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| 2. |
- Wang, QBS, et al.
(författare)
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The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force
- 2022
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1, s. 4830-
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 3. |
- Yabuta, Hikaru, et al.
(författare)
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Macromolecular organic matter in samples of the asteroid (162173) Ryugu
- 2023
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Ingår i: Science. - : American Association for the Advancement of Science. - 0036-8075 .- 1095-9203. ; 379:6634
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Tidskriftsartikel (refereegranskat)abstract
- Samples of the carbonaceous asteroid (162173) Ryugu were collected and brought to Earth by the Hayabusa2 spacecraft. We investigated the macromolecular organic matter in Ryugu samples and found that it contains aromatic and aliphatic carbon, ketone, and carboxyl functional groups. The spectroscopic features of the organic matter are consistent with those in chemically primitive carbonaceous chondrite meteorites that experienced parent-body aqueous alteration (reactions with liquid water). The morphology of the organic carbon includes nanoglobules and diffuse carbon associated with phyllosilicate and carbonate minerals. Deuterium and/or nitrogen-15 enrichments indicate that the organic matter formed in a cold molecular cloud or the presolar nebula. The diversity of the organic matter indicates variable levels of aqueous alteration on Ryugus parent body.
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| 4. |
- Fukuzawa, Hironobu, et al.
(författare)
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Real-time observation of X-ray-induced intramolecular and interatomic electronic decay in CH2I2
- 2019
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- The increasing availability of X-ray free-electron lasers (XFELs) has catalyzed the development of single-object structural determination and of structural dynamics tracking in real-time. Disentangling the molecular-level reactions triggered by the interaction with an XFEL pulse is a fundamental step towards developing such applications. Here we report real-time observations of XFEL-induced electronic decay via short-lived transient electronic states in the diiodomethane molecule, using a femtosecond near-infrared probe laser. We determine the lifetimes of the transient states populated during the XFEL-induced Auger cascades and find that multiply charged iodine ions are issued from short-lived (∼20 fs) transient states, whereas the singly charged ones originate from significantly longer-lived states (∼100 fs). We identify the mechanisms behind these different time scales: contrary to the short-lived transient states which relax by molecular Auger decay, the long-lived ones decay by an interatomic Coulombic decay between two iodine atoms, during the molecular fragmentation. © 2019, The Author(s).
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| 5. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 6. |
- Kumagai, Yoshiaki, et al.
(författare)
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Suppression of thermal nanoplasma emission in clusters strongly ionized by hard x-rays
- 2021
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Ingår i: Journal of Physics B. - : Institute of Physics Publishing (IOPP). - 0953-4075 .- 1361-6455. ; 54:4
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Tidskriftsartikel (refereegranskat)abstract
- Using electron and ion spectroscopy, we studied the electron and nuclear dynamics in similar to 50 000-atom large krypton clusters, following excitation with an intense hard x-ray pulse. Beyond the single pulse experiment, we also present the results of a time-resolved, x-ray pump-near-infrared probe measurement that allows one to learn about the time evolution of the system. After core ionization of the atoms by x-ray photons, trapped Auger and secondary electrons form a nanoplasma in which the krypton ions are embedded, according to the already published scenario. While the ion data show expected features, the electron emission spectra miss the expected pump-probe delay-dependent enhancement except for a slight enhancement in the energy range below 2 eV. Theoretical simulations help to reveal that, due to the deep trapping potential of the ions during the long time expansion accompanied by electron-ion recombination, thermal emission from the transient nanoplasma becomes quenched.
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| 7. |
- Otto, Katharina, et al.
(författare)
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MASCOT’s in situ analysis of asteroid Ryugu in the context of regolith samples and remote sensing data returned by Hayabusa2
- 2023
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Ingår i: Earth Planets and Space. - : Springer. - 1343-8832 .- 1880-5981. ; 75:1
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Tidskriftsartikel (refereegranskat)abstract
- The Hayabusa2 mission provided a unique data set of asteroid Ryugu that covers a wide range of spatial scale from the orbiter remote sensing instruments to the returned samples. The MASCOT lander that was delivered onto the surface of Ryugu aimed to provide context for these data sets by producing in situ data collected by a camera (MasCam), a radiometer (MARA), a magnetometer (MasMag) and a spectrometer (MicrOmega). In this work, we evaluate the success of MASCOT as an integrated lander to bridge the gap between orbiter and returned sample analysis. We find that MASCOT’s measurements and derivatives thereof, including the rock morphology, colour in the visible wavelengths, possible meteorite analogue, density, and porosity of the rock at the landing site are in good agreement with those of the orbiter and the returned samples. However, it also provides information on the spatial scale (sub-millimetres to centimetres) at which some physical properties such as the thermal inertia and reflectance undergo scale-dependent changes. Some of the in situ observations such as the presence of clast/inclusions in rocks and the absence of fine particles at the landing site was uniquely identified by MASCOT. Thus, we conclude that the delivery of an in situ instrument like MASCOT provides a valuable data set that complements and provides context for remote sensing and returned sample analyses.
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