Termination of Graphene Edges Created by Hydrogen and Deuterium Plasmas

Edge engineering is important for both fundamental research and applications as the device size decreases to nanometer scale. This is especially the case for graphene because a graphene edge shows totally different electronic properties depending on the atomic structure and the termination. It has recently been shown that an atomically precise zigzag edge can be obtained by etching graphene and graphite using hydrogen (H) plasma. However, edge termination had not been studied directly. In this study, termination of edges created by H-plasma is studied by high-resolution electron energy loss spectroscopy (HREELS) to show that the edge is $\mathrm{sp}^{2}$ bonded and the edge carbon atom is terminated by only one H atom. This suggests that an ideal zigzag edge, which is not only atomically precise but also $\mathrm{sp}^{2}$ bonding, can be obtained by H-plasma etching. Etching of the graphite surface with plasma of a different isotope, deuterium (D), is also studied by scanning tunneling microscopy (STM) to show that D-plasma anisotropically etches graphite less efficiently, although it can make defects more efficiently, than H-plasma.Comment: 8 pages, 5 figure

Stimulated emission from multilayer graphene

Monolayer graphene absorbs $\sim$ 2.3 percent of the incident visible light. This "small" absorption was used to emphasize visual transparency of graphene, but in fact it means that multilayer graphene absorbs sizable fraction of incident light, which causes non-negligible fluorescence. In this paper, we study the light emission properties of multilayer graphene composed of tens to hundreds of layers, because these are informative materials having interesting optical properties correlated closely with fluorescence. For example, it was recently predicted that 87-layer graphene absorbs infrared light at maximum efficiency and 20-layer graphene on silicon substrates exhibits zero reflectance (a total absence of backscattering) at a specific visible light wavelength. By modeling light emissions from multilayer graphene using a transfer matrix method, we could quantitatively explain the measured reflectivity from multilayer graphene on silicon substrates. We found sizable corrections, that cannot be classified as incoherent light emissions, to the reflectance of visible light. The new component originates from stimulated emission caused by absorption at each graphene layer, and it is a coherent sum over the amplitudes coming from all graphene layers with a common phase shift of $\pi$ relative to the incident light. The coherent corrections to the reflectance become dominant for samples thicker than 40-layers and thinner than 160-layers. Multilayer graphene thus functions as a partial coherent light source of various wavelengths and it may have surface-emitting laser applications.Comment: 9 pages, 9 figure

Endoscopic diagosis of gastric malignant lymphoma

To delineate the pitfalls and counter-measures in the endoscopic diagnosis of gastric malignant lymphoma (GML), reviewed were 32 cases of primary GML and 16 cases of systemic ML with gastric involvement (secondary GML). 1) Accurate diagnosis of GML had been made in only 13 cases of primary GML ; 18 cases had been diagnosed of gastric cancer (GC); the remaining one of benign ulcer (BU). Review of the endoscopic films, however, revealed more than two of the three findings characteristic, but not pathognomomic, of GML in 84 percent. This result indicates that possibility of GML must be kept in mind in the differential diagnosis of malignant lesions despite its rarity, because endoscopists tend to be predisposed with an impression of GC. 2) Follow-up examinations made in nine cases of primary GML revealed marked changes in endoscopic findings in three cases : healing of an ulcer lesion in one case, healing of an ulcer lesion on an unchanged tumor in another and enlargement of a tumor in the remaining one. The first case had been followed up for two years with an impression of BU. This result indicates that improvement of ulcer does not necessarily rule out GML because it can show "malignant cycle" just as GC. 3) Endoscopic biopsy performed in 30 cases of primary GML had led to accurate diagnosis in only 16 cases and erroneous diagnosis of GC in five and no malignancy in nine. Review of the cases revealed the importance of having suspicion of GML at first from endoscopic findings, because it can lead to an increase of the number of biopsy specimens, careful selection of biopsy sites, careful use of biopsy instruments to obtain good specimens and closer contact with pathologists. 4) Prospective studies on systemic ML revealed gastric involvement in 17 percent. Examinations of the GI tract, especially of the stomach is one of the important steps for staging of systemic ML and deciding therapeutic modalities. 5) It is extremely difficult to diffierentate primary GML and secondary GML from endoscopic findings alone, although there are a few findings characteristic of the latter

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

Daunorubicin can eliminate iPS-derived cancer stem cells via ICAD/CAD-independent DNA fragmentation

Aim: To identify a drug that can effectively eliminate these cancer stem cells (CSCs) and determine its mode of action.Methods: CSCs were obtained from mouse induced pluripotent stem cells (miPSCs) using cancer cell-conditioned media. Drug screening was performed on these cells or after transplantation into mice. Apoptosis was analyzed by flow cytometry and western blotting.Results: Drug screening studies showed that daunorubicin, a topoisomerase II inhibitor, is specifically cytotoxic to miPS-CSCs. Daunorubicin-induced apoptosis was found to be associated with p53 accumulation, activation of the caspase cascade, and oligonucleosomal DNA fragmentation. Treatment with the caspase inhibitor abolished daunorubicin-induced DNA fragmentation and was therefore considered to act downstream of caspase activation. This was also suppressed by treatment with a Ca2+-specific chelator, which suggested that CAD endonuclease does not contribute. Moreover, no obvious ICAD reduction/degradation was detected.Conclusion: Daunorubicin effectively eliminated CSCs, which are dependent on the p53/caspase signaling cascade. The current findings provided the basis for further studies on CSC-targeted drugs for the development of cancer treatment strategies