| 1. |
- Wortman, J. R., et al.
(författare)
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The 2008 update of the Aspergillus nidulans genome annotation: A community effort
- 2009
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1096-0937 .- 1087-1845. ; 46, s. S2-S13
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Tidskriftsartikel (refereegranskat)abstract
- The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology. (C) 2009 Elsevier Inc. All rights reserved.
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| 2. |
- Coutinho, P. M., et al.
(författare)
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Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae
- 2009
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1096-0937 .- 1087-1845. ; 46:Suppl 1, s. S161-S169
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Tidskriftsartikel (refereegranskat)abstract
- The plant polysaccharide degradative potential of Aspergillus nidulans was analysed in detail and compared to that of Aspergillus niger and Aspergillus oryzae using a combination of bioinformatics, physiology and transcriptomics. Manual verification indicated that 28.4% of the A. nidulans ORFs analysed in this study do not contain a secretion signal, of which 40% may be secreted through a non-classical method. While significant differences were found between the species in the numbers of ORFs assigned to the relevant CAZy families, no significant difference was observed in growth on polysaccharides. Growth differences were observed between the Aspergilli and Podospora anserina, which has a more different genomic potential for polysaccharide degradation, suggesting that large genomic differences are required to cause growth differences oil polysaccharides, Differences were also detected between the Aspergilli in the presence Of putative regulatory sequences in the promoters of the ORFs Of this Study and correlation of the presence Of putative XlnR binding sites to induction by xylose was detected for A. niger. These data demonstrate differences at genome content, Substrate specificity of the enzymes and gene regulation in these three Aspergilli, which likely reflect their individual adaptation to their natural biotope. (C) 2008 Elsevier Inc. All rights reserved.
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| 3. |
- Seiboth, F., et al.
(författare)
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Focusing XFEL SASE pulses by rotationally parabolic refractive x-ray lenses
- 2014
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Ingår i: Journal of Physics, Conference Series. - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 499:1, s. 012004-
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Tidskriftsartikel (refereegranskat)abstract
- Using rotationally parabolic refractive x-ray lenses made of beryllium, we focus hard x-ray free-electron laser pulses of the Linac Coherent Light Source (LCLS) down to a spot size in the 100 nm range. We demonstrated efficient nanofocusing and characterized the nanofocused wave field by ptychographic imaging [A. Schropp, et al., Sci. Rep. 3, 1633 (2013)] in the case of monochromatic LCLS pulses produced by a crystal monochromator that decreases the LCLS bandwidth down to ΔE/E 1.4 · 10-4. The full spectrum of LCLS pulses generated by self-amplified spontaneous emission (SASE), however, fluctuates and has a typical bandwidth of a few per mille (ΔE/E 2 · 10-3). Due to the dispersion in the lens material, a polychromatic nanobeam generated by refractive x-ray lenses is affected by chromatic aberration. After reviewing the chromaticity of refractive x-ray lenses, we discuss the influence of increased bandwidth on the quality of a nanofocused SASE pulse.
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| 4. |
- Hoppe, R., et al.
(författare)
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Full characterization of a focused wavefield with sub 100 nm resolution
- 2013
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Ingår i: Advances In X-Ray Free-Electron Lasers II. - : SPIE - International Society for Optical Engineering. - 9780819495808 ; , s. 87780G-
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Konferensbidrag (refereegranskat)abstract
- A hard x-ray free-electron laser (XFEL) provides an x-ray source with an extraordinary high peak-brilliance, a time structure with extremely short pulses and with a large degree of coherence, opening the door to new scientific fields. Many XFEL experiments require the x-ray beam to be focused to nanometer dimensions or, at least, benefit from such a focused beam. A detailed knowledge about the illuminating beam helps to interpret the measurements or is even inevitable to make full use of the focused beam. In this paper we report on focusing an XFEL beam to a transverse size of 125nm and how we applied ptychographic imaging to measure the complex wavefield in the focal plane in terms of phase and amplitude. Propagating the wavefield back and forth we are able to reconstruct the full caustic of the beam, revealing aberrations of the nano-focusing optic. By this method we not only obtain the averaged illumination but also the wavefield of individual XFEL pulses.
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| 5. |
- Pisanelli, I., et al.
(författare)
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Heterologous expression of an Agaricus meleagris pyranose dehydrogenase-encoding gene in Aspergillus spp. and characterization of the recombinant enzyme
- 2010
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 0175-7598 .- 1432-0614. ; 86:2, s. 599-606
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Tidskriftsartikel (refereegranskat)abstract
- Pyranose dehydrogenase (PDH) is a flavin-dependant sugar oxidoreductase found in the family Agaricaceae, basidiomycetes that degrade lignocellulose-rich forest litter, and is catalytically related to the fungal enzymes pyranose 2-oxidase and cellobiose dehydrogenase. It has broad substrate specificity and displays similar activities with most sugar constituents of lignocellulose including disaccharides and oligosaccharides, a number of (substituted) quinones, and metal ions are suitable electron acceptors rather than molecular oxygen. In contrast to pyranose 2-oxidase and cellobiose dehydrogenase, which oxidize regioselectively at C-2 and C-1, respectively, PDH is capable of oxidation on C-1 to C-4 as well as double oxidations, depending on the nature of the substrate. This makes it a very interesting enzyme for biocatalytic applications, as many of the reaction products are otherwise unaccessible by chemical or enzymatic means. PDH was characterized in detail in a limited number of fungi, and the first encoding genes were isolated only recently. We report here, for the first time, the heterologous expression of one of these genes, encoding the major PDH protein in Agaricus meleagris, in the filamentous fungi Aspergillus nidulans, and Aspergillus niger.
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| 6. |
- Schropp, Andreas, et al.
(författare)
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Full spatial characterization of a nanofocused x-ray free-electron laser beam by ptychographic imaging
- 2013
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 3, s. 1633-
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Tidskriftsartikel (refereegranskat)abstract
- The emergence of hard X-ray free electron lasers (XFELs) enables new insights into many fields of science. These new sources provide short, highly intense, and coherent X-ray pulses. In a variety of scientific applications these pulses need to be strongly focused. In this article, we demonstrate focusing of hard X-ray FEL pulses to 125 nmusing refractive x-ray optics. For a quantitative analysis of most experiments, the wave field or at least the intensity distribution illuminating the sample is needed. We report on the full characterization of a nanofocused XFEL beam by ptychographic imaging, giving access to the complex wave field in the nanofocus. From these data, we obtain the full caustic of the beam, identify the aberrations of the optic, and determine the wave field for individual pulses. This information is for example crucial for high-resolution imaging, creating matter in extreme conditions, and nonlinear x-ray optics.
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| 7. |
- Schropp, Andreas, et al.
(författare)
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Scanning coherent x-ray microscopy as a tool for XFEL nanobeam characterization
- 2013
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Ingår i: Proceedings of SPIE. - : SPIE. - 9780819496997
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Konferensbidrag (refereegranskat)abstract
- During the last years, scanning coherent x-ray microscopy, also called ptychography, has revolutionized nanobeam characterization at third generation x-ray sources. The method yields the complete information on the complex valued, nanofocused wave field with high spatial resolution. In an experiment carried out at the Matter in Extreme Conditions (MEC) instrument at the Linac Coherent Light Source (LCLS) we successfully applied the method to an attenuated nanofocused XFEL beam with a size of 180(h) × 150(v) nm2 (FWHM) in horizontal (h) and vertical direction (v), respectively. It was created by a set of 20 beryllium compound refractive lenses (Be-CRLs). By using a fast detector (CSPAD) to record the diffraction patterns and a fast implementation of the phase retrieval code running on a graphics processing unit (GPU), the applicability of the method as a real-time XFEL nanobeam diagnostic is highlighted.
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| 8. |
- Uhlén, Fredrik, et al.
(författare)
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Damage investigation on tungsten and diamond diffractive optics at a hard x-ray free-electron laser
- 2013
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Ingår i: Optics Express. - : Optical Society America. - 1094-4087. ; 21:7, s. 8051-8061
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Tidskriftsartikel (refereegranskat)abstract
- Focusing hard x-ray free-electron laser radiation with extremely high fluence sets stringent demands on the x-ray optics. Any material placed in an intense x-ray beam is at risk of being damaged. Therefore, it is crucial to find the damage thresholds for focusing optics. In this paper we report experimental results of exposing tungsten and diamond diffractive optics to a prefocused 8.2 keV free-electron laser beam in order to find damage threshold fluence levels. Tungsten nanostructures were damaged at fluence levels above 500 mJ/cm(2). The damage was of mechanical character, caused by thermal stress variations. Diamond nanostructures were affected at a fluence of 59 000 mJ/cm(2). For fluence levels above this, a significant graphitization process was initiated. Scanning Electron Microscopy (SEM) and mu-Raman analysis were used to analyze exposed nanostructures.
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