mass). For the remaining targets( Dra, 18 Del, and HD 14067) we exclude companions more massive than 30-60 M(sub Jup) at projected separations of 1-7. We examine whether these directly imaged companions or unidentified long-period companions can account for the RV trends observed around the six giants. We find that the Kozai mechanism can explain the high eccentricity of the inner planets Dra b, HD 5608 b, and HD 14067 b

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

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