| 1. |
- Alseekh, Saleh, et al.
(författare)
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Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices
- 2021
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Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 18:7, s. 747-756
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Forskningsöversikt (refereegranskat)abstract
- This Perspective, from a large group of metabolomics experts, provides best practices and simplified reporting guidelines for practitioners of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics. Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics-derived data.
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| 2. |
- Kusano, Miyako, et al.
(författare)
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Application of a metabolomic method combining one-dimensional and two-dimensional gas chromatography-time-of-flight/mass spectrometry to metabolic phenotyping of natural variants in rice
- 2007
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Ingår i: Journal of chromatography. B. - Amsterdam : Elsevier. - 1570-0232 .- 1873-376X. ; 855:1, s. 71-79
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Tidskriftsartikel (refereegranskat)abstract
- We have developed a comprehensive method combining analytical techniques of one-dimensional (I D) and two-dimensional (GC x GC) gas chromatography-time-of-flight (TOF)-mass spectrometry. This method was applied to the metabolic phenotyping of natural variants in rice for the 68 world rice core collection (WRC) and two other varieties. Ten metabolites were selected as metabolite representatives, and the selected ion current of each metabolite peak obtained from both techniques were statistically compared. Our method of combining I D- and GC x GC-TOF/MS is useful for the metabolic phenotyping of natural variants in rice for further studies in breeding programs.
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| 3. |
- Kusano, Miyako, et al.
(författare)
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Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana
- 2007
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Ingår i: BMC Systems Biology. - : Springer Science and Business Media LLC. - 1752-0509. ; 1:53, s. 1-17
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Metabolites are not only the catalytic products of enzymatic reactions but also the active regulators or the ultimate phenotype of metabolic homeostasis in highly complex cellular processes. The modes of regulation at the metabolome level can be revealed by metabolic networks. We investigated the metabolic network between wild-type and 2 mutant (methionine-over accumulation 1 [mto1] and transparent testa4 [tt4]) plants regarding the alteration of metabolite accumulation in Arabidopsis thaliana. RESULTS: In the GC-TOF/MS analysis, we acquired quantitative information regarding over 170 metabolites, which has been analyzed by a novel score (ZMC, z-score of metabolite correlation) describing a characteristic metabolite in terms of correlation. Although the 2 mutants revealed no apparent morphological abnormalities, the overall correlation values in mto1 were much lower than those of the wild-type and tt4 plants, indicating the loss of overall network stability due to the uncontrolled accumulation of methionine. In the tt4 mutant, a new correlation between malate and sinapate was observed although the levels of malate, sinapate, and sinapoylmalate remain unchanged, suggesting an adaptive reconfiguration of the network. Gene-expression correlations presumably responsible for these metabolic networks were determined using the metabolite correlations as clues. CONCLUSION: Two Arabidopsis mutants, mto1 and tt4, exhibited the following changes in entire metabolome networks: the overall loss of metabolic stability (mto1) or the generation of a metabolic network of a backup pathway for the lost physiological functions (tt4). The expansion of metabolite correlation to gene-expression correlation provides detailed insights into the systemic understanding of the plant cellular process regarding metabolome and transcriptome.
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| 4. |
- Masese, Titus, et al.
(författare)
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Honeycomb-Layered Oxides With Silver Atom Bilayers and Emergence of Non-Abelian SU(2) Interactions
- 2023
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Ingår i: Advanced Science. - : Wiley. - 2198-3844 .- 2198-3844. ; 10:6
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Tidskriftsartikel (refereegranskat)abstract
- Honeycomb-layered oxides with monovalent or divalent, monolayered cationic lattices generally exhibit myriad crystalline features encompassing rich electrochemistry, geometries, and disorders, which particularly places them as attractive material candidates for next-generation energy storage applications. Herein, global honeycomb-layered oxide compositions, Ag2M2TeO6 ((Formula presented.).) exhibiting (Formula presented.) atom bilayers with sub-valent states within Ag-rich crystalline domains of Ag6M2TeO6 and (Formula presented.) -deficient domains of (Formula presented.) ((Formula presented.)). The (Formula presented.) -rich material characterized by aberration-corrected transmission electron microscopy reveals local atomic structural disorders characterized by aperiodic stacking and incoherency in the bilayer arrangement of (Formula presented.) atoms. Meanwhile, the global material not only displays high ionic conductivity but also manifests oxygen-hole electrochemistry during silver-ion extraction. Within the (Formula presented.) -rich domains, the bilayered structure, argentophilic interactions therein and the expected (Formula presented.) sub-valent states ((Formula presented.), etc.) are theoretically understood via spontaneous symmetry breaking of SU(2)× U(1) gauge symmetry interactions amongst 3 degenerate mass-less chiral fermion states, justified by electron occupancy of silver (Formula presented.) and 5s orbitals on a bifurcated honeycomb lattice. This implies that bilayered frameworks have research applications that go beyond the confines of energy storage.
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| 5. |
- Masese, Titus, et al.
(författare)
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Mixed alkali-ion transport and storage in atomic-disordered honeycomb layered NaKNi 2 TeO 6
- 2021
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Honeycomb layered oxides constitute an emerging class of materials that show interesting physicochemical and electrochemical properties. However, the development of these materials is still limited. Here, we report the combined use of alkali atoms (Na and K) to produce a mixed-alkali honeycomb layered oxide material, namely, NaKNi2TeO6. Via transmission electron microscopy measurements, we reveal the local atomic structural disorders characterised by aperiodic stacking and incoherency in the alternating arrangement of Na and K atoms. We also investigate the possibility of mixed electrochemical transport and storage of Na+ and K+ ions in NaKNi2TeO6. In particular, we report an average discharge cell voltage of about 4 V and a specific capacity of around 80 mAh g–1 at low specific currents (i.e., < 10 mA g–1) when a NaKNi2TeO6-based positive electrode is combined with a room-temperature NaK liquid alloy negative electrode using an ionic liquid-based electrolyte solution. These results represent a step towards the use of tailored cathode active materials for “dendrite-free” electrochemical energy storage systems exploiting room-temperature liquid alkali metal alloy materials.
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| 6. |
- Morokuma, Tomoki, et al.
(författare)
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OISTER optical and near-infrared monitoring observations of peculiar radio-loud active galactic nucleus SDSSJ110006.07+442144.3
- 2017
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Ingår i: Nippon Tenmon Gakkai obun kenkyu hokoku. - : Oxford University Press (OUP). - 0004-6264. ; 69:5
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Tidskriftsartikel (refereegranskat)abstract
- We present monitoring campaign observations at optical and near-infrared (NIR) wavelengths for a radio-loud active galactic nucleus (AGN) at z = 0.840, SDSSJ110006.07+442144.3 (hereafter, J1100+4421), which was identified during a flare phase in late 2014 February. The campaigns consist of three intensive observing runs from the discovery to 2015 March, mostly within the scheme of the OISTER collaboration. Optical-NIR light curves and simultaneous spectral energy distributions (SEDs) are obtained. Our measurements show the strongest brightening in 2015 March. We found that the optical-NIR SEDs of J1100+4421 show an almost steady shape despite the large and rapid intranight variability. This constant SED shape is confirmed to extend to similar to 5 mu m in the observed frame using the archival WISE data. Given the lack of absorption lines and the steep power-law spectrum of alpha(upsilon) similar to -1.4, where f(v) proportional to v(alpha upsilon), synchrotron radiation by a relativistic jet with no or small contributions from the host galaxy and the accretion disk seemsmost plausible as an optical-NIR emission mechanism. The steep optical-NIR spectral shape and the large amplitude of variability are consistent with this object being a low.peak jet-dominated AGN. In addition, sub-arcsecond resolution optical imaging data taken with Subaru Hyper Suprime-Cam does not show a clear extended component and the spatial scales are significantly smaller than the large extensions detected at radio wavelengths. The optical spectrum of a possible faint companion galaxy does not show any emission lines at the same redshift, and hence a merging hypothesis for this AGN-related activity is not supported by our observations.
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| 7. |
- Redestig, Henning, et al.
(författare)
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Compensation for systematic cross-contribution improves normalization of mass spectrometry based metabolomics data
- 2009
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Ingår i: Analytical Chemistry. - Washington : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 81:19, s. 7974-7980
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Tidskriftsartikel (refereegranskat)abstract
- Most mass spectrometry based metabolomics studies are semiquantitative and depend on efficient normalization techniques to suppress systematic error. A common approach is to include isotope-labeled internal standards (ISs) and then express the estimated metabolite abundances relative to the IS. Because of problems such as insufficient chromatographic resolution, however, the analytes may directly influence estimates of the IS, a phenomenon known as cross-contribution (CC). Normalization using ISs that suffer from CC effects will cause significant loss of information if the interfering analytes are associated with the studied factors. We present a novel normalization algorithm, which compensates for systematic CC effects that can be traced back to a linear association with the experimental design. The proposed method was found to be superior at purifying the signal of interest compared to current normalization methods when applied to two biological data sets and a multicomponent dilution mixture. Our method is applicable to data from randomized and designed experiments that use ISs to monitor the systematic error.
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| 8. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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