| 1. |
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| 2. |
- Askebjer, P., et al.
(författare)
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On the age vs depth and optical clarity of deep ice at South Pole
- 1995
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Ingår i: Journal of Glaciology. - 0022-1430 .- 1727-5652. ; 41:139, s. 445-454
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Tidskriftsartikel (refereegranskat)abstract
- The first four strings of phototubes for the AMANDA high-energy neutrino observatory are now frozen in place at a depth of 800 to 1000 m in ice at the South Pole. During the 1995-96 season an additional six strings will be deployed at greater depths. Provided absorption, scattering, and refraction of visible light are sufficiently small, the trajectory of a muon into which a neutrino converts can be determined by using the array of phototubes to measure the arrival times of \v{C}erenkov light emitted by the muon. To help in deciding on the depth for implantation of the six new strings, we discuss models of age vs depth for South Pole ice, we estimate mean free paths for scattering from bubbles and dust as a function of depth, and we assess distortion of light paths due to refraction at crystal boundaries and interfaces between air-hydrate inclusions and normal ice. We conclude that the depth interval 1600 to 1800 m will be suitably transparent for the next six AMANDA strings and, moreover, that the interval 1600 to 2100 m will be suitably transparent for a future 1-km 3 observatory except possibly in a region a few tens of meters thick at a depth corresponding to a peak in the dust concentration at 60 kyr BP.
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| 3. |
- Coleman, Gareth A., et al.
(författare)
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A rooted phylogeny resolves early bacterial evolution
- 2021
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 372:6542
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Tidskriftsartikel (refereegranskat)abstract
- A rooted bacterial tree is necessary to understand early evolution, but the position of the root is contested. Here, we model the evolution of 11,272 gene families to identify the root, extent of horizontal gene transfer (HGT), and the nature of the last bacterial common ancestor (LBCA). Our analyses root the tree between the major clades Terrabacteria and Gracilicutes and suggest that LBCA was a free-living flagellated, rod-shaped double-membraned organism. Contrary to recent proposals, our analyses reject a basal placement of the Candidate Phyla Radiation, which instead branches sister to Chloroflexota within Terrabacteria. While most gene families (92%) have evidence of HGT, overall, two-thirds of gene transmissions have been vertical, suggesting that a rooted tree provides a meaningful frame of reference for interpreting bacterial evolution.
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| 4. |
- Murray, Alison E., et al.
(författare)
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Roadmap for naming uncultivated Archaea and Bacteria
- 2020
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Ingår i: Nature Microbiology. - : NATURE PUBLISHING GROUP. - 2058-5276. ; 5:8, s. 987-994
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Tidskriftsartikel (refereegranskat)abstract
- The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity. In this Consensus Statement, the authors discuss the issue of naming uncultivated prokaryotic microorganisms, which currently do not have a formal nomenclature system due to a lack of type material or cultured representatives, and propose two recommendations including the recognition of DNA sequences as type material.
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| 5. |
- Chiavassa, A., et al.
(författare)
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Radiative hydrodynamic simulations of red supergiant stars III. Spectro-photocentric variability, photometric variability, and consequences on Gaia measurements
- 2011
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 528, s. A120-
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Tidskriftsartikel (refereegranskat)abstract
- Context. It has been shown that convection in red supergiant stars (RSG) gives rise to large granules that cause surface inhomogeneities and shock waves in the photosphere. The resulting motion of the photocentre (on time scales ranging from months to years) could possibly have adverse effects on the parallax determination with Gaia. Aims. We explore the impact of the granulation on the photocentric and photometric variability. We quantify these effects in order to better characterise the error that could possibly alter the parallax. Methods. We use 3D radiative-hydrodynamics (RHD) simulations of convection with CO5BOLD and the post-processing radiative transfer code Optim3D to compute intensity maps and spectra in the Gaia G band [325-1030 nm]. Results. We provide astrometric and photometric predictions from 3D simulations of RSGs that are used to evaluate the possible degradation of the astrometric parameters of evolved stars derived by Gaia. We show in particular from RHD simulations that a supergiant like Betelgeuse exhibits a photocentric noise characterised by a standard deviation of the order of 0.1 AU. The number of bright giant and supergiant stars whose Gaia parallaxes will be altered by the photocentric noise ranges from a few tens to several thousands, depending on the poorly known relation between the size of the convective cells and the atmospheric pressure scale height of supergiants, and to a lower extent, on the adopted prescription for galactic extinction. In the worst situation, the degradation of the astrometric fit caused by this photocentric noise will be noticeable up to about 5 kpc for the brightest supergiants. Moreover, parallaxes of Betelgeuse-like supergiants are affected by an error of the order of a few percents. We also show that the photocentric noise, as predicted by the 3D simulation, does account for a substantial part of the supplementary "cosmic noise" that affects Hipparcos measurements of Betelgeuse and Antares.
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| 6. |
- Cruzalebes, P., et al.
(författare)
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Brightness Asymmetries of Cool Giants and Supergiants Measured with VLTI-AMBER
- 2015
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Ingår i: WHY GALAXIES CARE ABOUT AGB STARS III. - : ASTRONOMICAL SOC PACIFIC. - 9781583818794 ; , s. 109-110
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Konferensbidrag (refereegranskat)abstract
- We report on a search for asymmetries on the photospheres of 16 giants and supergiants. We found that all targets have surface-brightness asymmetries, but the most prominent ones are found along the upper AGB.
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| 7. |
- Cruzalebes, P., et al.
(författare)
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Fundamental parameters of 16 late-type stars derived from their angular diameter measured with VLTI/AMBER(star)
- 2013
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 434:1, s. 437-450
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Tidskriftsartikel (refereegranskat)abstract
- Thanks to their large angular dimension and brightness, red giants and supergiants are privileged targets for optical long-baseline interferometers. 16 red giants and supergiants have been observed with the VLTI/AMBER facility over a 2-year period, at medium spectral resolution (R = 1500) in the K band. The limb-darkened angular diameters are derived from fits of stellar atmospheric models on the visibility and the triple product data. The angular diameters do not show any significant temporal variation, except for one target: TX Psc, which shows a variation of 4 per cent using visibility data. For the eight targets previously measured by long-baseline interferometry (LBI) in the same spectral range, the difference between our diameters and the literature values is less than 5 per cent, except for TX Psc, which shows a difference of 11 per cent. For the eight other targets, the present angular diameters are the first measured from LBI. Angular diameters are then used to determine several fundamental stellar parameters, and to locate these targets in the Hertzsprung-Russell diagram (HRD). Except for the enigmatic Tc-poor low-mass carbon star W Ori, the location of Tc-rich stars in the HRD matches remarkably well the thermally-pulsating asymptotic giant branch, as it is predicted by the stellar evolution models. For pulsating stars with periods available, we compute the pulsation constant and locate the stars along the various sequences in the period-luminosity diagram. We confirm the increase in mass along the pulsation sequences, as predicted by theory, except for W Ori which, despite being less massive, appears to have a longer period than T Cet along the first-overtone sequence.
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| 8. |
- Cruzalebes, P., et al.
(författare)
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Measuring deviation from centrosymmetry for a source brightness distribution observed by spectro-interferometry
- 2014
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 443:4, s. 3550-3563
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Tidskriftsartikel (refereegranskat)abstract
- We report on the testing of the centrosymmetry parameter (CSP), an indicator of deviation from centrosymmetry of a source brightness distribution. This indicator is derived from the spectral distribution of the triple product measured over three baselines of an optical interferometer. Numerical simulations using parametric toy-models (separated or transiting binary, one-spot model), generated with the SPIDAST software, are applied to the VLTI/AMBER facility in the K band (2.2 mu m). The simulations show that, in case of centrosymmetry, the CSP parameter is in agreement with the usual phase of the spectral mean of the triple product (called GCP, global closure phase). To justify the preferential use of CSP rather than GCP, we show situations with asymmetric geometries for which GCP diagnoses centrosymmetry, while CSP does not. Using realistic Roche lobe-filling binary and hydrodynamic convective models, we show that CSP can also be used as an indicator for geometric similarity between physical and toy-models. Thus, dealing with real data, the toy-model parameters can be fitted on the measured CSP values, in order to assess the input-parameter values of the most suitable complex physical model that will be used to interpret the data.
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| 9. |
- Cruzalebes, P., et al.
(författare)
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SPIDAST : a new modular software to process spectrointerferometric measurements
- 2013
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 432:2, s. 1658-1671
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Tidskriftsartikel (refereegranskat)abstract
- Extracting stellar fundamental parameters from Spectrointerferometric (SPI) data requires reliable estimates of observables and with robust uncertainties (visibility, triple product, phase closure). A number of fine calibration procedures are necessary throughout the reduction process. Testing departures from centrosymmetry of brightness distributions is a useful complement. Developing a set of automatic routines called spidast (made available to the community) to reduce, calibrate and interpret raw data sets of instantaneous spectrointerferograms at the spectral channel level, we complement (and in some respects improve) the ones contained in the amdlib Data Reduction Software. Our new software spidast is designed to work in an automatic mode, free from subjective choices, while being versatile enough to suit various processing strategies. spidast performs the following automated operations: weighting of non-aberrant SPI data (visibility, triple product), fine spectral calibration (subpixel level), accurate and robust determinations of stellar diameters for calibrator sources (and their uncertainties as well), correction for the degradations of the interferometer response in visibility and triple product, calculation of the centrosymmetry parameter from the calibrated triple product, fit of parametric chromatic models on SPI observables, to extract model parameters. spidast is currently applied to the scientific study of 18 cool giant and supergiant stars, observed with the VLTI/AMBER facility at medium resolution in the K band. Because part of their calibrators have no diameter in the current catalogues, spidast provides new determinations of the angular diameters of all calibrators. Comparison of spidast final calibrated observables with amdlib determinations shows good agreement, under good and poor seeing conditions.
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| 10. |
- Abat, F, et al.
(författare)
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Current trends in tendinopathy : consensus of the ESSKA basic science committee. Part II
- 2018
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Ingår i: Journal of experimental orthopaedics. - : Springer. - 2197-1153. ; 5:38
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Tidskriftsartikel (refereegranskat)abstract
- The treatment of painful chronic tendinopathy is challenging. Multiple non-invasive and tendon-invasive methods are used. When traditional non-invasive treatments fail, the injections of platelet-rich plasma autologous blood or cortisone have become increasingly favored. However, there is little scientific evidence from human studies supporting injection treatment. As the last resort, intra- or peritendinous open or endoscopic surgery are employed even though these also show varying results. This ESSKA basic science committee current concepts review follows the first part on the biology, biomechanics and anatomy of tendinopathies, to provide a comprehensive overview of the latest treatment options for tendinopathy as reported in the literature.
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| 11. |
- Abat, F., et al.
(författare)
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Current trends in tendinopathy : consensus of the ESSKA basic science committee. Part I: biology, biomechanics, anatomy and anexercise-based approach
- 2017
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Ingår i: Journal of Experimental Orthopaedics. - : Springer. - 2197-1153. ; 4:1
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Forskningsöversikt (refereegranskat)abstract
- Chronic tendinopathies represent a major problem in the clinical practice of sports orthopaedic surgeons, sports doctors and other health professionals involved in the treatment of athletes and patients that perform repetitive actions. The lack of consensus relative to the diagnostic tools and treatment modalities represents a management dilemma for these professionals. With this review, the purpose of the ESSKA Basic Science Committee is to establish guidelines for understanding, diagnosing and treating this complex pathology.
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| 12. |
- Alfven, T, et al.
(författare)
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Low-level cadmium exposure and osteoporosis
- 2000
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Ingår i: Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research. - : Wiley. - 0884-0431. ; 15:8, s. 1579-1586
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Tidskriftsartikel (refereegranskat)
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| 13. |
- Moody, Edmund R. R., et al.
(författare)
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An estimate of the deepest branches of the tree of life from ancient vertically evolving genes
- 2022
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Ingår i: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Core gene phylogenies provide a window into early evolution, but different gene sets and analytical methods have yielded substantially different views of the tree of life. Trees inferred from a small set of universal core genes have typically supported a long branch separating the archaeal and bacterial domains. By contrast, recent analyses of a broader set of non-ribosomal genes have suggested that Archaea may be less divergent from Bacteria, and that estimates of inter-domain distance are inflated due to accelerated evolution of ribosomal proteins along the inter-domain branch. Resolving this debate is key to determining the diversity of the archaeal and bacterial domains, the shape of the tree of life, and our understanding of the early course of cellular evolution. Here, we investigate the evolutionary history of the marker genes key to the debate. We show that estimates of a reduced Archaea-Bacteria (AB) branch length result from inter-domain gene transfers and hidden paralogy in the expanded marker gene set. By contrast, analysis of a broad range of manually curated marker gene datasets from an evenly sampled set of 700 Archaea and Bacteria reveals that current methods likely underestimate the AB branch length due to substitutional saturation and poor model fit; that the best-performing phylogenetic markers tend to support longer inter-domain branch lengths; and that the AB branch lengths of ribosomal and non-ribosomal marker genes are statistically indistinguishable. Furthermore, our phylogeny inferred from the 27 highest-ranked marker genes recovers a clade of DPANN at the base of the Archaea and places the bacterial Candidate Phyla Radiation (CPR) within Bacteria as the sister group to the Chloroflexota.
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| 14. |
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| 15. |
- Dombrowski, Nina, et al.
(författare)
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Genomic diversity, lifestyles and evolutionary origins of DPANN archaea
- 2019
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Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 0378-1097 .- 1574-6968. ; 366:2
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Forskningsöversikt (refereegranskat)abstract
- Archaea-a primary domain of life besides Bacteriahave for a long time been regarded as peculiar organisms that play marginal roles in biogeochemical cycles. However, this picture changed with the discovery of a large diversity of archaea in non-extreme environments enabled by the use of cultivation-independent methods. These approaches have allowed the reconstruction of genomes of uncultivated microorganisms and revealed that archaea are diverse and broadly distributed in the biosphere and seemingly include a large diversity of putative symbiotic organisms, most of which belong to the tentative archaeal superphylum referred to as DPANN. This archaeal group encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, many members of DPANN may be obligately dependent on symbiotic interactions with other organisms and may even include novel parasites. In this contribution, we review the current knowledge of the gene repertoires and lifestyles of members of this group and discuss their placement in the tree of life, which is the basis for our understanding of the deep microbial roots and the role of symbiosis in the evolution of life on Earth.
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| 16. |
- Dombrowski, Nina, et al.
(författare)
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Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution
- 2020
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 11:1
-
Tidskriftsartikel (refereegranskat)abstract
- The recently discovered DPANN archaea are a potentially deep-branching, monophyletic radiation of organisms with small cells and genomes. However, the monophyly and early emergence of the various DPANN clades and their role in life's evolution are debated. Here, we reconstructed and analysed genomes of an uncharacterized archaeal phylum (Candidatus Undinarchaeota), revealing that its members have small genomes and, while potentially being able to conserve energy through fermentation, likely depend on partner organisms for the acquisition of certain metabolites. Our phylogenomic analyses robustly place Undinarchaeota as an independent lineage between two highly supported 'DPANN' clans. Further, our analyses suggest that DPANN have exchanged core genes with their hosts, adding to the difficulty of placing DPANN in the tree of life. This pattern can be sufficiently dominant to allow identifying known symbiont-host clades based on routes of gene transfer. Together, our work provides insights into the origins and evolution of DPANN and their hosts. The evolutionary relationships within Archaea remain unresolved. Here, the authors used genomic approaches to study the Undinarchaeota, a previously uncharacterized clade of DPANN, shed light on their position in an updated archaeal phylogeny and illuminate the history of archaeal genome evolution.
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| 17. |
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| 18. |
- Hertwig, Falk, et al.
(författare)
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Definition of Genetic Events Directing the Development of Distinct Types of Brain Tumors from Postnatal Neural Stem/Progenitor Cells.
- 2012
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Ingår i: Cancer Research. - 1538-7445. ; 72:13, s. 3381-3392
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Tidskriftsartikel (refereegranskat)abstract
- Although brain tumors are classified and treated based upon their histology, the molecular factors involved in the development of various tumor types remain unknown. In this study, we show that the type and order of genetic events directs the development of gliomas, central nervous system primitive neuroectodermal tumors, and atypical teratoid/rhabdoid-like tumors from postnatal mouse neural stem/progenitor cells (NSC/NPC). We found that the overexpression of specific genes led to the development of these three different brain tumors from NSC/NPCs, and manipulation of the order of genetic events was able to convert one established tumor type into another. In addition, loss of the nuclear chromatin-remodeling factor SMARCB1 in rhabdoid tumors led to increased phosphorylation of eIF2α, a central cytoplasmic unfolded protein response (UPR) component, suggesting a role for the UPR in these tumors. Consistent with this, application of the proteasome inhibitor bortezomib led to an increase in apoptosis of human cells with reduced SMARCB1 levels. Taken together, our findings indicate that the order of genetic events determines the phenotypes of brain tumors derived from a common precursor cell pool, and suggest that the UPR may represent a therapeutic target in atypical teratoid/rhabdoid tumors. Cancer Res; 72(13); 3381-92. ©2012 AACR.
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| 19. |
- Kellner, Siri, et al.
(författare)
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Genome size evolution in the Archaea
- 2018
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Ingår i: Emerging Topics in Life Sciences. - : Portland Press. - 2397-8554 .- 2397-8562. ; 2:4, s. 595-605
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Forskningsöversikt (refereegranskat)abstract
- What determines variation in genome size, gene content and genetic diversity at the broadest scales across the tree of life? Much of the existing work contrasts eukaryotes with prokaryotes, the latter represented mainly by Bacteria. But any general theory of genome evolution must also account for the Archaea, a diverse and ecologically important group of prokaryotes that represent one of the primary domains of cellular life. Here, we survey the extant diversity of Bacteria and Archaea, and ask whether the general principles of genome evolution deduced from the study of Bacteria and eukaryotes also apply to the archaeal domain. Although Bacteria and Archaea share a common prokaryotic genome architecture, the extant diversity of Bacteria appears to be much higher than that of Archaea. Compared with Archaea, Bacteria also show much greater genome-level specialisation to specific ecological niches, including parasitism and endosymbiosis. The reasons for these differences in long-term diversification rates are unclear, but might be related to fundamental differences in informational processing machineries and cell biological features that may favour archaeal diversification in harsher or more energy-limited environments. Finally, phylogenomic analyses suggest that the first Archaea were anaerobic autotrophs that evolved on the early Earth.
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| 20. |
- Kirsch, A., et al.
(författare)
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Mimikveränderungen während einer Traumatherapie : Explorative Studie zum Zusammenhang mimisch-affektiver Veränderungen mit therapeutischen Outcomes
- 2018
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Ingår i: Psychotherapeut (Berlin). - : Springer. - 0935-6185 .- 1432-2080. ; 63:1, s. 49-54
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Tidskriftsartikel (refereegranskat)abstract
- Background: Clinicians frequently describe changes in facial affective behavior during the treatment of posttraumatic stress disorder (PTSD). An increase in facial affective behavior is seen in association with a reduction of numbing symptoms. Objective: The purpose of this exploratory study was to demonstrate the changes in facial affective behavior (especially negative affects) during inpatient eye movement desensitization and reprocessing (EMDR) treatment and to examine to what extent these changes correspond to shifts in symptom severity. Material and methods: Facial affective behavior was coded during therapeutic sessions for 16 patients who were chronically traumatized during their youth, using the facial action coding system (FACS) for 3 time points, before, during and 1 year after treatment with EMDR. Data of the impact of event scale revised (IES-R), the symptom checklist (SCL-90-R), Beck depression inventory (BDI-V) and a questionnaire for dissociative symptoms (FDS) was documented for 16 female patients with a mean age of 39 years (SD = ±10). Results and conclusion: There was a significant change in facial affective behavior during and after treatment (χ2(2) = 5.73, p = 0.030). Total facial affective behavior and the expression of negative affect significantly increased 1 year after therapy; however, there were no significant correlations between the change of facial affective behavior during EMDR treatment and relevant outcome variables. Further research will show if monitoring facial affective behavior is useful to assess therapeutic success, especially with respect to social interactions. © 2017, Springer Medizin Verlag GmbH.
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| 21. |
- Krause, Susanne, et al.
(författare)
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The importance of biofilm formation for cultivation of a Micrarchaeon and its interactions with its Thermoplasmatales host
- 2022
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Micrarchaeota is a distinctive lineage assigned to the DPANN archaea, which includes poorly characterised microorganisms with reduced genomes that likely depend on interactions with hosts for growth and survival. Here, we report the enrichment of a stable co-culture of a member of the Micrarchaeota (Ca. Micrarchaeum harzensis) together with its Thermoplasmatales host (Ca. Scheffleriplasma hospitalis), as well as the isolation of the latter. We show that symbiont-host interactions depend on biofilm formation as evidenced by growth experiments, comparative transcriptomic analyses and electron microscopy. In addition, genomic, metabolomic, extracellular polymeric substances and lipid content analyses indicate that the Micrarchaeon symbiont relies on the acquisition of metabolites from its host. Our study of the cell biology and physiology of a Micrarchaeon and its host adds to our limited knowledge of archaeal symbioses. The Micrarchaeota lineage includes poorly characterized archaea with reduced genomes that likely depend on host interactions for survival. Here, the authors report a stable co-culture of a member of the Micrarchaeota and its host, and use multi-omic and physiological analyses to shed light on this symbiosis.
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| 22. |
- Leich, E., et al.
(författare)
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Gene expression and copy number profiling of follicular lymphoma biopsies from patients treated with first-line rituximab without chemotherapy
- 2023
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Ingår i: Leukemia and Lymphoma. - : Taylor & Francis. - 1042-8194 .- 1029-2403. ; 64:12, s. 1927-1937
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Tidskriftsartikel (refereegranskat)abstract
- The Nordic Lymphoma Study Group has performed two randomized clinical trials with chemotherapy-free first-line treatment (rituximab +/- interferon) in follicular lymphoma (FL), with 73% of patients alive and 38% without any need of chemotherapy after 10.6 years median follow-up. In order to identify predictive markers, that may also serve as therapeutic targets, gene expression- and copy number profiles were obtained from 97 FL patients using whole genome microarrays. Copy number alterations (CNAs) were identified, e.g. by GISTIC. Cox Lasso Regression and Lasso logistic regression were used to determine molecular features predictive of time to next therapy (TTNT). A few molecular changes were associated with TTNT (e.g. increased expression of INPP5B, gains in 12q23/q24), but were not significant after adjusting for multiple testing. Our findings suggest that there are no strong determinants of patient outcome with respect to GE data and CNAs in FL patients treated with a chemotherapy-free regimen (i.e. rituximab +/- interferon).
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| 23. |
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| 24. |
- Martijn, Joran, et al.
(författare)
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Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition
- 2020
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Ingår i: Nature Communications. - : NATURE RESEARCH. - 2041-1723. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Halobacteria (henceforth: Haloarchaea) are predominantly aerobic halophiles that are thought to have evolved from anaerobic methanogens. This remarkable transformation most likely involved an extensive influx of bacterial genes. Whether it entailed a single massive transfer event or a gradual stream of transfers remains a matter of debate. To address this, genomes that descend from methanogen-to-halophile intermediates are necessary. Here, we present five such near-complete genomes of Marine Group IV archaea (Hikarchaeia), the closest known relatives of Haloarchaea. Their inclusion in gene tree-aware ancestral reconstructions reveals an intermediate stage that had already lost a large number of genes, including nearly all of those involved in methanogenesis and the Wood-Ljungdahl pathway. In contrast, the last Haloarchaea common ancestor gained a large number of genes and expanded its aerobic respiration and salt/UV resistance gene repertoire. Our results suggest that complex and gradual patterns of gain and loss shaped the methanogen-to-halophile transition. A study of the first genomes of the marine Hikarchaeia, the closest known relatives of Haloarchaea, is presented. Their inclusion in ancestral reconstructions unveils an intermediate stage in the evolutionary transition from ancestral anaerobic methanogens to modern day aerobic halophiles.
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| 25. |
- Raina, Jean-Baptiste, et al.
(författare)
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Symbiosis in the microbial world : from ecology to genome evolution
- 2018
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Ingår i: BIOLOGY OPEN. - : The Company of Biologists. - 2046-6390. ; 7:2
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Forskningsöversikt (refereegranskat)abstract
- The concept of symbiosis - defined in 1879 by de Bary as 'the living together of unlike organisms' - has a rich and convoluted history in biology. In part, because it questioned the concept of the individual, symbiosis fell largely outside mainstream science and has traditionally received less attention than other research disciplines. This is gradually changing. In nature organisms do not live in isolation but rather interact with, and are impacted by, diverse beings throughout their life histories. Symbiosis is now recognized as a central driver of evolution across the entire tree of life, including, for example, bacterial endosymbionts that provide insects with vital nutrients and the mitochondria that power our own cells. Symbioses between microbes and their multicellular hosts also underpin the ecological success of some of the most productive ecosystems on the planet, including hydrothermal vents and coral reefs. In November 2017, scientists working in fields spanning the life sciences came together at a Company of Biologists' workshop to discuss the origin, maintenance, and long-term implications of symbiosis from the complementary perspectives of cell biology, ecology, evolution and genomics, taking into account both model and non-model organisms. Here, we provide a brief synthesis of the fruitful discussions that transpired.
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