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2.
  • Heywood, I., et al. (författare)
  • Inflation of 430-parsec bipolar radio bubbles in the Galactic Centre by an energetic event
  • 2019
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 573:7773, s. 235-237
  • Tidskriftsartikel (refereegranskat)abstract
    • The Galactic Centre contains a supermassive black hole with a mass of four million Suns1 within an environment that differs markedly from that of the Galactic disk. Although the black hole is essentially quiescent in the broader context of active galactic nuclei, X-ray observations have provided evidence for energetic outbursts from its surroundings2. Also, although the levels of star formation in the Galactic Centre have been approximately constant over the past few hundred million years, there is evidence of increased short-duration bursts3, strongly influenced by the interaction of the black hole with the enhanced gas density present within the ring-like central molecular zone4 at Galactic longitude |l| < 0.7 degrees and latitude |b| < 0.2 degrees. The inner 200-parsec region is characterized by large amounts of warm molecular gas5, a high cosmic-ray ionization rate6, unusual gas chemistry, enhanced synchrotron emission7,8, and a multitude of radio-emitting magnetized filaments9, the origin of which has not been established. Here we report radio imaging that reveals a bipolar bubble structure, with an overall span of 1 degree by 3 degrees (140 parsecs × 430 parsecs), extending above and below the Galactic plane and apparently associated with the Galactic Centre. The structure is edge-brightened and bounded, with symmetry implying creation by an energetic event in the Galactic Centre. We estimate the age of the bubbles to be a few million years, with a total energy of 7 × 1052 ergs. We postulate that the progenitor event was a major contributor to the increased cosmic-ray density in the Galactic Centre, and is in turn the principal source of the relativistic particles required to power the synchrotron emission of the radio filaments within and in the vicinity of the bubble cavities.
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3.
  • Wang, J., et al. (författare)
  • Final report of the CCQM-K145 : Toxic and essential elements in bovine liver
  • 2020
  • Ingår i: Metrologia. - : IOP Publishing Ltd. - 0026-1394 .- 1681-7575. ; 57:1 A
  • Tidskriftsartikel (refereegranskat)abstract
    • Liver plays a major role in metabolism and acts as a source of energy for the body by storing glycogen. With the growing interest and investigation in the biological effects in recent years, it is important and necessary to develop accurate and comparable analytical methods for elements in bio-samples. It has, however, been 10 years since the tissue sample (bovine liver) of CCQM-K49 key comparison. The purpose of CCQM-K145 is to ensure the comparable and traceable measurement results for essential and toxic elements such as P, S, Zn, Mn, Ni, Mo, Sr, Cr, Co, Pb, As and Hg in bovine liver among NMIs and other designated measurement bodies worldwide. The comparison was agreed by IAWG as 6th IAWG Benchmarking Exercise with Zn and Ni as exemplary elements at the meeting in Korea in the early October 2016. The results of CCQM-K145 are expected to cover the measurement capability and support CMCs claiming for inorganic elements in the similar biological tissue materials and food samples. 30 NMIs and DIs registered in CCQM-K145. With respect to the methodology, a variety of techniques such as IDMS, ICP-OES, ICP-MS(non-ID), AAS and NAA were adopted by the participants. For Zn, Ni, Sr, Pb and Hg measurements, most participants chose ID-ICP-MS method, which showed the better performance in terms of consistency and reliability of the measurement results. In aspect of the traceability for the measurement results in CCQM-K145, most participants used their own (in house) CRMs or other NMI's CRMs to guarantee trace to SI unit. Most participants used similar matrix CRMs for quality control or method validation. Base on different statistic way to calculate the reference mass fraction values and associated uncertainties for each measurand, removal of the suspected extreme values, and discussion at the IAWG meetings, the median values are proposed as the KCRV for Zn, Ni, Mn, Mo, Cr, Pb and Hg; the arithmetic mean values are proposed as the KCRV for P, S, Sr, Co and As. In general, the performances of the majority of CCQM-K145 participants are very good, illustrating their measurement capabilities for Zn, Ni, P, S, Mn, Mo, Sr, Cr, As, Co, Pb and Hg in a complex biological tissue matrix. Bovine liver contains many kinds of nutrients and microelements, it can be regarded as a typical representative material of biological tissue and food. In CCQM-K145, the analytes involved alkali metals and transition elements, metalloids/semi-metals and non metals with a range of mass fraction from mg/g to μg/kg. CCQM-K145 also tested the ability of NMIs/DIs to determine elements that were easy to be lost and polluted, and interfered significantly. The chemical pretreatment methods of samples used in the comparison is suitable for general food and biological matrix samples. A variety of measurement methods used in the comparison represent the main instrumental technology for elemental analysis. Therefore, for supporting CMC claim, CCQM-K145 is readily applicable to measurement of more elements in a wide range of biological materials (including liquids and solids) and meat products. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
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4.
  • Camilo, F., et al. (författare)
  • Revival of the Magnetar PSR J1622-4950: Observations with MeerKAT, Parkes, XMM-Newton, Swift, Chandra, and NuSTAR
  • 2018
  • Ingår i: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 856:2
  • Tidskriftsartikel (refereegranskat)abstract
    • New radio (MeerKAT and Parkes) and X-ray (XMM-Newton, Swift, Chandra, and NuSTAR) observations of PSR J1622-4950 indicate that the magnetar, in a quiescent state since at least early 2015, reactivated between 2017 March 19 and April 5. The radio flux density, while variable, is approximately 100 larger than during its dormant state. The X-ray flux one month after reactivation was at least 800 larger than during quiescence, and has been decaying exponentially on a 111 19 day timescale. This high-flux state, together with a radio-derived rotational ephemeris, enabled for the first time the detection of X-ray pulsations for this magnetar. At 5%, the 0.3-6 keV pulsed fraction is comparable to the smallest observed for magnetars. The overall pulsar geometry inferred from polarized radio emission appears to be broadly consistent with that determined 6-8 years earlier. However, rotating vector model fits suggest that we are now seeing radio emission from a different location in the magnetosphere than previously. This indicates a novel way in which radio emission from magnetars can differ from that of ordinary pulsars. The torque on the neutron star is varying rapidly and unsteadily, as is common for magnetars following outburst, having changed by a factor of 7 within six months of reactivation.
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5.
  • Echelmeier, A., et al. (författare)
  • Segmented flow generator for serial crystallography at the European X-ray free electron laser
  • 2020
  • Ingår i: Nature Communications. - : Nature Research. - 2041-1723. ; 11:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal suspension into the path of the XFEL, wasting a vast amount of sample due to the pulsed nature of all current XFEL sources. The European XFEL (EuXFEL) delivers femtosecond (fs) X-ray pulses in trains spaced 100 ms apart whereas pulses within trains are currently separated by 889 ns. Therefore, continuous sample delivery via fast jets wastes >99% of sample. Here, we introduce a microfluidic device delivering crystal laden droplets segmented with an immiscible oil reducing sample waste and demonstrate droplet injection at the EuXFEL compatible with high pressure liquid delivery of an SFX experiment. While achieving ~60% reduction in sample waste, we determine the structure of the enzyme 3-deoxy-D-manno-octulosonate-8-phosphate synthase from microcrystals delivered in droplets revealing distinct structural features not previously reported. 
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6.
  • Hartmann, S., et al. (författare)
  • Can single-cell and spatial omics unravel the pathophysiology of pre-eclampsia?
  • 2023
  • Ingår i: Journal of Reproductive Immunology. - : Elsevier. - 0165-0378 .- 1872-7603. ; 159
  • Tidskriftsartikel (refereegranskat)abstract
    • Pre-eclampsia is a leading cause of maternal and fetal morbidity and mortality. Characterised by the onset of hypertension and proteinuria in the second half of pregnancy, it can lead to maternal end-organ injury such as cerebral ischemia and oedema, pulmonary oedema and renal failure, and potentially fatal outcomes for both mother and fetus. The causes of the different maternal end-organ phenotypes of pre-eclampsia and why some women develop pre-eclampsia condition early in pregnancy have yet to be elucidated. Omics methods include proteomics, genomics, metabolomics, transcriptomics. These omics techniques, previously mostly used on bulk tissue and individually, are increasingly available at a single cellular level and can be combined with each other. Multi-omics techniques on a single-cell or spatial level provide us with a powerful tool to understand the pathophysiology of pre-eclampsia. This review will explore the status of omics methods and how they can and could contribute to understanding the pathophysiology of pre-eclampsia.
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7.
  • Crous, P.W., et al. (författare)
  • Fungal Planet description sheets: 1112–1181
  • 2020
  • Ingår i: Persoonia. - : Naturalis Biodiversity Center. - 0031-5850. ; 45, s. 251-409
  • Tidskriftsartikel (refereegranskat)abstract
    • Novel species of fungi described in this study include those from various countries as follows: Australia, Austroboletus asper on soil, Cylindromonium alloxyli on leaves of Alloxylon pinnatum, Davidhawksworthia quintiniae on leaves of Quintinia sieberi, Exophiala prostantherae on leaves of Prostanthera sp., Lactifluus lactiglaucus on soil, Linteromyces quintiniae (incl. Linteromyces gen. nov.) on leaves of Quintinia sieberi, Lophotrichus medusoides from stem tissue of Citrus garrawayi, Mycena pulchra on soil, Neocalonectria tristaniopsidis (incl. Neocalonectria gen. nov.) and Xyladictyochaeta tristaniopsidis on leaves of Tristaniopsis collina, Parasarocladium tasmanniae on leaves of Tasmannia insipida, Phytophthora aquae-cooljarloo from pond water, Serendipita whamiae as endophyte from roots of Eriochilus cucullatus, Veloboletus limbatus (incl. Veloboletus gen. nov.) on soil. Austria, Cortinarius glaucoelotus on soil. Bulgaria, Suhomyces rilaensis from the gut of Bolitophagus interruptus found on a Polyporus sp. Canada, Cantharellus betularum among leaf litter of Betula, Penicillium saanichii from house dust. Chile, Circinella lampensis on soil, Exophiala embothrii from rhizosphere of Embothrium coccineum. China, Colletotrichum cycadis on leaves of Cycas revoluta. Croatia, Phialocephala melitaea on fallen branch of Pinus halepensis. Czech Republic, Geoglossum jirinae on soil, Pyrenochaetopsis rajhradensis from dead wood of Buxus sempervirens. Dominican Republic, Amanita domingensis on litter of deciduous wood, Melanoleuca dominicana on forest litter. France, Crin- ipellis nigrolamellata (Martinique) on leaves of Pisonia fragrans, Talaromyces pulveris from bore dust of Xestobium rufovillosum infesting floorboards. French Guiana, Hypoxylon hepaticolor on dead corticated branch. Great Britain, Inocybe ionolepis on soil. India, Cortinarius indopurpurascens among leaf litter of Quercus leucotrichophora. Iran, Pseudopyricularia javanii on infected leaves of Cyperus sp., Xenomonodictys iranica (incl. Xenomonodictys gen. nov.) on wood of Fagus orientalis. Italy, Penicillium vallebormidaense from compost. Namibia, Alternaria mira- bibensis on plant litter, Curvularia moringae and Moringomyces phantasmae (incl. Moringomyces gen. nov.) on leaves and flowers of Moringa ovalifolia, Gobabebomyces vachelliae (incl. Gobabebomyces gen. nov.) on leaves of Vachellia erioloba, Preussia procaviae on dung of Procavia capensis. Pakistan, Russula shawarensis from soil on forest floor. Russia, Cyberlindnera dauci from Daucus carota. South Africa, Acremonium behniae on leaves of Behnia reticulata, Dothiora aloidendri and Hantamomyces aloidendri (incl. Hantamomyces gen. nov.) on leaves of Aloidendron dichotomum, Endoconidioma euphorbiae on leaves of Euphorbia mauritanica, Eucasphaeria pro- teae on leaves of Protea neriifolia, Exophiala mali from inner fruit tissue of Malus sp., Graminopassalora geisso- rhizae on leaves of Geissorhiza splendidissima, Neocamarosporium leipoldtiae on leaves of Leipoldtia schultzii,Neocladosporium osteospermi on leaf spots of Osteospermum moniliferum, Neometulocladosporiella seifertii on leaves of Combretum caffrum, Paramyrothecium pituitipietianum on stems of Grielum humifusum, Phytopythium paucipapillatum from roots of Vitis sp., Stemphylium carpobroti and Verrucocladosporium carpobroti on leaves of Carpobrotus quadrifolius, Suttonomyces cephalophylli on leaves of Cephalophyllum pilansii. Sweden, Coprinopsis rubra on cow dung, Elaphomyces nemoreus from deciduous woodlands. Spain, Polyscytalum pini-canariensis on needles of Pinus canariensis, Pseudosubramaniomyces septatus from stream sediment, Tuber lusitanicum on soil under Quercus suber. Thailand, Tolypocladium flavonigrum on Elaphomyces sp. USA, Chaetothyrina spondiadis on fruits of Spondias mombin, Gymnascella minnisii from bat guano, Juncomyces patwiniorum on culms of Juncus effusus, Moelleriella puertoricoensis on scale insect, Neodothiora populina (incl. Neodothiora gen. nov.) on stem cankers of Populus tremuloides, Pseudogymnoascus palmeri from cave sediment. Vietnam, Cyphellophora viet- namensis on leaf litter, Tylopilus subotsuensis on soil in montane evergreen broadleaf forest. Morphological and culture characteristics are supported by DNA barcodes.
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10.
  • Urgessa, Z. N., et al. (författare)
  • Low temperature near band edge recombination dynamics in ZnO nanorods
  • 2014
  • Ingår i: Journal of Applied Physics. - : American Institute of Physics (AIP). - 0021-8979 .- 1089-7550. ; 116:12, s. 123506-
  • Tidskriftsartikel (refereegranskat)abstract
    • The recombination dynamics of neutral donor bound excitons ((DX)-X-o: I-4, I-6/6a) and near band edge defect-related emission in solution grown ZnO nanorods are investigated using steady state and time-resolved photoluminescence (PL) measurements. The effects of annealing are also studied. Low temperature steady state PL shows a systematic removal of the I-4 line after annealing at 450 degrees C and the subsequent domination of I-6a in these PL spectra. Additionally, the time decay of the I-4, I-6/6a, free exciton (FX), and basal plane stacking fault-related (BSF) PL transitions are studied as a function of annealing temperature. For the various annealing temperatures studied, the PL decay is described by a bi-exponential profile with a fast component (contribution from the surface) and slow component (related to bulk recombination). The fast component dominates in the case of as-grown and low temperature annealed samples (anneal temperatures up to 300 degrees C), suggesting the presence of surface adsorbed impurities. For samples annealed above 400 degrees C, the effects of the surface are reduced. The sample annealed at 850 degrees C produced an overall enhancement of the crystal quality. The underlying mechanisms for the observed PL characteristics are discussed based on near surface band bending caused by surface impurities.
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  • Khranovskyy, Volodymyr, et al. (författare)
  • Comparative PL study of individual ZnO nanorods, grown by APMOCVD and CBD techniques
  • 2012
  • Ingår i: Physica. B, Condensed matter. - : Elsevier. - 0921-4526 .- 1873-2135. ; 407:10, s. 1538-1542
  • Tidskriftsartikel (refereegranskat)abstract
    • The photoluminescence properties of individual ZnO nanorods, grown by atmospheric pressure metalorganic chemical vapor deposition (APMOCV) and chemical bath deposition (CBD) are investigated by means of temperature dependent micro-PL. It was found that the low temperature PL spectra are driven by neutral donor bound exciton emission (DX)-X-0, peaked at 3.359 and 3.363 eV for APMOCVD and CBD ZnO nanorods, respectively. The temperature increase causes a red energy shift of the peaks and enhancement of the free excitonic emission (FX). The FX was found to dominate after 150 K for both samples. It was observed that while APMOCVD ZnO nanorods possess a constant low signal of visible deep level emission with temperature, the ZnO nanorods grown by CBD revealed the thermal activation of deep level emission (DLE) after 130 K. The resulting room temperature DLE was a wide band located at 420-550 nm. The PL properties of individual ZnO nanorods can be of importance for their forthcoming application in future optoelectronics and photonics.
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14.
  • Martin, DP, et al. (författare)
  • RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets
  • 2021
  • Ingår i: Virus evolution. - : Oxford University Press (OUP). - 2057-1577. ; 7:1, s. veaa087-
  • Tidskriftsartikel (refereegranskat)abstract
    • For the past 20 years, the recombination detection program (RDP) project has focused on the development of a fast, flexible, and easy to use Windows-based recombination analysis tool. Whereas previous versions of this tool have relied on considerable user-mediated verification of detected recombination events, the latest iteration, RDP5, is automated enough that it can be integrated within analysis pipelines and run without any user input. The main innovation enabling this degree of automation is the implementation of statistical tests to identify recombination signals that could be attributable to evolutionary processes other than recombination. The additional analysis time required for these tests has been offset by algorithmic improvements throughout the program such that, relative to RDP4, RDP5 will still run up to five times faster and be capable of analyzing alignments containing twice as many sequences (up to 5000) that are five times longer (up to 50 million sites). For users wanting to remove signals of recombination from their datasets before using them for downstream phylogenetics-based molecular evolution analyses, RDP5 can disassemble detected recombinant sequences into their constituent parts and output a variety of different recombination-free datasets in an array of different alignment formats. For users that are interested in exploring the recombination history of their datasets, all the manual verification, data management and data visualization components of RDP5 have been extensively updated to minimize the amount of time needed by users to individually verify and refine the program’s interpretation of each of the individual recombination events that it detects.
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15.
  • Martin, DP, et al. (författare)
  • RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets
  • 2021
  • Ingår i: Virus evolution. - : Oxford University Press (OUP). - 2057-1577. ; 7:1, s. veaa087-
  • Tidskriftsartikel (refereegranskat)abstract
    • For the past 20 years, the recombination detection program (RDP) project has focused on the development of a fast, flexible, and easy to use Windows-based recombination analysis tool. Whereas previous versions of this tool have relied on considerable user-mediated verification of detected recombination events, the latest iteration, RDP5, is automated enough that it can be integrated within analysis pipelines and run without any user input. The main innovation enabling this degree of automation is the implementation of statistical tests to identify recombination signals that could be attributable to evolutionary processes other than recombination. The additional analysis time required for these tests has been offset by algorithmic improvements throughout the program such that, relative to RDP4, RDP5 will still run up to five times faster and be capable of analyzing alignments containing twice as many sequences (up to 5000) that are five times longer (up to 50 million sites). For users wanting to remove signals of recombination from their datasets before using them for downstream phylogenetics-based molecular evolution analyses, RDP5 can disassemble detected recombinant sequences into their constituent parts and output a variety of different recombination-free datasets in an array of different alignment formats. For users that are interested in exploring the recombination history of their datasets, all the manual verification, data management and data visualization components of RDP5 have been extensively updated to minimize the amount of time needed by users to individually verify and refine the program’s interpretation of each of the individual recombination events that it detects.
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  • Saheed, S. A., et al. (författare)
  • Xylem - as well as phloem sustains severe damage due to feeding by the Russian wheat aphid
  • 2007
  • Ingår i: South African Journal of Botany. - : Elsevier BV. - 0254-6299 .- 1727-9321. ; 73:4, s. 593-599
  • Tidskriftsartikel (refereegranskat)abstract
    • Investigation of comparative effects of feeding damage by the Russian wheat aphid (RWA, biotype SAI, Diuraphis noxia Mordvilko) on leaf blades of susceptible and resistant wheat cultivars (Triticum aestivum L. var Betta and Betta-Dn1 respectively) were carried out to establish the level of ultrastructural damage caused by this aphid and the possible limitation of damage induced which could be ascribed to the resistance gene Dn1 over the susceptible cultivar. Ultrastructurally, Betta-Dn1 sustained less damage to the vascular tissue as well as to the mesophyll during the experimental period. Both inter- and intracellular probes resulted in considerable saliva deposition as the aphids probed for suitable feeding sites. Salivary tracks were observed between and within mesophyll, bundle sheath cells as well as the vascular tissue, including the xylem. Disruption of organelles and cytoplasm resulted from cell probing and sheath deposition. Cell and organelle damage was more evident in the non-resistant Betta cultivar. The aphids probed for and fed from thin-walled sieve tubes preferentially. Few thick-walled sieve tubes showed evidence of either aphid probing or feeding-related damage. Saliva was deposited when the aphids probed inter- and intracellularly for feeding sites. The aphids appeared preferentially to probe for and feed from thin-walled sieve tubes, as few thick-walled sieve tubes showed evidence of damage. Vessels, apparently probed for water, contained watery saliva that encased the secondary walls and scaled pit membranes between probed vessels and xylem parenchyma. The xylem probed by the RWA was rendered non-functional, probably contributing to symptoms of leaf roll, chlorosis and necrosis, which were observed within two weeks of infestation in the susceptible Betta cultivar. This damage was limited in the resistant Betta-Dn] cultivar during the same time frame.
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20.
  • Vogel, Jacob W., et al. (författare)
  • Connectome-based modelling of neurodegenerative diseases: towards precision medicine and mechanistic insight
  • 2023
  • Ingår i: Nature Reviews Neuroscience. - 1471-003X .- 1471-0048. ; 24:10, s. 620-639
  • Tidskriftsartikel (refereegranskat)abstract
    • Neurodegenerative diseases are the most common cause of dementia. Although their underlying molecular pathologies have been identified, there is substantial heterogeneity in the patterns of progressive brain alterations across and within these diseases. Recent advances in neuroimaging methods have revealed that pathological proteins accumulate along specific macroscale brain networks, implicating the network architecture of the brain in the system-level pathophysiology of neurodegenerative diseases. However, the extent to which 'network-based neurodegeneration' applies across the wide range of neurodegenerative disorders remains unclear. Here, we discuss the state-of-the-art of neuroimaging-based connectomics for the mapping and prediction of neurodegenerative processes. We review findings supporting brain networks as passive conduits through which pathological proteins spread. As an alternative view, we also discuss complementary work suggesting that network alterations actively modulate the spreading of pathological proteins between connected brain regions. We conclude this Perspective by proposing an integrative framework in which connectome-based models can be advanced along three dimensions of innovation: incorporating parameters that modulate propagation behaviour on the basis of measurable biological features; building patient-tailored models that use individual-level information and allowing model parameters to interact dynamically over time. We discuss promises and pitfalls of these strategies for improving disease insights and moving towards precision medicine. Neurodegenerative diseases show idiosyncratic spatial patterns of progressive protein malformations in the brain. In this Perspective, Vogel et al. discuss the role of inter-regional connectivity in constraining and modulating the spread of pathological proteins and provide a framework for patient-tailored prognostics.
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21.
  • Wiedorn, Max O., et al. (författare)
  • Megahertz serial crystallography
  • 2018
  • Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 9
  • Tidskriftsartikel (refereegranskat)abstract
    • The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a beta-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.
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