| 1. |
- Ito, H., et al.
(författare)
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Comparison of analytical methods for profiling N- and O-linked glycans from cultured cell lines
- 2016
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Ingår i: Glycoconjugate Journal. - : Springer Science and Business Media LLC. - 0282-0080 .- 1573-4986. ; 33:3, s. 405-415
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Tidskriftsartikel (refereegranskat)abstract
- The Human Disease Glycomics/Proteome Initiative (HGPI) is an activity in the Human Proteome Organization (HUPO) supported by leading researchers from international institutes and aims at development of disease-related glycomics/glycoproteomics analysis techniques. Since 2004, the initiative has conducted three pilot studies. The first two were N- and O-glycan analyses of purified transferrin and immunoglobulin-G and assessed the most appropriate analytical approach employed at the time. This paper describes the third study, which was conducted to compare different approaches for quantitation of N- and O-linked glycans attached to proteins in crude biological samples. The preliminary analysis on cell pellets resulted in wildly varied glycan profiles, which was probably the consequence of variations in the pre-processing sample preparation methodologies. However, the reproducibility of the data was not improved dramatically in the subsequent analysis on cell lysate fractions prepared in a specified method by one lab. The study demonstrated the difficulty of carrying out a complete analysis of the glycome in crude samples by any single technology and the importance of rigorous optimization of the course of analysis from preprocessing to data interpretation. It suggests that another collaborative study employing the latest technologies in this rapidly evolving field will help to realize the requirements of carrying out the large-scale analysis of glycoproteins in complex cell samples.
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| 2. |
- Chelban, V., et al.
(författare)
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PDXK mutations cause polyneuropathy responsive to pyridoxal 5′-phosphate supplementation
- 2019
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Ingår i: Annals of Neurology. - : Wiley. - 0364-5134 .- 1531-8249. ; 86:2, s. 225-240
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To identify disease-causing variants in autosomal recessive axonal polyneuropathy with optic atrophy and provide targeted replacement therapy. Methods: We performed genome-wide sequencing, homozygosity mapping, and segregation analysis for novel disease-causing gene discovery. We used circular dichroism to show secondary structure changes and isothermal titration calorimetry to investigate the impact of variants on adenosine triphosphate (ATP) binding. Pathogenicity was further supported by enzymatic assays and mass spectroscopy on recombinant protein, patient-derived fibroblasts, plasma, and erythrocytes. Response to supplementation was measured with clinical validated rating scales, electrophysiology, and biochemical quantification. Results: We identified biallelic mutations in PDXK in 5 individuals from 2 unrelated families with primary axonal polyneuropathy and optic atrophy. The natural history of this disorder suggests that untreated, affected individuals become wheelchair-bound and blind. We identified conformational rearrangement in the mutant enzyme around the ATP-binding pocket. Low PDXK ATP binding resulted in decreased erythrocyte PDXK activity and low pyridoxal 5′-phosphate (PLP) concentrations. We rescued the clinical and biochemical profile with PLP supplementation in 1 family, improvement in power, pain, and fatigue contributing to patients regaining their ability to walk independently during the first year of PLP normalization. Interpretation: We show that mutations in PDXK cause autosomal recessive axonal peripheral polyneuropathy leading to disease via reduced PDXK enzymatic activity and low PLP. We show that the biochemical profile can be rescued with PLP supplementation associated with clinical improvement. As B6 is a cofactor in diverse essential biological pathways, our findings may have direct implications for neuropathies of unknown etiology characterized by reduced PLP levels. ANN NEUROL 2019;86:225–240. © 2019 The Authors. Annals of Neurology published by Wiley Periodicals, Inc. on behalf of American Neurological Association.
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| 3. |
- Fukuzawa, H., et al.
(författare)
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Electron spectroscopy of rare-gas clusters irradiated by x-ray free-electron laser pulses from SACLA
- 2016
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Ingår i: Journal of Physics B-Atomic Molecular and Optical Physics. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 49:3
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Tidskriftsartikel (refereegranskat)abstract
- We have measured electron energy spectra and asymmetry parameters of Ar clusters and Xe clusters illuminated by intense x-rays at 5 and 5.5 keV. A velocity map imaging spectrometer was developed for this purpose and employed at an x-ray free-electron laser facility, SACLA in Japan. The cluster size dependence and the peak fluence dependence of the electron spectra and asymmetry parameters are discussed.
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| 4. |
- Furukawa, T., et al.
(författare)
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Cooling dynamics of photo-excited negative carbon cluster ions stored in an ion storage ring
- 2015
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Ingår i: Nuclear Instruments & Methods in Physics Research Section B-Beam Interactions with Materials and Atoms. - : Elsevier BV. - 0168-583X. ; 354, s. 192-196
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Tidskriftsartikel (refereegranskat)abstract
- A newly found fast radiative cooling process of C-6(-) is studied by simulation based on statistical sharing of the internal energy by the vibrational modes both in the electronic ground and excited states. For comparison, a contrasting slow cooling of C6H- is simulated by the same procedure. The simulation demonstrates a distinct difference in the time evolution of energy distributions between C-6(-) and C6H-, and well reproduces the observed fast cooling of C-6(-) by recurrent electronic transitions and the slow cooling of C6H- by vibrational de-excitation. (C) 2014 Elsevier B.V. All rights reserved.
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| 5. |
- Ito, G., et al.
(författare)
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Cooling Dynamics of Photoexcited C6 − and C6H−
- 2014
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 112
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Tidskriftsartikel (refereegranskat)abstract
- We report conclusive evidence of an efficient cooling mechanism via the electronic radiative transitions of hot small molecular anions isolated in vacuum. We stored C6− and C6H− in an ion storage ring and observed laser-induced electron detachment with delays up to several milliseconds. The terminal hydrogen atom caused a drastic change in the decay profiles. The decay of hotoexcited C6H− is slow and nonexponential, which can be explained by depletion cooling, whereas that for C6− occurs extremely fast, on a time scale below 0.1 ms and can only be explained by electronic radiative cooling via low-lying electronic excited states.
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| 6. |
- Shang, Z. Y., et al.
(författare)
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Weakened growth of cropland-N2O emissions in China associated with nationwide policy interventions
- 2019
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 25:11, s. 3706-3719
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Tidskriftsartikel (refereegranskat)abstract
- China has experienced rapid agricultural development over recent decades, accompanied by increased fertilizer consumption in croplands; yet, the trend and drivers of the associated nitrous oxide (N2O) emissions remain uncertain. The primary sources of this uncertainty are the coarse spatial variation of activity data and the incomplete model representation of N2O emissions in response to agricultural management. Here, we provide new data-driven estimates of cropland-N2O emissions across China in 1990-2014, compiled using a global cropland-N2O flux observation dataset, nationwide survey-based reconstruction of N-fertilization and irrigation, and an updated nonlinear model. In addition, we have evaluated the drivers behind changing cropland-N2O patterns using an index decomposition analysis approach. We find that China's annual cropland-N2O emissions increased on average by 11.2 Gg N/year(2) (p < .001) from 1990 to 2003, after which emissions plateaued until 2014 (2.8 Gg N/year(2), p = .02), consistent with the output from an ensemble of process-based terrestrial biosphere models. The slowdown of the increase in cropland-N2O emissions after 2003 was pervasive across two thirds of China's sowing areas. This change was mainly driven by the nationwide reduction in N-fertilizer applied per area, partially due to the prevalence of nationwide technological adoptions. This reduction has almost offset the N2O emissions induced by policy-driven expansion of sowing areas, particularly in the Northeast Plain and the lower Yangtze River Basin. Our results underline the importance of high-resolution activity data and adoption of nonlinear model of N2O emission for capturing cropland-N2O emission changes. Improving the representation of policy interventions is also recommended for future projections.
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| 7. |
- Shiromaru, H., et al.
(författare)
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Cooling dynamics of carbon cluster anions
- 2015
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Ingår i: Journal of Physics: Conference Series. - : IOP Publishing. - 1742-6596 .- 1742-6588. ; 635
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Tidskriftsartikel (refereegranskat)abstract
- A series of ion storage experiments on small carbon cluster anions was conducted to understand size-dependent cooling processes. The laser-induced delayed electron detachment time profile show clear even/odd alternation due to the presence of the electronic cooling. The time evolution of the internal energy distribution was simulated for Cn- (n=4 to 7) with a common procedure taking vibrational and electronic cooling into account.
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| 8. |
- Tachibana, T., et al.
(författare)
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Nanoplasma Formation by High Intensity Hard X-rays
- 2015
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Using electron spectroscopy, we have investigated nanoplasma formation from noble gas clusters exposed to high-intensity hard-x-ray pulses at similar to 5 keV. Our experiment was carried out at the SPring-8 Angstrom Compact free electron LAser (SACLA) facility in Japan. Dedicated theoretical simulations were performed with the molecular dynamics tool XMDYN. We found that in this unprecedented wavelength regime nanoplasma formation is a highly indirect process. In the argon clusters investigated, nanoplasma is mainly formed through secondary electron cascading initiated by slow Auger electrons. Energy is distributed within the sample entirely through Auger processes and secondary electron cascading following photoabsorption, as in the hard x-ray regime there is no direct energy transfer from the field to the plasma. This plasma formation mechanism is specific to the hard-x-ray regime and may, thus, also be important for XFEL-based molecular imaging studies. In xenon clusters, photo-and Auger electrons contribute more significantly to the nanoplasma formation. Good agreement between experiment and simulations validates our modelling approach. This has wide-ranging implications for our ability to quantitatively predict the behavior of complex molecular systems irradiated by high-intensity hard x-rays.
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| 9. |
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| 10. |
- Kajihara, H., et al.
(författare)
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Taxonomic Identity of a Tetrodotoxin-Accumulating Ribbon-worm Cephalothrix simula (Nemertea: Palaeonemertea): A Species Artificially Introduced from the Pacific to Europe
- 2013
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Ingår i: Zoological Science. - : Zoological Society of Japan. - 0289-0003. ; 30:11, s. 985-997
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Tidskriftsartikel (refereegranskat)abstract
- We compared the anatomy of the holotype of the palaeonemertean Cephalothrix simula (Iwata, 1952) with that of the holotypes of Cephalothrix hongkongiensis Sundberg, Gibson and Olsson, 2003 and Cephalothrix fasciculus (Iwata, 1952), as well as additional specimens from Fukue (type locality of C. simula) and Hiroshima, Japan. While there was no major morphological discordance between these specimens, we found discrepancies between the actual morphology and some statements in the original description of C. simula with respect to supposedly species-specific characters. Our observation indicates that these three species cannot be discriminated by the anatomical characters so far used to distinguish congeners. For objectivity of scientific names, topogenetypes of the mitochondrial cytochrome c oxidase subunit I (COI) sequences are designated for C. simula, C. hongkongiensis, and C. fasciculus. Analysis of COI sequence showed that the Hiroshima population can be identified as C. simula, which has been found in previous studies from Trieste, Italy, and also from both the Mediterranean and Atlantic coasts of the Iberian Peninsula, indicating an artificial introduction via (1) ballast water, (2) ship-fouling communities, or (3) the commercially cultured oyster Crassostrea gigas (Thunberg, 1793) brought from Japan to France in 1970s. Cephalothrix simula is known to be toxic, as it contains large amounts of tetrodotoxin (TTX). We report here that the grass puffer Takifugu niphobles (Jordan and Snyder, 1901)-also known to contain TTX-consumes C. simula. We suggest that the puffer may be able to accumulate TTX by eating C. simula.
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