| 1. |
- Hibbett, D. S., et al.
(författare)
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A higher-level phylogenetic classification of the Fungi
- 2007
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Ingår i: Mycological Research. - : Elsevier BV. - 0953-7562 .- 1469-8102. ; 111, s. 509-547
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Tidskriftsartikel (refereegranskat)abstract
- A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecarioromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotiria. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella. (c) 2007 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.
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| 2. |
- Raiteri, C. M., et al.
(författare)
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WEBT and XMM-Newton observations of 3C 454.3 during the post-outburst phase - Detection of the little and big blue bumps
- 2007
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 473:3, s. 819-827
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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.
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| 3. |
- Sodergren, Erica, et al.
(författare)
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The genome of the sea urchin Strongylocentrotus purpuratus.
- 2006
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 314:5801, s. 941-52
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Tidskriftsartikel (refereegranskat)abstract
- We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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| 4. |
- Janson, Peter C. J., et al.
(författare)
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CpG methylation of the IFNG gene as a mechanism to induce immunosupression in tumor-infiltrating lymphocytes
- 2008
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Ingår i: Journal of Immunology. - 0022-1767 .- 1550-6606. ; 181:4, s. 2878-2886
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Tidskriftsartikel (refereegranskat)abstract
- The execution of appropriate gene expression patterns during immune responses is of eminent importance where CpG methylation has emerged as an essential mechanism for gene silencing. We have charted the methylation status of regulatory elements in the human IFNG gene encoding the signature cytokine of the Th1 response. Surprisingly, human naive CD4(+) T lymphocytes displayed hypermethylation at the IFNG promoter region, which is in sharp contrast to the completely demethylated status of this region in mice. Th1 differentiation induced demethylation of the IFNG promoter and the upstream conserved nucleotide sequence 1 enhancer region, whereas Th2-differentiated lymphocytes remained hypermethylated. Furthermore, CD19(+) B lymphocytes displayed hypomethylation at the IFNG promoter region with a similar pattern to Th1 effector cells. When investigating the methylation status among tumor-infiltrating CD4(+) T lymphocytes from patients with colon cancer, we found that tumor-infiltrating lymphocytes cells are inappropriately hypermethylated, and thus not confined to the Th1 lineage. In contrast, CD4(+) T cells from the tumor draining lymph node were significantly more demethylated than tumor-infiltrating lymphocytes. We conclude that there are obvious interspecies differences in the methylation status of the IFNG gene in naive CD4(+) T lymphocytes, where Th1 commitment in human lymphocytes involves demethylation before IFNG expression. Finally, investigations of tumor-infiltrating lymphocytes and CD4(+) cells from tumor draining lymph node demonstrate methylation of regulatory regions within key effector genes as an epigenetic mechanism of tumor-induced immunosupression.
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| 5. |
- Janson, Peter C. J., et al.
(författare)
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FOXP3 Promoter Demethylation Reveals the Committed Treg Population in Humans
- 2008
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 3:2, s. e1612-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Naturally occurring thymus derived regulatory T cells (Tregs) are central in the maintenance of self-tolerance. The transcription factor FOXP3 is crucial for the suppressive activity of Tregs and is considered the most specific marker for this population. However, human non regulatory T cells upregulate FOXP3 transiently upon activation which calls for other means to identify the Treg population. Since epigenetic mechanisms are involved in the establishment of stable gene expression patterns during cell differentiation, we hypothesized that the methylation profile of the FOXP3 promoter would allow the distinction of truly committed Tregs. Methodology/Principal Findings: Human CD4(+) CD25(hi) Tregs displayed a demethylated FOXP3 promoter (1.4%+/-0.95% SEM methylated) in contrast to CD4(+) CD25(lo) T cells which were partially methylated (27.9%+/-7.1%). Furthermore, stimulated CD4(+)CD25(lo) T cells transiently expressed FOXP3 but remained partially methylated, suggesting promoter methylation as a mechanism for regulation of stable FOXP3 expression and Treg commitment. In addition, transient FOXP3 expressing cells exhibited suppressive abilities that correlate to the methylation status of the FOXP3 promoter. As an alternative to bisulphite sequencing, we present a restriction enzyme based screening method for the identification of committed Tregs and apply this method to evaluate the effect of various culturing conditions. We show that a partial demethylation occurs in long-term cultures after activation, whereas the addition of TGF-beta and/or IL-10 does not induce any additional change in methylation level. Conclusions/Significance: The unique FOXP3 promoter methylation profile in Tregs suggests that a demethylated pattern is a prerequisite for stable FOXP3 expression and suppressive phenotype. Presently, FOXP3 is used to identify Tregs in several human diseases and there are future implications for adoptive Treg transfer in immunotherapy. In these settings there is a need to distinguish true Tregs from transiently FOXP3(+) activated T cells. The screening method we present allows this distinction and enables the identification of cells suitable for in vitro expansions and clinical use.
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| 6. |
- Thorn, Colin E., et al.
(författare)
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Comparison of radiocarbon dating of buried paleosols using arbuscular mycorrhizae spores and bulk soil samples
- 2009
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Ingår i: The Holocene. - : SAGE Publications. - 0959-6836 .- 1477-0911. ; 19:7, s. 1031-1037
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Tidskriftsartikel (refereegranskat)abstract
- Ten paleosols from four separate soil pits located in Karkevagge, a glaciated trough in Swedish Lapland, were dated using radiocarbon. Each soil was dated using both conventional bulk soil organic material (SOM) and a pure sample of arbuscular mycorrhizae (AM) fungal spores. The latter are produced by ubiquitous mycorrhizal fungi associated with the roots of many plant genera and may be viewed as a fossil material that has not interacted with any soil constituent subsequent to its emplacement in the soil - at a time presumed to mark the cessation of a favorable soil-forming environment. Regional deglaciation is presumed to have been about 10 000 BP, while a cosmogenic exposure date obtained from the valley floor in Karkevagge dated at 13 100 +/- 1638 BP. The youngest paleosol, buried at similar to 6 cm in soil pit M3, produced a spore date of 0-281 cal. yr BP (1 sigma). However, bulk SOM dates of the same paleosol A horizon gave widely divergent dates and varied with the sample pretreatment, ie, the combustion temperature and the acid-base treatment. For example, the bulk SOM dates for that paleosol ranged from a post-bomb date of 0-314 cal. yr BP (1 sigma) to 2366-2710 cal. yr BP (1 sigma) when subjected to different pretreatments (acid only, acid-base-acid) and the ignition temperatures (400, 800, or 900 degrees C). The oldest paleosol in the set, buried at similar to 61 cm in soil pit M6, dated at 5479-5698 cal. yr BP (1 sigma) using spores, but beyond calibration using bulk SOM. The spore dates were all within the range to be expected of postglacial paleosols, but the bulk SOM dates were frequently beyond the generally accepted time of deglaciation. In addition, all of the spore dates followed a conventional age/depth pattern while the bulk SOM dates did not. There are known possible sources of geogenic carbon contamination in Karkevagge which may well account for the obviously invalid older bulk SOM dates. An additional complication is that the spore dates vary somewhat with their density and diameter. However, where other types of fossil or charcoal are unavailable it appears that the enormously broad distribution of spores and their lack of interaction within the soil and persistence may well offer the prospect of an unusually useful radiocarbon dating medium within paleosols.
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| 7. |
- Thorn, Stefan, 1971, et al.
(författare)
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Trapezius muscle rest time during standardised computer work - A comparison of female computer users with and without self-reported neck/shoulder complaints
- 2007
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Ingår i: Journal of Electromyography and Kinesiology. - : Elsevier BV. - 1873-5711 .- 1050-6411. ; 17:4, s. 420-427
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Tidskriftsartikel (refereegranskat)abstract
- Work related musculoskeletal disorders (WMSDs) in the shoulder/neck area are a common and increasing problem among European computer workers, especially women. Long-term low-level workloads with low degree of muscle rest are a potential risk factor for developing WMSDs. The purpose of the present study of female computer users (age 45-65 years) in Denmark and Sweden was to investigate if subjects with self-reported neck/shoulder complaints (cases, N = 35) show less trapezius muscle relative rest time (RRT) than controls (N = 44) when performing standardised short-term computer work tasks in controlled laboratory conditions. Surface electromyography (EMG) signals were recorded bilaterally from the upper trapezius muscles during a type, edit, precision and colour word stress task. Besides RRT, 10th percentile RMS values were calculated. On the average, 15 of the cases and 18 of the controls showed analysable EMG files per task. For the colour word stress task, the results showed lower RRT values and higher 10th percentile RMS amplitude levels among cases compared to controls. No such signs could be found for the other tasks performed. The present results indicate an increased motor response to a psychological stressor among subjects with self-reported neck/shoulder complaints. (c) 2006 Elsevier Ltd. All rights reserved.
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