| 1. |
- Abdo, A. A., et al.
(författare)
-
Multi-wavelength observations of the flaring gamma-ray blazar 3C 66A in 2008 October
- 2011
-
Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 726:1, s. 43-
-
Tidskriftsartikel (refereegranskat)abstract
- The BL Lacertae object 3C 66A was detected in a flaring state by the Fermi Large Area Telescope (LAT) and VERITAS in 2008 October. In addition to these gamma-ray observations, F-GAMMA, GASP-WEBT, PAIRITEL, MDM, ATOM, Swift, and Chandra provided radio to X-ray coverage. The available light curves show variability and, in particular, correlated flares are observed in the optical and Fermi-LAT gamma-ray band. The resulting spectral energy distribution can be well fitted using standard leptonic models with and without an external radiation field for inverse Compton scattering. It is found, however, that only the model with an external radiation field can accommodate the intra-night variability observed at optical wavelengths.
|
|
| 2. |
- Ackermann, M., et al.
(författare)
-
MULTI-WAVELENGTH OBSERVATIONS OF BLAZAR AO 0235+164 IN THE 2008-2009 FLARING STATE
- 2012
-
Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 751:2
-
Tidskriftsartikel (refereegranskat)abstract
- The blazarAO 0235+164 (z=0.94) has been one of the most active objects observed by Fermi Large Area Telescope (LAT) since its launch in Summer 2008. In addition to the continuous coverage by Fermi, contemporaneous observations were carried out from the radio to gamma-ray bands between 2008 September and 2009 February. In this paper, we summarize the rich multi-wavelength data collected during the campaign (including F-GAMMA, GASP-WEBT, Kanata, OVRO, RXTE, SMARTS, Swift, and other instruments), examine the cross-correlation between the light curves measured in the different energy bands, and interpret the resulting spectral energy distributions in the context of well-known blazar emission models. We find that the gamma-ray activity is well correlated with a series of near-IR/optical flares, accompanied by an increase in the optical polarization degree. On the other hand, the X-ray light curve shows a distinct 20 day high state of unusually soft spectrum, which does not match the extrapolation of the optical/UV synchrotron spectrum. We tentatively interpret this feature as the bulk Compton emission by cold electrons contained in the jet, which requires an accretion disk corona with an effective covering factor of 19% at a distance of 100 R-g. We model the broadband spectra with a leptonic model with external radiation dominated by the infrared emission from the dusty torus.
|
|
| 3. |
- Abdo, A. A., et al.
(författare)
-
FERMI Large Area Telescope and multi-wavelength observations of the flaring activity of PKS 1510-089 between 2008 september and 2009 june
- 2010
-
Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 721:2, s. 1425-1447
-
Tidskriftsartikel (refereegranskat)abstract
- We report on the multi-wavelength observations of PKS 1510-089 (a flat spectrum radio quasar (FSRQ) at z = 0.361) during its high activity period between 2008 September and 2009 June. During this 11 month period, the source was characterized by a complex variability at optical, UV, and gamma-ray bands, on timescales down to 6-12 hr. The brightest gamma-ray isotropic luminosity, recorded on 2009 March 26, was similar or equal to 2 x 1048 erg s-1. The spectrum in the Fermi Large Area Telescope energy range shows a mild curvature described well by a log-parabolic law, and can be understood as due to the Klein-Nishina effect. The. -ray flux has a complex correlation with the other wavelengths. There is no correlation at all with the X-ray band, a weak correlation with the UV, and a significant correlation with the optical flux. The. -ray flux seems to lead the optical one by about 13 days. From the UV photometry, we estimated a black hole mass of similar or equal to 5.4 x 10(8)M(circle dot) and an accretion rate of similar or equal to 0.5M(circle dot) yr(-1). Although the power in the thermal and non-thermal outputs is smaller compared to the very luminous and distant FSRQs, PKS 1510-089 exhibits a quite large Compton dominance and a prominent big blue bump (BBB) as observed in the most powerful gamma-ray quasars. The BBB was still prominent during the historical maximum optical state in 2009 May, but the optical/ UV spectral index was softer than in the quiescent state. This seems to indicate that the BBB was not completely dominated by the synchrotron emission during the highest optical state. We model the broadband spectrum assuming a leptonic scenario in which the inverse Compton emission is dominated by the scattering of soft photons produced externally to the jet. The resulting model-dependent jet energetic content is compatible with a scenario in which the jet is powered by the accretion disk, with a total efficiency within the Kerr black hole limit.
|
|
| 4. |
- Abdo, A. A., et al.
(författare)
-
The spectral energy distribution of fermi bright blazars
- 2010
-
Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 716:1, s. 30-70
-
Tidskriftsartikel (refereegranskat)abstract
- We have conducted a detailed investigation of the broadband spectral properties of the gamma-ray selected blazars of the Fermi LAT Bright AGN Sample (LBAS). By combining our accurately estimated Fermi gamma-ray spectra with Swift, radio, infra-red, optical, and other hard X-ray/gamma-ray data, collected within 3 months of the LBAS data taking period, we were able to assemble high-quality and quasi-simultaneous spectral energy distributions (SED) for 48 LBAS blazars. The SED of these gamma-ray sources is similar to that of blazars discovered at other wavelengths, clearly showing, in the usual log nu-log nu F-nu representation, the typical broadband spectral signatures normally attributed to a combination of low-energy synchrotron radiation followed by inverse Compton emission of one or more components. We have used these SED to characterize the peak intensity of both the low-and the high-energy components. The results have been used to derive empirical relationships that estimate the position of the two peaks from the broadband colors (i.e., the radio to optical, alpha(ro), and optical to X-ray, alpha(ox), spectral slopes) and from the gamma-ray spectral index. Our data show that the synchrotron peak frequency (nu(S)(peak)) is positioned between 10(12.5) and 10(14.5) Hz in broad-lined flat spectrum radio quasars (FSRQs) and between 10(13) and 10(17) Hz in featureless BL Lacertae objects. We find that the gamma-ray spectral slope is strongly correlated with the synchrotron peak energy and with the X-ray spectral index, as expected at first order in synchrotron-inverse Compton scenarios. However, simple homogeneous, one-zone, synchrotron self-Compton (SSC) models cannot explain most of our SED, especially in the case of FSRQs and low energy peaked (LBL) BL Lacs. More complex models involving external Compton radiation or multiple SSC components are required to reproduce the overall SED and the observed spectral variability. While more than 50% of known radio bright high energy peaked (HBL) BL Lacs are detected in the LBAS sample, only less than 13% of known bright FSRQs and LBL BL Lacs are included. This suggests that the latter sources, as a class, may be much fainter gamma-ray emitters than LBAS blazars, and could in fact radiate close to the expectations of simple SSC models. We categorized all our sources according to a new physical classification scheme based on the generally accepted paradigm for Active Galactic Nuclei and on the results of this SED study. Since the LAT detector is more sensitive to flat spectrum gamma-ray sources, the correlation between nu(S)(peak) and gamma-ray spectral index strongly favors the detection of high energy peaked blazars, thus explaining the Fermi overabundance of this type of sources compared to radio and EGRET samples. This selection effect is similar to that experienced in the soft X-ray band where HBL BL Lacs are the dominant type of blazars.
|
|
| 5. |
- Abdo, A. A., et al.
(författare)
-
FERMI DISCOVERY OF GAMMA-RAY EMISSION FROM NGC 1275
- 2009
-
Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 699:1, s. 31-39
-
Tidskriftsartikel (refereegranskat)abstract
- We report the discovery of high-energy (E > 100 MeV) gamma-ray emission from NGC 1275, a giant elliptical galaxy lying at the center of the Perseus cluster of galaxies, based on observations made with the Large Area Telescope (LAT) of the Fermi Gamma-ray Space Telescope. The positional center of the gamma-ray source is only approximate to 3' away from the NGC 1275 nucleus, well within the 95% LAT error circle of approximate to 5'. The spatial distribution of gamma-ay photons is consistent with a point source. The average flux and power-law photon index measured with the LAT from 2008 August 4 to 2008 December 5 are F-gamma = (2.10 +/- 0.23) x 10(-7) ph (>100 MeV) cm(-2) s(-1) and Gamma = 2.17 +/- 0.05, respectively. The measurements are statistically consistent with constant flux during the four-month LAT observing period. Previous EGRET observations gave an upper limit of F-gamma < 3.72 x 10(-8) ph (>100 MeV) cm(-2) s(-1) to the gamma-ray flux from NGC 1275. This indicates that the source is variable on timescales of years to decades, and therefore restricts the fraction of emission that can be produced in extended regions of the galaxy cluster. Contemporaneous and historical radio observations are also reported. The broadband spectrum of NGC 1275 is modeled with a simple one-zone synchrotron/synchrotron self-Compton model and a model with a decelerating jet flow.
|
|
| 6. |
- Lister, M. L., et al.
(författare)
-
gamma-RAY AND PARSEC-SCALE JET PROPERTIES OF A COMPLETE SAMPLE OF BLAZARS FROM THE MOJAVE PROGRAM
- 2011
-
Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 742:1, s. 27-
-
Tidskriftsartikel (refereegranskat)abstract
- We investigate the Fermi Large Area Telescope gamma-ray and 15 GHz Very Long Baseline Array radio properties of a joint gamma-ay and radio-selected sample of active galactic nuclei (AGNs) obtained during the first 11 months of the Fermi mission (2008 August 4-2009 July 5). Our sample contains the brightest 173 AGNs in these bands above declination -30 degrees during this period, and thus probes the full range of gamma-ray loudness (gamma-ray to radio band luminosity ratio) in the bright blazar population. The latter quantity spans at least 4 orders of magnitude, reflecting a wide range of spectral energy distribution (SED) parameters in the bright blazar population. The BL Lac objects, however, display a linear correlation of increasing gamma-ray loudness with synchrotron SED peak frequency, suggesting a universal SED shape for objects of this class. The synchrotron self-Compton model is favored for the gamma-ray emission in these BL Lac objects over external seed photon models, since the latter predict a dependence of Compton dominance on Doppler factor that would destroy any observed synchrotron SED-peak-gamma-ray-loudness correlation. The high-synchrotron peaked (HSP) BL Lac objects are distinguished by lower than average radio core brightness temperatures, and none display large radio modulation indices or high linear core polarization levels. No equivalent trends are seen for the flat-spectrum radio quasars (FSRQs) in our sample. Given the association of such properties with relativistic beaming, we suggest that the HSP BL Lac objects have generally lower Doppler factors than the lower-synchrotron peaked BL Lac objects or FSRQs in our sample.
|
|
| 7. |
- Hayashida, M., et al.
(författare)
-
THE STRUCTURE AND EMISSION MODEL OF THE RELATIVISTIC JET IN THE QUASAR 3C 279 INFERRED FROM RADIO TO HIGH-ENERGY gamma-RAY OBSERVATIONS IN 2008-2010
- 2012
-
Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 754:2, s. 114-
-
Tidskriftsartikel (refereegranskat)abstract
- We present time-resolved broadband observations of the quasar 3C 279 obtained from multi-wavelength campaigns conducted during the first two years of the Fermi Gamma-ray Space Telescope mission. While investigating the previously reported gamma-ray/optical flare accompanied by a change in optical polarization, we found that the optical emission appears to be delayed with respect to the gamma-ray emission by about 10 days. X-ray observations reveal a pair of isolated flares separated by similar to 90 days, with only weak gamma-ray/optical counterparts. The spectral structure measured by Spitzer reveals a synchrotron component peaking in the mid-infrared band with a sharp break at the far-infrared band during the gamma-ray flare, while the peak appears in the millimeter (mm)/submillimeter (sub-mm) band in the low state. Selected spectral energy distributions are fitted with leptonic models including Comptonization of external radiation produced in a dusty torus or the broad-line region. Adopting the interpretation of the polarization swing involving propagation of the emitting region along a curved trajectory, we can explain the evolution of the broadband spectra during the gamma-ray flaring event by a shift of its location from similar to 1 pc to similar to 4 pc from the central black hole. On the other hand, if the gamma-ray flare is generated instead at sub-pc distance from the central black hole, the far-infrared break can be explained by synchrotron self-absorption. We also model the low spectral state, dominated by the mm/sub-mm peaking synchrotron component, and suggest that the corresponding inverse-Compton component explains the steady X-ray emission.
|
|
| 8. |
- Raiteri, C. M., et al.
(författare)
-
WEBT and XMM-Newton observations of 3C 454.3 during the post-outburst phase - Detection of the little and big blue bumps
- 2007
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 473:3, s. 819-827
-
Tidskriftsartikel (refereegranskat)abstract
- Context. The quasar-type blazar 3C 454.3 was observed to undergo an unprecedented optical outburst in spring 2005, affecting the source brightness from the near-IR to the X-ray frequencies. This was first followed by a millimetric and then by a radio outburst, which peaked in February 2006. Aims. In this paper we report on follow-up observations to study the multiwavelength emission in the post-outburst phase. Methods. Radio, near-infrared, and optical monitoring was performed by the Whole Earth Blazar Telescope (WEBT) collaboration in the 2006-2007 observing season. XMM-Newton observations on July 2-3 and December 18-19, 2006 added information on the X-ray and UV states of the source. Results. The source was in a faint state. The radio flux at the higher frequencies showed a fast decreasing trend, which represents the tail of the big radio outburst. It was followed by a quiescent state, common at all radio frequencies. In contrast, moderate activity characterized the near-IR and optical light curves, with a progressive increase of the variability amplitude with increasing wavelength. We ascribe this redder-when-brighter behaviour to the presence of a ""little blue bump"" due to line emission from the broad line region, which is clearly visible in the source spectral energy distribution (SED) during faint states. Moreover, the data from the XMM- Newton Optical Monitor reveal a rise of the SED in the ultraviolet, suggesting the existence of a "" big blue bump"" due to thermal emission from the accretion disc. The X-ray spectra are well fitted with a power- law model with photoelectric absorption, possibly larger than the Galactic one. However, the comparison with previous X-ray observations would imply that the amount of absorbing matter is variable. Alternatively, the intrinsic X-ray spectrum presents a curvature, which may depend on the X-ray brightness. In this case, two scenarios are possible. i) There is no extra absorption, and the X-ray spectrum hardens at low energies, the hardening being more evident in bright states; ii) there is a constant amount of extra absorption, likely in the quasar environment, and the X-ray spectrum softens at low energies, at least in faint X-ray states. This softening might be the result of a flux contribution by the high-frequency tail of the big blue bump.
|
|
| 9. |
- Pavlides, Michael, et al.
(författare)
-
Liver investigation: Testing marker utility in steatohepatitis (LITMUS): Assessment & validation of imaging modality performance across the NAFLD spectrum in a prospectively recruited cohort study (the LITMUS imaging study): Study protocol
- 2023
-
Ingår i: Contemporary Clinical Trials. - : ELSEVIER SCIENCE INC. - 1551-7144 .- 1559-2030. ; 134
-
Tidskriftsartikel (refereegranskat)abstract
- Non-alcoholic fatty liver disease (NAFLD) is the liver manifestation of the metabolic syndrome with global prevalence reaching epidemic levels. Despite the high disease burden in the population only a small proportion of those with NAFLD will develop progressive liver disease, for which there is currently no approved pharmacotherapy. Identifying those who are at risk of progressive NAFLD currently requires a liver biopsy which is problematic. Firstly, liver biopsy is invasive and therefore not appropriate for use in a condition like NAFLD that affects a large proportion of the population. Secondly, biopsy is limited by sampling and observer dependent variability which can lead to misclassification of disease severity. Non-invasive biomarkers are therefore needed to replace liver biopsy in the assessment of NAFLD. Our study addresses this unmet need. The LITMUS Imaging Study is a prospectively recruited multi-centre cohort study evaluating magnetic resonance imaging and elastography, and ultrasound elastography against liver histology as the reference standard. Imaging biomarkers and biopsy are acquired within a 100-day window. The study employs standardised processes for imaging data collection and analysis as well as a real time central monitoring and quality control process for all the data submitted for analysis. It is anticipated that the high-quality data generated from this study will underpin changes in clinical practice for the benefit of people with NAFLD. Study Registration: clinicaltrials.gov: NCT05479721
|
|
| 10. |
- Crossfield, Ian J. M., et al.
(författare)
-
197 CANDIDATES AND 104 VALIDATED PLANETS IN K2's FIRST FIVE FIELDS
- 2016
-
Ingår i: Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 226:1
-
Tidskriftsartikel (refereegranskat)abstract
- We present 197 planet candidates discovered using data from the first year of the NASA K2 mission (Campaigns 0-4), along with the results of an intensive program of photometric analyses, stellar spectroscopy, high-resolution imaging, and statistical validation. We distill these candidates into sets of 104 validated planets (57 in multi-planet systems), 30 false positives, and 63 remaining candidates. Our validated systems span a range of properties, with median values of R-P = 2.3 R-circle plus, P = 8.6 days, T-eff = 5300 K, and Kp = 12.7 mag. Stellar spectroscopy provides precise stellar and planetary parameters for most of these systems. We show that K2 has increased by 30% the number of small planets known to orbit moderately bright stars (1-4 R-circle plus, Kp = 9-13. mag). Of particular interest are 76 planets smaller than 2 R-circle plus, 15 orbiting stars brighter than Kp = 11.5. mag, 5 receiving Earth-like irradiation levels, and several multi-planet systems-including 4 planets orbiting the M dwarf K2-72 near mean-motion resonances. By quantifying the likelihood that each candidate is a planet we demonstrate that our candidate sample has an overall false positive rate of 15%-30%, with rates substantially lower for small candidates (<2 R-circle plus) and larger for candidates with radii >8 R-circle plus and/or with P < 3 days. Extrapolation of the current planetary yield suggests that K2 will discover between 500 and 1000 planets in its planned four-year mission, assuming sufficient follow-up resources are available. Efficient observing and analysis, together with an organized and coherent follow-up strategy, are essential for maximizing the efficacy of planet-validation efforts for K2, TESS, and future large-scale surveys.
|
|
| 11. |
- Britzen, S., et al.
(författare)
-
A ring accelerator? Unusual jet dynamics in the IceCube candidate PKS 1502+106
- 2021
-
Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 503:3, s. 3145-3178
-
Tidskriftsartikel (refereegranskat)abstract
- On 2019/07/30.86853 UT, IceCube detected a high-energy astrophysical neutrino candidate. The Flat Spectrum Radio Quasar PKS 1502+106 is located within the 50 per cent uncertainty region of the event. Our analysis of 15 GHz Very Long Baseline Array (VLBA) and astrometric 8 GHz VLBA data, in a time span prior and after the IceCube event, reveals evidence for a radio ring structure that develops with time. Several arc-structures evolve perpendicular to the jet ridge line. We find evidence for precession of a curved jet based on kinematic modelling and a periodicity analysis. An outflowing broad line region (BLR) based on the C IV line emission (Sloan Digital Sky Survey) is found. We attribute the atypical ring to an interaction of the precessing jet with the outflowing material. We discuss our findings in the context of a spine-sheath scenario where the ring reveals the sheath and its interaction with the surroundings (narrow line region, NLR, clouds). We find that the radio emission is correlated with the gamma-ray emission, with radio lagging the gamma-rays. Based on the gamma-ray variability time-scale, we constrain the gamma-ray emission zone to the BLR (30-200 r(g)) and within the jet launching region. We discuss that the outflowing BLR provides the external radiation field for gamma-ray production via external Compton scattering. The neutrino is most likely produced by proton-proton interaction in the blazar zone (beyond the BLR), enabled by episodic encounters of the jet with dense clouds, i.e. some molecular cloud in the NLR.
|
|
| 12. |
- Hardy, Timothy, et al.
(författare)
-
The European NAFLD Registry : A real-world longitudinal cohort study of nonalcoholic fatty liver disease
- 2020
-
Ingår i: Contemporary Clinical Trials. - : Elsevier. - 1551-7144 .- 1559-2030. ; 98
-
Tidskriftsartikel (refereegranskat)abstract
- Non-Alcoholic Fatty Liver Disease (NAFLD), a progressive liver disease that is closely associated with obesity, type 2 diabetes, hypertension and dyslipidaemia, represents an increasing global public health challenge. There is significant variability in the disease course: the majority exhibit only fat accumulation in the liver but a significant minority develop a necroinflammatory form of the disease (non-alcoholic steatohepatitis, NASH) that may progress to cirrhosis and hepatocellular carcinoma. At present our understanding of pathogenesis, disease natural history and long-term outcomes remain incomplete. There is a need for large, well characterised patient cohorts that may be used to address these knowledge gaps and to support the development of better biomarkers and novel therapies. The European NAFLD Registry is an international, prospectively recruited observational cohort study that aims to establish a large, highly-phenotyped patient cohort and linked bioresource. Here we describe the infrastructure, data management and monitoring plans, and the standard operating procedures implemented to ensure the timely and systematic collection of high-quality data and samples. Already recruiting subjects at secondary/tertiary care centres across Europe, the Registry is supporting the European Union IMI2-funded LITMUS Liver Investigation: Testing Marker Utility in Steatohepatitis consortium, which is a major international effort to robustly validate biomarkers that diagnose, risk stratify and/or monitor NAFLD progression and liver fibrosis stage. The European NAFLD Registry has the demonstrable capacity to support research and biomarker development at scale and pace.
|
|
| 13. |
- Diéguez-Uribeondo, Javier, et al.
(författare)
-
Re-evaluation of the enigmatic species complex Saprolegnia diclina-Saprolegnia parasitica based on morphological, physiological and molecular data
- 2007
-
Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 44:7, s. 585-601
-
Tidskriftsartikel (refereegranskat)abstract
- The phylogenetic relationships among isolates of the Saprolegnia diclina-Saprolegnia parasitica complex were investigated based on ITS rDNA sequences, and correlated with morphological and physiological characters. The isolates studied belong to five phylogenetically separate clades. The majority of presumed parasitic isolates, mostly isolated from fish lesions, fell within a clade that comprises isolates which has been variously named as S. diclina Type 1, S. parasitica, Saprolegnia salmonis or just as unnamed Saprolegnia sp. Presence of bundles of long-hooked hairs on secondary cysts, high frequency of retracted germination, and oogonia production at 7 degrees C (when occurring) were characteristic of this clade. A single isolate identified as S. diclina Type 2 clustered in a clade along with Saprolegnia ferax isolates. The isolates identified as S. diclina s. str. (S. diclina Type 3) distributed in two clades and appeared closely related to Saprolegnia multispora and to a number of Chilean isolates identified as Saprolegnia australis. The ITS sequences of clade I were almost identical even though the isolates were of diverse geographical origins and showed physiological and morphological differences and variations in their pathogenicity. This suggest these species reproduces clonally even in apparently sexually competent isolates. Adaptation to parasitism in Saprolegnia might have occurred at spore level by the development of long-hooked hairs to facilitate host attachment and selection of a retracting germination. The use of the name S. parasitica should be assigned to isolates of clade I that contained isolates forming cysts with bundles of long-hooked hairs.
|
|
| 14. |
- Fuller, Franklin D, et al.
(författare)
-
Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers
- 2017
-
Ingår i: Nature Methods. - : Macmillan Publishers Ltd.. - 1548-7091 .- 1548-7105. ; 14, s. 443-449
-
Tidskriftsartikel (refereegranskat)abstract
- X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.
|
|
| 15. |
- Gilbert, F., et al.
(författare)
-
Sediment reworking by the burrowing polychaete Hediste diversicolor modulated by environmental and biological factors across the temperate North Atlantic. A tribute to Gaston Desrosiers
- 2021
-
Ingår i: Journal of Experimental Marine Biology and Ecology. - : Elsevier BV. - 0022-0981. ; 541
-
Tidskriftsartikel (refereegranskat)abstract
- Particle mixing and irrigation of the seabed by benthic fauna (bioturbation) have major impacts on ecosystem functions such as remineralization of organic matter and sediment-water exchange. As a tribute to Prof. Gaston Desrosiers by the Nereis Park association, eighteen laboratories carried out a collaborative experiment to acquire a global snapshot of particle reworking by the polychaete Hediste diversicolor at 16 sites surrounding the Northern Atlantic. Organisms and soft sediments were collected during May - July at different geographical locations and, using a common laboratory protocol, particulate fluorescent tracers (`luminophores') were used to quantify particle transport over a 10-day period. Particle mixing was quantified using the maximum penetration depth of tracers (MPD), particle diffusive coefficients (D-b), and non-local transport coefficients (r). Non-local coefficients (reflecting centimeter scale transport steps) ranged from 0.4 to 15 yr(-1), and were not correlated across sites with any measured biological (biomass, biovolume) or environmental parameters (temperature, grain size, organic matter). Maximum penetration depths (MPD) averaged similar to 10.7 cm (6.5-14.5 cm), and were similar to the global average bioturbation depth inferred from short-lived radiochemical tracers. MPD was also not correlated with measures of size (individual biomass), but increased with grain size and decreased with temperature. Bio-diffusion (D-b) correlated inversely with individual biomass (size) and directly with temperature over the environmental range (Q(10) similar to 1.7; 5-21 degrees C). The transport data were comparable in magnitude to rates reported for localized H. diversicolor populations of similar size, and confirmed some but not all correlations between sediment reworking and biological and environmental variables found in previous studies. The results imply that measures of particle reworking activities of a species from a single location can be generally extrapolated to different populations at similar conditions.
|
|
| 16. |
- Kern, Jan, et al.
(författare)
-
Structures of the intermediates of Kok’s photosynthetic water oxidation clock
- 2018
-
Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 563, s. 421-425
-
Tidskriftsartikel (refereegranskat)abstract
- Inspired by the period-four oscillation in flash-induced oxygen evolution of photosystem II discovered by Joliot in 1969, Kok performed additional experiments and proposed a five-state kinetic model for photosynthetic oxygen evolution, known as Kok’s S-state clock or cycle1,2. The model comprises four (meta)stable intermediates (S0, S1, S2 and S3) and one transient S4 state, which precedes dioxygen formation occurring in a concerted reaction from two water-derived oxygens bound at an oxo-bridged tetra manganese calcium (Mn4CaO5) cluster in the oxygen-evolving complex3–7. This reaction is coupled to the two-step reduction and protonation of the mobile plastoquinone QB at the acceptor side of PSII. Here, using serial femtosecond X-ray crystallography and simultaneous X-ray emission spectroscopy with multi-flash visible laser excitation at room temperature, we visualize all (meta)stable states of Kok’s cycle as high-resolution structures (2.04–2.08 Å). In addition, we report structures of two transient states at 150 and 400 µs, revealing notable structural changes including the binding of one additional ‘water’, Ox, during the S2→S3 state transition. Our results suggest that one water ligand to calcium (W3) is directly involved in substrate delivery. The binding of the additional oxygen Ox in the S3 state between Ca and Mn1 supports O–O bond formation mechanisms involving O5 as one substrate, where Ox is either the other substrate oxygen or is perfectly positioned to refill the O5 position during O2 release. Thus, our results exclude peroxo-bond formation in the S3 state, and the nucleophilic attack of W3 onto W2 is unlikely.
|
|
| 17. |
- Martinez, Arturo O., et al.
(författare)
-
Stellar and Planetary Parameters for K2's Late-type Dwarf Systems from C1 to C5
- 2017
-
Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 837:1
-
Tidskriftsartikel (refereegranskat)abstract
- The NASA K2 mission uses photometry to find planets transiting stars of various types. M dwarfs are of high interest since they host more short-period planets than any other type of main-sequence star and transiting planets around M dwarfs have deeper transits compared to other main-sequence stars. In this paper, we present stellar parameters from K and M dwarfs hosting transiting planet candidates discovered by our team. Using the SOFI spectrograph on the European Southern Observatory's New Technology Telescope, we obtained R approximate to 1000 J-, H-, and K-band (0.95-2.52 mu m) spectra of 34 late-type K2 planet and candidate planet host systems and 12 bright K4-M5 dwarfs with interferometrically measured radii and effective temperatures. Out of our 34 late-type K2 targets, we identify 27 of these stars as M dwarfs. We measure equivalent widths of spectral features, derive calibration relations using stars with interferometric measurements, and estimate stellar radii, effective temperatures, masses, and luminosities for the K2 planet hosts. Our calibrations provide radii and temperatures with median uncertainties of 0.059 R-circle dot (16.09%) and 160 K (4.33%), respectively. We then reassess the radii and equilibrium temperatures of known and candidate planets based on our spectroscopically derived stellar parameters. Since a planet's radius and equilibrium temperature depend on the parameters of its host star, our study provides more precise planetary parameters for planets and candidates orbiting late-type stars observed with K2. We find a median planet radius and an equilibrium temperature of approximately 3 R-circle plus and 500 K, respectively, with several systems (K2-18b and K2-72e) receiving near-Earth-like levels of incident irradiation.
|
|
| 18. |
- Rabe, Patrick, et al.
(författare)
-
X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis
- 2021
-
Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 7:34
-
Tidskriftsartikel (refereegranskat)abstract
- Isopenicillin N synthase (IPNS) catalyzes the unique reaction of L-delta-(alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV) with dioxygen giving isopenicillin N (IPN), the precursor of all natural penicillins and cephalosporins. X-ray free-electron laser studies including time-resolved crystallography and emission spectroscopy reveal how reaction of IPNS:Fe(II):ACV with dioxygen to yield an Fe(III) superoxide causes differences in active site volume and unexpected conformational changes that propagate to structurally remote regions. Combined with solution studies, the results reveal the importance of protein dynamics in regulating intermediate conformations during conversion of ACV to IPN. The results have implications for catalysis by multiple IPNS-related oxygenases, including those involved in the human hypoxic response, and highlight the power of serial femtosecond crystallography to provide insight into long-range enzyme dynamics during reactions presently impossible for nonprotein catalysts.
|
|
| 19. |
- Young, Iris D., et al.
(författare)
-
Structure of photosystem II and substrate binding at room temperature
- 2016
-
Ingår i: Nature. - : Macmillan Publishers Ltd.. - 0028-0836 .- 1476-4687. ; 540:7633, s. 453-457
-
Tidskriftsartikel (refereegranskat)abstract
- Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4)1, in which S1 is the dark-stable state and S3 is the last semi-stable state before O–O bond formation and O2 evolution2,3. A detailed understanding of the O–O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site4–6. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL7 provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions8,9, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states10. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site10–13. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O–O bond formation mechanisms.
|
|
| 20. |
- Alonso Aller, Elisa, et al.
(författare)
-
Monitoring of a protected multi-specific tropical seagrass meadow reveals a pattern of decline and recovery
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- In a changing environment, there is an increasing interest to monitor ecosystems to understand their responses to environmental change. Seagrass meadows are highly important ecosystems, but at the same time they are under a constant threat from human activities, as well as climate impacts, and marked declines have been observed worldwide. Despite increasing efforts, monitoring of multi-specific tropical seagrass meadows is scarce, particularly in developing regions. Here we analysed data from the first 10 years of a monitoring programme in a marine protected area in Zanzibar (Tanzania) to assess temporal changes in seagrass cover and species composition and to detect potential drivers of change. The seagrass meadow experienced a strong gradual decline in seagrass cover and changes in species composition, followed by a period of recovery. However, the timing and length of these temporal patterns varied in space (between transects). Of the climate variables considered, cloud cover, temperature, storm occurrence, sunspot activity and the height of the diurnal low tide seemed to influence seagrass cover, although only to a small extent, suggesting that the monitored seagrass meadow may be influenced by other unmeasured factors. Considering our results, seagrass meadows seem to be highly dynamic at small spatial scales even in the absence of major local anthropogenic impacts. Further monitoring programmes should be developed in the region to gain a better understanding of seagrass temporal variability and causes of change.
|
|
| 21. |
- Alonso Aller, Elisa, et al.
(författare)
-
Temporal variability of a protected multispecific tropical seagrass meadow in response to environmental change
- 2019
-
Ingår i: Environmental Monitoring and Assessment. - : Springer Science and Business Media LLC. - 0167-6369 .- 1573-2959. ; 191
-
Tidskriftsartikel (refereegranskat)abstract
- In a changing environment, there is an increasing interest to monitor ecosystems to understand their responses to environmental change. Seagrass meadows are highly important ecosystems that are under constant pressure from human activities and climate impacts, with marked declines observed worldwide. Despite increasing efforts, monitoring of multispecific tropical seagrass meadows is scarce, particularly in low-income regions. Based on data from a monitoring programme in a marine protected area in Zanzibar (Tanzania), we assessed temporal changes in seagrass cover and species composition during a 10-year period in relation to local variability in environmental variables. We observed a strong, gradual decline in seagrass cover and changes in species composition, followed by a period of recovery. However, the timing and length of these temporal patterns varied in space (between transects). Multiple environmental variables—cloud cover, temperature, storm occurrence, sunspot activity, and tidal amplitude and height—influenced seagrass cover, although only to a minor extent, suggesting that the monitored seagrass meadow may be influenced by other unmeasured factors (e.g. water currents and sediment movement). Our results show that seagrass meadows can be highly dynamic at small (10–50m) spatial scales, even in the absence of major local anthropogenic impacts. Our findings suggest that high-resolution monitoring programmes can be highly valuable for the detection of temporal changes in multispecific seagrass meadows; however, to understand the causes of change, there is a need of long-term (> 10years) data series that include direct measurements of environmental variables and extreme events.
|
|
| 22. |
- Armandi, Angelo, et al.
(författare)
-
Serum ferritin levels can predict long-term outcomes in patients with metabolic dysfunction-associated steatotic liver disease
- 2024
-
Ingår i: Gut. - : BMJ PUBLISHING GROUP. - 0017-5749 .- 1468-3288.
-
Tidskriftsartikel (refereegranskat)abstract
- Objective Hyperferritinaemia is associated with liver fibrosis severity in patients with metabolic dysfunction-associated steatotic liver disease (MASLD), but the longitudinal implications have not been thoroughly investigated. We assessed the role of serum ferritin in predicting long-term outcomes or death. Design We evaluated the relationship between baseline serum ferritin and longitudinal events in a multicentre cohort of 1342 patients. Four survival models considering ferritin with confounders or non-invasive scoring systems were applied with repeated five-fold cross-validation schema. Prediction performance was evaluated in terms of Harrell's C-index and its improvement by including ferritin as a covariate. Results Median follow-up time was 96 months. Liver-related events occurred in 7.7%, hepatocellular carcinoma in 1.9%, cardiovascular events in 10.9%, extrahepatic cancers in 8.3% and all-cause mortality in 5.8%. Hyperferritinaemia was associated with a 50% increased risk of liver-related events and 27% of all-cause mortality. A stepwise increase in baseline ferritin thresholds was associated with a statistical increase in C-index, ranging between 0.02 (lasso-penalised Cox regression) and 0.03 (ridge-penalised Cox regression); the risk of developing liver-related events mainly increased from threshold 215.5 mu g/L (median HR=1.71 and C-index=0.71) and the risk of overall mortality from threshold 272 mu g/L (median HR=1.49 and C-index=0.70). The inclusion of serum ferritin thresholds (215.5 mu g/L and 272 mu g/L) in predictive models increased the performance of Fibrosis-4 and Non-Alcoholic Fatty Liver Disease Fibrosis Score in the longitudinal risk assessment of liver-related events (C-indices>0.71) and overall mortality (C-indices>0.65). Conclusions This study supports the potential use of serum ferritin values for predicting the long-term prognosis of patients with MASLD.
|
|
| 23. |
- Hjartaker, A, et al.
(författare)
-
Consumption of dairy products in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort: data from 35955 24-hour dietary recalls in 10 European countries
- 2002
-
Ingår i: Public Health Nutrition. - 1475-2727. ; 5:6B, s. 1259-1271
-
Tidskriftsartikel (refereegranskat)abstract
- Objectives: To describe and compare the consumption of dairy products in cohorts included in the European Prospective Investigation into-Cancer and Nutrition (EPIC). Methods: Data from single 24-hour dietary recall interviews collected through a highly standardised computer-based program (EPIC-SOFT) in 27 redefined centres in 10 European countries between 1995 and 2000. From a total random sample of 36 900, 22 924 women and 13 031 men were selected after exclusion of subjects under 35 and over 74 years of age. Results: A high total consumption of dairy products was reported in most of the centres in Spain and in the UK cohort sampled from the general population, as well as in the Dutch, Swedish and Danish centres. A somewhat low consumption was reported in the Greek centre-and in some of the Italian centres (Ragusa and Turin). In all centres and for both sexes, milk constituted the dairy sub-group with the largest proportion (in grams) of total dairy consumption, followed by yoghurt and other fermented milk products, and cheese. Still, there was a wide range in the contributions of the different dairy sub-groups between centres. The Spanish and Nordic centres generally reported a high consumption of milk,, the Swedish and Dutch centres reported a high consumption of yoghurt and other fermented milk products, whereas the highest consumption of cheese was reported in the French centres. Conclusion: The results demonstrate both quantitative and qualitative disparities in dairy product consumption among the EPIC centres. This offers a sound starting point for analyses of associations between dairy intake and chronic diseases such as cancer.
|
|
| 24. |
- John, Juliane, et al.
(författare)
-
Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b–NrdI complex monitored by serial femtosecond crystallography
- 2022
-
Ingår i: eLIFE. - 2050-084X. ; 11
-
Tidskriftsartikel (refereegranskat)abstract
- Redox reactions are central to biochemistry and are both controlled by and induce protein structural changes. Here, we describe structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b–NrdI complex, a di-metal carboxylate-flavoprotein system, as part of the mechanism generating the essential catalytic free radical of the enzyme. Femtosecond crystallography at an X-ray free electron laser was utilized to obtain structures at room temperature in defined redox states without suffering photoreduction. Together with density functional theory calculations, we show that the flavin is under steric strain in the R2b–NrdI protein complex, likely tuning its redox properties to promote superoxide generation. Moreover, a binding site in close vicinity to the expected flavin O2 interaction site is observed to be controlled by the redox state of the flavin and linked to the channel proposed to funnel the produced superoxide species from NrdI to the di-manganese site in protein R2b. These specific features are coupled to further structural changes around the R2b–NrdI interaction surface. The mechanistic implications for the control of reactive oxygen species and radical generation in protein R2b are discussed.
|
|
| 25. |
- John, Juliane, et al.
(författare)
-
Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b–NrdI complex monitored by serial femtosecond crystallography
- 2022
-
Ingår i: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 11
-
Tidskriftsartikel (refereegranskat)abstract
- Redox reactions are central to biochemistry and are both controlled by and induce protein structural changes. Here, we describe structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b–NrdI complex, a di-metal carboxylate-flavoprotein system, as part of the mechanism generating the essential catalytic free radical of the enzyme. Femtosecond crystallography at an X-ray free electron laser was utilized to obtain structures at room temperature in defined redox states without suffering photoreduction. Together with density functional theory calculations, we show that the flavin is under steric strain in the R2b–NrdI protein complex, likely tuning its redox properties to promote superoxide generation. Moreover, a binding site in close vicinity to the expected flavin O2 interaction site is observed to be controlled by the redox state of the flavin and linked to the channel proposed to funnel the produced superoxide species from NrdI to the di-manganese site in protein R2b. These specific features are coupled to further structural changes around the R2b–NrdI interaction surface. The mechanistic implications for the control of reactive oxygen species and radical generation in protein R2b are discussed.
|
|
| 26. |
- Lebrette, Hugo, 1986-, et al.
(författare)
-
Structure of a ribonucleotide reductase R2 protein radical
- 2023
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 382:6666, s. 109-113
-
Tidskriftsartikel (refereegranskat)abstract
- Aerobic ribonucleotide reductases (RNRs) initiate synthesis of DNA building blocks by generating a free radical within the R2 subunit; the radical is subsequently shuttled to the catalytic R1 subunit through proton-coupled electron transfer (PCET). We present a high-resolution room temperature structure of the class Ie R2 protein radical captured by x-ray free electron laser serial femtosecond crystallography. The structure reveals conformational reorganization to shield the radical and connect it to the translocation path, with structural changes propagating to the surface where the protein interacts with the catalytic R1 subunit. Restructuring of the hydrogen bond network, including a notably short O-O interaction of 2.41 angstroms, likely tunes and gates the radical during PCET. These structural results help explain radical handling and mobilization in RNR and have general implications for radical transfer in proteins.
|
|
| 27. |
- Oshima, A., et al.
(författare)
-
Mutation profile of the CDH23 gene in 56 probands with Usher syndrome type I
- 2008
-
Ingår i: Human Mutation. - New York, N.Y. : Wiley-Liss. - 1059-7794 .- 1098-1004. ; 29:6, s. E37-E46
-
Tidskriftsartikel (refereegranskat)abstract
- Mutations in the human gene encoding cadherin 23 (CDH23) cause Usher syndrome type 1D (USH1D) and nonsyndromic hearing loss. Individuals with Usher syndrome type I have profound congenital deafness, vestibular areflexia and usually begin to exhibit signs of RP in early adolescence. In the present study, we carried out the mutation analysis in all 69 exons of the CDH23 gene in 56 Usher type 1 probands already screened for mutations in MYO7A. A total of 18 of 56 subjects (32.1%) were observed to have one or two CDH23 variants that are presumed to be pathologic. Twenty one different pathologic genome variants were observed of which 15 were novel. Out of a total of 112 alleles, 31 (27.7%) were considered pathologic. Based on our results it is estimated that about 20% of patients with Usher syndrome type I have CDH23 mutations.
|
|
| 28. |
- Srinivas, Vivek, et al.
(författare)
-
High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States
- 2020
-
Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 142:33, s. 14249-14266
-
Tidskriftsartikel (refereegranskat)abstract
- Soluble methane monooxygenase (sMMO)is a multicomponent metalloenzyme that catalyzes the conversion of methane to methanol at ambient temperature using a nonheme, oxygen-bridged dinuclear iron cluster in the active site. Structural changes in the hydroxylase component (sMMOH) containing the diiron cluster caused by complex formation with a regulatory component (MMOB) and by iron reduction are important for the regulation of O-2 activation and substrate hydroxylation. Structural studies of metalloenzymes using traditional synchrotron-based X-ray crystallography are often complicated by partial X-ray-induced photoreduction of the metal center, thereby obviating determination of the structure of the enzyme in pure oxidation states. Here, microcrystals of the sMMOH:MMOB complex from Methylosinus trichosporium OB3b were serially exposed to X-ray free electron laser (XFEL) pulses, where the <= 35 fs duration of exposure of an individual crystal yields diffraction data before photoreduction-induced structural changes can manifest. Merging diffraction patterns obtained from thousands of crystals generates radiation damage-free, 1.95 angstrom resolution crystal structures for the fully oxidized and fully reduced states of the sMMOH:MMOB complex for the first time. The results provide new insight into the manner by which the diiron cluster and the active site environment are reorganized by the regulatory protein component in order to enhance the steps of oxygen activation and methane oxidation. This study also emphasizes the value of XFEL and serial femtosecond crystallography (SFX) methods for investigating the structures of metalloenzymes with radiation sensitive metal active sites.
|
|
